bluuebunny/crossref_metadata_2025 huggingface dataset:
A study on technologies that enable high-speed communication regardless of the interface standard between the host devices and peripheral devices
Authors: Jung So Ki
Published: March 2021

Recently, I/O interfaces for connecting a computer to peripheral devices have emerged to provide 10Giga services for communication companies. Therefore, Intel has developed Thunderbolt cables, which enable electrical signals and high-speed data transfer to facilitate 10Giga services. Thunderbolt is a type of input–output interface that is used to connect computers and peripherals. It is capable of high-speed input/output(I/O), incurs lower overheads than USB, and supports data, images, and voice simultaneously. As these are very recent standards, they have not been applied to many computers. Moreover, no device exists to use interfaces having a different protocols while differentiating between Thunderbolt and USB devices. Therefore, if both interfaces are mutually incompatible, the user must utilize Thunderbolt or USB devices separately. For this reason, a device that automatically identifies Thunderbolt or USB and automatically adapts to the user’s environment is required. In this study, Thunderbolt MAC and a MAC are alternately connected to each other via an electrical Multiplexer to auto detect link information and connect to Host. Then, based on the determined result, the Thunderbolt to PCIe bridge or the USB to PCIe bridge is electrically connected to the PCIe BUS to which the Multiplexer is connected.
Application of sequential quadratic programming for obtaining optimal obstacle avoidance posture and end position of a 7-axis robotic manipulator
Authors: Huang T Y , Chen W J
Published: March 2021

This paper used sequential quadratic programming (SQP) method to obtain the optimal obstacle avoidance posture and end position of a 7-axis robotic manipulator. By applying restraining conditions, obstacle information, and finishing point coordinates, a homogeneous transformation matrix was firstly used to construct a space for limited movement for the first and sixth axes of the robotic manipulator. Subsequently, we determined whether the terminal point was within reach of the robotic manipulator and calculated the angle of each axis. Finally, the MATLAB software was used to conduct a simulation and verification. In this study, the SQP method was used to introduce inequality constraints into the computation and conducted the iterative method. The simulation results revealed that the method can obtain avoidance of obstacle postures and select optimal values from the iteration results of multiple initial values to avoid the local optimal problem. Overall, the research findings are that the functions and applicability of the 7-axis robotic manipulator can be extended in industry when applied in future intelligent manufacturing.
Characterization and overexpression of esterases-encoding Lip900 and Lip3954 through metagenomic sequencing of paddy soil
Authors: Chen Yu Pei , Lee Pei Chi , Wu Hong Tan , Wang Guey Horng , Tsai Chai Fang , Young Chiu Chung
Published: March 2021

A lot of industrial genes can be explored from the metagenomic sequences. In this study, metagenome sequencing of paddy soil was carried out, and several putative open reading frames (ORFs) involved in the lipolytic activity can be identified. Lipolytic enzymes are widely used in different industrial applications, such as biodiesel production, bioremediation, and waste treatment. To verify the lipolytic enzymes of assembly ORFs, two putative genes encoding esterase, namely Lip900 and Lip3594, which shared 47.6% and 43.7% identities with the uncharacterized esterase proteins, were synthesized and constructed with pET-30a for Escherichia coli overexpression. Lip900 and Lip3594 belonging to VI and XII families were successfully obtained and characterized. The results of recombinant proteins indicated that Lip900 and Lip3594 preferred to hydrolyze short-length p-nitrophenyl (p-NP) esters such as p-NP butyrate (C4). The optimal temperature and pH for both Lip900 and Lip3594 were 30°C and pH 7, respectively. Nevertheless, Lip3594 had a higher relative activity than Lip900 when the temperature was over 40°C. The effect of various reagents on Lip900 and Lip3594 activities was determined. The inhibition of Lip900 and Lip3594 was observed in the presence of MgSO4, MnSO4, NiSO4, and sodium dodecyl sulfate (SDS). However, the addition of ethylenediaminetetraacetic acid (EDTA) can improve the lipolytic activity, indicating these esterases without metal ions as the cofactor. Moreover, Lip900 and Lip3594 were resistant to methanol, ethanol, and butanol. Over 81.6% of the relative activity of Lip900 can be attained when these organic solvents of alcohol were added to 10%. These results revealed that Lip900 and Lip3594 have potential applications in various industries.
Generalized proportional integral disturbance observer-based fuzzy sliding mode control for active magnetic bearing system
Authors: Giap Van Nam , Huang Shyh Chour
Published: March 2021

