bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Envelope Glycoprotein Domain III (ED III) Based on Surface-Enhanced Raman Scattering for Dengue Diagnosis
Authors: Novaznursyah Costrada Aldo , Felicia  , Siti Aminah Nina , Fitriyah Masduki Fifi , Herman  , Natalia Dessy , Djamal Mitra 
Published: February 2024

Abstract
Surface-enhanced Raman Scattering (SERS) based ED III protein detection has been conducted as a dengue virus diagnosis. ED III is one of the ectodomains of the envelope located along the surface of the dengue virus and acts as a receptor for the virus with its host cells. The SERS substrate used in this study is On-Spec-lite SERS by NECTEC and fabricated as a grating surface coated with gold. The imaging results from SEM show that the average radius of gold nanoparticles on OnSpec-lite SERS is 60 nm. On the grating-Au surface, the grating period is 588 nm with 50 nm thickness of gold thin film. OnSpec-lite SERS has a more significant increase in Raman intensity than the grating-Au surface when detecting ED III using Raman spectroscopy. The amino acids in the ED III Raman bands are Glycine, Alanine, Histidine, and Proline. The highest intensity Raman band that appears is 850 cm-1. Based on the research done in dengue virus detection, ED III has a typical Raman peak of 850 cm-1 which is the Raman band of Glycine and Alanine with CCN symmetry stretching vibration mode (𝑣(CCN)). This distinctive characteristic of ED III can be used as a diagnostic to detect dengue virus.
Optimization of Semiconductor-Based SRR Metamaterials as Sensors
Authors: Soerbakti Yan , Saktioto  , Sulistyo Rini Ari , Astuti Budi , Syamsudhuha  , Anita Sofia , Suyanto Hery , Rati Yolanda 
Published: February 2024

Abstract
The development of hybrid sensor media is needed to achieve more efficient, sensitive, and accurate performance. Efforts to modify the structure of conventional metamaterials are carried out by integrating semiconductor materials which aim to improve the characteristics of optical properties, electrical properties, and sensitivity as sensors. This study aims to analyze and investigate changes in the optical properties of semiconductor-based metamaterials. The research was conducted through simulation and numerical methods to design and characterize the SRR metamaterial geometry, with a modified Nicolson-Ross-Weir approach, especially the optical parameters of refractive index. The single-cell square pattern SRR metamaterial geometry with a ring radius of 2.2 – 2.8 mm on quartz glass substrate designed at a smaller wavelength based on a maximum frequency source of 9 GHz. The square SRR metamaterial is integrated with several semiconductor materials such as silicon (Si), gallium arsenide (GaAs), and aluminum nitride (AlN). Changes in radius size cause a redshift with respect to radius enlargement. The increasing ring radius of SRR causes a higher resonance depth of the refractive index. Combining hybrid semiconductors with metamaterial results in more negative metamaterial properties as the refractive index becomes larger and negative. The addition of semiconductor material to the metamaterial substrate causes a negative refractive index to shift to a lower frequency.
Photoacoustic Imaging using Diode Laser for Soft Tissue Visualization
Authors: Tasmara Fikhri A. , Wahyuni Eka , Silalahi Harry M. , Widyaningrum R , Setiawan A , Mitrayana  
Published: February 2024

Abstract
This study aimed to develop a photoacoustic imaging system using a diode laser as a radiation source, and a condenser microphone as a soft-tissue image detector. These tools were set in a static position and combined with the mechanic component to move the object table in the X-Y direction and were controlled by a computer with a LabView program. The result showed the built photoacoustic imaging system was used to analyze soft tissue using a diode laser in the frequency range of over 15 kHz with a 24%-47% duty cycle modulation. Furthermore, the minimum shift of the mechanic component X-Y stage was 0.02 mm, the sampling data rate was 1 second/pixel, and the image showed soft tissue intensity is generally higher than non-biological materials.
Computing the endomorphism ring of an elliptic curve over a number field
Authors: Cremona John , Sutherland Andrew 
Published: February 2024

We describe deterministic and probabilistic algorithms to determine whether or not a given monic irreducible polynomial

H
∈

Z

[
X
]

H\in \mathbb {Z}[X]

is a Hilbert class polynomial, and if so, which one. These algorithms can be used to determine whether a given algebraic integer is the

j
j

-invariant of an elliptic curve with complex multiplication (CM), and if so, the associated CM discriminant. More generally, given an elliptic curve

E
E

over a number field, one can use them to compute the endomorphism ring of

E
E

. Our algorithms admit simple implementations that are asymptotically and practically faster than previous approaches.
Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis
Authors: Xu Wang , Zhang Houfang , Guo Wenhan , Jiang Lijun , Zhao Yunjie , Peng Yunhui 
Published: February 2024

