bluuebunny/crossref_metadata_2025 huggingface dataset:
Design verification through tolerance stack up analysis of mechanical assembly for 3d printed components
Authors: Jafrin Beryl R , Saravanan A N , Annamalai K , Janardhan Reddy K
Published: April 2021

Automobile sector encounters new challenges and hurdles every day. New design trends and day-by-day technology advancement from research, push companies to develop new competitive models. Automobile manufacturing is one of the most competitive business domains where every organization will thrive to prove themselves in the society and market. In order to increase the production rate of the company, automobile manufactures can increase the efficiency of their research and development process enabling them to get their product in the market with less time and better quality. Additive manufacturing is being used in the prototyping, tool and dies making process due to less time, labour efforts and cost. But the hurdles faced by company in additive manufacturing are poor dimensional accuracies and tolerances. Automotive industries find difficult to get their exact dimensional tolerance values resulting in failure of the component. In this paper authors demonstrated tolerances stack-up analysis through a case study of critical 3D printed components and its assembly used in automobile. This paper provides a review of role and future scope of additive manufacturing in automobile industries.
Investigation on the Effect of Charge Carriers in Chemical Shift Anisotropy of Si Single Crystal
Authors: Viswanathan E. , Padma Prasad K. , Ganapathy S.
Published: April 2021

The Chemical Shift Anisotropy (CSA) of single crystalline silicon (Si) was investigated using 29Si static NMR for commercially procured p-type and n-type silicon. The observed CSA has been distributed between -80 ppm to -90 ppm for n-type and p-type Si. The NMR parameters such as Isotropic Chemical Shift (5iso), Chemical Shift Anisotropy tensor (ΔS) and the asymmetry parameter (77) of the CSA were extracted by using DMFIT with the CSA-static model. The ΔS and
rj
are found to be -1.73 ppm and 0.3 ppm respectively for the n-type and the asymmetry parameter of the CSA was found one order different from p-type material. The changes observed in CSA pattern and spin-lattice relaxation (T
1) time are ascribed to strength (mobility) of the shallow donor level and shallow acceptor level effects in the Fermi contact term.
Experimental Investigations on the Drilling of Titanium Metal Matrix Composite
Authors: Arun Rajesh M , Bala Kumar S S , Ashok R , Vijay Sekar K S
Published: April 2021

Titanium Metal Matrix Composites have high specific strength and offer high stiffness compared with Nickel alloys and steel. While maintaining equivalent strength, it can reduce 50% weight relative to other super alloys. In this work, preparation of Silicon Carbide reinforced Titanium Metal Matrix Composite by powder metallurgy and drilling of the composite to evaluate the drilling forces are discussed and the effect of drilling process parameters on thrust force, surface finish and chip formation is studied.
Design and analysis of energy-efficient solar panel cooling system using computational fluid dynamics
Authors: Vaishnav Sarthak , Kapadiya Vivek , Harish R. , Mohan R.
Published: April 2021

This paper highlights the design of an effective liquid cooling system that utilizes the heat generated from the solar panel as a cooling medium to maintain the optimal desired temperature of the solar panel. The coolant for this finned cooling system is selected based on its vaporizing temperature range and thermal cycle characteristics. For analysis purposes, a CAD model is generated in Solidworks CAD package, and further meshing and numerical simulations are performed using Ansys Fluent software. Flow and heat transfer characteristics of the cooling system are investigated by plotting stream functions, velocity, and temperature distributions inside the system. Probing of variations in temperature, pressure and turbulent kinetic energy along vertical as well as longitudinal direction is graphically analysed. Thus, elucidating characteristic of parametric conditions under observation. This study’s results can be the potential background for designing an efficient solar panel cooling system with superior thermal performance.
Effect of Shape Imperfections on Collapse Moment of Strain Hardened Pipe Bends under in-plane Opening Bending Moment
Authors: Sai Santosh Pavan Kumar M. , Christo Michael T.
Published: April 2021

The effect of ovality and variable wall thickness on the collapse load of pipe bends subjected to in-plane opening moment is investigated using Finite Element (FE) analysis for an elastic plastic material. The collapse load was estimated from the moment-rotation curves using Twice-Elastic-Slope method. The presence of ovality reduced the collapse load by 13.1% for a model having bend characteristic 0.1, thus making its effect critical. The presence of thinning had no significant effect on the collapse load. Based on the FE results, a mathematical equation is proposed to estimate the collapse load of strain-hardened pipe bends for a range of bend characteristic from 0.1 to 0.6, considering the effect of ovality.
CT Guided Liver Tumor Biopsy Framework
Authors: Mourya G K , Bhatia D , Gogoi M , Handique A
Published: April 2021