This paper presents a generalized proportional integral disturbance observer-based a combination of a fuzzy logic control and sliding mode control for the suspension active magnetic bearing system. Firstly, a generalized disturbance observer based on proportional and integral is built to estimate the parameters variation and the outside disturbances. In order to guarantee the system-state will be stabilized on pre-defined states, a disturbance feedback is constructed with a low pass filter. Subsequently, the proportional integral derivative surface sliding mode control is designed. Finally, the Fuzzy logic controller is constructed to determine the hitting controller gain. The stability analysis is given following the Lyapunov law. The proposed control structure can guarantee the system transient response quite good, no overshoot value, and settling time is quite narrow. Two testing cases of the proposed controller with and without the generalized disturbance observe is compared.
Flow characteristics and heat transfer performance of a multi-layer winding hose system: theory and experimentation
Authors: Qiang Haiyan , Li Wanli , Wang Yanran , Li Guanyuan , Xu Junqi
Published: March 2021

This paper investigates the flow characteristics and heat transfer performance of a multi-layer winding hose system (MLWH) that is widely used in double-wheel trench cutters. Numerical analysis with Fluent 15.0 was performed to investigate the laminar fluid flow characteristics for the multi-layer winding hose system, especially for the study the effect of the Reynolds number and radius of curvature on the fluid flow. The radius of curvature of the multi-layer winding hydraulic hose was gradually increased in the range of 1 to 3. The Reynolds number varied between 167 and 1510. According to numerical analysis, the curvature-induced centrifugal force is found to have a significant influence on pressure drop and heat transfer. An experimental platform was presented to simulate the working conditions for the multi-layer winding hose system and collect experimental data for comparison with numerical data. The results show that the flow characteristics and heat transfer performance of the multi-layer winding hose system is strongly influenced by the Reynolds number and radius of curvature.
A smart model of the rural village planning
Authors: Wu P , Lin Y
Published: March 2021

The smart model of rural village planning is to build a digital platform to connect agriculture and industry through big data. The process starts with the construction of a big data agricultural platform, then planning and designing the physical environment of the smart village, and the third stage is the creation of a multi-industry alliance and co-operation model. For combining agricultural demand and physical access information data, the cloud database can obtain the required information and achieve the exact goal of increasing agricultural income. In addition, agricultural tourism uses the urban planning concept to carry out village layout, and develops qualitative and quantitative regulations, ecology, landscape and tourism data in scientific calculations to control the intensity of land use that can be supported by rural areas and provide the best tourism condition and ecological environment. The project also builds a shared economic model in which enterprises contribute to assisting farmers in housing repairs and invite them to participate in operations. Thus, farmers are transformed into inheritors and educators, and they are able to participate in the operation of the village as a teacher, so that the culture of sustainable agriculture can continue.
Building an asynchronous HTML5-related competency-based guided e-learning system
Authors: Li Cheng Hsiu
Published: March 2021

Improving learner behavior and attitude is one method for improving learning quality. However, every student has unique characteristics, which makes the prediction of how learning behavior alters learning effects challenging. Humans obtain knowledge through cognitive learning, which can be effectively taught using asynchronous e-learning systems. However, these systems require self-study and include tedious processes that can affect learner motivation and the overall learning effect. This study implemented an HTML5-related competency-based guided e-learning (CBGE) system with an embedded competency-based guided learning (CBGL) mechanism to implement a personalized learning environment. Moreover, learner behaviors were recorded in a log dataset for data mining. The results revealed that the participants were satisfied with the CBGL mechanism and e-course design. The cognitive ability of the participants significantly improved after the experiment. Moreover, the growth in cognitive ability of the participants who completed the guiding process was significantly higher than that of the participants who did not finish the guiding process. This indicates that cognitive ability was improved through the CBGE system and the completion of the CBGL process provided a significantly more pronounced learning effect. A decision tree technique was also employed to construct a predictive model of the learning effect that could help learners achieve the learning objective. The predictive model revealed that learners who used the CBGE system could not achieve the learning objective without passing the stage tests a minimum of 2.5 times. Thus, the number of times that the stage tests were passed was the critical factor in achieving the learning objective.
Research on zero waste garment engineering design in sustainable environment
Authors: Shih Jhan Rong , Hung Chien Jen , Chiu Feng Tzu
Published: March 2021

