bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of regeneration process of spent bleaching earth
Authors: Pranowo D , Dewanti B S D , Fatimah H , Setyawan H Y
Published: July 2020

The bleaching process is critical to improving the colour, flavour, taste, and stability of the final oil products of palm oil. The bleaching process uses bleaching earth (BE), which after several cycles, becomes a waste called Spent Bleaching Earth (SBE). Impurities cover the surface of SBE from the purification process. Regeneration by utilizing acid can increase the absorption capacity of SBE. The purpose of this research is to obtain the optimal combination of nitric acid concentration and heating temperature in the regeneration process of SBE. Response Surface Method (RSM) with Central Composite Design (CCD) was employed, using two factors of concentration of nitric acid and the heating temperature. The responses analysed in this research include colour, absorption efficiency, and yield. The obtained optimum condition in the treatment was found in the concentration of nitric acid (0.75 M) and a heating temperature of 430.8°C. The results of this research indicated colour absorption efficiency of 95.7557%, the yield of 52.4846%. The verified optimal solution obtained was 94.68% of absorption efficiency and 51.43% of yield. The Regenerated Spent Bleaching Earth (RSBE) optimum conditions compared to BE. The colour absorption efficiency utilizing BE was 96.77%, 2% higher than that of RSBE at 94.68%. The value of RSBE colour absorption efficiency in optimum conditions similar to that of the BE.
Effect of plant sound wave technology to increase productivity of mustard greens (Brassica juncea L.)
Authors: Hendrawan Y , Anniza K N , Prasetyo J , Damayanti R , Djoyowasito G
Published: July 2020

Plant sound wave technology (PSWT) is the use of sound waves to improve crop productivity and quality through optimization of stomata opening so that plants are able to absorb nutrients and water optimally. The purpose of this study is to test PSWT to increase the vegetative growth of mustard greens (Brassica juncea L.). The type of music used in PSWT is Javanese gamelan entitled Puspawarna. PSWT exposure time is given to plants in the morning and evening. The frequencies used are 3-5 kHz, 7-9 kHz, and 11-13 kHz. The mixture of organic planting media i.e. roasted husk, cocopeat, and moss with a ratio of 2: 2: 1 for soil, organic planting media, and organic fertilizer. Observations were made on plant height, plant length, wet weight, stomata opening, leaf chlorophyll, leaf area, and the number of plant leaves. The results showed that the frequency and the mixture of organic planting media significantly affected the wet weight, plant length, stomata opening, plant height, leaf chlorophyll, leaf area, and the number of leaves. The best PSWT method for growing mustard greens is using a frequency of 3-5 kHz with moss as the organic planting media. The maximum yield of vegetative growth resulted in the most optimal stomatal openings of 70.84–159.46 µm, with a plant height of 19.47 cm, plant length of 29.47 cm, leaf area of 31.99 cm2, number of leaves is 5.33 strands, leaf chlorophyll of 31.60 cci, and wet weight of 5.01 g.
Composting of chicken manure for biofertiliser production: a case study in Kidal Village, Malang Regency
Authors: Suhartini S , Wijana S , Surjono  , Wardhani N W S , Muttaqin S
Published: July 2020

Kidal Village, located in Malang Regency, has around 106 traditional chicken poultries with hens chicken population of 1,463,720 chickens, producing of 85.8 tonnes chicken manure per day. Currently the chicken manure is remained untreated and left on the bottom of the chicken cage over one-year period. Such practice has resulted odour problems especially to those area nearby the chicken poultry. The aim of this study is to investigate the potential of valorizing chicken manure for biofertiliser, as well as the impact of co-composting of chicken manure (CiM) and cow manure (CoM) with blotong (B) on the compost physic-chemical quality. Randomized block design (RBD) was used in this study with factor of feedstock composition and C/N ratio. Composting was carried out under aerobic condition, with manual turning over, for 30 days period. The results demonstrated that CiM, CoM and blotong has high organic content, but lower C/N value. Blotong has higher moisture content (MC), which is suitable as co-composting feedstock to increase MC value of the mixture. This study also observed that all treatments combination have similar trends in terms of changes in temperature, pH and MC during composting process. The quality of resulted compost were well within the Indonesian standard value for organic compost (SNI 19-7030-2004), indicating that composting of chicken manure or cow manure with and without blotong may become potential alternative routes for tackling pollution problems from the untreated manure.
Anaerobic digestion of fungally pre-treated oil palm empty fruit bunches: energy and carbon emission footprint
Authors: Hidayat N , Suhartini S , Utami R N , Pangestuti M B
Published: July 2020