Abstract
Nucleosomes represent hubs in chromatin organization and gene regulation and interact with a plethora of chromatin factors through different modes. In addition, alterations in histone proteins such as cancer mutations and post-translational modifications have profound effects on histone/nucleosome interactions. To elucidate the principles of histone interactions and the effects of those alterations, we developed histone interactomes for comprehensive mapping of histone–histone interactions (HHIs), histone–DNA interactions (HDIs), histone–partner interactions (HPIs) and DNA–partner interactions (DPIs) of 37 organisms, which contains a total of 3808 HPIs from 2544 binding proteins and 339 HHIs, 100 HDIs and 142 DPIs across 110 histone variants. With the developed networks, we explored histone interactions at different levels of granularities (protein-, domain- and residue-level) and performed systematic analysis on histone interactions at a large scale. Our analyses have characterized the preferred binding hotspots on both nucleosomal/linker DNA and histone octamer and unraveled diverse binding modes between nucleosome and different classes of binding partners. Last, to understand the impact of histone cancer-associated mutations on histone/nucleosome interactions, we complied one comprehensive cancer mutation dataset including 7940 cancer-associated histone mutations and further mapped those mutations onto 419,125 histone interactions at the residue level. Our quantitative analyses point to histone cancer-associated mutations' strongly disruptive effects on HHIs, HDIs and HPIs. We have further predicted 57 recurrent histone cancer mutations that have large effects on histone/nucleosome interactions and may have driver status in oncogenesis.
Establishment and comparison of human term placenta–derived trophoblast cells
Authors: Vidal Manuel S , Radnaa Enkhtuya , Vora Natasha , Khanipov Kamil , Antich Cristina , Ferrer Marc , Urrabaz-Garza Rheanna , Jacob Jeena E , Menon Ramkumar 
Published: February 2024

Abstract
Research on the biology of fetal–maternal barriers has been limited by access to physiologically relevant cells, including trophoblast cells. In this study, we describe the development of a human term placenta–derived cytotrophoblast immortalized cell line (hPTCCTB) derived from the basal plate. Human-term placenta–derived cytotrophoblast immortalized cell line cells are comparable to their primary cells of origin in terms of morphology, marker expression, and functional responses. We demonstrate that these can transform into syncytiotrophoblast and extravillous trophoblasts. We also compared the hPTCCTB cells to immortalized chorionic trophoblasts (hFM-CTC), trophoblasts of the chorionic plate, and BeWo cells, choriocarcinoma cell lines of conventional use. Human-term placenta–derived cytotrophoblast immortalized cell line and hFM-CTCs displayed more similarity to each other than to BeWos, but these differ in syncytialization ability. Overall, this study (1) demonstrates that the immortalized hPTCCTB generated are cells of higher physiological relevance and (2) provides a look into the distinction between the spatially distinct placental and fetal barrier trophoblasts cells, hPTCCTB and hFM-CTC, respectively.
Probabilistic k-swap method for uniform graph generation beyond the configuration model
Authors: Tabourier Lionel , Karadayi Julien 
Published: February 2024

Abstract
Generating graphs with realistic structural characteristics is an important challenge for complex networks analysis, as these graphs are the null models that allow to describe and understand the properties of real-world networks. However, the field lacks systematic means to generate samples of graphs with predefined structural properties, because it is difficult to devise a method that is both flexible and guarantees to get a uniform sample, that is where any graph of the target set has the same probability to be represented in the sample. In practice, it limits the experimental investigation to a handful of models, including the well-known Erdős–Rényi graphs or the configuration model. The aim of this paper is to provide such a method: we design and implement a Monte Carlo Markov Chain process which is both flexible and satisfies the uniformity condition. Its assumptions are that: (1) the graphs are simple, (2) their degree sequence is fixed and (3) the user has at least one graph of the set available. Within these limitations, we prove that it is possible to generate a uniform sample of any set of such graphs. We provide an implementation in python and extensive experiments to show that this method is practically operational in several relevant cases. We use it with five specific set of constraints and verify that the samples obtained are consistent with existing methods when such a method is available. In those cases, we report that state-of-the-art methods are usually faster, as our method favours versatility at the cost of a lower efficiency. Also, the implementation provided has been designed so that users may adapt it to relevant constraints for their own field of work.
Evaluation of a novel cuffless photoplethysmography-based wristband for measuring blood pressure according to the regulatory standards
Authors: van Vliet Mariska , Monnink Stefan H J , Kuiper Mathijs J , Constandse Jan C , Hoftijzer Dieke , Ronner Eelko 
Published: February 2024

Abstract

Aims
Elevated blood pressure (BP) is a key risk factor in cardiovascular diseases. However, obtaining reliable and reproducible BP remains a challenge. This study, therefore, aimed to evaluate a novel cuffless wristband, based on photoplethysmography (PPG), for continuous BP monitoring.

