bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the Performance of Spline Interpolation Method in Mapping and Estimating the Total Suspended Solids over the Coastal Water of Pulau Tuba, Kedah
Authors: Kamaruddin S A , Hashim A R , Zainol Z E , Ahmad A , Abd.Aziz K A , Roslani M A , Shuhaime N , Tajam J , Hamid H A , Mat Nazir E N
Published: July 2022

The purpose of this paper is to evaluate the performance of the spline interpolation method in predicting and mapping the concentration of Total Suspended Solids (TSS) in the surface water of Pulau Tuba, Kedah. Thirty sampling points were set up and geolocated using the Geographic Positioning System (GPS). Gravimetric analyses were used to determine the TSS level. Fifty percent of the total sampling points were randomly chosen for developing spatial models using regularised and tension spline methods. The research found that the tension spline methods outperform the regularised spline method. The Mean Squared Error (MSE), Root Mean Squared Error (RMSE), Mean Absolute Error (MAE), and Mean Absolute Error Percentage (MAPE) were reported at 351.641, 18.752, 15.81, and 21.51%, respectively. This study’s findings are critical in the domains of spatial statistics and interpolation for creating a precise map of water properties.
Application of GIS and MCDM on Natural Environment Effect toward the Durability of Water pipe: A Conceptual Study
Authors: Rashid Firdaus Abd , Othman Ainon Nisa , Sulaiman Saiful Aman , Naharudin Nabilah
Published: July 2022

Utility is considered as one of the most important systems in all countries. A structured network is defined as a network comprising specific components and subsystems. Leakage of water pipes is a common problem around the world. It is understood that water is a valuable resource to all living things. The aim of this study is to estimate the durability of water pipe based on natural environment factor in Selangor, Malaysia. There are several proposed objectives listed such as to identify the parameters that affect the durability of the pipe, to develop GIS modelling to predict the durability of water pipelines and to generate durability of pipeline prediction maps to the study area. The criteria such as temperature, soil moisture, soil type, acidity, resistivity, landuse and slope were selected from the expert opinion and also from the previous study. The method used is Analytical Hierarchy Process (AHP) and GIS. AHP technique were used to calculate the weightage for each of the criteria. In this study, map of the mildsteel waterpipe durability estimation can be produced using ArcGIS.
Monitoring of Rice Growth Phases Using Multi-Temporal Sentinel-2 Satellite Image
Authors: Badrul Hisham Nurul Hasniati , Hashim Nurhanisah , Saraf Noraain Mohamed , Talib Noorfatekah
Published: July 2022

Rice is the primary source of nutrition food of more than half of the world’s population, and it is hugely important in the global economic growth, food security, water use, and climate change. The need for satellite systems to monitor rice crops and assist in rice crop management is gaining in popularity. The European Space Agency’s (ESA) launched Sentinel-2 A + B twin platform’s which enhanced the temporal, spatial, and spectral resolution, opening the way for their widely use in crop monitoring. Aside from the technical features of the Sentinel-2 A and B constellation, the easily accessible type of information they generate as well as the appropriate support software have been significant improvements for rice crop monitoring. In this study, the spectral reflectance has been analysed to find how far their potential in determining rice growth phases. The highest spectrum in reflectance was observed in the near infrared (NIR) region (842 nm). Because of the structure of mesophyll cells tissues and the inner backscatter of air spaces, moisture content, and air–water abstraction layers within the leaves, the reflectance in the NIR region seems to be much larger than in the visible band. The multi-temporal vegetation index namely Normalized Difference Vegetation Index (NDVI), Soil Adjusted Vegetation Index (SAVI), and Normalized Difference Moisture Index (NDMI) have derived from ten Sentinel-2 images cover the entire rice season. These indices have been tested to determine the rice growth phases over the rice season. The spatial distribution of each tested indices is displayed in the map output. The maps are then analysed and compared to determine the potential of each index in determining rice growth phases. It was discovered in this study that there was a quadratic correlation between all of the tested indices and rice age. The Normalized Difference Vegetation Index (NDVI) is the most accurate vegetation index for estimating rice growth phases, followed by SAVI and NDMI.
Oil Palm Plantation Land Cover and Age Mapping Using Sentinel-2 Satellite Imagery and Machine Learning Algorithms
Authors: Jarayee A N , Shafri H Z M , Ang Y , Lee Y P , Bakar S A , Abidin H , Lim H S , Abdullah R
Published: July 2022

Nowadays, there are various techniques and methods used in land cover classification using remote sensing data especially in oil palm monitoring. This study discussed the oil palm mapping using satellite imagery (Sentinel-2) and classification of land cover features using machine learning algorithms such as linear support vector classifier (LSVC), random forests (RF) and deep neural network (DNN). A total 13218 sampling points (80% of the total sampling points used as training samples and 20% applied as testing samples) were randomly selected in the study area which were then classified into six land cover features; water, bare soil, forest, immature oil palm (the age of 2-8 year), mature oil palm (age >8 year) and built-up area. These data were validated by using spectral reflectance, Google Earth Pro and ground checking. The accuracy assessment was conducted by a confusion matrix method. The results showed that classification of land features using DNN with batch size 32 and epoch 100 has the highest accuracy which is 99.35% for overall accuracy and 98.49% kappa accuracy. This study demonstrated various machine learning algorithms that may be used to detect and classify the maturity of oil palm trees, which is vital to record in tree inventories for effective plantation management.
Evaluating Oil Palm Cultivation using Geospatial Approach in Kerdau, Temerloh District
Authors: Abdul Rahim Haris , Bidin Verinus
Published: July 2022