Oil palm empty fruit bunches (OPEFB) is one of the abundant lignocellulosic biomass in Indonesia. However, high lignin content in EFOB has becoming one of the obstacles in valorising it as bioenergy resources, as it is hardly broken down by the microorganisms. Therefore, pre-treatment is often needed to enhance the biodegradation process of organic content in OPEFB. The biological pre-treatment is besieged to enhance the utilisation of OPEFB as bioenergy resources. This study was aimed to investigate the impact of fungal pre-treatment on the OPEFB characteristics and its methane potential, and to estimate the energy and carbon emission saving from anaerobic digestion (AD) of OPEFB. In this study, OPEFB was treated using Phanerocheate chrysosporium under the standard condition and incubated for 7 and 14 days. The energy and carbon emission footprint were calculated using AD Assessment Tool (ADAT) software. The results showed that fungal pre-treatment was able to increase organic matter and enhance methane potential. Estimation on energy (i.e. electrical and heat), however, indicated a lower energy balance and carbon emissions saving for fungal pre-treated OPEFB. The higher moisture content (MC) on treated OPEFB may reduce the biogas and methane production. Yet, further research is still required to have an in-depth understanding of improving the efficacy of biogas production from OPEFB by incorporating other green pre-treatment approaches.
Effect of sonic bloom frequency on the growth of red amaranth (Alternanthera amoena Voss)
Authors: Susilo B , Fitriani Y F
Published: July 2020

Red amaranth (Alternanthera amoena Voss) is able to be used not only as food plants but also as herbal plants. Due to a high nutrient content of red amaranth, the demand of this plant is continue to increase. Even though this plant has high demand, its productivity is relatively low. The Sonic-bloom was experimented to be applied on the red amaranth cultivation to improve the productivity. The purpose of this research is to determine the effect of various frequencies and duration of sonic-bloom exposure on the growth of the red amaranth plant (Alternanthera amoena Voss). The frequencies were set at two levels i.e. 3000-5000Hz and 7000-9000 Hz with the exposure duration were 15, 30, 45, 60 and 75 minutes respectively. The results showed that the frequency and duration of exposure have a significant influence on the cultivation parameters of red amaranth plants. Frequency treatment of 3000-5000 Hz and 7000-9000 Hz produced plants with 25.93 cm and 18.83 cm of height, 13 strands of leaves, 42 cm and 30.6 cm of plants length, 2841.01 μm2 and 3688.51 μm2 of stomata area, and 14.84 gr and 7.58 gr of wet plant weight respectively. These results were significantly different compared to the control (without sonic bloom treatment) that have 8.53 cm of height, 7-13 strands of leaves, 14.87 cm of plants length, 972.98 μm2 of stomata area, and 0.55 gr of wet weight. The best treatment in this study is the frequency of 3000-5000 Hz with exposure duration of 75 minutes, concluding that Sonic Bloom technology is able to improve the productivity of red amaranth plants.
The design and application of cracker dough kneading machine for increasing productivity and quality of mackerel crackers in Tambakasri village Malang
Authors: Hendrawan Y , Sandra S , Utami H N , Damayanti R
Published: July 2020

Mackerel cracker is a type of fish crackers with the basic ingredients of mackerel fish. The potential of mackerel fish production reaches 5000 tons/year. Moreover, it is supported by the Indonesian government’s policies which currently make the marine sector a superior program, so that business licensing of marine and fishery products can be faster. Mackerel cracker processing industry in Tambakasri village, Malang, Indonesia is still facing problems in its production process. This research was conducted in a small and medium-sized enterprise (SMEs) Yuan Mina Kartika which produces various fish crackers. The constraints in the SMEs include 1) the amount of production that has not been optimal, because of the inadequate production tools; 2) the process of refining fish that still uses traditional tools; 3) the process of kneading is done manually so that it takes a long time and produces uneven mackerel fish mixture. The purpose of this study is to develop and to test a cracker dough kneading machine to increase the productivity and quality of cracker products. Dough kneading machine uses a kneading system that is driven using an electric motor and transmission. Engine capacity is designed for 100 kg/hour using 1.5 HP with some outputs of dough tube. The test results showed a significant increase in time efficiency in the kneading process as well as the quality of the cracker dough which was better than the manual method.
Implementation of drinking water treatment device for primary school students and teachers (Case study at SDIT Insantama Malang, Indonesia)
Authors: Putranto A W , Izza N , Wibisono Y , Argo B D
Published: July 2020

The education and health sectors are placed in the top position of Indonesian goverment priority scales, since both have positive relationship and should be developed together. Education and health sector collaboration actually creates a health awareness for children as early as possible, which starts at the age of primary school. Unfortunately, the drinking water treatment device that can be operated continuously with low cost or energy for elementary students are never be found in Malang, Indonesia. This study aimed to install the drinking water treatment device based on membrane filtration and UV sterilization at primary school and also to analyze of teachers and students satisfaction toward the device applied. In this study, the importance performance analysis (IPA) and consumer satisfaction index (CSI) are used as a method for analyzing of teachers and students satisfaction. The data was collected from 100 respondents and 13 attributes were analyzed. The IPA results showed that maintenance of the device attribute was categorized as priority for improvement (quadrant I). Attributes that are categorized into quadrant II (maintain achievement) were appearance, freshness, taste, volume precision and quality testing in laboratory. While attributes that are categorized as second priority for improvement (quadrant III) are flavor, color, volume, hygiene of water and affordability. The attributes of practicality of use and the ergonomic design were categorized into quadrant IV or high level of performance implementation. The consumer satisfaction level by using CSI was 76%, indicating a high customer satisfaction level on the water produced by drinking water treatment device installed in their school.
The design of website-based sugarcane forecasting information system
Authors: Effendi M , Yuliani D D , Setyawan D T , Effendi U
Published: July 2020

