bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted optimization of regulatory DNA sequences with neural editing architectures
Authors: Gupta Anvita , Kundaje Anshul 
Published: July 2019

AbstractTargeted optimizing of existing DNA sequences for useful properties, has the potential to enable several synthetic biology applications from modifying DNA to treat genetic disorders to designing regulatory elements to fine tune context-specific gene expression. Current approaches for targeted genome editing are largely based on prior biological knowledge or ad-hoc rules. Few if any machine learning approaches exist for targeted optimization of regulatory DNA sequences.Here, we propose a novel generative neural network architecture for targeted DNA sequence editing – the EDA architecture – consisting of an encoder, decoder, and analyzer. We showcase the use of EDA to optimize regulatory DNA sequences to bind to the transcription factor SPI1. Compared to other state-of-the-art approaches such as a textual variational autoencoder and rule-based editing, EDA significantly improves predicted binding of SPI1 of genomic sequences with the minimal set of edits. We also use EDA to design regulatory elements with optimized grammars of CREB1 binding sites that can tune reporter expression levels as measured by massively parallel reporter assays (MPRA). We analyze the properties of the binding sites in the edited sequences and find patterns that are consistent with previously reported grammatical rules which tie gene expression to CRE binding site density, spacing and affinity.
Infection ofBorrelia burgdorferisensu lato of small mammals in Yunnan Province, China
Authors: He Zhi-hai , Jiang Bao-gui , Gao Zi-hou , Shao Zong-ti , Zhang Yun , Liu Zheng-xiang , Li Yu-qiong , Pu En-nian , Tang Li , Yao Ming-guo , Jia Na , von Fricken Michael E. , Jiang Jia-fu , Cao Wu-chun , Du Chun-hong 
Published: July 2019

AbstractBackgroundLyme disease is caused byBorrelia burgdorferisensulato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases ofB. burgdorferiinfections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Yunnan Province, Southwestern China. Yunnan Province is a tropical area with a diverse topographic range and sustains a high biodiversity of small mammals that could potentially play an important role in the transmission of a variety ofB. burgdorferigenospecies.Methods3659 small mammals were captured in 159 sample siteslocated 23 countries inYunnan Province and screened for BBSL infection by nested PCR based on 5S-23S rRNA intergenic spacer gene of BBSL.Univariate and multivariate forward stepwise logistic regression analysis was used to access the association between infections and related risk factors.ResultsInfection with BBSL was confirmed in 3.99%(146/3659) of small mammals. Significant differences in prevalence rates of BBSL were observed at varying landscape types and altitudes.Small mammals in forested areas had higher prevalence rates than other landscape types as did small mammals found at altitudes greater than 2500 meters. The 5S-23S rRNA intergenic spacergene revealed that there were 5 genotype of BBSL, includingB. afzelii, B. burgdorferisensustricto, B.japonica, B.gariniiand B.valaisiana, which demonstrate the genetic diversity and regional distribution.ConclusionsThere exists a wide distribution and genetic diversity of endemic BBSL in Southwestern China, warranting further investigations and monitoring of clinical disease in individuals presenting with symptoms of Lyme disease in these areas.Author summaryLyme disease is caused byBorrelia burgdorferisensu lato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases ofBorrelia burgdorferisensu lato infections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Southwestern China. This study documents potential small mammal reservoir hosts collected from a large of sample sites from different landscape types and altitudes, with PCR and sequencing identifying the wide distribution and genetic diversity of endemicBorrelia burgdorferisensu lato in Southwestern China. This was the first report thatB. japonicawas detected inApodemus dracoandNiviventer excelsiorin China. This study adds to body of literature onBorrelia burgdorferisensu lato in China. This work will provide insight regarding small mammals to target for surveillance and we access the association between gender, developmental stage of rodents, environmental landscape and altitude to better prevent human exposure.
Conjugated linoleic acid as a novel insecticide targeting the agricultural pestLeptinotarsa decemlineata
Authors: Clements Justin , Groves Russell L. , Cava JoAnn , Barry Caroline , Chapman Scott , Olson Jake M. 
Published: July 2019