Oil palm is one of the cultivation that synonyms in Malaysia. Malaysia become one of the biggest palm oil producer globally after Indonesia. In order to achieve successful yield per year, oil palm need constant effort and labor to monitor them accordingly. Manual method in monitoring the palm oil consumes large amount of time and energy. Palm oil comes from the fleshy fruit of oil palms. Unrefined palm oil is sometimes referred to as red palm oil because of its reddish-orange color. Remote sensing technique utilizes usage of satellite imageries to analyzes healthiness and canopy features of palm oil plantation. There are several advantage in determining palm oil condition through multispectral and texture analysis in ERDAS Imagine and Envi. Utilizing Landsat-8 imagery, monitoring palm oil cultivation and yield can be effectively implemented in Malaysia. In this study, we will use three vegetation indices which are Normalized Differential Vegetation Index (NDVI), Soil Adjusted Vegetation Index (SAVI), and Ratio Vegetation Index (RVI). This study will demonstrate that selected satellite-derived vegetation indices can be used to estimate oil palm yields with reliable accuracy. In this work, the ability of selected vegetation indices, derived from a single-date archived high resolution satellite imagery, to estimate oil palm yields at the management block scale was demonstrated. This technique applied to determine the condition of the palm oil tree. Using remote sensing technique, the value of the vegetation indices will be determined and analyzed. Result from this process, palm oil condition can be evaluated. This study provides an important benchmark for applying remote sensing technology in the management of plantation-scale oil palm. Oil palm yield estimation based on empirical models, as described in this work, can be computerized using a simple spreadsheet interface so as to facilitate optimal agronomic intervention, particularly with regard to crop harvesting, crop stress alleviation and input application. However, it’s important to note that palm oil should not be confused with palm kernel oil. While both originate from the same plant, palm kernel oil is extracted from the seed of the fruit. It provides different health benefits.
Detection of in-Car-Abandoned Children via Deep Learning
Authors: Norman M. , Pauzi MFM. , Ismail MH. , Mohamad Z. , Rahim A. , Mohd FA. , Shafri HZM
Published: July 2022

Cases of children died in vehicle have been increased each year. Such incident sometimes may happen incidentally especially when children are seated at the rear seats and the problem occurs due to lacking of existing system in detecting children image in a car. Consequently, this study aims to detect the existence of "in-car-abandoned children" using deep learning algorithm. A set of children images model will be classified into two (2) classes; children and no-children via Convolutional Neural Network (CNN) classifier by integrating with programming language, namely TensorFlow. Interestingly, the proposed method can automatically learn pattern features and reduce the incompleteness caused by artificial design features. As a result, a model of sensor that can detect the whole children’s body in various poses with automatic tagging to the children’s image is designed. Accordingly, this study can assist to improve current vehicle systems and create awareness among parents regarding the importance of children’s safety.
A phantom-based study and clinical implementation of brainlab’s treatment planning system for radiosurgical treatments of arteriovenous malformations
Authors: Shrestha Nishan , Narayanasamy Ganesh , Kalantari Faraz , Sabouri Pouya , Xia Fen , Zhong Su
Published: July 2022

Purpose. Development of a simple, phantom-based methodology allowing for pilot applications for the Elements TPS cranio-vascular module and clinical implementation prior to AVM treatments. Methods. A customized phantom was developed to be visible in MRI and CT images. High resolution digital subtraction angiograms (DSAs) and CT images of the phantom were acquired and imported into the Brainlab Elements treatment planning system. A clinical treatment plan with 5 arcs was generated in cranial vascular planning module and delivered to the phantom using a Varian TrueBeam STx Linac equipped with HD-MLCs and Brainlab ExacTrac imaging system for non-coplanar setup verification. The delivered dose was verified using a calibrated ionization chamber placed in the phantom. Upon verification of the TPS workflow, three patients with AVM who have been treated to date at our center using the Brainlab’s cranial vascular module for AVM are presented here for retrospective review. Results. The difference between the planed and measured dose by the ionization chamber was found to be less than 1%. Following a successful dose verification study, a clinical workflow was created. Currently, three AVM patients have been treated successfully. Clinical aspects of imaging and treatment planning consideration are presented in retrospective setting. Conclusions. Dose verification of the Brainlab Elements cranial vascular planning module for intracranial SRS treatments of AVM on Varian TrueBeam was successfully implemented using a custom-made phantom with <1% discrepancy. The Brainlab Elements’ cranial vascular module was successfully implemented in clinical workflow to treat patients with AVM. This manuscript provides a guideline for clinical implementation of frameless Linac-based AVM treatment using the Brainlab Elements TPS.
Evolution of edge turbulent transport induced by L-mode detachment in the HL-2A tokamak
Authors: WU Ting , NIE Lin , YU Yi , GAO Jinming , LI Junyan , MA Huicong , WEN Jie , KE Rui , WU Na , HUANG Zhihui , LIU Liang , ZHENG Dianlin , YI Kaiyang , GAO Xiaoyan , WANG Weice , CHENG Jun , YAN Longwen , CAI Laizhong , WANG Zhanhui , XU Min
Published: July 2022