Liver tumor biopsy is the first step of a liver cancer diagnosis. Accuracy of liver cancer diagnosis depends upon how precisely the sample is collected from the right location. The ultrasound-guided biopsy procedure is subjective and painful to patient. CT guided biopsy framework assists medical experts in planning biopsy needle path before performing the procedure. In this framework, first, CT image acquired, and 3D models are created for liver, skin, liver tumor, bone, and liver blood vessels using 3Dirac CT datasets. Second, an algorithm designed for biopsy needle insertion path recommendation. At the last 3D simulation generated. Needle insertion starts from the skin and ends at the tumor site. The recommended needle path does not carry bone and major blood vessels. The designed framework suggests two possible paths that medical experts can select and allow to make a further modification in that path. 3D simulation of needle insertion shown to medical experts for the evaluation. According to their comments, methods are producing promising results. The proposed framework may utilize for teaching-learning procedures for junior medical experts. Automatic biopsy needle path recommendations are perquisites for generating augmented reality tools and robotic biopsy systems.
Finite element analysis of the slot milling of carbon fiber reinforced polymer composites
Authors: Prakash C , Vijay Sekar K S
Published: April 2021

Carbon Fiber Reinforced Polymer (CFRP) composites are widely used for making the components and primary structures in the field of aircraft, aerospace, automobile, medical, construction and many essential items which we use every day. These composite laminates are light in weight without compromising its strength. Hence, CFRP composites attract the researchers and the modern industries to investigate more on it. Industries rely on conventional machining process to achieve required shape and size, but CFRP composites show intrinsic behaviour while machining because of its non homogeneous properties. Selecting the appropriate tool and the cutting conditions for machining the CFRP composite, influences more in achieving the desired shape, size with close tolerance. In this paper, a 3D Finite Element Model is developed to simulate the slot milling process and to predict the cutting forces for the different cutting conditions. The reliability and accuracy of 3D FE analysis depend on the friction coefficient and failure model used in the FE model. These FE input parameters were applied in a wider range and analysis was carried out. The cutting forces obtained from the FE results are correlated with the experimental results to validate and to evaluate the influence of the FEM parameters. The outcome of this investigation is to suggest a suitable Failure model and the Friction coefficient, which ensures the reliability of the FE Model.
Experimental and Numerical Study on Ergonomic Evaluation of Automotive Seating Comfort
Authors: Anand V , Dongale Amit , Jebaseelan Davidson , Jagannath M. , Michael Christo
Published: April 2021

Automotive car seats play a vital role in providing optimum comfort to the occupants when it comes to vehicle comfort. The objective of this study was to perform an experimental and numerical investigation of the ergonomic evaluation of automotive seating comfort. A questionnaire survey was carried out on car drivers driving two different cars namely Tata Indica and Maruti Swift, to understand the perception of drivers on seating comfort. Posture monitoring techniques using Kinect camera and pressure mapping systems were used to analyze the sitting posture and sitting angle. A multibody dynamics analysis technique was used to evaluate the human body exposed to vehicle vibration. The vertical vibration transmissibility was measured from different body segments using this model. Also, with the help of a multibody dynamics simulation model, the results were compared and validated with existing literature. This study suggests suitable sitting posture and sitting angle derived with the help of multibody dynamics simulation along with the experimental investigation, which would reduce the fatigue of the driver when exposed to prolonged driving.
Researches on energy-efficient plasma conversion of fibreglass waste into new ecological materials for building industry
Authors: Antonescu I , Isopescu D N , Cucoş I , Caunii V , Alecu I C , Lupu M L
Published: April 2021

The paper presents the researches, prototype laboratory equipment and technologies developed by the authors for the plasma conversion of fiberglass waste into useful materials for building industry. The aim was to increase the energy efficiency of conversion processes and to obtain technologies and materials with better proprieties for civil engineering appliances and reduced impact on the environment.
Multi-criteria optimization for a residential horizontal ground heat exchanger
Authors: Bulmez A M , Ciofoaia V , Pleşcan C , Bolocan S I , Şerban A
Published: April 2021

Ground source heat pumps (GSHP) are the most efficient heat pump systems currently in use for residential sector today. Although these systems outperform all other heat pump systems when considering the energy source, the installation costs represent an ongoing issue. For the market to increase in this area, multi-criteria optimization for the ground heat exchanger (GHE) is the main research topic today. The main objective of this study is to search ways to optimize the horizontal ground heat exchanger focusing on two distinct viewpoints: physical and energetic optimization. To achieve this goal, the entropy generation number and the coefficient of performance based on several configuration are studied. Using the Pareto optimal set obtained from two objectives provides useful information about the design optimization. In comparison with traditional single objective optimization, multi-criteria optimization avoids cost increase when regarding only the performance or performance decrease when regarding only the cost. The results indicate that the use of a cheaper heat source such as solar panels to mitigate the energy needed for peak loads during the heating and cooling systems can reduce the horizontal ground heat exchanger size and therefore the installation cost. A hybrid solar assisted ground source heat pump system, using more than one renewable energy source, shows a much higher flexibility for residential purposes than a heat pump system that uses only one renewable energy source.
Analysis of the most determining factors from Romanian urban regulation, at the state level, in relation to sanitation, hygiene and health throughout recent history
Authors: Cazacu Ch , Chitonu C , Muntean R
Published: April 2021

