bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct estimation of petrophysical properties from elastic parameter: A Case Study on the Batu Raja Formation
Authors: Pranatikta Krishna A. , Winardhi Sonny , Prastama Rizky A. 
Published: December 2024

Abstract
Rock physics analysis is a method to characterize petrophysical properties of rocks based on their elastic behaviour. However, this approach requires complete information on mineral composition of the matrix, pore-filling fluids, and in-situ conditions of the reservoir. Recently, a new approach was introduced to model the rock physics of clastic sediments using only acoustic impedance (AI) and the ratio between P- and S-wave velocity (Vp/Vs ratio) for predicting fluid saturation and porosity without requiring detailed Voigt-Reuss-Hill and/or Hashin-Shtrikman bounds and Gassmann fluid substitution. In this study, we combine AI and Vp/Vs ratio to form pseudo elastic impedance attributes that based on attribute rotation scheme. We apply the approach to carbonate sediments in the Batu Raja formation. We combined AI and Vp/Vs ratio to produce SCPEI (Simple Curved Pseudo Elastic Impedance) and SPEIL (Simple Pseudo Elastic Impedance for Lithology) attribute to obtain better estimation of water saturation and porosity, respectively. This new approach provides a way of estimating the two main petrophysical properties, namely porosity and water saturation, from elastic properties commonly derived from seismic inversion.
Remote Sensing of Gas Characteristics in 2018 Gamalama Eruption
Authors: Suhermat Mamat , Anarta Draniswari Windi , Santoso Imam 
Published: December 2024

Abstract
The area of Mount Gamalama is located near densely populated settlements and vital objects such as airports and ports. The eruption of Mount Gamalama in 2018 had a significant impact on aviation activities and social activities of the surrounding communities in the eruption area. The eruption caused airport closures and flight cancellations which impacted population mobility and the local economy. In addition, the eruption also caused losses in the agricultural and tourism sectors. The increase in SO2 gas concentration can indicate the presence of magma activity rising to the surface and can be an early indicator for early eruption detection. Additionally, the measurement of gas characteristics can also provide information on gas flow patterns and volcanic ash cloud movement in the atmosphere that can impact human health and safety as well as air transportation. Therefore, measuring gas characteristics using remote sensing technology is important to improve our understanding of volcano behavior and strengthen early warning systems to reduce disaster risks. This study utilized the GEE (Google Earth Engine) platform with Sentinel-5P satellite data to determine SO2 gas characteristics before and after the 2018 Gamalama’s eruption. SO2 gas concentrations from Mount Gamalama’s eruptions can be monitored using Sentinel-5P satellite imagery. The highest SO2 levels are observed at the crater, with the distribution affected by factors such as data collection timing, wind direction, and volcanic activity.
ANOVA-based performance evaluation of hybrid fibre-reinforced ECC with quarry dust in structural repair applications
Authors: George Mareena , Sathyan Dhanya 
Published: December 2024

Abstract
Engineered cementitious composites (ECC) are high-performance materials known for their exceptional ductility and micro-cracking behaviour due to the inclusion of small percentages of synthetic fibres. This characteristic makes ECC a promising alternative to conventional concrete. However, the high cost of silica sand, a key component of ECC, and the limited availability of polyvinyl alcohol fibres hinder its widespread adoption. Quarry dust powder (QDP), a byproduct of the manufactured sand production process, presents a significant environmental challenge due to its disposal. This study focuses on checking the suitability of quarry dust powder in replacing the silica sand of ECC. Quarry dust powder with particle size <150 μm is added by 5,10,15% by the total weight of the mix and its statistical significance is analysed using ANOVA. Also, the hybridization of fibre is done using 50% Polyvinyl Alcohol fibre (PVA)- 50% Polypropylene fibre (PP) combination and 50% PVA -50% Steel fibre (ST) combination of the total fibre content. The water binder ratio is varied by 0.35,0.32, 0.30.0.28. The acceptability of the ECC is checked by comparing its density, compressive strength, flexural strength, uniaxial tension test and sorptivity test. The repair property of the mix is analysed using bond strength tests like the splitting prism test and slant shear test. The pozzolanic activity of quarry dust powder is analysed using the strength activity index. An optimum mix is determined according to the findings as 10% of the total mix as quarry dust powder, 50% PVA-50%PP combination of total fibre and 0.3 water binder ratio. A surface plot is created using response surface plot to get a graphical representation of all parameters. Interaction plots and main effects plots are used as tools for visualizing and understanding the effects of dependent and independent variables. ANOVA models are developed for each parameter for future research in this area.
Identification and analysis of reference-independent movement event-related desynchronization
Authors: de Melo Gabriel Chaves , Castellano Gabriela , Forner-Cordero Arturo 
Published: December 2024