With life becoming more convenient and rich, the pollution caused by human beings is far beyond our imagination. This study focuses on the clothing industry, which is closely related to human life, and its ecological pollution and waste of resources. It attempts to combine environmental issues to create clothing that can convey the concept of a sustainable environment and a more friendly Earth 2050: The Future of Energy. Different from the previous green environmental protection design, the current fashion trend is not only to promote environmental protection, but also to emphasize blue economy. In environmental protection, find out the industrial and economic values that meet various costs to achieve sustainable operation. In this study, the concept of environmental sustainability is brought into the clothing project. The goal is that the manufacturing process will not produce cloth waste. All cloth will go through the life course of clothing. The clothing project of “zero waste”will be built. The consumed resources will be fully utilized. In this research design, water resources, which is the most threatening issue of human sustainable environment, are used as the main design axis with blue as the image. Pollution and optimization issues faced by water resources are applied to clothing design thinking, presenting a series of clothing with zero waste structure, and implementing good behaviors of “sustainable” environment in life.
Hydraulic-mechanical modeling research on coseismic fracture behavior
Authors: Chung Chih Cheng , Chen Chi Jen , Wu Yuan Chieh
Published: March 2021

We establish hydraulic-mechanical modeling technique combined with simulation of fracture coseismic behavior based on discrete element method and well accepted equations to investigate the influence of earthquake on pore pressure and transmissivity of fractures. This study concludes 2 models with different hydraulic boundary condition, one designed for stable region with low hydraulic gradient (Mode I) while the other designed for regions with high hydraulic gradient (Model II). Model I shows that pore pressure of fractures interact with aperture and can be summarized into two possible patterns. Besides, the post-seismic transmissivity is 29∼138 % of pre-seismic transmissivity depending on location of fractures. Results of Model II indicate that pore pressure is controlled by the inflow of groundwater at the beginning of earthquake and later becomes dominated by opening and closure of aperture. Because of high hydraulic gradient and pore pressure boundary condition set into Model II, post-seismic transmissivity is 102∼1989 % of pre-seismic transmissivity. With this technique, well-established source parameter and site-specific hydraulic conditions, we are able to evaluate the possible post-seismic pore pressure and transmissivity of fractures which can be applied to underground facilities designing and evaluation of pollution transportation.
Development and application of an internet of things door lock Network Bridge for classroom access control management
Authors: Li Cheng Hsiu , Chen Chi Yu , Huang Xuan Rui , Tsai Ting Fu , Liu Bo Yang
Published: March 2021

School classroom doors are usually managed using conventional machine locks. This can cause inconvenience for the borrowing and returning of keys. In addition, issues on the copying and embezzlement of keys are persistent. To avoid these problems, schools have replaced conventional locks with card readers and magnetic locks to manage classroom access; users need only a RFID card to enter and exit classrooms. However, the hardware and software equipment required for such control schemes is expensive and entails cumbersome installation processes. This study developed an innovative Internet of Things (IoT) door lock network bridge, which can be installed on conventional electronic locks to transform it into IoT locks. The developed bridge can be integrated with a customized web-based classroom access information system and QR code scanning to establish a low-cost classroom access control system. The system can be provided to schools to perform user management, lock management, and lock matching. Each door in the school is assigned with a unique QR code for unlocking. Users only need to use the QR code scanner on their smart phone to send relevant information required for unlocking a door to the web-based classroom access information system, which then performs user and lock matching verification. Verified users can then unlock the door and enter the venue. The proposed classroom access control system does not require card readers or RFID cards. The cable installation of the system is simplified through by using wireless connections, thereby greatly reducing the time, cost, and human resource required for installation. In addition, users and locks can be matched directly using the proposed system. This greatly improves the convenience of classroom management in schools.
Development of a model for the mass loss rate of chemical erosion in fracture intersection with the deposition hole
Authors: Chiou Jia Sheng , Wang Chung Yue , Wu Yuan Chieh
Published: March 2021

The erosion of bentonite buffer in a fracture intersecting a deposition hole will affect the safety function. The purpose of this study was to build up a model which was to predict the rate of erosion of buffer/backfill, and this research focused on the KTH model which was developed by SKB. The KTH model consists of fluid pressure, sodium concentration, and smectite volume fraction, which is governed by Darcy’s Law and advection-diffusion equations respectively, and the mutual dependencies of these variables were considered. This model was implemented using the COMSOL Multiphysics, and the results show the different behavior of sodium concentration and smectite in various seeping water velocity, the erosion rate increases with the seeping water velocity, but the distance to the smectite rim border decreases with the water velocity. The KTH considers the relationship between sodium and smectite, and with scalability. it lays a foundation for the evaluation buffer/backfill mass loss by erosion.
Compounding sterile products during a personal protective equipment shortage
Authors: Wollitz Amanda Danielle , Hong Christine , Blanco Fernando
Published: March 2021

Purpose

To describe our pharmacy department’s plan for conservation of personal protective equipment (PPE) during the coronavirus disease 2019 (COVID-19) pandemic to ensure continued availability of sterile compounded products.