Construction represents an important branch of the Romanian economy. The construction branch must be characterized by flexibility and diversity, attributes that favor change, through generation, continuous development and rapid transposition into practice of new ideas. The demands of society are becoming more and more severe throughout the all countries of the world. Expectations and needs are becoming increasingly explicit for issues such as: health and safety of the place where we live or work environmental protection, operational safety.
Using E-waste in asphalt mixtures – a laboratory investigation
Authors: Dragomir M L , Cadar R D , Boitor R M
Published: April 2021

Incorporating electronic waste (E-waste) in a new asphalt mixture is a subjected connected to the recycling process of PCB (Printed Circuit Boards), in which PCB waste is turned into a powder. The aim of the paper is to present the performance of the new asphalt pavement obtained by using PCB waste to substitute lime filler in a share of 100%. First, laboratory analyses are performed to determine the composition of PCB. Then, the feasibility of using PCB waste in the asphalt pavement industry is analysed in a series of laboratory investigations conducted on asphalt concrete BA16 rul 50/70 (AC16) that is a standard asphalt mixture in Romania. The following tests are performed on the new material: cyclic compression-dynamic flow, rutting test, and Marshall Stability and flow. The conclusion after the first experimental stage of this research is that the mixture containing PCB is softer than the control/witness mixture containing lime filler. Further investigations regarding the use of E-waste in road asphalt pavements will be conducted to find a way to reduce the use of new raw materials in the road construction industry.
Validation of AE tomography based on model tests of soil specimen with heterogeneous elastic wave velocity distribution
Authors: Nakamura K , Kobayashi Y , Oda K , Shigemura S , Ikebata K
Published: April 2021

In order to investigate the progressive failure of soil-structures, non-destructive inspections have been applied in recent. Use of Acoustic Emission (AE), the elastic wave which is generated by the occurrence of cracks, is attractive in this field to detail the progressive failure if the measurement is conducted with sufficiently small time interval. Although this technique potentially detects the cracks clearly, conventional methods of AE source localization consider that elastic wave velocity distribution is homogenous, and there are the limitations of its application due to the diffraction and the refraction of elastic wave if the heterogeneity of the elastic wave velocity distribution is not negligible. In this study, AE-Tomography (AET), which performs the identification elastic wave velocity distribution and the localization of AE sources with consideration of the diffraction and the refraction of elastic wave, is validated about the performance of the identification of the elastic wave velocity distribution and the AE sources localizations on numerical tests and model tests. Artificial AE events are generated in the soil specimen that have some parts of different relative density and validation of AET is conducted by using the arrival times of the artificial AE. According to the results of the validation, it is suggested that AET identifies elastic wave velocity distributions and AE source locations adequately on the heterogeneous elastic wave velocity distributions.
Restoration and preservation of the authentic traditional housing model. Case study - the peasant house in the Danube Delta area
Authors: Pericleanu B D , Pericleanu M , Grămescu A M
Published: April 2021

The paper develops a new concept, relatively unique in approaching the concept of rehabilitation of the peasant house at the beginning of the XXI century, namely the traditional architecture of the Danube Delta as a system of integrated research, preservation of cultural and historical values. As it is known, the Vernacular Heritage Charter, ratified in 1999 in Mexico, draws attention to the fact that vernacular architecture around the world is valuable and requires protection, positive attitude in preserving, preserving and transmitting technologies, materials, architecture combined with authentic elements can even unique. This valuable built fund is increasingly subject to the pressures generated by urbanization, globalization (a phenomenon that affects local specificity) and lack of information or interest. The vernacular architecture of the Delta area was executed empirically, within the community using local materials, techniques and traditional crafts is what the Austrian American architect Bernard Rudofsky called it, in the title of his 1964 book, "Architecture without architects". The heritage reflected in the built environment of the villages in the Delta belongs to a type of vernacular architecture, and, of course, shares the general characteristics of the genre: a close communion with the natural landscape and the society in which it was "born". If we talk about contemporary ideology in architecture, in the context of very present discourses on sustainable development and sustainability (in absolutely all areas). The paper presents two approaches; high-tech, which supports the use of modern materials and advanced technology in construction and the low-tech approach, which aims at methods and techniques with low impact on the environment. The authors detail the concept of restoration corresponding to traditional materials and technologies.
Principles regarding integrated conservation of historical and archaeological sites to capitalize in the urban location
Authors: Simion A G , Gramescu A M , Pericleanu B D
Published: April 2021

The promotion in Romania of the integrated conservation of the historical / archaeological sites from the urban areas represents a vector of the recognition of the importance of the archaeological patrimony, as a source of non-renewable and public development. The starting point of the article is to analyse the state of the built heritage, of the historical and natural sites in the peninsular area of Constanta in order to propose solutions for conservation / rehabilitation and their enhancement. The article will outline some principles of major importance: the need for an in-depth historical and archaeological study that precedes any intervention or enhancement, the obligation to respect with the utmost rigor the authenticity of the remains, preserving their original substance, the requirement that public accessibility not harm the quality of the sites, as the case may be, their integration in the urban structure. Case study - the wall of the Tomis fortress.
Study on heat treatment and coating of copper screw female in friction pair of rock drill
Authors: Wang Y Y , Zhao M , Zhang X L
Published: April 2021