AbstractThe Colorado Potato Beetle,Leptinotarsa decemlineata, is a major agricultural pest of solanaceous crops in the United States. Historically, a multitude of insecticides have been used to control problematic populations. Due to increasing resistance to insecticides, novel compounds and methodologies are warranted for the control of beetle populations. Mixed-isomer conjugated linoleic acid has been studied in-depth for its beneficial properties to mammalian systems. At the same time, studies have demonstrated that conjugated linoleic acid can manipulate fatty acid composition in non-mammalian systems, resulting in embryo mortality. Consequently, experiments were conducted to assess the effects of foliar-applied conjugated linoleic acid on larval growth, embryogenesis, and feeding preference in Colorado potato beetle. Both maternal and deterrent effects of dietary conjugated linoleic acid were assessed. Conjugated linoleic acid demonstrated desirable insecticidal properties, including increased larval mortality, slowed larval development, antifeedant effects, and decreased egg viability after maternal ingestion.
Pyruvate Kinase M Links Glucose Availability to Protein Synthesis
Authors: Kejiou Nevraj S. , Ilan Lena , Aigner Stefan , Luo Enching , Rabano Ines , Rajakulendran Nishani , Najafabadi Hamed S. , Angers Stephane , Yeo Gene W. , Palazzo Alexander F. 
Published: July 2019

AbstractHow human cells coordinate various metabolic processes, such as glycolysis and protein translation, remains unclear. One key insight is that various metabolic enzymes have been found to associate with mRNAs, however whether these enzymes regulate mRNA biology in response to changes in cellular metabolic state remains unknown. Here we report that the glycolytic enzyme, pyruvate kinase M (PKM), inhibits the translation of 7% of the transcriptome in response to elevated levels of glucose and pyruvate. Our data suggest that in the presence of glucose and pyruvate, PKM associates with ribosomes that are synthesizing stretches of polyacidic nascent polypeptides and stalls the elongation step of translation. PKM-regulated mRNAs encode proteins required for the cell cycle and may explain previous results linking PKM to cell cycle regulation. Our study uncovers an unappreciated link between glycolysis and the ribosome that likely coordinates the intake of glycolytic metabolites with the regulation of protein synthesis and the cell cycle.
Machine Learning for Prioritization of Thermostabilizing Mutations for G-protein Coupled Receptors
Authors: Muk S. , Ghosh S. , Achuthan S. , Chen X. , Yao X. , Sandhu M. , Griffor M. C. , Fennell K. F. , Che Y. , Shanmugasundaram V. , Qiu X. , Tate C. G. , Vaidehi N. 
Published: July 2019

AbstractAlthough the three-dimensional structures of G-protein-coupled receptors (GPCRs), the largest superfamily of drug targets, have enabled structure-based drug design, there are no structures available for 87% of GPCRs. This is due to the stiff challenge in purifying the inherently flexible GPCRs. Identifying thermostabilized mutant GPCRs via systematic alanine scanning mutations has been a successful strategy in stabilizing GPCRs, but it remains a daunting task for each GPCR. We developed a computational method that combines sequence, structure and dynamics based molecular properties of GPCRs that recapitulate GPCR stability, with four different machine learning methods to predict thermostable mutations ahead of experiments. This method has been trained on thermostability data for 1231 mutants, the largest publicly available dataset. A blind prediction for thermostable mutations of the Complement factor C5a Receptor retrieved 36% of the thermostable mutants in the top 50 prioritized mutants compared to 3% in the first 50 attempts using systematic alanine scanning.Statement Of SignifiganceG-protein-coupled receptors (GPCRs), the largest superfamily of membrane proteins play a vital role in cellular physiology and are targets to blockbuster drugs. Hence it is imperative to solve the three dimensional structures of GPCRs in various conformational states with different types of ligands bound. To reduce the experimental burden in identifying thermostable GPCR mutants, we report a computational framework using machine learning algorithms trained on thermostability data for 1231 mutants and features calculated from analysis of GPCR sequences, structure and dynamics to predict thermostable mutations ahead of experiments. This work represents a significant advancement in the development, validation and testing of a computational framework that can be extended to other class A GPCRs and helical membrane proteins.
A survey on data-driven process monitoring and diagnostic methods for variation reduction in multi-station assembly systems
Authors: Liu Yinhua , Sun Rui , Jin Sun 
Published: July 2019