PPE shortages impacted hospitals throughout the nation in the early months of the COVID-19 pandemic response. The PPE requirement for sterile compounding and need to maintain supplies within the pharmacy cleanroom are often overlooked. A sustained supply of PPE is critical to ensure an uninterrupted supply of compounded medications to our patient population. Multiple conservation strategies, including staffing changes, communication, adjustments to training, and even reuse of select PPE, can assist with conservation.

Conclusion

PPE in pharmacy cleanrooms is critical for the continued provision of sterile compounds with appropriate beyond-use dates and effective patient care. Pharmacy departments must employ multiple conservation strategies to ensure PPE is available for continued compounding of sterile products, and early planning and implementation of conservation strategies are key.
Comparison of Changes in Nasal Skin Sensation After Primary and Revision Rhinoplasty Procedures Using Semmes-Weinstein Monofilament Testing
Authors: Akyigit Abdulvahap , Keleş Erol , Yıldırım Yavuz Sultan Selim , Karlıdağ Turgut , Eroglu Orkun , Kaygusuz İrfan , Sakallıoglu Oner , Yalcın Sinasi
Published: March 2021

Background

Numbness of the nasal skin is one of the most common complications following rhinoplasty.

Objectives

The present study investigated postoperative changes in nasal skin sensation among primary and revision rhinoplasty patients and evaluated the recovery outcomes for both groups.

Methods

A prospective, randomized blinded study was undertaken involving 100 primary and 34 revision open rhinoplasty patients and 50 volunteers as control group. Semmes-Weinstein monofilament testing was performed on 7 designated nasal points preoperatively and at postoperative months 1, 3, 6, and 12, and the results were evaluated.

Results

Among the primary rhinoplasty patients, the change in reduced sensation on pressure to the tip and infratip over time was significant (P < 0.001), whereas there was no statistically significant difference for the other points. Among the revision rhinoplasty patients, the change in reduced sensation on pressure to the tip, infratip, and base of columella over time was significant (P < 0.001), whereas there was no statistically significant difference at the other points. In a comparison of the revision and primary rhinoplasty patients at all timepoints, a statistically significant reduction in sensation was noted on the application of pressure to all points in the revision patient group (P < 0.001).

Conclusions

This study found that the sense of touch on pressure returned to normal, aside from at the tip and infratip, by the end of month 12 in primary rhinoplasty patients. The revision rhinoplasty patients, in turn, were observed to have reduced sensation on pressure by the end of month 12, with the greatest reduction at the tip, infratip, and columellar base.

Level of Evidence: 3
Orange peel extract reduces the inflammatory state of skeletal muscle after downhill running via an increase in IL-1RA
Authors: Suzuki Toshihide , Shimizu Makoto , Yamauchi Yoshio , Sato Ryuichiro
Published: March 2021

It has been reported that orange peel extract (OPE) and the 4 major polymethoxyflavones (PMFs) in OPE have a protective effect against downhill running (DR)-induced skeletal muscle inflammation. However, the mechanism is not well understood. We investigated the potential of OPE and PMF compounds for increasing anti-inflammatory cytokine levels. The plasma interleukin-1 receptor antagonist (IL-1RA) level was increased 1 and 8 h after OPE administration in rats. Nobiletin induced the secretion of IL-1RA from C2C12 myotubes. In the inflammatory state of skeletal muscle after DR, OPE administration reduced nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB) expression, NF-κB-DNA binding, and monocyte chemotactic protein-1 mRNA levels, but these effects were all abrogated by the intravenous administration of IL-1RA neutralizing antibody. These results indicated that OPE reduces skeletal muscle inflammatory state after DR via an increase in IL-1RA, and that IL-1 receptor signaling is important for skeletal muscle inflammation after DR.
Increased C-Peptide Immunoreactivity in Insulin Autoimmune Syndrome (Hirata Disease) Due to High Molecular Weight Proinsulin
Authors: Kay Richard G , Barker Peter , Burling Keith , Cohen Mark , Halsall David , Reimann Frank , Gribble Fiona M , Semple Robert K , Church David
Published: March 2021

Background

Determination of C-peptide is important in the investigation of unexplained hyperinsulinemic hypoglycemia because a high C-peptide concentration usually indicates endogenous insulin hypersecretion. Insulin autoimmune syndrome (IAS) denotes hyperinsulinemic hypoglycemia due to insulin-binding antibodies that prolong insulin half-life. C-peptide clearance is considered to be unaffected, and although a marked C-peptide immunoreactivity in hypoglycemic samples has been reported, it has been suspected to be artifactual. High-resolution mass spectrometry enables examination of the basis of C-peptide-immunoreactivity in IAS.