This paper presents the characteristics of L-mode detachment, together with the behavior of edge turbulent transport and plasma confinement on the HL-2A tokamak. Partially detached and pronounced detached states have been achieved in L-mode plasma. Stored energy was maintained before and after detachment. Edge turbulence and its transport have increased obviously in the partially detached state. In the pronounced detached state, redistribution of the density and temperature profiles due to detachment leads to low amplitude of electron temperature and pressure, as well as very weak edge turbulence and transport. Despite strong plasma radiation in the pronounced detached state, reduced edge turbulent transport contributes to maintaining stored energy in detached L-mode plasma in HL-2A. Different detachment states play an important role in the redistribution of density and temperature profiles, which requires further study.
Numerical study of viscosity and heat flux role in heavy species dynamics in Hall thruster discharge
Authors: SHASHKOV Andrey , LOVTSOV Alexander , TOMILIN Dmitri , KRAVCHENKO Dmitrii
Published: July 2022

A two- and three-dimensional velocity space axisymmetric hybrid-PIC model of Hall thruster discharge called Hybrid2D has been developed. The particle-in-cell (PIC) method was used for neutrals and ions (heavy species), and fluid dynamics on a magnetic field-aligned (MFA) mesh was used for electrons. A time-saving method for heavy species moment interpolation on a MFA mesh was developed. The method comprises using regular rectangle and irregular triangle meshes, connected to each other on a pre-processing stage. The electron fluid model takes into account neither inertia terms nor viscous terms and includes an electron temperature equation with a heat flux term. The developed model was used to calculate all heavy species moments up to the third one in a stationary case. The analysis of the viscosity and the heat flux impact on the force and energy balance has shown that for the calculated geometry of the Hall thruster, the viscosity and the heat flux terms have the same magnitude as the other terms and could not be omitted. Also, it was shown that the heat flux is not proportional to the temperature gradient and, consequently, the highest moments should be calculated to close the neutral fluid equation system. At the same time, ions can only be modeled as a cold non-viscous fluid when the sole aim of modeling is the calculation of the operating parameters or distribution of the local parameters along the centerline of the discharge channel. This is because the magnitude of the viscosity and the temperature gradient terms are negligible at the centerline. However, when a simulation’s focus is either on the radial divergence of the plume or on magnetic pole erosion, three components of the ion temperature should be taken into consideration. The non-diagonal terms of ion pressure tensor have a lower impact than the diagonal terms. According to the study, a zero heat flux condition could be used to close the ion equation system in calculated geometry.
Energy bounds for a fourth-order equation in low dimensions related to wave maps
Authors: Schmid Tobias
Published: July 2022

For compact, isometrically embedded Riemannian manifolds

N
↪

R

L

N \hookrightarrow \mathbb {R}^L

, we introduce a fourth-order version of the wave maps equation. By energy estimates, we prove an a priori estimate for smooth local solutions in the energy subcritical dimension

n
=
1

n = 1

,

2
2

. The estimate excludes blow-up of a Sobolev norm in finite existence times. In particular, combining this with recent work of local well-posedness of the Cauchy problem, it follows that for smooth initial data with compact support, there exists a (smooth) unique global solution in dimension

n
=
1

n=1

,

2
2

. We also give a proof of the uniqueness of solutions that are bounded in these Sobolev norms.
The 𝑀_{𝑑}-approximation property and unitarisability
Authors: Vergara Ignacio
Published: July 2022

We define a strengthening of the Haagerup–Kraus approximation property by means of the subalgebras of Herz–Schur multipliers

M
d

(
G
)

M_d(G)

(

d
≥
2

d\geq 2

) introduced by Pisier. We show that unitarisable groups satisfying this property for all

d
≥
2

d\geq 2

are amenable. Moreover, we show that groups acting properly on finite-dimensional CAT(0) cube complexes satisfy

M
d

M_d

-AP for all

d
≥
2

d\geq 2

. We also give examples of non-weakly amenable groups satisfying

M
d

M_d

-AP for all

d
≥
2

d\geq 2

.
Non-isogenous abelian varieties sharing the same division fields
Authors: Lombardo Davide
Published: July 2022

Two abelian varieties

A
1

,

A
2

A_1, A_2

over a number field

K
K

are strongly iso-Kummerian if the torsion fields

K
(

A
1

[
d
]
)

K(A_1[d])

and

K
(

A
2

[
d
]
)

K(A_2[d])

coincide for all

d
≥
1

d \geq 1

. For all

g
≥
4

g \geq 4

we construct geometrically simple, strongly iso-Kummerian

g
g

-dimensional abelian varieties over number fields that are not geometrically isogenous. We also discuss related examples and put significant constraints on any further iso-Kummerian pair.
Green groupoids of 2-Calabi–Yau categories, derived Picard actions, and hyperplane arrangements
Authors: Jørgensen Peter , Yakimov Milen
Published: July 2022

We present a construction of (faithful) group actions via derived equivalences in the general categorical setting of algebraic 2-Calabi–Yau triangulated categories.