Sugarcane (Saccharum officianarum) is widely used as raw material for sugar and MSG. Data on sugarcane production has not been used optimally, except for administrative purposes. The production data can be used to predict the yield of sugar cane of which can be utilized by cooperatives and farmers. This research was conducted to design an information system that can be used to forecast sugarcane yields in the working area of KUD Subur Malang, Indonesia. The information system design process is carried out by implementing Machine Learning. The results of sugarcane yield forecasting using machine learning implementation in KUD Subur showed the best results using the gradient boosting algorithm with 68% model accuracy. Web-based yield forecasting information system can be used as a production forecasting tool for KUD Subur to improve its business processes. Sugarcane forecasting information system can be well received by users.
2D 1T′-MoS2-WS2 van der Waals heterostructure for hydrogen evolution reaction: dispersion-corrected density functional theory calculations
Authors: Obligacion Joseph Kyle A , Putungan Darwin Barayang
Published: July 2020

Dispersion-corrected density functional theory calculations were implemented to investigate structural characteristics, as well as the hydrogen evolution reaction (HER) capability of 2D 1T′ phase MoS2-WS2 van der Waals heterostructures. Two van der Waals corrections were utilized in the study, namely DFT-D3 (semi-empirical-based) and vdW-DF2-B86R (ab-initio-based) corrections. Results show that the DFT-D3 correction stabilized the binding of the monolayers consistent with experimental observations, with binding energy per unit cell of -0.54 eV/cell. The Gibbs free energy of hydrogen adsorption ΔG

ads,H
, which is the lone descriptor of HER, were calculated for the two known adsorption sites in the 1T′ phase, termed S1 (sulfur site with elongated bonds, more active for HER) and S2 (sulfur site with compressed bonds, less active for HER). It is revealed that at the van der Waals region, the S1 and S2 sites, acting as a single adsorption site, become active for HER, with significantly lowered value of ΔG

ads,H
at 0.20-0.24 eV. This is linked to the synergistic interaction of the two sites in adsorbing hydrogen. In terms of electronic structure, the enhanced states in the vicinity of the Fermi level for the interacting S1 and S2 sites at the van der Waals region resulted from orbital hybridization among 3p states of the sulfur sites from the inner top and bottom surfaces. The merging of the two sites at the van der Waals region would result to HER efficiency that is expected to be higher by a factor of 2 compared to that on the top and bottom surfaces. This work has showed that 2D heterostructures could be of importance in catalysis, particularly in HER. Furthermore, it is showed that building a 2D heterostructure could be a good alternative to the application of strain in improving HER capability of 1T′ 2D materials without compromising the adsorption properties of other sites.
Unsupervised classification of single-molecule data with autoencoders and transfer learning
Authors: Vladyka Anton , Albrecht Tim
Published: July 2020

Datasets from single-molecule experiments often reflect a large variety of molecular behaviour. The exploration of such datasets can be challenging, especially if knowledge about the data is limited and a priori assumptions about expected data characteristics are to be avoided. Indeed, searching for pre-defined signal characteristics is sometimes useful, but it can also lead to information loss and the introduction of expectation bias. Here, we demonstrate how Transfer Learning-enhanced dimensionality reduction can be employed to identify and quantify hidden features in single-molecule charge transport data, in an unsupervised manner. Taking advantage of open-access neural networks trained on millions of seemingly unrelated image data, our results also show how Deep Learning methodologies can readily be employed, even if the amount of problem-specific, ‘own’ data is limited.
A rapid point-of-care ultrasound marker for muscle mass and muscle strength in older adults
Authors: Madden Kenneth M , Feldman Boris , Arishenkoff Shane , Meneilly Graydon S
Published: July 2020

Background/Objectives

Sarcopenia is defined as the gradual age-associated loss of both muscle quantity and strength in older adults, and is associated with increased mortality, falls, fractures and hospitalisations. Current sarcopenia criteria use dual-energy X-ray absorptiometry (DXA) measures of muscle mass, a test that cannot be performed at the bedside, unlike point-of-care ultrasound (PoCUS). We examined the association between ultrasonic measures of muscle thickness (MT, vastus medialis muscle thickness) and measures of muscle quantity and strength in older adults.

Methods

A total of 150 older adults (age ≥ 65; mean age 80.0 ± 0.5 years, 66 women, 84 men) were recruited sequentially from geriatric medicine clinics. Each subject had lean body mass (LBM, by bioimpedance assay), grip strength, mid-arm biceps circumference (MABC), gait speed and MT measured. All initial models were adjusted for biological sex.

Results

In our final parsimonious models, MT showed a strong significant correlation with all measures of muscle mass, including LBM (Standardised β = 0.204 ± 0.058, R2 = 0.577, P < 0.001) and MABC (Standardised β = 0.141 ± 0.067, R2 = 0.417, P = 0.038). With respect to measures of muscle quality, there was a strong significant correlation with grip strength (Standardised β = 0.118 ± 0.115, R2 = 0.511, P < 0.001) but not with subject performance (gait speed).

Conclusions

MT showed strong correlations with both measures of muscle mass (LBM and MABC) and with muscle strength (grip strength). Although more work needs to be done, PoCUS shows potential as a screening tool for sarcopenia in older adults.
Identification of critical factors for forming collaborative relationships between physicians and pharmacists
Authors: Turner Kyle M , Nelson Cory A , Pestka Deborah L , Sorensen Todd D
Published: July 2020

Purpose

The purpose of this study was to identify and describe strategies that have successfully achieved collaboration among physicians and pharmacists providing comprehensive medication management (CMM) to support development of CMM services.