Aiming at the copper screw female parts of the rock drill friction pair that are made of tin bronze and easy to wear, the material, hardness, the metallographic structure and other comparative studies have conducted in-depth research on the formation mechanism of the application of thermal spraying technology on the copper spiral female parts of the rock drill product. The copper spiral female in the friction pair of the rock drill after heat treatment and thermal spraying has been tested on site by the customer. With better results, it is hoped that it can be used as a reference for the study of other friction pairs in rock drill products.
Optimization of diamond circular saw blade by vibration noise analysis
Authors: Wu T , Wang D , Zhao M
Published: April 2021

The vibration noise analysis and optimization of diamond circular saw blade is presented. The position of hole of the diamond circular saw blade matrix with diameter of 500 mm is established by analyzing the vibration and noise through experiment, and then making matrix topology optimization to the blade by ANSYS. The research content is divided into three parts. The noise analysis of diamond saw blade. Study on vibration characteristics of diamond saw blades. The optimization design of diamond saw blade. The study on the noise and vibration characteristics of diamond circular saw blade provides some reference for the design and technological parameter of blades. The successful application of the topology optimization has certain reference value to production and manufacturing of saw blades.
Study of two-phase transportation mode of liquefied natural gas through a pipeline by the gravitational method
Authors: Zhmakin V , Samoylov A
Published: April 2021

The given paper considers the choice of method and technology of liquefied natural gas transportation from an isothermal LNG storage facility via a pipeline to a transport cryogenic tank. Theoretical studies have been performed, including mathematical modeling of thermal and hydro-dynamic processes during the transportation of liquefied natural gas with partial evaporation through a pipeline. A new method for calculating the transportation of liquefied natural gas with partial evaporation through a pipeline using the gravitational method has been proposed in the paper.
Photocatalytic disinfection of bacteria under visible light irradiation by BiFeO3 photocatalyst
Authors: Daub N A , Aziz F , Mohd Zain N A , Lau W J , Yusof N , Salleh W N W , Jaafar J
Published: April 2021

BiFeO3 nanoparticles was synthesized by sol gel auto combustion. The as-synthesized BiFeO3 were characterized by X-ray diffraction (XRD), UV-Vis diffuse reflectance spectra (DRS) and Brunauer-Emmett-Teller (BET) analysis. The disinfection activities towards Gram-positive Staphylococcus aureus (S.aureus) were examined under visible light irradiation. The results showed a complete inactivation of 3 × 106 CFU/mL S.aureus was achieved within 20 min. The disruption of bacterial cell structure was observed by Transmission electron microscope (TEM). The cells were severely damaged after being exposed to BiFeO3 under visible light irradiation. Hence, the results demonstrated the potential application of perovskite-type photocatalyst, BiFeO3 in photocatalytic disinfection of various microorganisms.
The role of g-C3N4 in round-the-clock photocatalysis for POME
Authors: Razali N A M , Salleh W N W , Rosman N , Ismail H , Ahmad S Z N , Aziz F , Lau W J , Ismail A F
Published: April 2021

The main drawback of conventional palm oil mill effluent (POME) treatment is that the process is time and space-consuming. Besides, the treatment produces highly polluted wastewater that pollutes the environment if discharged directly. Photocatalytic process has significant potential to degrade recalcitrant organic pollutants and has recently attracted tremendous attention. However, current approaches mainly focus on visible light condition, which is still an ineffective treatment for POME. In this study, POME was successfully degraded using graphitic carbon nitride (g-C3N4) photocatalyst synthesised by calcination. The prepared photocatalyst was characterised by ultraviolet-visible diffuse reflectance (UV-Vis DRS) spectroscopy and scanning electron microscopy (SEM). The SEM results revealed the morphology of g-C3N4 photocatalyst. g-C3N4 could act as a visible-light-driven (VLD) photocatalyst with the highest photocatalytic efficiency of 71% under visible light. The present work highlights the potential of g-C3N4 towards the degradation of POME under visible light and dark condition. The highly enhanced photocatalytic performance is attributed to g-C3N4, but it does not work well in round-the-clock photocatalysis. However, g-C3N4 can work as the band alignment to drive separate photogenerated charge carriers, leading to effective photocatalytic degradation. g-C3N4 photocatalyst may be considered as an ideal candidate for treating POME.
Study on the effect of air gap on physico-chemical and performance of PVDF hollow fibre membrane
Authors: Zakria H S , Othman M H D , Kamaludin R , Jilani A
Published: April 2021