To each algebraic 2-Calabi–Yau category

C

\mathscr {C}

satisfying standard mild assumptions, we associate a groupoid

G

C

\mathscr {G}_{ \mathscr {C} }

, named the green groupoid of

C

\mathscr {C}

, defined in an intrinsic homological way. Its objects are given by a set of representatives

m
r
i
g

C

mrig\mathscr {C}

of the equivalence classes of basic maximal rigid objects of

C

\mathscr {C}

, arrows are given by mutation, and relations are given by equating monotone (green) paths in the silting order. In this generality we construct a homomorphsim from the green groupoid

G

C

\mathscr {G}_{ \mathscr {C} }

to the derived Picard groupoid of the collection of endomorphism rings of representatives of

m
r
i
g

C

mrig\mathscr {C}

in a Frobenius model of

C

\mathscr {C}

; the latter canonically acts by triangle equivalences between the derived categories of the rings.

We prove that the constructed representation of the green groupoid

G

C

\mathscr {G}_{ \mathscr {C} }

is faithful if the index chamber decompositions of the split Grothendieck groups of basic maximal rigid objects of

C

\mathscr {C}

come from hyperplane arrangements. If

Σ
2

≅
i
d

\Sigma ^2 \cong id

and

C

\mathscr {C}

has finitely many equivalence classes of basic maximal rigid objects, we prove that

G

C

\mathscr {G}_{ \mathscr {C} }

is isomorphic to a Deligne groupoid of a hyperplane arrangement and that the representation of this groupoid is faithful.
Unleashing the power of STEAM
Authors: Ma Yiran , Walsh Kevin
Published: July 2022

Archaeoastronomy, or “the science of stars and stones”, is not only an engaging subject for high-school students, argue Yiran Ma and Kevin Walsh, it is also the ideal candidate for an expanded multidisciplinary approach: STEAM.
Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer
Authors: Liang Jing , Li Zong-Wei , Yue Cai-Tong , Hu Zhuo , Cheng Han , Liu Ze-Xian , Guo Wei-Feng
Published: July 2022

Finding personalized biomarkers for disease prediction of patients with cancer remains a massive challenge in precision medicine. Most methods focus on one subnetwork or module as a network biomarker; however, this ignores the early warning capabilities of other modules with different configurations of biomarkers (i.e. multi-modal personalized biomarkers). Identifying such modules would not only predict disease but also provide effective therapeutic drug target information for individual patients. To solve this problem, we developed a novel model (denoted multi-modal personalized dynamic network biomarkers (MMPDNB)) based on a multi-modal optimization mechanism and personalized dynamic network biomarker (PDNB) theory, which can provide multiple modules of personalized biomarkers and unveil their multi-modal properties. Using the genomics data of patients with breast or lung cancer from The Cancer Genome Atlas database, we validated the effectiveness of the MMPDNB model. The experimental results showed that compared with other advanced methods, MMPDNB can more effectively predict the critical state with the highest early warning signal score during cancer development. Furthermore, MMPDNB more significantly identified PDNBs containing driver and biomarker genes specific to cancer tissues. More importantly, we validated the biological significance of multi-modal PDNBs, which could provide effective drug targets of individual patients as well as markers for predicting early warning signals of the critical disease state. In conclusion, multi-modal optimization is an effective method to identify PDNBs and offers a new perspective for understanding tumor heterogeneity in cancer precision medicine.
High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression
Authors: Ke Hongjie , Ren Zhao , Qi Jianfei , Chen Shuo , Tseng George C , Ye Zhenyao , Ma Tianzhou
Published: July 2022

Motivation

The advancement of high-throughput technology characterizes a wide variety of epigenetic modifications and noncoding RNAs across the genome involved in disease pathogenesis via regulating gene expression. The high dimensionality of both epigenetic/noncoding RNA and gene expression data make it challenging to identify the important regulators of genes. Conducting univariate test for each possible regulator–gene pair is subject to serious multiple comparison burden, and direct application of regularization methods to select regulator–gene pairs is computationally infeasible. Applying fast screening to reduce dimension first before regularization is more efficient and stable than applying regularization methods alone.

Results

We propose a novel screening method based on robust partial correlation to detect epigenetic and noncoding RNA regulators of gene expression over the whole genome, a problem that includes both high-dimensional predictors and high-dimensional responses. Compared to existing screening methods, our method is conceptually innovative that it reduces the dimension of both predictor and response, and screens at both node (regulators or genes) and edge (regulator–gene pairs) levels. We develop data-driven procedures to determine the conditional sets and the optimal screening threshold, and implement a fast iterative algorithm. Simulations and applications to long noncoding RNA and microRNA regulation in Kidney cancer and DNA methylation regulation in Glioblastoma Multiforme illustrate the validity and advantage of our method.

Availability and implementation

The R package, related source codes and real datasets used in this article are provided at https://github.com/kehongjie/rPCor.