Methods

A 2-phase, mixed-methods approach was employed to identify successful strategies for building pharmacist–physician relationships in primary care clinic settings. Phase I used a qualitative approach to identify strategies deemed successful in building relationships with physicians. An advisory group of pharmacists with experience building CMM practices assisted in the development of minimum criteria characterizing pharmacists as having strong collaborative relationships. Semi-structured interviews were conducted with 10 interviewees meeting established criteria. Researchers coded interview transcripts and identified the resulting strategies. Phase II employed a survey instrument to determine how frequently identified strategies are used and evaluate the relative level of perceived impact of each strategy, which was distributed to a national audience of pharmacists practicing in ambulatory care settings. Responses from pharmacists meeting prespecified criteria were included in the analysis.

Results

Thirty-three strategies were identified and grouped into 8 themes. In phase II, 104 survey respondents met defined criteria and were eligible to endorse use of identified strategies and rate their relative influence.

Conclusions

Thirty-three strategies were identified and grouped into 8 themes to aid pharmacists practicing CMM in developing stronger collaborative relationships with physician colleagues. A national sampling found many of these strategies were employed by a majority of pharmacists, who had found them to be influential in creating collaborative relationships.
Intramuscular Insertion of a Radiofrequency Microneedling Device for Facial Rejuvenation: A New Technique and Case Reports
Authors: Kornstein Andrew N
Published: July 2020

Skin laxity and dynamic rhytids that signify facial aging are due, in part, to atrophic changes and volume redistribution in the underlying layers of the face: the bone and soft tissue. A microneedling device that delivers bipolar radiofrequency (RF) energy directly to the reticular dermis has been shown to yield rejuvenated, tighter skin in 100% of patients. Herein, the author describes a modification to the standard dermal technique in which the skin is gently gathered with the nondominant hand, and the microneedling device is tilted to deliver RF energy to the mimetic muscles—including the frontalis, orbicularis oculi, and orbicularis oris—as well as the dermis. Muscle penetration was inferred by intraoperative bleeding and postoperative bruising, neither of which is typical of standard RF microneedling. Preliminary findings suggest that the modified procedure may yield greater aesthetic benefits than achieved with dermal application alone, including subtle lifting of the brow and oral commissure, upper-lip shortening with vermilion eversion, tightening of the lower-lid fat pads, and reduction in lateral-canthal rhytids. Although this modified technique will need to be optimized and evaluated in large, controlled studies, the initial results presented herein are encouraging.

Level of Evidence: 5
A Comparative Nesting Study of Red-tailed Hawks and Harris’ Hawks in Southern Arizona
Authors: Mader William J.
Published: July 2020

I studied the nesting of Red-tailed Hawks in the Sonoran Desert of Arizona in 1969-1976, emphasizing its ecology relative to the Harris' Hawk, a species that I have found to be sometimes polyandrous and have nest helpers. Red-tails averaged 2.32 eggs per clutch (59 nests) and Harris' Hawks 2.96 (50 nests). The clutch size distributions of the two species were significantly different. Nest success was 81% for Red-tails and 68% for Harris' Hawks, but may actually be slightly lower because a nest was considered successful if a chick was raised to an age of at least 28 days but not always to fledging. For Red-tails, the average number of chicks produced was 1.55 per nest attempt (42 nests) and for Harris' Hawks 1.60 (50 nests). Red-tails nested exclusively in saguaro cacti, but the more agile Harris' Hawks used not only easily accessible saguaro sites but enclosed tree sites as well. Nest site availability seemed to have no significant role in population regulation. The nesting cycle of the Red-tailed Hawk, from egg laying to fledging, was from February to June; for Harris' Hawks it was from February to early December (because of second broods). Optimum habitat and greater hunting versatility in the Harris' Hawk may allow it a less restricted breeding season in saguaro-palo verde desert than the Red-tail by providing essential food resources. These two factors, and nest helping if it is common, probably contribute to maximizing the productivity of Harris' Hawks in an arid environment with variable food resources.
Sexual Size Dimorphism and Survival of Male and Female Blackbirds (Icteridae)
Authors: Searcy William A. , Yasukawa Ken
Published: July 2020

In a between-species comparison of icterids, male survival decreases relative to female survival as the degree of sexual size dimorphism increases. This result is consistent with the hypothesis that male size is limited by survival selection in icterids; the degree of size dimorphism is known to correlate with the degree of polygyny in icterids, however, so the decreased relative survival of males in dimorphic species may be caused by some correlate of polygyny other than large size.