PurposeDriven by the development in sensing techniques and information and communications technology, and their applications in the manufacturing system, data-driven quality control methods play an essential role in the quality improvement of assembly products. This paper aims to review the development of data-driven modeling methods for process monitoring and fault diagnosis in multi-station assembly systems. Furthermore, the authors discuss the applications of the methods proposed and present suggestions for future studies in data mining for quality control in product assembly.Design/methodology/approachThis paper provides an outline of data-driven process monitoring and fault diagnosis methods for reduction in variation. The development of statistical process monitoring techniques and diagnosis methods, such as pattern matching, estimation-based analysis and artificial intelligence-based diagnostics, is introduced.FindingsA classification structure for data-driven process control techniques and the limitations of their applications in multi-station assembly processes are discussed. From the perspective of the engineering requirements of real, dynamic, nonlinear and uncertain assembly systems, future trends in sensing system location, data mining and data fusion techniques for variation reduction are suggested.Originality/valueThis paper reveals the development of process monitoring and fault diagnosis techniques, and their applications in variation reduction in multi-station assembly.
Study on the effect of surface tannic acid/silane conversion film on properties of epoxy resin coatings
Authors: Xing Tianji , Ying Lixia , Wu Chunxi , Fu Zhen , Wang Guixiang 
Published: July 2019

Purpose
The purpose of this paper is to improve binding force between the coating and the steel substrate by using chemical modification on the steel surface; at the same time, it can also increase the corrosion resistance of the coating.

Design/methodology/approach
The main components of the conversion film include tannic acid, sodium molybdate and silane coupling agent KH560. After the preparation was completed, the samples were tested and analyzed, including surface morphology, conversion film components, bonding force with organic resins and corrosion resistance. Finally, it drew a conclusion that the conversion film can greatly improve the bonding strength of the steel substrate and epoxy resin.

Findings
When the content of tannic acid is 4 g/L meanwhile the content of KH560 is 20 g/L, the conversion film has the strongest binding force with epoxy resin, from 2.15 Mpa of untreated steel to 4.60 Mpa, growth of 140 per cent. At the same time, the resulting conversion film also improves the corrosion resistance of the steel surface by a small margin.

Originality/value
A method of enhancing the bond between an epoxy coating and steel is provided. Verify the mechanism of this method.
Enhanced corrosion resistance of Cr-Mn ASS by low temperature salt bath nitriding technique for the replacement of convectional Cr-Ni ASS
Authors: Tandon Vipin , Patil Awanikumar P. , Rathod Ramesh C. 
Published: July 2019

Purpose
The purpose of this paper is to enhance the corrosion resistance of Cr-Mn austenitic stainless steel (ASS) via low temperature salt bath nitriding and to replace the convectional Cr-Ni ASS with newly developed enhanced corrosion resistive Cr-Mn ASS.

Design/methodology/approach
The low temperature salt bath nitriding was performed on Cr-Mn ASS at 450°C for 3 h in potassium nitrate salt bath.

Findings
The present paper compares the corrosion resistance of salt bath nitrided Cr-Mn ASS with convectional Cr-Ni ASSs (316 L and 304 L ASSs) in 3.5 per cent NaCl by electrochemical techniques. The electrochemical impedance spectroscopy result shows the increase in film resistance and potentiodynamic polarization results show the enhanced corrosion resistance of nitrided Cr-Mn ASS, which is almost equivalent to that of 316 L and 304 L ASSs. This is attributed to the formation of nitrogen supersaturated dense nitride layer. The present results therefore suggest that the nitrided Cr-Mn ASS may replace costly convectional Cr-Ni ASSs for commercial and industrial applications.