Supplementary information

Supplementary data are available at Bioinformatics online.
Impact of climate change on the elevational and latitudinal distributions of populations of Tipulidae (Diptera) in Wales, United Kingdom
Authors: Devlin Jack J , Thomas Robert J , Long Sarah E , Boardman Pete , Dupuis Julian R
Published: July 2022

As dominant features of most ecosystems, insects are responsive to changes in climate, both over short temporal scales (e.g. seasonal fluctuations in abundance) and over longer evolutionary scales (e.g. decade-scale changes in patterns of biodiversity). One such taxonomic group that is sensitive to changing climate are the craneflies (Diptera: Tipulidae). Here, we used aggregated biodiversity data to examine elevational and latitudinal distributions of adult Tipulidae between 1976 and 2019 in Wales, UK, and we related these distributions to climatic patterns. Our analyses showed that species with earlier-emerging adults were most affected by weather conditions in the year before observation. Specifically, as temperature increased, observed elevation increased in high-precipitation conditions, remained stable in average-precipitation conditions and decreased in low-precipitation conditions. For species with later-emerging adults, associations were seen between elevation and weather conditions in the year of observation. Observed latitude generally exhibited a negative association with maximum temperature in the year before observation, with observations of Tipulidae trending southwards during the 43-year study period. Our results support consideration of emergence phenology, weather and habitat data when predicting species distributional changes attributable to climate change, which is vital in understanding the selection pressures that species face in a changing environment.
Rising from the Ashes: The Biogeographic Origins of Modern Coral Reef Fishes
Authors: Cantalice Kleyton M , Alvarado-Ortega Jesús , Bellwood David R , Siqueira Alexandre C
Published: July 2022

During the excavation of Mayan tombs, little did the archaeologists know that the fossils they discovered in the tomb stones would fundamentally alter our understanding of the earliest origins of coral reef fishes. Located just 500 kilometers from the point where an asteroid impact reconfigured the world's biological systems 66 million years ago, we find the earliest origins of three typical reef fish groups. Their presence in Mexico just 3 million years after this impact finally reconciles the conflict between the fossil and phylogenetic evidence for the earliest origins of reef fishes. The incorporation of these fossils into a global reconstruction of fish evolutionary history reveals a new picture of the early biogeography of reef fishes, with strong Atlantic links. From locations associated with biological destruction and societal collapse, we see evidence of the origins of one of the world's most diverse and spectacular marine ecosystems: coral reefs.
Multi-method investigation of factors influencing amyloid onset and impairment in three cohorts
Authors: Betthauser Tobey J , Bilgel Murat , Koscik Rebecca L , Jedynak Bruno M , An Yang , Kellett Kristina A , Moghekar Abhay , Jonaitis Erin M , Stone Charles K , Engelman Corinne D , Asthana Sanjay , Christian Bradley T , Wong Dean F , Albert Marilyn , Resnick Susan M , Johnson Sterling C ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2022

Alzheimer’s disease biomarkers are becoming increasingly important for characterizing the longitudinal course of disease, predicting the timing of clinical and cognitive symptoms, and for recruitment and treatment monitoring in clinical trials. In this work, we develop and evaluate three methods for modelling the longitudinal course of amyloid accumulation in three cohorts using amyloid PET imaging. We then use these novel approaches to investigate factors that influence the timing of amyloid onset and the timing from amyloid onset to impairment onset in the Alzheimer's disease continuum.

Data were acquired from the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Baltimore Longitudinal Study of Aging (BLSA) and the Wisconsin Registry for Alzheimer's Prevention (WRAP). Amyloid PET was used to assess global amyloid burden. Three methods were evaluated for modelling amyloid accumulation using 10-fold cross-validation and holdout validation where applicable. Estimated amyloid onset age was compared across all three modelling methods and cohorts. Cox regression and accelerated failure time models were used to investigate whether sex, apolipoprotein E genotype and e4 carriage were associated with amyloid onset age in all cohorts. Cox regression was used to investigate whether apolipoprotein E (e4 carriage and e3e3, e3e4, e4e4 genotypes), sex or age of amyloid onset were associated with the time from amyloid onset to impairment onset (global clinical dementia rating ≥1) in a subset of 595 ADNI participants that were not impaired before amyloid onset.

Model prediction and estimated amyloid onset age were similar across all three amyloid modelling methods. Sex and apolipoprotein E e4 carriage were not associated with PET-measured amyloid accumulation rates. Apolipoprotein E genotype and e4 carriage, but not sex, were associated with amyloid onset age such that e4 carriers became amyloid positive at an earlier age compared to non-carriers, and greater e4 dosage was associated with an earlier amyloid onset age. In the ADNI, e4 carriage, being female and a later amyloid onset age were all associated with a shorter time from amyloid onset to impairment onset. The risk of impairment onset due to age of amyloid onset was non-linear and accelerated for amyloid onset age >65. These findings demonstrate the feasibility of modelling longitudinal amyloid accumulation to enable individualized estimates of amyloid onset age from amyloid PET imaging. These estimates provide a more direct way to investigate the role of amyloid and other factors that influence the timing of clinical impairment in Alzheimer's disease.
Rare humanATP6V1Avariants provide unique insights into V-ATPase functions
Authors: Groszer Matthias
Published: July 2022

This scientific commentary refers to ‘Phenotypic and genetic spectrum of ATP6V1A encephalopathy: a disorder of lysosomal homeostasis’ by Guerrini et al. (https://doi.org/10.1093/brain/awac145).
Local neurodynamics as a signature of cortical areas: new insights from sleep
Authors: Armonaite Karolina , Nobili Lino , Paulon Luca , Balsi Marco , Conti Livio , Tecchio Franca
Published: July 2022

Sleep crucial for the animal survival is accompanied by huge changes in neuronal electrical activity over time, the neurodynamics.