Methods

Precipitation of plasma with polyethylene glycol was followed by C-peptide immunoassay. Plasma peptides extracted by solvent precipitation were characterized by nano-LC–MS/MS and analyzed using an untargeted data-dependent method. Peptides related to proinsulin, in amino acid sequence, were identified using proprietary bioinformatics software and confirmed by repeat LC–MS/MS analysis. Gel filtration chromatography coupled to LC–MS/MS was used to identify proinsulin-related peptides present in IAS immunocomplexes. Results were compared with those from C-peptide immunoassay.

Results

Polyethylene glycol precipitation of IAS plasma, but not control plasma, depleted C-peptide immunoreactivity consistent with immunoglobulin-bound C-peptide immunoreactivity. LC–MS/MS detected proinsulin and des 31,32 proinsulin at higher abundance in IAS plasma compared with control plasma. Analysis by gel filtration chromatography coupled to LC–MS/MS demonstrated proinsulin and des 31,32 proinsulin, but no C-peptide, in plasma immunocomplexes.

Conclusions

Antibody binding can enrich proinsulin and des 31,32 proinsulin in IAS immunocomplexes. Proinsulin cross-reactivity in some C-peptide immunoassays can lead to artifactually increased C-peptide results.
The Efficacy and Safety of Switching From Originator Infliximab to Single or Double Switch Biosimilar Among a Nationwide Cohort of Inflammatory Bowel Disease Patients
Authors: Khan Nabeel , Patel Dhruvan , Pernes Tyler , Patel Manthankumar , Trivedi Chinmay , Medvedeva Elina , Xie Dawei , Yang Yu-Xiao
Published: March 2021

Background

Data on safety and efficacy of switching to Renflexis (SB2) from originator Infliximab (IFX) (single switch) or from originator IFX to Inflectra (CT-P13) to Renflexis (double switch) are limited.

Methods

We conducted a retrospective cohort study in a nationwide cohort of patient with inflammatory bowel disease (IBD) in remission who were switched to SB2. The main exposure was the treatment course of SB2. There are 2 levels in this variable: single switch (IFX to SB2) and double switch (IFX to CT-P13 to SB2). The outcome is SB2 drug discontinuation rate and/or not being in remission after 1 year. Logistic regression was used to estimate the adjusted and unadjusted odds ratios with 95% confidence intervals to study the efficacy difference between single switch and double switch.

Results

A total of 271 IBD patients were started on SB2. Among them 52 (19.2%) patients did not achieve remission at 1 year and 14 (5.1%) patients had to discontinue SB2 due to adverse events). In logistic regression analysis after controlling for covariates, there was no statistically significant difference observed in regard to efficacy or safety of the single switch versus double switch to SB2 (adjusted odds ratio for double switch compared to single switch = 1.33 (95% confidence interval 0.74–2.41, P = 0.3432).

Conclusions

Among IBD patients in remission, double switch was equally effective as compared to a single switch. This will help reassure the gastroenterologists who have concerns regarding the safety and efficacy of switching between multiple biosimilars for treating IBD.
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning
Authors: Kropiwnicki Eryk , Evangelista John E , Stein Daniel J , Clarke Daniel J B , Lachmann Alexander , Kuleshov Maxim V , Jeon Minji , Jagodnik Kathleen M , Ma’ayan Avi
Published: March 2021

Understanding the underlying molecular and structural similarities between seemingly heterogeneous sets of drugs can aid in identifying drug repurposing opportunities and assist in the discovery of novel properties of preclinical small molecules. A wealth of information about drug and small molecule structure, targets, indications and side effects; induced gene expression signatures; and other attributes are publicly available through web-based tools, databases and repositories. By processing, abstracting and aggregating information from these resources into drug set libraries, knowledge about novel properties of drugs and small molecules can be systematically imputed with machine learning. In addition, drug set libraries can be used as the underlying database for drug set enrichment analysis. Here, we present Drugmonizome, a database with a search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis. Utilizing the data within Drugmonizome, we also developed Drugmonizome-ML. Drugmonizome-ML enables users to construct customized machine learning pipelines using the drug set libraries from Drugmonizome. To demonstrate the utility of Drugmonizome, drug sets from 12 independent SARS-CoV-2 in vitro screens were subjected to consensus enrichment analysis. Despite the low overlap among these 12 independent in vitro screens, we identified common biological processes critical for blocking viral replication. To demonstrate Drugmonizome-ML, we constructed a machine learning pipeline to predict whether approved and preclinical drugs may induce peripheral neuropathy as a potential side effect. Overall, the Drugmonizome and Drugmonizome-ML resources provide rich and diverse knowledge about drugs and small molecules for direct systems pharmacology applications.