Polyvinylidene fluoride (PVDF) was chosen in this study as the main material in fabricating membrane due to its excellent chemical resistance and good thermal stability. Combination of triethyl phosphate (TEP) with DMAc produce better structure of membrane which safer and provide high mechanical strength for membrane. Surface modified PVDF hollow fibre membrane (HFM) was prepared using dry-wet spinning technique by varying air gap namely 10 cm, 20 cm and 30 cm. The morphology was evaluated using scanning electron microscopy (SEM), atomic force microscopy (AFM), mercury intrusion porosimetry (MIP), contact angle, tensile test and performing water flux testing. From the characterization data, PVDF HFM with 3 wt.% PEG 400, HFM 3-10 and HFM 3-20 referred as microfiltration membrane with pore size range 0.1-0.8 µm. While, HFM 3-30 act as ultrafiltration membrane with pore size ranging 0.01-0.1 µm. Experimental results revealed that by increasing the air gap from 10 cm to 30 cm, the porosity and finger-like length decreased due to the higher elongational stress that shift the pores from broad to narrow. Thus, PVDF HFM at 10 cm air gap, HFM 3-10 achieve the highest water flux due to the higher porosity, longer finger-like length and hydrophilicity achieved. The modified HFM at shorter air gap was found to be a promising membrane structure for excellence water performance and eco-friendly to environment.
Retraction: Lean manufacturing analysis to reduce waste on production process of fan products (IOP Conf. Ser.: Mater. Sci. Eng.
308 012004)
Authors: Siregar I , Nasution A A , Andayani U , Sari R M , Syahputri K , Anizar
Published: April 2021

IOP Publishing Limited ("IOPP") is retracting this paper at the request of the author, who has stated that the work contains material or data without authorisation for use.

Retraction published: 27 April 2021
Propagation of priors for more accurate and efficient spectroscopic functional fits and their application to ferroelectric hysteresis
Authors: Creange N , Kelley K P , Smith C , Sando D , Paull O , Valanoor N , Somnath S , Jesse S , Kalinin S V , Vasudevan R K
Published: April 2021

Multi-dimensional spectral-imaging is a mainstay of the scanning probe and electron microscopies, micro-Raman, and various forms of chemical imaging. In many cases, individual spectra can be fit to a specific functional form, with the model parameter maps, providing direct insight into material properties. Since spectra are often acquired across a spatial grid of points, spatially adjacent spectra are likely to be similar to one another; yet, this fact is almost never used when considering parameter estimation for functional fits. On datasets tried here, we show that by utilizing proximal information, whether it be in the spatial or spectral domains, it is possible to improve the reliability and increase the speed of such functional fits by ∼2–3×, as compared to random priors. We explore and compare three distinct new methods: (a) spatially averaging neighborhood spectra, and propagating priors based on functional fits to the averaged case, (b) hierarchical clustering-based methods where spectra are grouped hierarchically based on response, with the priors propagated progressively down the hierarchy, and (c) regular clustering without hierarchical methods with priors propagated from fits to cluster means. Our results highlight that utilizing spatial and spectral neighborhood information is often critical for accurate parameter estimation in noisy environments, which we show for ferroelectric hysteresis loops acquired on a prototypical PbTiO3 thin film with piezoresponse spectroscopy. This method is general and applicable to any spatially measured spectra where functional forms are available. Examples include exploring the superconducting gap with tunneling spectroscopy, using the Dynes formula, or current–voltage curve fits in conductive atomic force microscopy mapping. Here we explore the problem for ferroelectric hysteresis, which, given its large parameter space, constitutes a more difficult task than, for example, fitting current–voltage curves with a Schottky emission formula (Chiu 2014 Adv. Mater. Sci. Eng.
2014 578168).
Abdominal Laser Lipolysis Using a Microprocessor-Controlled Robotic Arm With Noncontact Heating and Cooling
Authors: Fiala Thomas
Published: April 2021

Background

A novel FDA-cleared device uses a 1064-nm laser to noninvasively induce apoptosis for lipolysis of subcutaneous abdominal fat while maintaining comfortable skin temperatures with a proprietary jet cooling system (eon; Dominion Aesthetic Technologies, Inc., San Antonio, TX). A programmable articulated robotic arm moves the treatment head without any subject contact, maintaining an appropriate 3-dimensional treatment path, compensating for patient movement.

Objectives

The goal of this prospective, single center, open-label study was to demonstrate the safety and effectiveness of this device for reducing subcutaneous abdominal fat when operated with an updated power delivery curve.

Methods

Male and female subjects with Fitzpatrick skin types I to VI (N = 26) were treated. Four abdominal zones up to 150 cm2 each, customized in size and location for body habitus, were treated. Each zone underwent a single 20-minute treatment session. Follow-up visits occurred after 6 and 12 weeks. A standardized protocol was used to obtain ultrasound measurement of subcutaneous abdominal fat thickness, abdominal circumference, reported patient satisfaction and digital images.

Results

The mean treatment area was 378.5 cm2. At Week 12, there was a 21.6% or 6.3 mm mean reduction in abdominal subcutaneous fat thickness and a 4.1-cm (1.6-inch) mean reduction in abdominal circumference. Most subjects (84.6%) were satisfied or very satisfied with their results. The mean pain score was 2.5 on an 11-point ordinal scale. There were no nonresponders. Only 2 adverse events were noted: mild transient erythema (n = 1, 3.8%) and localized subcutaneous firmness (n = 1, 3.8%) which resolved without intervention within 12 weeks.

Conclusions

This contact-free device is safe and effective for reducing subcutaneous abdominal fat and represents an improvement on the prior treatment protocol.