Survival estimates based on records of recovery of dead birds show positive correlations between male size and male survival and between female size and female survival, but survival estimates based on recaptures of live birds fail to show such relationships.
Timing of Shorebird Migration in Relation to Prey Depletion
Authors: Schneider David C. , Harrington Brian A.
Published: July 2020

The southward departure of migratory shorebirds (Charadrii) before the collapse of food supplies on the breeding grounds would seem to disprove the hypothesis that migratory timing is a trait actively maintained by selective pressures created by seasonal production of food supplies. In this study we looked at seasonal changes in the food supplies of shorebirds at a migratory stopover to see if dwindling food supplies here might explain early arrival from Arctic breeding grounds. For the three earliest migrants through Plymouth, Massachusetts we found substantial reductions of prey densities (7-90%) during migration (July-September). Reductions in prey density were not substantial before September for a later migrant. Caging experiments showed that the reductions in density of infaunal prey were due to predation. If these reductions are sufficient to cause energetic deficits among late arrivals, then competition may be an important selective agent in shaping migratory patterns.
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning
Authors: Tang Yi-Jun , Pang Yi-He , Liu Bin
Published: July 2020

Motivation

Related to many important biological functions, intrinsically disordered regions (IDRs) are widely distributed in proteins. Accurate prediction of IDRs is critical for the protein structure and function analysis. However, the existing computational methods construct the predictive models solely in the sequence space, failing to convert the sequence space into the ‘semantic space’ to reflect the structure characteristics of proteins. Furthermore, although the length-dependent predictors showed promising results, new fusion strategies should be explored to improve their predictive performance and the generalization.

Results

In this study, we applied the Sequence to Sequence Learning (Seq2Seq) derived from natural language processing (NLP) to map protein sequences to ‘semantic space’ to reflect the structure patterns with the help of predicted residue–residue contacts (CCMs) and other sequence-based features. Furthermore, the Attention mechanism was used to capture the global associations between all residue pairs in the proteins. Three length-dependent predictors were constructed: IDP-Seq2Seq-L for long disordered region prediction, IDP-Seq2Seq-S for short disordered region prediction and IDP-Seq2Seq-G for both long and short disordered region predictions. Finally, these three predictors were fused into one predictor called IDP-Seq2Seq to improve the discriminative power and generalization. Experimental results on four independent test datasets and the CASP test dataset showed that IDP-Seq2Seq is insensitive with the ratios of long and short disordered regions and outperforms other competing methods.

Availability and implementation

For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bliulab.net/IDP-Seq2Seq/. It is anticipated that IDP-Seq2Seq will become a very useful tool for identification of IDRs.

Supplementary information

Supplementary data are available at Bioinformatics online.
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports
Authors: Bressem Keno K , Adams Lisa C , Gaudin Robert A , Tröltzsch Daniel , Hamm Bernd , Makowski Marcus R , Schüle Chan-Yong , Vahldiek Janis L , Niehues Stefan M
Published: July 2020

Motivation

The development of deep, bidirectional transformers such as Bidirectional Encoder Representations from Transformers (BERT) led to an outperformance of several Natural Language Processing (NLP) benchmarks. Especially in radiology, large amounts of free-text data are generated in daily clinical workflow. These report texts could be of particular use for the generation of labels in machine learning, especially for image classification. However, as report texts are mostly unstructured, advanced NLP methods are needed to enable accurate text classification. While neural networks can be used for this purpose, they must first be trained on large amounts of manually labelled data to achieve good results. In contrast, BERT models can be pre-trained on unlabelled data and then only require fine tuning on a small amount of manually labelled data to achieve even better results.

Results

Using BERT to identify the most important findings in intensive care chest radiograph reports, we achieve areas under the receiver operation characteristics curve of 0.98 for congestion, 0.97 for effusion, 0.97 for consolidation and 0.99 for pneumothorax, surpassing the accuracy of previous approaches with comparatively little annotation effort. Our approach could therefore help to improve information extraction from free-text medical reports.

Availability  and implementation

We make the source code for fine-tuning the BERT-models freely available at https://github.com/fast-raidiology/bert-for-radiology.

Supplementary information

Supplementary data are available at Bioinformatics online.
netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling
Authors: Dong Zhengyang , Alterovitz Gil
Published: July 2020

Motivation

Single-cell RNA sequencing allows us to study cell heterogeneity at an unprecedented cell-level resolution and identify known and new cell populations. Current cell labeling pipeline uses unsupervised clustering and assigns labels to clusters by manual inspection. However, this pipeline does not utilize available gold-standard labels because there are usually too few of them to be useful to most computational methods. This article aims to facilitate cell labeling with a semi-supervised method in an alternative pipeline, in which a few gold-standard labels are first identified and then extended to the rest of the cells computationally.

Results

We built a semi-supervised dimensionality reduction method, a network-enhanced autoencoder (netAE). Tested on three public datasets, netAE outperforms various dimensionality reduction baselines and achieves satisfactory classification accuracy even when the labeled set is very small, without disrupting the similarity structure of the original space.