Database URL: https://maayanlab.cloud/drugmonizome/.
CA125 but not NT-proBNP predicts the presence of a congestive intrarenal venous flow in patients with acute heart failure
Authors: Núñez-Marín Gonzalo , de la Espriella Rafael , Santas Enrique , Lorenzo Miguel , Miñana Gema , Núñez Eduardo , Bodí Vicent , González Miguel , Górriz José Luis , Bonanad Clara , Sanchis Juan , Bayés-Genís Antoni , Núñez Julio
Published: March 2021

Background

Intrarenal venous flow (IRVF) measured by Doppler ultrasound has gained interest as a potential surrogate marker of renal congestion and adverse outcomes in heart failure. In this work, we aimed to determine if antigen carbohydrate 125 (CA125) and plasma amino-terminal pro-B-type natriuretic peptide (NT-proBNP) are associated with congestive IRVF patterns (i.e., biphasic and monophasic) in acute heart failure (AHF).

Methods and results

We prospectively enrolled a consecutive cohort of 70 patients hospitalized for AHF. Renal Doppler ultrasound was assessed within the first 24-h of hospital admission. The mean age of the sample was 73.5 ± 12.3 years; 47.1% were female, and 42.9% exhibited heart failure with preserved ejection fraction. The median (interquartile range) for NT-proBNP and CA125 were 6149 (3604–12 330) pg/mL and 64 (37–122) U/mL, respectively. The diagnostic performance of both exposures for identifying congestive IRVF patterns was tested using the receiving operating curve (ROC). The cut-off for CA125 of 63.5 U/mL showed a sensibility and specificity of 67% and 74% and an area under the ROC curve of 0.71. After multivariate adjustment, CA125 remained non-linearly and positively associated with congestive IRVF (P-value = 0.008) and emerged as the most important covariate explaining the variability of the model (R2: 47.5%). Under the same multivariate setting, NT-proBNP did not show to be associated with congestive IRVF patterns (P-value = 0.847).

Conclusions

CA125 and not NT-proBNP is a useful marker for identifying patients with AHF and congestive IRVF patterns.
Machine learning phenotyping of scarred myocardium from cine in hypertrophic cardiomyopathy
Authors: Mancio Jennifer , Pashakhanloo Farhad , El-Rewaidy Hossam , Jang Jihye , Joshi Gargi , Csecs Ibolya , Ngo Long , Rowin Ethan , Manning Warren , Maron Martin , Nezafat Reza
Published: March 2021

Aims

Cardiovascular magnetic resonance (CMR) with late-gadolinium enhancement (LGE) is increasingly being used in hypertrophic cardiomyopathy (HCM) for diagnosis, risk stratification, and monitoring. However, recent data demonstrating brain gadolinium deposits have raised safety concerns. We developed and validated a machine-learning (ML) method that incorporates features extracted from cine to identify HCM patients without fibrosis in whom gadolinium can be avoided.

Methods and results

An XGBoost ML model was developed using regional wall thickness and thickening, and radiomic features of myocardial signal intensity, texture, size, and shape from cine. A CMR dataset containing 1099 HCM patients collected using 1.5T CMR scanners from different vendors and centres was used for model development (n=882) and validation (n=217). Among the 2613 radiomic features, we identified 7 features that provided best discrimination between +LGE and −LGE using 10-fold stratified cross-validation in the development cohort. Subsequently, an XGBoost model was developed using these radiomic features, regional wall thickness and thickening. In the independent validation cohort, the ML model yielded an area under the curve of 0.83 (95% CI: 0.77–0.89), sensitivity of 91%, specificity of 62%, F1-score of 77%, true negatives rate (TNR) of 34%, and negative predictive value (NPV) of 89%. Optimization for sensitivity provided sensitivity of 96%, F2-score of 83%, TNR of 19% and NPV of 91%; false negatives halved from 4% to 2%.

Conclusion

An ML model incorporating novel radiomic markers of myocardium from cine can rule-out myocardial fibrosis in one-third of HCM patients referred for CMR reducing unnecessary gadolinium administration.
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event
Authors: Fan Zheng , Yuan Tao , Liu Piao , Wang Lu-Yu , Jin Jian-Feng , Zhang Feng , Zhang Zhi-Sheng
Published: March 2021

Background

The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event.

Results

We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes.