Here, drawing on intracranial stereo-electroencephalographic (sEEG) recordings from the Montreal Neurological Institute (MNI), we analyzed local neurodynamics in the waking state at rest and during the N2, N3, and rapid eye movement (REM) sleep phases. Higuchi fractal dimension (HFD)—a measure of signal complexity—was studied as a feature of the local neurodynamics of the primary motor (M1), somatosensory (S1), and auditory (A1) cortices. The key working hypothesis, that the relationships between local neurodynamics preserve in all sleep phases despite the neurodynamics complexity reduces in sleep compared with wakefulness, was supported by the results. In fact, while HFD awake > REM > N2 > N3 (P < 0.001 consistently), HFD in M1 > S1 > A1 in awake and all sleep stages (P < 0.05 consistently). Also power spectral density was studied for consistency with previous investigations. Meaningfully, we found a local specificity of neurodynamics, well quantified by the fractal dimension, expressed in wakefulness and during sleep. We reinforce the idea that neurodynamic may become a new criterion for cortical parcellation, prospectively improving the understanding and ability of compensatory interventions for behavioral disorders.
A sequence labeling framework for extracting drug–protein relations from biomedical literature
Authors: Luo Ling , Lai Po-Ting , Wei Chih-Hsuan , Lu Zhiyong
Published: July 2022

Automatic extracting interactions between chemical compound/drug and gene/protein are significantly beneficial to drug discovery, drug repurposing, drug design and biomedical knowledge graph construction. To promote the development of the relation extraction between drug and protein, the BioCreative VII challenge organized the DrugProt track. This paper describes the approach we developed for this task. In addition to the conventional text classification framework that has been widely used in relation extraction tasks, we propose a sequence labeling framework to drug–protein relation extraction. We first comprehensively compared the cutting-edge biomedical pre-trained language models for both frameworks. Then, we explored several ensemble methods to further improve the final performance. In the evaluation of the challenge, our best submission (i.e. the ensemble of models in two frameworks via major voting) achieved the F1-score of 0.795 on the official test set. Further, we realized the sequence labeling framework is more efficient and achieves better performance than the text classification framework. Finally, our ensemble of the sequence labeling models with majority voting achieves the best F1-score of 0.800 on the test set.

Database URL

https://github.com/lingluodlut/BioCreativeVII_DrugProt
Serum Retinol Binding Protein 4 as a Potential Biomarker for Sarcopenia in Older Adults
Authors: Chang Chen-Lu , Li Yan-Ru , Wang Zhi-Yue , Li Mei-Lin , Jia Kai-Yue , Sun Hui-Xian , Wang Quan , Zhao Can , Lu Xiang , Gao Wei
Published: July 2022

Sarcopenia is characterized by progressive loss of muscle mass and function due to aging. Retinol-binding protein 4 (RBP4) is an adipokine with pro-inflammatory effects. However, the change of RBP4 concentration and its role in sarcopenia remains unclear. The aim of this study was to evaluate the association of serum RBP4 level with sarcopenia in the older adults. A total of 816 community-dwelling older adults aged ≥60 years were enrolled. Serum RBP4 was measured by enzyme-linked immunosorbent assay. Appendicular skeletal muscle mass index (ASMI), grip strength, and gait speed were measured. We found that serum RBP4 levels were higher in patients with sarcopenia when compared with those without sarcopenias (44.3 [33.9–57.7] vs 38.0 [28.0–48.4] μg/mL). Receiver operating characteristic curve analysis indicated that the optimal cutoff value of serum RBP4 level that predicted sarcopenia was 38.79 μg/mL with a sensitivity of 67.8% and a specificity of 53.3%. Multivariate logistic regression analysis showed that the subjects with a higher level of RBP4 had a higher risk of sarcopenia (adjusted odds ratio [OR] = 2.036, 95% CI = 1.449–2.861). Serum RBP4 concentration was negatively correlated with grip strength (r = −.098), gait speed (r = −.186), and AMSI (r = −.096). Moreover, serum RBP4 levels were higher in patients with severe sarcopenia when compared with those with moderate sarcopenia (49.0 [37.3–61.2] vs 40.4 [31.3–51.2] μg/mL). Taken together, our results demonstrate that serum RBP4 level is correlated with the risk and severity of sarcopenia in the older adults, indicating that RBP4 might serve as a surrogate biomarker for the screening and evaluation of sarcopenia.
Increased Macrophage-Specific Arterial Infiltration Relates to Noncalcified Plaque and Systemic Immune Activation in People With Human Immunodeficiency Virus
Authors: Toribio Mabel , Wilks Moses Q , Hedgire Sandeep , Lu Michael T , Cetlin Madeline , Wang Melissa , Alhallak Iad , Durbin Claudia G , White Kevin S , Wallis Zoey , Schnittman Samuel R , Stanley Takara L , El-Fakhri Georges , Lee Hang , Autissier Patrick , Zanni Markella V , Williams Kenneth C , Grinspoon Steven K
Published: July 2022

Background

Persistent immune activation is thought to contribute to heightened atherosclerotic cardiovascular disease (ASCVD) risk among people with human immunodeficiency virus (PWH).