Level of Evidence: 4
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data
Authors: Lu Yang Young , Bilmes Jeff , Rodriguez-Mias Ricard A , Villén Judit , Noble William Stafford
Published: April 2021

Motivation

Tandem mass spectrometry data acquired using data independent acquisition (DIA) is challenging to interpret because the data exhibits complex structure along both the mass-to-charge (m/z) and time axes. The most common approach to analyzing this type of data makes use of a library of previously observed DIA data patterns (a ‘spectral library’), but this approach is expensive because the libraries do not typically generalize well across laboratories.

Results

Here, we propose DIAmeter, a search engine that detects peptides in DIA data using only a peptide sequence database. Although some existing library-free DIA analysis methods (i) support data generated using both wide and narrow isolation windows, (ii) detect peptides containing post-translational modifications, (iii) analyze data from a variety of instrument platforms and (iv) are capable of detecting peptides even in the absence of detectable signal in the survey (MS1) scan, DIAmeter is the only method that offers all four capabilities in a single tool.

Availability and implementation

The open source, Apache licensed source code is available as part of the Crux mass spectrometry analysis toolkit (http://crux.ms).

Supplementary information

Supplementary data are available at Bioinformatics online.
TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings
Authors: Peres da Silva Rafael , Suphavilai Chayaporn , Nagarajan Niranjan
Published: April 2021

Motivation

Large-scale cancer omics studies have highlighted the diversity of patient molecular profiles and the importance of leveraging this information to deliver the right drug to the right patient at the right time. Key challenges in learning predictive models for this include the high-dimensionality of omics data and heterogeneity in biological and clinical factors affecting patient response. The use of multi-task learning techniques has been widely explored to address dataset limitations for in vitro drug response models, while domain adaptation (DA) has been employed to extend them to predict in vivo response. In both of these transfer learning settings, noisy data for some tasks (or domains) can substantially reduce the performance for others compared to single-task (domain) learners, i.e. lead to negative transfer (NT).

Results

We describe a novel multi-task unsupervised DA method (TUGDA) that addresses these limitations in a unified framework by quantifying uncertainty in predictors and weighting their influence on shared feature representations. TUGDA’s ability to rely more on predictors with low-uncertainty allowed it to notably reduce cases of NT for in vitro models (94% overall) compared to state-of-the-art methods. For DA to in vivo settings, TUGDA improved over previous methods for patient-derived xenografts (9 out of 14 drugs) as well as patient datasets (significant associations in 9 out of 22 drugs). TUGDA’s ability to avoid NT thus provides a key capability as we try to integrate diverse drug-response datasets to build consistent predictive models with in vivo utility.

Availabilityand implementation

https://github.com/CSB5/TUGDA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Regional Networks of Biological Field Stations to Study Climate Change
Authors: Stuble Katharine L , Des Roches Simone , Ambrose Anthony , Brown Kevin C , Cooper Helen , Hilton Timothy , Sinervo Barry , Fox Laurel R
Published: April 2021

Field stations are platforms for documenting patterns and processes in ecosystems and are critical for understanding how anthropogenic climate change reshapes nature. Although networks of field stations have been used to identify patterns at continental to global scales, these broad, sparsely distributed networks miss variation in climate change at local and regional scales. We propose that regional-scale research networks are essential for addressing the myriad of ecological and evolutionary challenges—including management and mitigation options—that cannot be answered by more broadly distributed networks or by individual field sites. We discuss our experiences leveraging natural areas throughout California at the Institute for the Study of Ecological and Evolutionary Climate Impacts. We then explore benefits and challenges of networking research at spatial scales congruent with regional patterns of climate variation and climate change, the challenges of sustained infrastructure and research support, and opportunities for future regional-scale research networks.
O1: DISCOVERING NOVEL THERAPEUTICS TO TREAT ACUTE TRAUMATIC COAGULOPATHY (ATC)
Authors: Thaventhiran A , Thiemermann C , Brohi K , Tremoleda JL , Davenport RA
Published: April 2021

Introduction

In the UK, 17,000 people die from injury each year, with uncontrolled bleeding the most significant cause of preventable mortality. Acute Traumatic Coagulopathy (ATC) exacerbates bleeding through the failure of blood-clotting with accelerated clot breakdown that mechanistically is driven by activated Protein C (aPC). No targeted therapy to treat the underlying cause of ATC exists with treatment limited to blood component resuscitation and antifibrinolytic drugs to prevent premature clot breakdown.

Method

Two hundred fifty-four bleeding trauma patients had Factor V and aPC measured on arrival and during resuscitation. A preclinical ATC model was used to test the novel therapeutic recombinant Factor V (rFV), which is resistant to aPC mediated cleavage. Mice underwent combined injury and pressure controlled-blood loss with intervention at 30-minutes to represent a clinically relevant model. Coagulopathy was measured by ROTEM and biomarkers of coagulation/fibrinolysis.