Conclusions

The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.
Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
Authors: Blamey Ben , Toor Salman , Dahlö Martin , Wieslander Håkan , Harrison Philip J , Sintorn Ida-Maria , Sabirsh Alan , Wählby Carolina , Spjuth Ola , Hellander Andreas
Published: March 2021

Background

Large streamed datasets, characteristic of life science applications, are often resource-intensive to process, transport and store. We propose a pipeline model, a design pattern for scientific pipelines, where an incoming stream of scientific data is organized into a tiered or ordered “data hierarchy". We introduce the HASTE Toolkit, a proof-of-concept cloud-native software toolkit based on this pipeline model, to partition and prioritize data streams to optimize use of limited computing resources.

Findings

In our pipeline model, an “interestingness function” assigns an interestingness score to data objects in the stream, inducing a data hierarchy. From this score, a “policy” guides decisions on how to prioritize computational resource use for a given object. The HASTE Toolkit is a collection of tools to adopt this approach. We evaluate with 2 microscopy imaging case studies. The first is a high content screening experiment, where images are analyzed in an on-premise container cloud to prioritize storage and subsequent computation. The second considers edge processing of images for upload into the public cloud for real-time control of a transmission electron microscope.

Conclusions

Through our evaluation, we created smart data pipelines capable of effective use of storage, compute, and network resources, enabling more efficient data-intensive experiments. We note a beneficial separation between scientific concerns of data priority, and the implementation of this behaviour for different resources in different deployment contexts. The toolkit allows intelligent prioritization to be `bolted on' to new and existing systems – and is intended for use with a range of technologies in different deployment scenarios.
Runs of homozygosity are associated with staging of periodontitis in isolated populations
Authors: Mezzavilla Massimo , Navarra Chiara Ottavia , Di Lenarda Roberto , Gasparini Paolo , Bevilacqua Lorenzo , Robino Antonietta
Published: March 2021

Periodontitis is a common inflammatory disease characterized by a complex etiology, which is the result of a combination of genetic and environmental factors. Genetic variants linked to the periodontitis disease were already investigated, however, little was known regarding the severity of this disease. Recently, long runs of homozygosity (ROH) were associated with several multifactorial diseases. Therefore, in our work, we tried to assess the role of ROH and periodontitis status. We found an association between the excess of homozygosity owing to ROH and staging of periodontitis. More in detail, the total amount of homozygosity owing to ROH is positively associated with an increased severity of periodontitis (P = 0.0001). Regression tree analysis showed the impact of ROH burden in discriminating individuals with mild periodontitis stages I and II and periodontitis stages III and IV (P < 0.001). Furthermore, ROH mapping highlights several regions associated with a severe status of periodontitis (odds ratio > 1). Among them, we found a total of 33 genes. Interestingly, some of these genes were previously associated with granulocyte or platelet measures, both linked to the onset and the progression of periodontal disease. Our results suggest the not only single variants association test could help to risk assessment but even individual genomic features; furthermore, our ROH mapping highlighted the possible role of multiple genes in periodontal development.
Learning by doing: collaborative conceptual modelling as a path forward in ecosystem-based management
Authors: DePiper Geret , Gaichas Sarah , Muffley Brandon , Ardini Greg , Brust Jeffrey , Coakley Jessica , Dancy Kiley , Elliott G Warren , Leaning Dustin C , Lipton Douglas , McNamee Jason , Perretti Charles , Rootes-Murdy Kirby , Wilberg Michael J
Published: March 2021

Managers, stakeholders, and scientists recognize the need for collaborative, transparent, integrated approaches to complex resource management issues, and frameworks to address these complex issues are developing. Through the course of 2019, the Mid-Atlantic Fishery Management Council developed a conceptual model of ecosystem linkages and risks for summer flounder, a species of recreational and commercial fisheries importance. The proximal aim of the model was to develop a list of integrated management questions that could be refined and addressed through a future quantitative management strategy evaluation. As such, this conceptual model served as a scoping tool. However, the true value of the conceptual model lays elsewhere: familiarizing resource managers historically focused on single-species management with the potential utility of an ecosystem approach to management. This paper details the goals and development of the conceptual model and situates this process in the broader context of best practices for collaborative open science and scientific reproducibility. Further, it highlights a successful path by which the shift towards ecosystem-based management can be actuated.
Pricing formulas for perpetual American options with general payoffs
Authors: Rodrigo Marianito R
Published: March 2021