Availability and implementation

The code of netAE is available on GitHub: https://github.com/LeoZDong/netAE.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prospective investigations of concentration–clinical response for immunosuppressive drugs provide the scientific basis for therapeutic drug monitoring
Authors: Shaw Leslie M , Kaplan Bruce , Brayman Kenneth L
Published: July 2020

The performance of prospective concentration–clinical response investigations during the early stages of the development of new therapeutic agents can provide a more rigorous basis for therapeutic drug monitoring than the traditional retrospective review of drug concentrations vs clinical outcome. Here we discuss the application of the multicenter randomized concentration-controlled clinical trial study design, and related study designs, as applied to older commonly used and monitored drugs and to two new immunosuppressant drugs, mycophenolate mofetil and tacrolimus. Such studies can provide a more rigorous basis for assessing the risk/benefit associated with a target drug concentration in the individual patient and for designing future prospective pharmacokinetic and therapeutic drug monitoring investigations.
Bone formation and resorption biological markers in cosmonauts during and after a 180-day space flight (Euromir 95)
Authors: Caillot-Augusseau Anne , Lafage-Proust Marie-Héléne , Soler Claude , Pernod Josiane , Dubois Francis , Alexandre Christian
Published: July 2020

Long-term spaceflights induce bone loss as a result of profound modifications of bone remodeling, the modalities of which remain unknown in humans. We measured intact parathyroid hormone (PTH) and serum calcium; for bone formation, serum concentrations of bone alkaline phosphatase (BAP), intact osteocalcin (iBGP), and type 1 procollagen propeptide (PICP); for resorption, urinary concentrations (normalized by creatinine) of procollagen C-telopeptide (CTX), free and bound deoxypyridinoline (F and B D-Pyr), and Pyr in a 36-year-old cosmonaut (RTO), before (days −180, −60, and −15), during (from days 10 to 178, n = 12), and after (days +7, +15, +25, and +90) a 180-day spaceflight, in another cosmonaut (ASW) before and after the flight. Flight PTH tended to decrease by 48% and postflight PTH increased by 98%. During the flight, BAP, iBGP, and PICP decreased by 27%, 38%, and 28% respectively in CM1, and increased by 54%, 35%, and 78% after the flight. F D-Pyr and CTX increased by 54% and 78% during the flight and decreased by 29% and 40% after the flight, respectively. We showed for the first time in humans that microgravity induced an uncoupling of bone remodeling between formation and resorption that could account for bone loss.
Calibrated user-friendly reverse transcriptase-PCR assay: quantitation of epidermal growth factor receptor mRNA
Authors: Bor Mustafa Vakur , Sørensen Boe Sandahl , Rammer Paul , Nexø Ebba
Published: July 2020

We report a competitive reverse transcriptase-PCR (RT-PCR) assay and a calibrated user-friendly RT-PCR assay (CURT-PCR) for epidermal growth factor receptor (EGFR) mRNA. A calibrator was prepared from isolated rat liver RNA, and the amount of EGFR mRNA was determined by competitive RT-PCR. In CURT-PCR, a calibration curve was developed by plotting the ratio between the amount of PCR product originating from the calibrator and the RNA internal standard vs the amount of EGFR mRNA present in the calibrator. A fixed amount of RNA internal standard was coamplified with the EGFR mRNA present in the calibrator or in the sample, using the same primer set. The primers were chosen in regions of the EGFR mRNA that show 100% homology between human, rat, and mouse. The amount of EGFR in the unknown samples was calculated from the calibration curve based on the ratio between PCR product originating from the sample and the corresponding RNA internal standard. Competitive RT-PCR and CURT-PCR were used for rat liver samples from 21 different animals. Comparable results were obtained by the two methods. The imprecision of the CURT-PCR method was 8% (n = 20), and the imprecision of the traditional competitive RT-PCR was 16% (n = 17). We conclude that the CURT-PCR method developed is suitable for routine applications such as quantitation of EGFR expression in tumor biopsies. The imprecision is relatively low. Furthermore, the use of a calibration curve makes it possible to analyze a large number of samples in one analytical run and to accept or reject the results according to existing rules for quality assurance.
Development and validation of an automated latex-enhanced immunoassay for prealbumin
Authors: Holownia Peter , Newman David J , Thakkar Hansa , Bedzyk William D , Crane Helen , Olabiran Yemi , Davey Carol L , Price Christopher P
Published: July 2020

The measurement of circulating prealbumin has been shown to be clinically useful in the assessment of nutritional status, both as an initial screen and in the monitoring of nutritional recovery. We describe a fully automated, noncompetitive, homogenous, light-scattering immunoassay that has been developed for this analyte on a Dimension® (Dade) analyzer. A sheep anti-prealbumin IgG fraction was covalently coupled to 40-nm chloromethyl styrene particles and, after the addition of sample, polyethylene glycol-assisted immunoagglutination was monitored by turbidimetry. The prealbumin working assay range was 8–550 mg/L at a sample volume of 2 μL and a reaction time of 6.5 min. When data were analyzed using ANOVA, total and within-run assay imprecision values (CVs) were 1–5%, and calibration and reagent stabilities were in excess of 40 days. Mean analytical recoveries were 102% ± 4% (SD), and there was no lack of parallelism. Hemolysis, lipemia, and bilirubin did not interfere. Both plasma anticoagulated with heparin or EDTA and serum from plain or serum-separation tubes were acceptable as sample matrices. Comparison with the Beckman Array® method gave a Passing and Bablok regression of: Dimension analyzer = 1.01Beckman + 7.1 (n = 103), using a common calibrator. We conclude that the prealbumin method is appropriate for clinical use according to the analytical criteria used in this study.
Spectroscopic and Clinical Aspects of Noninvasive Glucose Measurements
Authors: Khalil Omar S
Published: July 2020