Methods and results
Predictions by a PPG-guided algorithm were compared to arterial BP measurements (in the sub-clavian artery), obtained during cardiac catheterization. Eligible patients were included and screened based on AAMI/European Society of Hypertension (ESH)/ISO Universal Standard requirements. The machine learning-based BP algorithm required three cuff-based initialization measurements in combination with ∼100 features (signal-derived and patient demographic-based). Ninety-seven patients and 420 samples were included. Mean age, weight, and height were 67.1 years (SD 11.1), 83.4 kg (SD 16.1), and 174 cm (SD 10), respectively. Systolic BP was ≤100 mmHg in 48 samples (11%) and ≥160 mmHg in 106 samples (25%). Diastolic BP was ≤70 mmHg in 222 samples (53%) and ≥85 mmHg in 99 samples (24%). The algorithm showed mean errors of ±3.7 mmHg (SD 4.4 mmHg) and ±2.5 mmHg (SD 3.7 mmHg) for systolic and diastolic BP, respectively. Similar results were observed across all genders and skin colours (Fitzpatrick I-VI).

Conclusion
This study provides initial evidence for the accuracy of a PPG-based BP algorithm in combination with a cuffless wristband across a range of BP distributions. This research complies with the AAMI/ESH/ISO Universal Standard, however, further research is required to evaluate the algorithms performance in light of the remaining European Society of Hypertension recommendations.

Clinical trial registration
www.clinicaltrials.gov, NCT05566886.
Electrocardiogram-based prediction of conduction disturbances after transcatheter aortic valve replacement with convolutional neural network
Authors: Jia Yuheng , Li Yiming , Luosang Gaden , Wang Jianyong , Peng Gang , Pu Xingzhou , Jiang Weili , Li Wenjian , Zhao Zhengang , Peng Yong , Feng Yuan , Wei Jiafu , Xu Yuanning , Liu Xingbin , Yi Zhang , Chen Mao 
Published: February 2024

Abstract

Aims
Permanent pacemaker implantation and left bundle branch block are common complications after transcatheter aortic valve replacement (TAVR) and are associated with impaired prognosis. This study aimed to develop an artificial intelligence (AI) model for predicting conduction disturbances after TAVR using pre-procedural 12-lead electrocardiogram (ECG) images.

Methods and results
We collected pre-procedural 12-lead ECGs of patients who underwent TAVR at West China Hospital between March 2016 and March 2022. A hold-out testing set comprising 20% of the sample was randomly selected. We developed an AI model using a convolutional neural network, trained it using five-fold cross-validation and tested it on the hold-out testing cohort. We also developed and validated an enhanced model that included additional clinical features. After applying exclusion criteria, we included 1354 ECGs of 718 patients in the study. The AI model predicted conduction disturbances in the hold-out testing cohort with an area under the curve (AUC) of 0.764, accuracy of 0.743, F1 score of 0.752, sensitivity of 0.876, and specificity of 0.624, based solely on pre-procedural ECG images. The performance was better than the Emory score (AUC = 0.704), as well as the logistic (AUC = 0.574) and XGBoost (AUC = 0.520) models built with previously identified high-risk ECG patterns. After adding clinical features, there was an increase in the overall performance with an AUC of 0.779, accuracy of 0.774, F1 score of 0.776, sensitivity of 0.794, and specificity of 0.752.

Conclusion
Artificial intelligence–enhanced ECGs may offer better predictive value than traditionally defined high-risk ECG patterns.
The Lutheran Experience in the Ottoman Middle East: Stephan Gerlach (1546–1612) and the History of Lutheran Accommodation
Authors: Calis Richard 
Published: February 2024

Abstract
This article examines what it meant to be Lutheran in the early modern Middle East. Its point of departure is a letter in which Stephan Gerlach, a sixteenth-century Lutheran chaplain to the imperial ambassador in Istanbul, asked his superiors about the type of behaviour that befitted him as a Lutheran. Was he allowed to wear a Turkish turban to see mosques and learn about Islam? Was it permissible for him in exceptional circumstances to accept communion under both kinds from a Roman Catholic monk? Was he allowed to postpone the Sunday sermon to attend Greek Orthodox ceremonies? Reconstructing how sixteenth-century Lutherans who had business in the early modern Middle East tried to resolve such issues not only affords new insights into the Lutheran experience in the Ottoman Empire; it also raises a set of fundamental questions about late sixteenth-century Lutheranism itself. Did Lutherans in this period develop forms of religious accommodation similar to those of early modern Catholics? Did travel in the Eastern Mediterranean demand a more flexible and more fluid form of Lutheranism? Could one even adhere to Lutheranism’s core principles so far away from the place where the movement had first taken root? Through an examination of various Lutheran treatises and travelogues, I show that sixteenth-century Lutheranism did not develop an official policy of accommodation. Instead, Lutheran responses to questions about accommodation, (dis)simulation and conformity were often makeshift and idiosyncratic, because Lutheranism formulated little to no official guidance on the movement as a lived religion.
KDM1A genotyping and expression in 146 sporadic somatotroph pituitary adenomas
Authors: Chasseloup Fanny , Regazzo Daniela , Tosca Lucie , Proust Alexis , Kuhn Emmanuelle , Hage Mirella , Jublanc Christel , Mokhtari Karima , Dalle Nogare Mattia , Avallone Serena , Ceccato Filippo , Tachdjian Gerard , Salenave Sylvie , Young Jacques , Gaillard Stephan , Parker Fabrice , Boch Anne-Laure , Chanson Philippe , Bouligand Jerome , Occhi Gianluca , Kamenický Peter 
Published: February 2024