An American option gives the holder the right, but not the obligation, to buy/sell an underlying asset from/to the writer at an agreed strike price at any time on or before the expiry date. Options are mainly used for speculation and hedging. The pricing of options is a fundamental problem in mathematical finance. One of the attractions of options is that they can be used to construct a wide range of trading strategies characterized by different payoff functions. As a preliminary step in the valuation of American options for a variety of trading strategies, in this article the pricing of perpetual American options with general payoffs is considered, where the perpetual American call and put are special cases. Four broad classes of payoff functions are identified for which analytical pricing formulas can be derived by utilizing a Mellin transform technique and an optimization procedure. Depending on the class of payoff functions considered, free boundary problems with one or two boundaries are obtained. Illustrative examples are provided and benchmarked numerically with the binomial method. The characterization of different payoffs for perpetual American options considered in this article will be instrumental in the identification and pricing of new free boundary problems for (non-perpetual) American-style financial derivatives.
Integrating oscillator-based circadian clocks with crop growth simulations
Authors: Lochocki Edward B , McGrath Justin M
Published: March 2021

Circadian rhythms play critical roles in plant physiology, growth, development and survival, and their inclusion in crop growth models is essential for high-fidelity results, especially when considering climate change. Commonly used circadian clock models are often inflexible or result in complex outputs, limiting their use in general simulations. Here we present a new circadian clock model based on mathematical oscillators that easily adapts to different environmental conditions and produces intuitive outputs. We then demonstrate its utility as an input to Glycine max development models. This oscillator clock model has the power to simplify the inclusion of circadian cycles and photoperiodic effects in crop growth models and to unify experimental data from field and controlled environment observations.
Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)
Authors: Gearner Olivia M , Kamiński Marcin J , Kanda Kojun , Swichtenberg Kali , Smith Aaron D
Published: March 2021

Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.
Novel photochromic inhibitor for mitotic kinesin Eg5 which forms multiple isomerization states
Authors: Alrazi Islam Md , Sadakane Kei , Maruta Shinsaku
Published: March 2021

The mitotic kinesin Eg5 is a plus-end directed homotetrameric molecular motor essential for the formation of bipolar spindles during cell division. Kinesin Eg5 is overexpressed in cancer cells and hence considered as a target for cancer therapy; the inhibitors specific for Eg5 have been developed as anticancer drugs. In this study, we synthesized a novel functional photoresponsive inhibitor composed of spiropyran and azobenzene derivatives to control Eg5 function with multistage inhibitory activity accompanied by the formation of different isomerization states. The photochromic inhibitor spiropyran-sulfo-azobenzene (SPSAB) exhibited three isomerization states: spiro (SP)-trans, merocyanine (MC)-cis and MC-trans, upon exposure to visible light, ultraviolet and in the dark, respectively. SPSAB-induced reversible changes in the inhibitory activity of ATPase and motor activities correlating with photoisomerization among the three states. Among the three isomerization states of SPSAB, the SP-trans isomer showed potent inhibitory activity at an IC50 value of 30 µM in the basal ATPase assay. MC-trans and MC-cis exhibited less inhibitory activity at IC50 values of 38 and 86 µM, respectively. The results demonstrated that the novel photochromic inhibitor enabled precise control of Eg5 function at three different levels using light irradiation.
The 2019 International Society of Hip Preservation (ISHA) physiotherapy agreement on assessment and treatment of femoroacetabular impingement syndrome (FAIS): an international consensus statement
Authors: Takla Amir , O'Donnell John , Voight Michael , Byrd Thomas , Dienst Michael , Martin Rob Roy , Philippon Marc J , Enseki Keelan , Andrade Tony , Safran Marc , Christoforetti John Joseph , Martin Hal , Grant Louise , Campbell Ashley , Ryan Mark , Tyler Tim , McGovern Ryan P , Bizzini Mario , Kohlrieser David
Published: March 2021

The 2019 International Society of Hip Preservation (ISHA) physiotherapy agreement on femoroacetabular impingement syndrome (FAIS) was intended to build an international physiotherapy consensus on the assessment, non-surgical physiotherapy treatment, pre-/post-operative management, and return to sport decisions for those patients with FAIS. The panel consisted of 11 physiotherapists and 8 orthopaedic surgeons. There is limited evidence regarding the use of physiotherapy in the overall management of those with FAIS. Therefore, a group of ISHA member physiotherapists, who treat large numbers of FAIS patients and have extensive experience in this area, constructed a consensus statement to guide physiotherapy-related decisions in the overall management of those with FAIS. The consensus was conducted using a modified Delphi technique. Six major topics were the focus of the consensus statement: (i) hip assessment, (ii) non-surgical physiotherapy management, (iii) pre-habilitation prior to hip arthroscopy, (iv) post-operative physiotherapy rehabilitation, (v) stages of post-operative rehabilitation and (vi) return to sports criteria/guidelines after surgery.