Methods

Participants (≥18 years) with or without human immunodeficiency virus (HIV) and without history of clinical ASCVD were enrolled. We hypothesized that increased macrophage-specific arterial infiltration would relate to plaque composition and systemic immune activation among PWH. We applied a novel targeted molecular imaging approach (technetium-99m [99mTc]–tilmanocept single photon emission computed tomography [SPECT]/CT) and comprehensive immune phenotyping.

Results

Aortic 99mTc-tilmanocept uptake was significantly higher among PWH (n = 20) than participants without HIV (n = 10) with similar 10-year ASCVD risk (P = .02). Among PWH, but not among participants without HIV, noncalcified aortic plaque volume related directly to aortic 99mTc-tilmanocept uptake at different uptake thresholds. An interaction (P = .001) was seen between HIV status and noncalcified plaque volume, but not calcified plaque (P = .83). Systemic levels of caspase-1 (P = .004), CD14–CD16+ (nonclassical/patrolling/homing) monocytes (P = .0004) and CD8+ T cells (P = .005) related positively and CD4+/CD8+ T-cell ratio (P = .02) inversely to aortic 99mTc-tilmanocept uptake volume.

Conclusions

Macrophage-specific arterial infiltration was higher among PWH and related to noncalcified aortic plaque volume only among PWH. Key systemic markers of immune activation relating to macrophage-specific arterial infiltration may contribute to heightened ASCVD risk among PWH.

Clinical Trials Registration

NCT02542371.
Effects of Sublethal Concentrations of Insecticides on Survival and Reproduction of TwoBactroceraSpecies (Diptera: Tephritidae)
Authors: Nian Xiaoge , Luo Yaru , Ye Hui , He Xinyu , Wu Shujie , He Yurong , Wang Desen
Published: July 2022

The melon fruit fly, Bactrocera cucurbitae (Coquillett) and the pumpkin fruit fly, Bactrocera tau (Walker) (Diptera: Tephritidae), are important invasive pests on Cucurbitaceous hosts. The acute toxicity of five insecticides to females of these two fruit fly species was bio-assayed by membrane method, and effects of their sublethal concentration on the survival, reproduction, and ovary development of females were evaluated in the laboratory. Results showed that based on the LC50 values, both B. cucurbitae and B. tau were the most susceptible to trichlorfon. After treatment with sublethal concentration (LC30) of trichlorfon, abamectin+β-cypermethrin, spinetoram, and lambda-cyhalothrin, the female survival days of the two Bactrocera species were significantly shortened compared with the control. Moreover, the fecundity of two Bactrocera species was remarkably decreased, after exposure to abamectin+β-cypermethrin and trichlorfon LC30. However, the sublethal concentration (LC30) of insecticides had no significant influence on the egg hatchability of the fruit flies. Furthermore, after treatment with abamectin+β-cypermethrin LC30, the ovary length, width, and egg load of B. cucurbitae were significantly lower than that of the control; however, only the ovarian length and egg load of B. tau were significantly decreased on the 16th and 20th day. In conclusion, abamectin+β-cypermethrin has an excellent insecticidal activity against B. cucurbitae and B. tau.
Identifying priority areas for bat conservation in the Western Ghats mountain range, peninsular India
Authors: Raman Sreehari , Shameer Thekke Thumbath , Pooja Ushakumari , Hughes Alice C
Published: July 2022

Understanding patterns of species distribution and diversity plays a vital role in biodiversity conservation. Such documentation is frequently lacking for bats, which are relatively little studied and often threatened. The Western Ghats biodiversity hotspot in peninsular India is a bat hotspot with 63 species. We conducted a comprehensive bat survey across the southern Western Ghats and used maximum entropy modeling (MaxEnt) to model the potential distribution of 37 bat species for which sufficient data were available. We generated binary maps of each species using species-specific thresholds to estimate suitable habitat areas and overlaid binary maps of species to produce bat hotspots (we use the term “bat hotspot” for regions that were suitable for more than 25 bat species). We also estimated species richness across protected area networks in the southern Western Ghats to assess the level of protection. The highest levels of species richness were found mainly along the southmost Periyar–Agastyamalai landscape. The study also identified a 1,683 km2 area of potential bat hotspot and 726 km2 (43%) of the total bat hotspots are currently within the protected area network. However, more than 50% of suitable habitats for each of the 37 species remain unprotected. Therefore, conservation decisions are needed to take into account both bat hotspots and species with restricted distributions.
Isocitrate Dehydrogenase Mutations Are Associated with Different Expression and DNA Methylation Patterns of OLIG2 in Adult Gliomas
Authors: Mo Huan , Magaki Shino , Deisch Jeremy K , Raghavan Ravi
Published: July 2022