Frequent determination of glucose concentrations in diabetic patients is an important tool for diabetes management. This requires repetitive lancing and finger bleeding. Use of noninvasive (NI) detection techniques offers several advantages, such as the absence of pain and exposure to sharp objects and biohazard materials, the potential for increased frequency of testing, and hence, tighter control of the glucose concentrations, and the potential for a closed-loop system including a monitor and an insulin pump. These potential advantages have led to considerable interest in the commercialization of NI glucose monitoring devices. Review of the scientific, patent, and commercial literature indicates that the spectroscopic basis for NI determination of glucose is not yet well established, and attempts at commercialization may be several steps ahead of our understanding the origin and characteristics of an in vivo glucose-specific or glucose-related signal. Several technologies have potential for leading to viable measuring devices, but most of the data are based on in vitro experimentation. Because of the technical complexity of in vivo glucose measurements, this review aims at discussing the gap between the established need and current technology limitations.
Multicenter Clinical and Analytical Evaluation of the AxSYM Troponin-I Immunoassay to Assist in the Diagnosis of Myocardial Infarction
Authors: Apple Fred S , Maturen Andrew J , Mullins Richard E , Painter Pennell C , Pessin-Minsley Melissa S , Webster Robert A , Spray Flores Jennifer , DeCresce Robert , Fink Daniel J , Buckley Patrice M , Marsh Julie , Ricchiuti Vincent , Christenson Robert H
Published: July 2020

We evaluated the AxSYM troponin I (cTnI) immunoassay for assisting in the detection of acute myocardial infarction (AMI). At four sites, the total imprecision (CV) over 20 days was 6.3–10.2%. The minimum detectable concentration was 0.14 ± 0.05 μg/L. Comparison of cTnI measurements between the AxSYM and Stratus (n = 406) over the dynamic range of the AxSYM assay demonstrated good correlation, r = 0.881, with a proportional bias: AxSYM cTnI = 3.50(Stratus cTnI) − 1.10. The confidence intervals (95%) for the slope and intercept were 3.39–3.64 and −1.32 to −0.95, respectively. The expected cTnI concentration in healthy individuals was ≤0.5 μg/L, whereas the ROC curve-determined cutoff for AMI was 2.0 μg/L. This gave a diagnostic sensitivity of 91.8% and specificity of 92.4% when tested in serial samples collected within 24 h of admission in 633 patients presenting with chest pain, of which 122 had an AMI. The concordances of the AxSYM cTnI with the Stratus cTnI, OPUS cTnI, and Access cTnI were 95.3%, 95.1%, and 94.3%, respectively, from patients with suspected AMI. The AxSYM cTnI demonstrated excellent clinical specificity, ≥96%, in skeletal muscle injury, chronic renal disease, and same-day noncardiac surgery patients.
Home Range and Territoriality of Two Hawaiian Honeycreepers, the ‘ĀKohekohe and Maui Parrotbill
Authors: Pratt Thane K. , Simon John C. , Farm Brian P. , Berlin Kim E. , Kowalsky James R.
Published: July 2020

Hawaiian honeycreepers have radiated into a diversity of trophic niches and patterns of space-use. We investigated space-use in two honeycreeper species, the ‘Ākohekohe (Palmeria dolei), an endangered nectarivore, and Maui Parrotbill (Pseudonestor xanthophrys), an endangered wood excavator, by mapping the home ranges and dispersion of color-banded individuals at a study site in relatively undisturbed montane cloud forest on Maui Island, Hawai‘i. With 20% of outlying points excluded, home-range size averaged much smaller for adult male ‘Ākohekohe (0.56 ha) than for male Maui Parrotbill (2.26 ha). In both species, a female's home range mostly overlapped that of her mate. Adult male Maui Parrotbill defended year-round home ranges from which they excluded conspecifics except for their mates and dependent offspring. Although our data suggest that ‘Ākohekohe also maintained all-purpose territories, the evidence is less convincing because these birds were seen feeding in the home ranges of other individuals. By defending all-purpose territories, these two species depart from the more common honeycreeper pattern of sharing large, undefended home ranges.

Rango de Hogar y Territorialidad en Dos Mieleros de Hawai, Palmeria dolei y Pseudonestor xanthophrys

Resumen. Los mieleros de Hawai han radiado en una gran diversidad de nichos tróficos y patrones de uso del espacio. Investigamos el uso del espacio en dos especies amenazadas de mieleros, Palmeria dolei, un nectarívoro, y Pseudonestor xanthophrys, un excavador de madera. Mapeamos los rangos de hogar y dispersión de individuos marcadas con bandas de colores en un sitio relativamente no perturbado de bosque montano nublado, en la Isla Maui, Hawai. Excluyendo el 20% de los valores extremos, el tamaño promedio de los rangos de hogar de los machos adultos de P. dolei fue mucho menor (0.56 ha) que el de los machos de P. xanthophrys (2.26 ha). En ambas especies, el rango de hogar de la hembra se sobrepuso en gran parte al rango del macho. Los machos adultos de P. xanthophrys defendieron su territorio durante todo el año excluyendo a individuos conespecíficos con excepción de sus parejas y crías dependientes. A pesar que nuestros datos indican que P. dolei también mantuvo territorios, la evidencia es menos convincente debido a que estas aves fueron observadas forrajeando en rangos de hogar de otros individuos. Las dos especies estudiadas defienden sus territorios, lo cual las diferencia del patrón común observado en los mieleros, que consiste en compartir extensos rangos de hogar no defendidos.
P3394Carotid plaque neovascularization correlates to increased intraplaque blood-like tissue in acute coronary syndrome
Authors: Mantella L E , Colledanchise K N , Hetu M F , Weller M , Herr J E , Feinstein S B , Johri A M
Published: July 2020