Originality/value
Ever-increasing price of nickel (Ni) is driving the industries to use Ni-free or low-Ni austenitic stainless steels (ASSs). But its corrosion resistance is relatively poor as compared to conventional Cr-Ni ASSs. However, its corrosion resistance can be improved by nitriding. The low temperature salt bath nitriding of Cr-Mn ASS and its electrochemical behavior in 3.5 per cent NaCl has not been studied. The present research paper is beneficial for industries to use low cost Cr-Mn, enhance its corrosion resistance and replace the use of costly conventional Cr-Ni ASSs.
Effect of microstructure on corrosion of welded joints of X80 steel in water saturated supercritical CO2
Authors: Deng Hongda , Cao Xianlong , Yan Yongbo , Xie Kuanya 
Published: July 2019

Purpose
The purpose of this paper is to research whether microstructure varieties of zones at welded joints pose a tremendous effect on its corrosion in SC-CO2.

Design/methodology/approach
The interrelation between the corrosion and microstructure of base metal (BM), fine grain heat affected zone (FHAZ), coarse grain heat affected zone and weld metal (WM) in welded of X80 steel in water saturated supercritical CO2 was studied by using optical microscope, weight loss test, electrochemical measurements and surface analytical techniques.

Findings
The all subzones of X80 weld joints were attacked by SC-CO2 corrosion and showed flower-like corrosion scale spots consisted of granular FeCO3. The most severe corrosion appeared at WM due to lower proportion of ferrite to pearlite, but the slightest corrosion displayed at BM. GHAZ with larger grains and more polygonal ferrite exhibited more severe corrosion than that at BM. Due to its smaller grain, FHAZ displayed comparatively more severe corrosion to that at BM.

Originality/value
There exists close interrelation between the corrosion and microstructure of the welded carbon steel in water saturated supercritical CO2.
Impact of consultant obstetric presence on serious incidents
Authors: Shawer Sherif , Rowbotham Shirley , Heazell Alexander , Kelly Teresa , Vause Sarah 
Published: July 2019

Purpose
Many organisations, including the Royal College of Obstetricians and Gynaecologists, have recommended increasing the number of hours of consultant obstetric presence in UK National Health Service maternity units to improve patient care. St Mary’s Hospital, Manchester implemented 24-7 consultant presence in September 2014. The paper aims to discuss these issues.

Design/methodology/approach
To assess the impact of 24-7 consultant presence upon women and babies, a retrospective review of all serious clinical intrapartum incidents occurring between September 2011 and September 2017 was carried out by two independent reviewers; disagreements in classification were reviewed by a senior Obstetrician. The impact of consultant presence was classified in a structure agreed a priori.

Findings
A total of 72 incidents were reviewed. Consultants were directly involved in the care of 75.6 per cent of cases before 24-7 consultant presence compared to 96.8 per cent afterwards. Negative impact due to a lack of consultant presence fell from 22 per cent of the incidents before 24-7 consultant presence to 9.7 per cent after implementation. In contrast, positive impact of consultant presence increased from 14.6 to 32.3 per cent following the introduction of 24-7 consultant presence.

Practical implications
Introduction of 24-7 consultant presence reduced the negative impact caused by a lack of, or delay in, consultant presence as identified by serious untoward incident (SUI) reviews. Consultant presence was more likely to have a positive influence on care delivery.

Originality/value
This is the first assessment of the impact of 24-7 consultant presence on the SUIs in obstetrics.
A wireless IOT system towards gait detection technique using FSR sensor and wearable IOT devices
Authors: Achanta Sampath Dakshina Murthy , T. Karthikeyan , R. Vinoth Kanna 
Published: July 2019

Purpose
The recent advancement in gait analysis combines internet of things that provides better observations of person living behavior. The biomechanical model used for elderly and physically challenged persons is related to gait-related parameters, and the accuracy of the existing systems significantly varies according to different person abilities and their challenges. The paper aims to discuss these issues.