Abstract
Characterization of the electroencephalography (EEG) signals related to motor activity, such as alpha- and beta-band motor event-related desynchronizations (ERDs), is essential for Brain Computer Interface (BCI) development. Determining the best electrode combination to detect the ERD is crucial for the success of the BCI. Considering that the EEG signals are bipolar, this involves the choice of the main and reference electrodes. So far, no strategy to guarantee signals free of the activity from the reference electrode has achieved consensus among the scientific community. Therefore, mapping the ERD in terms of the spatial distribution of the main and reference electrodes can provide additional perspectives for the BCI field. The goal of this work is to identify subject-specific channels where ERD is temporally coupled to the initiation of an upper-limb motor task. We defined a criterion to determine the presence of the ERD linked to the movement onset and searched, separately for each subject, for the single channel with the most prominent ERD. The search was conducted over all available channels composed by a pair of electrodes, and the selected signals were analyzed according to their temporal and spatial characteristics. We found that alpha- and beta-band ERD temporarily linked to movement onset can be detected in atypical channels (pairs of electrodes) across the scalp. The selected channels were different across subjects. Four ERD temporal patterns were observed in terms of the initiation instant of the ERD. These patterns revealed that the M1 cortex seems to be related to later ERDs. Moreover, they were also associated to different cortical processes related to the motor task. To the best of our knowledge, this is the first time these findings are reported. Aiming at BCI development, further experiments with more subjects and with motor-imagery tasks are desirable for more robustness and applicability of these findings.
Printed textile metasurfaces for gain and directivity enhancement
Authors: Kajenski Adria , Strack Guinevere , Khushrushahi Shahriar , Akyurtlu Alkim 
Published: December 2024

Abstract
Wearable printed electronics are of significant recent interest for use in on-body communication devices, including antennas that are readily integrated into textiles using additive manufacturing. Directly printing the device onto textile reduces the need for costly, time-intensive processing steps; however, textile substrates impose design and performance limitations given that the design must be compatible with on-body usage and must also remain below maximum safe radiation levels. Herein, we present a passive solution for improving the performance of a commercial off the shelf omnidirectional antenna using textile metasurfaces. A modular system was developed for gain enhancement and pattern shaping using three metasurface elements with a band stop resonance at 6 GHz, where reflection is used to enhance gain. The versatility of a wearable metasurface is demonstrated for two of the designs which also offer a band pass at 2.4 GHz. Radiation pattern measurements conducted in an anechoic chamber showed that the metasurface achieved a gain improvement of up to 7.2 dB. This methodology enables a wearable, low-profile, passive, and non-destructive system for the improvement of existing wearable communication devices.
NetREm Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation
Authors: Khullar Saniya , Huang Xiang , Ramesh Raghu , Svaren John , Wang Daifeng 
Published: December 2024

Abstract

Motivation
Transcription factor (TF) coordination plays a key role in gene regulation via direct and/or indirect protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF coordination and gene regulation of various cell types remains unclear.

Results
To address this, we introduce our innovative computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for gene regulation. NetREm leverages network-constrained regularization using prior knowledge of PPIs among TFs to analyze single-cell gene expression data, uncovering cell-type coordinating TFs and identifying new TF-target gene candidate links. NetREm’s performance is validated using simulation studies and benchmarked across several datasets in humans, mice, and yeast. Further, we showcase NetREm’s ability to prioritize valid novel human TF-TF coordination links in 9 peripheral blood mononuclear and 42 immune cell sub-types. We apply NetREm to examine cell types in central and peripheral nerve systems (e.g. neuronal, glial, Schwann cells) as well as in Alzheimer’s disease. Top predictions are validated with experimental data from rat, mouse, and human models. Additional functional genomics data helps link genetic variants to TF-TF coordination.

Availability and implementation
https://github.com/SaniyaKhullar/NetREm
Relative contributions of genetic and environmental factors to palatal morphology: a longitudinal twin study
Authors: Giri Jamal , Bockmann Michelle , Brook Alan , Gurr Angela , Palmer Lyle , Brook O’Donnell Matthew , Hughes Toby 
Published: December 2024

Abstract

Objectives
This study aimed to determine the genetic and environmental contributions to phenotypic variations of palatal morphology during development.

Methods
Longitudinal three-dimensional digital maxillary dental casts of 228 twin pairs (104 monozygotic and 124 dizygotic) at primary, mixed, and permanent dentition stages were included in this study. Landmarks were placed on the casts along the midpoints of the dento-gingival junction on the palatal side of each tooth and the mid-palatine raphe using MeshLab. Palatal widths, depths, length, area, and volume were measured using those landmarks. Univariate genetic structural equation modelling was performed on twin data at each stage of dental development.