Background

The assessment of carotid plaque composition has attracted great interest as a tool to predict plaque vulnerability and subsequent risk of cardiovascular events. These vulnerable plaque lesions are characterized by the presence of intraplaque neovascularization (IPN). Previously, grayscale pixel ranges of ultrasound images have been correlated to various human tissue types. Thus, using these ranges, it is possible to assess the composition of atherosclerotic plaque non-invasively.

Purpose

This study sought to determine the relationship between carotid plaque composition and the degree of neovascularization in patients presenting with acute coronary syndrome (ACS), when compared to patients with stable angina.

Methods

A carotid focused vascular ultrasound was performed in 92 participants who had recently undergone coronary angiography due to stable angina or ACS. In 81 participants found to have atherosclerotic plaque in at least one carotid artery, plaque composition was assessed for tissue-like types by pixel distribution analysis: grayscale ranges 0–4 (blood), 8–26 (fat), 41–76 (muscle), 112–196 (fibrous), and 211–255 (calcium) (Figure 1). Participants also received microbubble contrast to assess IPN. IPN was graded based on the presence and location of microbubbles within each plaque (0, not visible; 1, peri-adventitial; 2, plaque core) and averaged to obtain an overall score. An independent t-test was used to compare continuous variables. Pearson pairwise correlations were used to assess associations between IPN and tissue composition.

Results

In the overall sample population, increased average IPN score correlated with increased plaque % blood tissue type (rho=0.28; p=0.01). Patients presenting with ACS (n=32) had increased neovascularization (IPN score of 1.47 vs 1.09; p=0.4), compared to patients with stable angina. In addition, ACS patients with an IPN score ≥1.25 had higher levels of plaque % blood (1.97% vs 0.75%; p=0.02).In ACS patients only, % blood increased with IPN score (r=0.34; p=0.06) and % fibrous tissue decreased with IPN score (r=−0.42; p=0.02).

Figure 1

Conclusion

The proportion of blood-like tissue in carotid plaque is associated with neovascularization and is increased in ACS patients. This may indicate hemorrhage within the plaque leading to rupture. Increased fibrous tissue may have a protective role, stabilizing the plaque when present. This data suggests that carotid plaque composition may be used as an imaging biomarker for cardiovascular risk, and its incorporation into routine screening practices may improve patient risk stratification.

Acknowledgement/Funding

CIHR CGS-Doctoral Award, Heart and Stroke Foundation of Canada, Canada Foundation for Innovation
P312The acute impact of a high altitude ultra-trail race on the ECG
Authors: D'Ascenzi F , Zorzi A , Anselmi F , Ibrahim A , Spera L , Ceccon C , Mondillo S , Corrado D , Antonini-Canterin F , Pagliani L
Published: July 2020

Background

Ultra-endurance competitions are becoming increasingly popular but the consequences of ultra-endurance sports activity on the heart rhythm is still a debated issue. Some authors demonstrated that athletes engaging in ultra-endurance sports show a transient rise in cardiac biomarkers and right ventricular dysfunction after a competition, suggesting the possibility of an adverse arrhythmic remodeling and an increased risk of sudden cardiac death. The aim of our study was to evaluate the effects on heart rhythm of an ultraendurance high-altitude race.

Methods

The study was performed during the 2018 North Face® Lavaredo Ultra Trail mountain run. We recorded the ECG with the FDA-approved MyDiagnostick device. Recordings were performed at baseline the day before the run and immediately after the run in the available athletes. The ECG was analyzed for heart rate, QRS duration, QT interval duration corrected according to the Bazett formula and presence of at least one beat of presumed ventricular origin (PVB).

Results

A total of 545 athletes (83% males, mean age: 40±9 years), 241 running the 120 Km race and 304 running the 50 Km race, were included in the study. At baseline, athletes showed a mean heart rate of 64±14 bpm and a mean QRS duration of 92±18 ms. Three (0.5%) showed at least one PVB. Analysis of QTc interval duration showed a mean value of 412±25 ms. After the race, athletes showed a higher heart rate (91±13 bpm, p<0.001), a similar QRS duration (94±16 ms, p=0.32) and a longer QTc interval duration (447±25 ms, p<0.001), as compared to baseline data. The number of athletes showing at least 1 PVB significantly increased to 18 (3.3%, p=0.004) as compared to pre-race evaluation. Athletes engaged in the 120 Km run showed a slightly longer post-run QTc interval (450±24 versus 444±25 ms, p=0.009) while the post-run QRS duration was similar between the two groups. The presence of PVBs after the race was not correlated with the duration of QTc interval.

Conclusions

In this study we found an increased number of PVBs and a prolonged QTc duration after an ultra-endurance competition. Increased ventricular ectopic activity and QT prolongation recorded shortly after an intense and prolonged exercise could contribute to the increased risk of arrhythmias occurring after the finish line.