Result

Admission levels of FV were 38% lower (83 vs 134u/dL, p<0.0001), deteriorated during resuscitation to 65% of normal after transfusion of eight RBC units and were inversely related to aPC levels. Compared to vehicle, animals treated with rFV had reduced coagulopathy (Clot Strength at 5 minutes: 31 vs 24mm, p<0.01) and significantly improved survival (80% vs 44%, p≤ 0.001).

Conclusion

FV falls significantly during bleeding in trauma patients and in the murine model, rFV improved coagulation suggesting it may represent a potential therapeutic target for ATC.

Take-home message

Directly targeting the cause of ATC represents a novel therapeutic strategy in trauma and may improve survival after major haemorrhage by directly improving clot function.
O3: EVALUATION OF A 3D PRINTED BIO-ARTIFICIAL MUSCLE-ORGANOID FOR TRAUMA RESEARCH
Authors: Staruch RMT , Spear AM , Edwards J , Rickard R , Thompson M
Published: April 2021

Introduction

Organoid models serve as a robust platform for investigating injury and disease in vitro. Currently, representative models of injury are lacking to investigate the effects of traumatic damage to organs and tissues. Here we describe a three-dimensional in vitro model of high strain rate loading seen in traumatic blast injury.

Method

3D printing resins were tested for Young's Modulus & Poisson Ratio using a universal testing Organoids were then loaded into a 3D Printed bioreactor for high strain rate loading using a split Hopkinson pressure bar device. machine and digital image. Euler beam theory was used to evaluate post deflection. C2C12 myoblasts were seeded in fibrin hydrogels around 3D printed posts using a custom designed jig. High strain rate loading was applied to constructs, then qPCR & Fluorescent Live/Dead staining was utilised to demonstrate cell alignment and myotube formation.

Result

Young's modulus of Flexible resin was 11.51Mpa. Differentiated C2C12 myoblasts were capable of alignment between posts and expression of key markers of differentiation shown by qPCR & imaging. MYH5, MYH2 & MYH1 all had a > 1.5 old increase in expression compared to undifferentiated controls. Organoids were capable of survival in bioreactor casings for over 24 hours and were intact after application of high strain rate loading.

Conclusion

This work demonstrates the first use of a 3D printed organoid in vitro model to investigate high strain rate loading for trauma research. This organoid is capable of high throughput analysis to facilitate genomic and protein level expression analysis.

Take-home message

This work demonstrates the first use of a 3D printed organoid in vitro model to investigate high strain rate loading for trauma research.
O4: A NOVEL BOWEL DISEASE MODEL: PHENOTYPIC DIVERSITY OF CONTROL VS FAP ORGANOIDS
Authors: Martin I , Wu Y , Patel R , Kalra P , K S Clark , von A Roon , Latchford A , Moore JG
Published: April 2021

Introduction

The lifetime risk of colorectal cancer in familial adenomatous polyposis (FAP) approaches 100%. In patients who have undergone prophylactic colectomy, duodenal cancer is 100-300 times more common than in the general population, and an important cause of death. We aimed to develop in vitro models of mucosal crypt-derived organoids from patients with FAP.

Method

Biopsies from apparent healthy duodenal mucosa of FAP patients undergoing upper gastrointestinal endoscopy or surgery yielded crypts that were immobilised in Matrigel Basement Membrane Matrix (Corning) and cultured in IntestiCult Organoid Growth Medium (StemCell Technologies) to generate organoids for further morphologic and immunocytochemistry analyses (Dako and Abcam antibodies).

Result

Duodenal crypt-derived organoids from one healthy volunteer formed ring structures (days 1 -2) that progressed to expected branched structures (days 4-7). FAP-derived organoids from 9 patients all generated organoids with aberrant morphologies. These organoids expressed markers of Paneth cells (lysozyme), proliferation (Ki-67), goblet cells (Muc-2) and the single cell layer of mucosal epithelium (CK18).

Conclusion

This is the first report of duodenal crypt-derived organoids generated from FAP patients. Aberrant organoid morphologies were observed in all 9 patients. Immunocytochemistry confirmed markers of duodenal epithelium, suggesting a promising in vitro model to study disease aetiology in FAP.

Take-home message

This is a step towards a personalised model of disease for patients with familial adenomatous polyposis.
O19: FROZEN GEL-PACKS REDUCE POST-OPERATIVE PAIN AND NARCOTIC USAGE IN PATIENTS UNDERGOING SURGERY FOR BREAST CANCER
Authors: Ravindhran B , AM Hema , Vijaykumar M
Published: April 2021

Introduction

Adequate post-operative analgesia is important for recovery, early rehabilitation and patient satisfaction. We aimed to prove that patients undergoing surgery for breast cancer who receive cryotherapy via frozen gel-packs in the immediate postoperative period would report lower pain, require lesser narcotics and pain medication.

Method

This prospective randomized study was conducted at our tertiary care referral centre in South India. The pre-operative characteristics, intra-operative variables and post-operative outcomes were compared between two sets of matched cases and controls. Cryotherapy was delivered via frozen gel-packs for 12 hours immediately following surgery. Pain relief was assessed with the visual analog pain scale(VAS). Comparisons between groups were measured by the chi-square test, Fischer's-exact test, Independent samples t-test or Mann-Whitney U test as appropriate.