Results
Except for anterior depth, all palatal dimensions increased significantly from the primary to permanent dentition stages. The phenotypic variance for most of the palatal dimensions during development was best explained by a model, including additive genetic and non-shared environment variance components. Variance in volume and area in the primary dentition stage was best explained by a model including additive genetic, shared environment, and non-shared environment variance components. For posterior palatal depth and width, narrow-sense heritability estimates were above 0.8 for all dental developmental stages. In contrast, heritability estimates for other palatal traits fluctuated during development.

Limitation
This study was limited to twins of European ancestry.

Conclusions
Additive genetic and non-shared environmental factors primarily influenced palatal morphology during development. While the genetic influence on different aspects of the palate varied throughout development, it was particularly strong in the posterior region of the palate and during the permanent dentition stage.
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine
Authors: He Yalan , Lai Jiyin , Wang Qian , Pan Bingyue , Li Siyuan , Zhao Xilong , Wang Ziyi , Zhang Yongbao , Tang Yujie , Han Junwei 
Published: December 2024

Abstract

Background
Single-sample pathway enrichment analysis is an effective approach for identifying cancer subtypes and pathway biomarkers, facilitating the development of precision medicine. However, the existing approaches focused on investigating the changes in gene expression levels but neglected somatic mutations, which play a crucial role in cancer development.

Findings
In this study, we proposed a novel single-sample mutation-based pathway analysis approach (ssMutPA) to infer individualized pathway activities by integrating somatic mutation data and the protein–protein interaction network. For each sample, ssMutPA first uses local and global weighted strategies to evaluate the effects of genes from mutations according to the network topology and then calculates a single-sample mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. To illustrate the performance of ssMutPA, we applied it to 33 cancer cohorts from The Cancer Genome Atlas database and revealed patient stratification with significantly different prognosis in each cancer type based on the ssMutPES profiles. We also found that the identified characteristic pathways with high overlap across different cancers could be used as potential prognosis biomarkers. Moreover, we applied ssMutPA to 2 melanoma cohorts with immunotherapy and identified a subgroup of patients who may benefit from therapy.

Conclusions
We provided evidence that ssMutPA could infer mutation-based individualized pathway activity profiles and complement the current individualized pathway analysis approaches focused on gene expression data, which may offer the potential for the development of precision medicine. ssMutPA is available at https://CRAN.R-project.org/package=ssMutPA.
Mitogenome comparative analysis of 3 Myotis species endemic to Mexico and detecting selection in OXPHOS genes
Authors: Gutiérrez Edgar G , Ortega Jorge 
Published: December 2024

Abstract
Concerning metabolic demands, powered flight stands out as a mode of locomotion characterized by exceptionally high energy requirements. Bats exhibit distinct anatomical and physiological features associated with flight, prompting the anticipation of adaptive evolution in protein-coding genes within their mitochondrial genomes crucial for the oxidative phosphorylation pathway. In this study, the complete mitogenomes of 3 Myotis species endemic to Mexico were obtained and evaluated to obtain signatures of adaptive evolution in genes encoding mitochondrial proteins. The mitochondrial genomes span 17,147; 17,148; and 17,171 bp in size of M. findleyi, M. vivesi, and M. planiceps, respectively. A phylogenetic analysis focusing on the 13 protein-coding genes supports the delimitation of several clades included in the genus Myotis. Notably, Branch Models propose that Cox1, Cytb, and Nad4 may be subject to more robust purifying selection compared to other mitochondrial genes, while the Nad5 gene likely experiences positive selection pressure. The statistical analysis supports that Branch-Site Models contribute insights into 5 genes featuring amino acid sites potentially under selection pressure. Further analysis revealed episodic diversifying selection in Cox3 and signatures of diversifying/positive selection in 5 genes. This research significantly advances our understanding of the adaptive evolution of mitochondrial protein-coding genes in chiropterans, shedding light on their potential role in sustaining active flight.
Policy effect evaluation under counterfactual neighbourhood intervention in the presence of spillover
Authors: Lee Youjin , Hettinger Gary , Mitra Nandita 
Published: December 2024

Abstract
Policy interventions can spill over to units of a population that is not directly exposed to the policy but are geographically close to the units receiving the intervention. In recent work, investigations of spillover effects on neighbouring regions have focused on estimating the average treatment effect of a particular policy in an observed setting. Our research question broadens this scope by asking what policy consequences would the treated units have experienced under counterfactual exposure settings. When we only observe treated unit(s) surrounded by controls—as is common when a policy intervention is implemented in a single city or state—this effect inquires about the policy effects under a counterfactual neighbourhood policy status that we do not, in actuality, observe. In this work, we extend difference-in-differences approaches to spillover settings and develop identification conditions required to evaluate policy effects in counterfactual treatment scenarios. These causal quantities are policy-relevant for designing effective policies for populations subject to various neighbourhood statuses. We develop several estimators that have desirable properties. We provide an illustrative data application to the Philadelphia beverage tax study.
Labour-Saving or Labour-Demanding? Replicating the Illumination of the 1459 Durandus
Authors: Ikeda Mayumi 
Published: December 2024

