bluuebunny/crossref_metadata_2025 huggingface dataset:
I-Superfamily Conotoxins: Sequence and Structure Analysis
Authors: Mondal Sukanta , Vijayan Ramachandran , Shichina Kannambath , Babu Rajasekaran Mohan , Ramakumar Suryanarayanarao
Published: January 2025

I-superfamily conotoxins have four-disulfide bonds with cysteine arrangement C-C-CC-CC-C-C, and they inhibit or modify ion channels of nerve cells. They have been characterized only recently and are relatively less well studied compared to other superfamily conotoxins. We have detected selective and sensitive sequence pattern for I-superfamily conotoxins. The availability of sequence pattern should be useful in protein family classification and functional annotation. We have built by homology modeling, a theoretical structural 3D model of ViTx from Conus virgo, a typical member of I-superfamily conotoxins. The modeling was based on the available 3D structure of Janus-atracotoxin-Hv1c of Janus-atracotoxin family whose members have been suggested as possible biopesticides. A study comparing the theoretically modeled structure of ViTx, with experimentally determined structures of other toxins, which share functional similarity with ViTx, reveals the crucial role of C-terminal region of ViTx in blocking therapeutically important voltage-gated potassium channels.
Hunting for Insect-Specific Protein Domains
Authors: Matute Daniel R. , Barreto-Hernandez Emiliano , Falquet Laurent
Published: January 2025

Automatically finding new protein domains is a challenge when using the complete collection of known proteins (i.e., UniProt). By limiting the taxonomic range to class insecta, including two full proteomes (A. gambiae and D. melanogaster), we reduced the size of the search space in the hope of finding taxon-specific domains. The MKDOM2 program (http://prodes.toulouse.inra.fr/prodom/xdom/mkdom2.html) was used to cluster the insect proteins into potential domains that were analyzed manually in a second step. We analyzed 219 potential domains, of which 2 were insect-specific. We show that it is possible to find new domains or to extend known domains using a semi-automated method; however the goal to detect class-specific domains was only partially achieved in the sense that the new domains we found were not all insect-specific domains.

The files used as input and the resulting output files, as well as extensive descriptions of the domains, are available as supplementary data from http://bioinf.ibun.unal.edu.co/insecta/.
Noise Reduction from Genotyping Microarrays Using Probe Level	Information
Authors: Komura Daisuke , Nishimura Kunihiro , Ishikawa Shumpei , Panda Binaya , Huang Jing , Nakamura Hiroshi , Ihara Sigeo , Hirose Michitaka , Jones Keith W. , Aburatani Hiroyuki
Published: January 2025

Genomic copy number change is one of the important phenomenon observed in cancer and other genetic disorders. Recently oligonucleotide microarrays have been used to analyze changes in the copy number. Although high density microarrays provide genome wide useful data on copy number, they are often associated with substantial amount of experimental noise that could affect the performance of the analyses.

We used the high density oligonucleotide genotyping microarrays in our experiments that uses redundant probe tiling approach for individual SNPs. We found that the noise in the genotyping microarray data is associated with several experimental steps during target preparation and devised an algorithm that takes into account those experimental parameters. Additionally, defective probes that do not hybridize well to the target and therefore could not be modified inherently were detected and omitted automatically by using the algorithm. When we applied the algorithm to actual datasets, we could reduce the noise substantially without compressing the dynamic range. Additionally, combinatorial use of our noise reduction algorithm and conventional breakpoint detection algorithm successfully detected a microamplification of c-myc which was overlooked in the raw data.

The algorithm described here is freely available with the software upon request to all non-profit researchers.
Efficient Secondary Database Driven Annotation Using Model	Organism Sequences
Authors: Faria-Campos Alessandra C. , Campos Sérgio V.A. , Prosdocimi Francisco , Franco Glaura C. , Franco Glória R. , Ortega J. Miguel
Published: January 2025

The use of sequences from specific organisms for annotation requires that it does not represent great loss of information and that the sequences available suffice for annotation. In order to investigate whether or not sequences from model organisms may suffice for annotation of sequences from the trematode Schistosoma mansoni, we performed local BLAST searches of S. mansoni sequences against other organisms sequences present in the NCBI database nr. Results have been inserted into a relational database and hits to sequences from three model organisms, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens have been computed and compared to hits to sequences from other organisms present in nr; score values of each alignment have also been registered. Our observations have shown that a large fraction of orthologous proteins exists in the set of sequences from the three model organisms selected, and therefore a similar fraction of transcripts can be annotated when using either nr or model organism datasets. Moreover, hits to model organisms' sequences are largely as informative as nr. Results suggest that model organisms provide a reliable set of sequences to use as a reference database for S. mansoni sequence annotation, showing the clear possibility of using a restricted dataset of expected better quality for functional annotation and therefore supporting secondary database driven annotation approaches.
SPLITS: A New Program for Predicting Split and Intron-Containing	tRNA Genes at the Genome Level
Authors: Sugahara Junichi , Yachie Nozomu , Sekine Yasuhiko , Soma Akiko , Matsui Motomu , Tomita Masaru , Kanai Akio
Published: January 2025