Result

81 patients were included in the study( Study-group=41 and control-group=40). For the primary outcome, mean postoperative pain score on postoperative days(PODs) 1(5.13±0.648 vs. 4.44±.502; t (79) = 5.3; p<0.001) and POD 5(4.1±0.9 vs. 3.29±.642; t (79)=3.26; p<0.001) were significantly lower in the cryotherapy group. The overall post-operative narcotic requirement(morphine equivalence) was reduced in the cryotherapy group(61.32±9.4 vs 55.8±11; t(79) = 2.421; p=0.018). The overall paracetamol requirement(grams) was also reduced in the cryotherapy group(2.1±.38 vs 1.9±.36; t(79) = 2.66; p=0.009). No significant difference was seen in the NSAID use between the groups. The cryotherapy group also demonstrated earlier functional recovery and lesser shoulder and arm stiffness(p=0.015).

Conclusion

Cryotherapy is a simple, cost-effective adjuvant to standard postoperative pain management which reduces pain, narcotics and promotes early rehabilitation.

Take-home message

Ice packs are a simple, cost-effective adjuvant to standard postoperative pain management which reduces pain, narcotic use and promotes early rehabilitation.
O29: PREDICTING RESPONSE TO NEOADJUVANT THERAPY IN OESOPHAGEAL ADENOCARCINOMA PRE-TREATMENT BIOPSIES
Authors: Lloyd M , Izadi F , Rahman S , Walker R , Hayden A , Harrington J , Grace B , Horne J , Machado M , Underwood T
Published: April 2021

Aims

We currently cannot predict which patients with locally advanced oesophageal adenocarcinoma will be amongst the 15-20% to gain a clinically important response to neoadjuvant therapy (NAT). This pilot study aimed to identify differentially expressed genes from oesophageal adenocarcinoma pre-treatment biopsies between responders and non-responders to NAT and develop methodology for predicting response.

Method

Response to NAT was assessed pathologically using Tumour Regression Grading (TRG). Pre-treatment formalin-fixed paraffin embedded samples were analysed with two nuclease protection assays (EdgeSeq, HTG = Oncology Biomarker Panel (OBP) and Precision Immuno-Oncology Panel (PIP)). Sequencing was performed on the NextSeq500 (Illumina).

Result

Whilst there was no difference in pre-treatment characteristics, responders (TRG1-2, n=26) had significantly better post-treatment pathology and overall survival than non-responders (TRG4-5, n=30). Genes up-regulated in responders were involved in regulating cell cycling, whereas genes up-regulated in non-responders were involved in cytokine signalling and the immune response. Neuronal artificial network models could predict response to NAT with overall accuracy of 73% and 68% for the OBP and PIP, respectively, which is promising considering the small sample size. As no model will be 100% accurate, we developed a model that could take patient's views into consideration with an adjustable probability threshold for classification.

Conclusion

This pilot study informs a biologically sound hypothesis for the basis of response to NAT and suggests prediction from pre-treatment biopsies may be possible using EdgeSeq. We now aim to validate these results in a larger study to inform a bespoke classifier of response to enable delivery of precision therapy.

Take-home message

In oesophageal adenocarcinoma, responders and non-responders to neoadjuvant therapy have different expression profiles. Through using EdgeSeq in larger studies, we may be able to predict which patients will respond to treatment, allowing for delivery of precision therapy.
O34: WHO SHOULD BE FOLLOWING UP IN PATIENTS WITH PROSTATE CANCER USING PSAS?
Authors: Lami M , Jackson G
Published: April 2021

Introdution

Prostate cancer patients are usually followed up using serial PSA testing. NICE provides guidelines for PSA follow up however whether this should be in primary care or secondary care is ambiguous. Consequently, there is a concern that PSAs are being missed. The primary aim of this study was to understand whether PSAs were being missed.

Method

A retrospective study was carried out at Whitehill General Practice. Patients were identified using codes for prostate cancer through Egton Medical Information Systems (EMIS) software. Data for patients followed up with PSAs between 2015-2019 was collected manually from documentation. Chi-squared statistical testing was used.

Result

47 patients had prostate cancer follow up with repeat PSAs. 45% patients were followed up solely by primary care whilst 40% had primary care follow up directed by specialists.

7 patients were excluded from further analysis. 35% of patients had missed PSAs, of which 18% had no reason documented. Furthermore, 19% had missed PSAs with solely primary care follow up. The difference in missed PSAs between solely primary care follow up versus those directed regularly by specialists was not significant (chi-squared 0.0177, p>0.05).

Conclusion

PSAs are being missed because of a lack of a recall system. An ‘out of hospital’ recall system through a local administrative hub would allow for follow up standardisation. Involving patients in their follow up care should also be considered. By placing the responsibility centrally rather than to individual clinicians provides multiple fail safes to reduce missed follow ups.

Take-home message

An ‘out of hospital’ recall system through a local administrative hub would allow for follow up standardisation. Involving patients in their follow up care needs to also be considered.