Abstract
This paper examines the illumination of a group of ten surviving copies of the Rationale divinorum officiorum of Guillelmus Durandus published by Johann Fust and Peter Schöffer in 1459. It considers the methods employed for replicating the design of the illumination of this group, focusing on the opening page for Book Seven (fol. 140r), a page that uniquely demonstrates several patterns of design. Three related designs, called here Versions A, B, and C, are identified on fol. 140r. Version A is the original design, from which Versions B and C seem to have been created independently. Typically, mechanical methods for transferring designs were used to support and/or speed up the illuminator’s work, but in the Durandus they were employed so rigorously that the process must have hindered the illuminators. The impetus for the adoption of these methods, therefore, must have come from the publishers, whose goal was to produce perfect ‘illuminated facsimiles’.
Repeatability of an extended phenotype: Potential causes and consequences of nest variation in Troglodytes aedon (Northern House Wren)
Authors: Carr Chandler E G , Swanson Zoë M , Reichard Dustin G 
Published: December 2024

ABSTRACT
Construction behavior is an aspect of the extended phenotype that allows organisms to build structures that alter their environments in potentially beneficial ways. Although individuals vary in the expression of this extended phenotype (e.g., structure morphology), the repeatability of construction behaviors remains understudied, especially among free-living populations. Many oviparous taxa construct nests, making them of particular interest because variation in nest architecture may directly affect fitness. Using a free-living, cavity-nesting songbird, Troglodytes aedon (Northern House Wren), as our model, we estimated the contribution of the primary builder (the female) to nest variability by measuring the repeatability of nest morphology between successive clutches. We further examined whether nest morphology was related to the dimensions of the nesting cavity, breeding date, or nest success. We found the composition of the cup lining to be a highly repeatable feature of the nesting female’s nest, although the size and composition of the structural platform appeared more related to the dimensions of the cavity. Nest morphology remained variable throughout the breeding season, showing no significant correlations with breeding date, and it was unrelated to clutch size or offspring survival. Our study suggests that variation in construction behavior is likely the product of multiple factors including the preferences of the builder and physical constraints. The absence of any clear links between construction behavior and fitness indicates that nest morphology is not under strong selection. As a result, diverse female building preferences may explain the extreme among-individual variation in nest structure in this species.
Progressive Multicomponent Intervention for Older Adults in Home Health Settings Following Hospitalization: Randomized Clinical Trial
Authors: Garbin Alexander J , Falvey Jason R , Cumbler Ethan , Derlein Danielle , Currier Deborah , Nordon-Craft Amy , Will Robert , Olivos Maegan , Forster Jeri E , Mangione Kathleen K , Stevens-Lapsley Jennifer E 
Published: December 2024

Abstract

Objectives
Reduced physical function following hospitalization places older adults at risk of adverse health events. Many older adults receive home health physical therapy to reverse their deconditioning; however, optimal approaches to improve physical function are currently not known. This study aimed to evaluate the effectiveness of a home health care approach comprised of high-intensity exercise, enhanced care transition, and protein supplementation.

Methods
Eligible participants included adults aged 65 years or older referred to home health care following hospitalization. Two hundred older adults who are medically complex were enrolled and were randomized 1:1 to (1) a high-intensity progressive, multi-component (PMC) intervention or (2) enhanced usual care (UC) comparison group. All participants received 12 visits over 60 days. The primary study outcome was change in the Short Physical Performance Battery (SPPB) from baseline to 60 days. Secondary outcomes included gait speed (usual, fast), modified Physical Performance Test, grip strength, Fatigue Severity Scale, Falls Efficacy Scale-International, physical activity (step count), and adverse events (falls, emergency department visits, hospitalizations). All outcomes were collected at baseline, then 30, 60, 90, and 180 days post baseline.

Results
There was no difference in 60-day SPPB change between groups with both groups experiencing significant improvements (PMC = 1.53 [95% CI: 1.00–2.05]; enhanced UC = 1.39 [95% CI = 0.89–1.88]). Differences were also not observed in secondary measures or adverse events at any time point.

Conclusion
An intervention consisting of high-intensity exercise, enhanced care transition, and protein supplementation was not associated with greater functional improvement at 60 days compared to enhanced UC in older adults receiving home health physical therapy.

Impact
The findings of this study demonstrate that a high-intensity progressive, multi-component intervention results in similar physical functional changes as an enhanced UC intervention in older adults who are medically complex and receiving home health care following hospital-associated deconditioning.