Design/methodology/approach
Deployment of wearable sensors in gait analysis provides a better solution while tracking the changes of the personal style, and this proposed model uses an electronics system using force sensing resistor and body sensors.

Findings
Experimental results provide an average gait recognition of 95 percent compared to the existing neural network-based gait analysis model based on the walking speeds and threshold values.

Originality/value
The sensors are used to monitor and update the predicted values of a person for analysis. Using IoT a communication process is performed in the research work by identifying a physically challenged person even in crowded areas.
Age-related productivity decrease in high-waged and low-waged employees
Authors: Roosaar Liis , Masso Jaan , Varblane Urmas 
Published: July 2019

Purpose
The purpose of this paper is to clarify whether the age-productivity curve is different for low-waged and high-waged employees.

Design/methodology/approach
Productivity growth is decomposed at the firm level into contributions by hired, separated and staying workers. Based on a matched employer-employee database of Estonian firms from 2006 to 2014 and considering the age as well as wages of employees, a panel data model with fixed effects is constructed to show the relative productivity of each cohort of employees.

Findings
High-waged employees appeared to be relatively more productive than low-waged employees and middle-aged were more productive than young or old employees. However, the productivity difference between young and old employees was not statistically significant. The age-productivity curve of high-waged employees appeared to be flatter than that of low-waged employees. Only in knowledge intensive services were the low-waged old employees statistically significantly less productive than high-waged old employees. In the manufacturing industry, the young were more productive than in services, in knowledge intensive services the old were less productive than in traditional services.

Research limitations/implications
The productivity of employees is only analysed for cohorts of employees.

Practical implications
Employers can be encouraged to hire older employees because old employees are shown to remain at least as productive as young employees.

Originality/value
The decomposition of labour productivity at the firm level is further developed, as the statistical difference between the productivity of different groups of employees is analysed.
Green Banking and Islam: two sides of the same coin
Authors: Bukhari Syed Asim Ali , Hashim Fathyah , Amran Azlan Bin , Hyder Kalim 
Published: July 2019

Purpose
Currently, one of the most important dilemmas facing mankind is environmental degradation and natural resource shortage. The adoption of Green Banking practices has been identified as a solution to the growing environmental problems all over the world. However, an important issue being faced by both the conventional and Islamic banking industry is the creation of stakeholder engagement in Green Banking practices. The purpose of this paper is to propose the use of Islamic principles in developing an emotional attachment between Green Banking practices and the Muslim consumer market to facilitate Green Banking adoption.

Design/methodology/approach
Based on the theory of self-congruity, the authors have proposed a framework to analyze the congruity between Islamic principles and Green Banking. The argument is built on secondary data by identifying the Environmental, Social and Governance (ESG) dimensions of Green Banking and proving its congruence with teachings of the Holy Qur’an and Sunnah.

Findings
It is observed that the doctrine of Islam established for mankind 1,400 years ago consists of the same principles that are now being implemented in the shape of Green Banking. The dimensions of Green Banking are in line with Islamic teachings and, thus, can easily be adopted and marketed by banks, especially Islamic banks, targeting the Muslim consumers. The congruence of Green Banking with Islamic principles can play a major role in fostering the growth of this imperative ideology for the Green Muslim consumers. Islamic banks can market green products and services on the basis of religious congruity to the Muslim consumer market and create greater acceptability and loyalty.

Research limitations/implications
The proposed model has not been empirically tested.

Originality/value
Limited research exists in the area of Green Banking adoption, especially in Muslim countries. Up until now, academic research has not been conducted on the congruity between the principles of Islam and Green Banking dimensions. This paper attempts to add to the unsaturated research area of Green Banking adoption by Islamic banks and how Islamic banks can gain a competitive advantage by building on the congruity between Green Banking and Islam.