Abstract

Importance
A paradoxical increase of growth hormone (GH) following oral glucose load has been described in ∼30% of patients with acromegaly and has been related to the ectopic expression of the glucose-dependent insulinotropic polypeptide (GIP) receptor (GIPR) in somatotropinomas. Recently, we identified germline pathogenic variants and somatic loss of heterozygosity of lysine demethylase 1A (KDM1A) in patients with GIP-dependent primary bilateral macronodular adrenal hyperplasia with Cushing's syndrome. The ectopic expression of GIPR in both adrenal and pituitary lesions suggests a common molecular mechanism.

Objective
We aimed to analyze KDM1A gene sequence and KDM1A and GIPR expressions in somatotroph pituitary adenomas.

Settings
We conducted a cohort study at university hospitals in France and in Italy. We collected pituitary adenoma specimens from acromegalic patients who had undergone pituitary surgery. We performed targeted exome sequencing (gene panel analysis) and array-comparative genomic hybridization on somatic DNA derived from adenomas and performed droplet digital PCR on adenoma samples to quantify KDM1A and GIPR expressions.

Results
One hundred and forty-six patients with sporadic acromegaly were studied; 72.6% presented unsuppressed classical GH response, whereas 27.4% displayed a paradoxical rise in GH after oral glucose load. We did not identify any pathogenic variant in the KDM1A gene in the adenomas of these patients. However, we identified a recurrent 1p deletion encompassing the KDM1A locus in 29 adenomas and observed a higher prevalence of paradoxical GH rise (P = .0166), lower KDM1A expression (4.47 ± 2.49 vs 8.56 ± 5.62, P &lt; .0001), and higher GIPR expression (1.09 ± 0.92 vs 0.43 ± 0.51, P = .0012) in adenomas from patients with KDM1A haploinsufficiency compared with those with 2 KDM1A copies.

Conclusions and relevance
Unlike in GIP-dependent primary bilateral macronodular adrenal hyperplasia, KDM1A genetic variations are not the cause of GIPR expression in somatotroph pituitary adenomas. Recurrent KDM1A haploinsufficiency, more frequently observed in GIPR-expressing adenomas, could be responsible for decreased KDM1A function resulting in transcriptional derepression on the GIPR locus.
Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution
Authors: Fornaini Nicola R , Černohorská Halina , do Vale Martins Lívia , Knytl Martin 
Published: February 2024

Abstract
Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.
Deep attributes: innovative LSTM-based seismic attributes
Authors: Roncoroni G , Forte E , Pipan M 
Published: February 2024

SUMMARY
Seismic attributes are derived measures from seismic data that help characterize subsurface geological features and enhance the interpretation of subsurface structures: we propose to exploit the hidden layers of Long–Short Time Memory neural network predictions as possible new reflection seismic attributes. The idea is based on the inference process of a neural network, which in its hidden layers stores information related to different features embedded in the input data and which usually are not considered. Neural network applications typically ignore such intermediate steps because the main interest lies in the final output, which is considered as the exclusive exploitable feature of the process. On the contrary, here we analyse the possibility to exploit the intermediate prediction steps, hereafter referred as ‘deep attributes’ because they are produced by a deep learning algorithm, to highlight features and emphasize characteristics embedded in the data but neither recognizable by traditional interpretation, nor evident with classical attributes or multi-attribute approaches. Nowadays, classical signal attributes are numerous and used for different purposes; we here propose an original strategy to calculate attributes previously never exploited, which are potentially complementary or a good alternative to the classical ones.
We tested the proposed procedure on synthetic and field 2-D and 3-D reflection seismic data sets to test and demonstrate the stability, affordability and versatility of the entire approach. Furthermore, we evaluated the performance of deep attributes on a 4-D seismic data set to assess the applicability and effectiveness for time-monitoring purposes and comparing them with the sweetness attribute.