Isocitrate dehydrogenase (IDH) mutant gliomas are associated with a better prognosis in comparison to adult IDH wild-type glioma and glioma-CpG island methylator phenotypes. Although OLIG2 is mainly expressed in oligodendrocytes in normal adult brain, it is expressed in both astrocytomas and oligodendrogliomas. Utilizing the clinical, DNA methylation, and RNA-sequencing data from the Cancer Genome Atlas (TCGA) for lower-grade glioma and glioblastoma cohorts, we explored the association between IDH mutation status and OLIG2 expression on transcription, DNA methylation, and gene target levels. Compared to IDH wild-type gliomas, IDH mutant gliomas showed consistently higher expression of OLIG2 transcripts. OLIG2 overexpression is a good surrogate marker for IDH mutation with an AUC of 0.90. At the DNA methylation level, IDH-mutant gliomas showed hyper- and hypomethylation foci upstream of the OLIG2 transcription start site. Underexpressed OLIG2 target genes in IDH mutant glioma were enriched in cell cycle-related pathways. Thus, the differential expression of OLIG2 between IDH mutant and wild-type gliomas reflects involvement in multiple pathways in tumorigenesis.
How China's Cognitive Warfare Works: A Frontline Perspective of Taiwan's Anti-Disinformation Wars
Authors: Hung Tzu-Chieh , Hung Tzu-Wei
Published: July 2022

Cognitive warfare—controlling others’ mental states and behaviors by manipulating environmental stimuli—is a significant and ever-evolving issue in global conflict and security, especially during the COVID-19 crisis. In this article, we aim to contribute to the field by proposing a two-dimensional framework to evaluate China's cognitive warfare and explore promising ways of counteracting it. We first define the problem by clarifying relevant concepts and then present a case study of China's attack on Taiwan. Next, based on predictive coding theory from the cognitive sciences, we offer a framework to explain how China's cognitive warfare works and to what extent it succeeds. We argue that this framework helps identify vulnerable targets and better explains some of the conflicting data in the literature. Finally, based on the framework, we predict China's strategy and discuss Taiwan's options in terms of cognitive and structural interventions.
Suffering to Save Lives: Torture, Cruelty, and Moral Disengagement in Australia’s Offshore Detention Centres
Authors: Barnes Jamal
Published: July 2022

Since Australia re-established offshore processing on Manus Island and Nauru in 2012, there have been ongoing reports that asylum seekers and refugees are being subjected to torture and cruel, inhuman or degrading treatment or punishment (CIDT). People in detention have endured indefinite detention, inadequate provision of health care, and sexual, physical, and mental harm as the government attempts to ‘stop the boats’ and prevent deaths at sea. How can Australia continue to violate the UN Convention against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment, while at the same time, promote its offshore detention policies worldwide? This article explores how Australia has engaged in moral disengagement from the pain and suffering of people in detention. Examining self-deception strategies such as denial of torture, denial of responsibility, and denial of wrongdoing, it shows not only how Australia privileged migration deterrence goals over human rights considerations, but utilized legal and humanitarian arguments to evade accountability and deny the existence of, and responsibility and wrongdoing for, torture and CIDT. This article explores the under-examined issue of moral disengagement to show how it is exacerbating the vulnerability of asylum seekers and refugees to torture and CIDT along their migration journeys.
Development of the

B

last

O

rdnance and

O

ccupational Exposure

M

easure for Self-Reported Lifetime Blast Exposures
Authors: Sours Rhodes Chandler , Sandlain Rebecca , Ollinger John , Bryden Daniel , Dittmer Travis , DeGraba Thomas J , Teslovich Theresa
Published: July 2022

Introduction

To address the military gap in the standardized collection of lifetime blast exposures across clinical and research endeavors, researchers at the National Intrepid Center of Excellence (NICoE) completed a quality improvement project that utilized systematic, iterative focus groups that leveraged the input from various stakeholders including subject matter experts, clinical providers, and service members (SMs) to develop a comprehensive, self-report blast exposure inventory that could be completed within 5-10 minutes. This manuscript outlines the process of the development of this inventory.

Materials and Methods

This project included three phases of focus groups that occurred at the NICoE between August 2020 and March 2021 to collect feedback and input from relevant military stakeholders. The study team utilized related assessments available in the literature, together with clinical experience with the NICoE patient population, to inform the development of an initial draft inventory. Phase 1 consisted of blast injury research subject matter experts who had extensive experience researching and providing clinical care to SMs exposed to blast. Phase 2 consisted of NICoE clinicians across numerous clinical specialties. Phase 3 included current active duty patients in the NICoE intensive outpatient program.

Results

Following completion of the focus groups, a lifetime blast exposure inventory was developed in the form of a single page table including incoming, outgoing, training, and operational exposures and broken down by levels of weapon systems as well as breaching and explosive ordnance disposal exposures. In addition, select questions related to the first and most recent blast exposures and experience as an instructor for explosive ordnance disposal- and breaching-related training were included.

Conclusions

Researchers at the NICoE developed a self-report blast exposure inventory through a quality improvement project that included active, ongoing participation and feedback of clinical experts and military SMs. The end result is a brief, single page inventory that can be administered within 5-10 minutes. Although additional research is needed to refine and validate the inventory, the project team believes that the tool begins to address a long-standing gap in the DoD in the standardized collection of lifetime blast exposures.