In the archaea, some tRNA precursors contain intron(s) not only in the anticodon loop region but also in diverse sites of the gene (intron-containing tRNA or cis-spliced tRNA). The parasite Nanoarchaeum equitans, a member of the Nanoarchaeota kingdom, creates functional tRNA from separate genes, one encoding the 5'-half and the other the 3'-half (split tRNA or trans-spliced tRNA). Although recent genome projects have revealed a huge amount of nucleotide sequence data in the archaea, a comprehensive methodology for intron-containing and split tRNA searching is yet to be established. We therefore developed SPLITS, which is aimed at searching for any type of tRNA gene and is especially focused on intron-containing tRNAs or split tRNAs at the genome level. SPLITS initially predicts the bulge-helix-bulge splicing motif (a well-known, required structure in archaeal pre-tRNA introns) to determine and remove the intronic regions of tRNA genes. The intron-removed DNA sequences are automatically queried to tRNAscan-SE. SPLITS can predict known tRNAs with single introns located at unconventional sites on the genes (100%, tRNAs with double introns (85.7%, and known split tRNAs (100%). Our program will be very useful for identifying novel tRNA genes after completion of genome projects. The SPLITS source code is freely downloadable at http://splits.iab.keio.ac.jp/.
Identification of Transcriptional Regulators Using Binding Site	Enrichment Analysis
Authors: Kim Tae-Min , Jung Myeong Ho
Published: January 2025

To understand the transcriptional regulatory network in eukaryotic cells, it is essential to identify functional cis-regulatory sequences that interact with trans-acting factors. A number of algorithms have been developed to predict common cis-regulatory elements for co-regulated genes with similar expression patterns. However, previous methods usually deal with disjoint gene groups partitioned or clustered by arbitrary cutoffs, which might cause information losses. To preclude the defining step of gene set, we adopted enrichment analysis and termed the method binding site enrichment analysis (BSEA). BSEA was first applied for publicly available ChIP-on-chip data of c-MYC, MAX and E2F transcription factors, identifying significant enrichment for signatures of corresponding factors and potential co-activators. Using time-scaled expression profiling of 3T3-L1 adipogenesis, we observed enrichment for signatures of known adipogenic factors such as C/EBPα, C/EBPβ and PPARγ, temporally coincident with previous reports. BSEA was also applied to tissue-specific expression profiles of human and mouse, identifying well-known tissue-specific transcription factors such as HNF-4 in liver and MEF-2 in heart along with other putative tissue-specific regulators. With extended versatility coping with various kinds of microarray dataset, BSEA can identify key regulators for global microarray data in which transcriptional regulation plays a major role. As a generalized method, BSEA would help to elucidate the transcriptional regulatory networks, the primary challenges in functional genomics.
In Silico Analysis of the Lateral Organ	Junction (LOJ) Gene and Promoter of Arabidopsis Thaliana
Authors: Saha Dipnarayan , Prasad Anand M. , Sujatha Thankeswaran P. , Kumar Vajinder , Jain Pradeep K. , Bhat Sripad R. , Srinivasan Ramamurthy
Published: January 2025

A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of few genes involved in lateral organ development and meristem related expression reveals few common relevant regulatory motifs. The coding region of the LOJ gene is intron-less and contains 19 PPR units. Based on in silico analysis, LOJ protein is predicted to be hydrophobic in nature and targeted to mitochondria. A partial 3D model of the LOJ protein has been suggested using a homology-based modeling program.
Coding Potential Prediction in Wolbachia Using	Artificial Neural Networks
Authors: Lambros Skarlas , Panos Ioannidis , Spiridon Likothanassis
Published: January 2025

Ab initio coding potential prediction in a bacterial genome is an important step in determining an organism's transcriptional regulatory function. Extensive studies of genes structure have been carried out in a few species such as.

Escherichia coli, fewer resources exist in newly sequenced genomes like Wolbachia. A model of gene prediction trained on one species may not reflect the properties of other, distantly related prokaryotic organisms. These issues were encountered in the course of predicting genes in the genome of Wolbachia, very important gramnegative bacteria that form intracellular inherited infections in many invertebrates. We describe a coding potential predictor based on artificial neural networks and we compare its performance by using different architectures, learning algorithms and parameters. We rely on a dataset of positive samples constructed from coding sequences and on a negative dataset consisted of all the intergenic regions that were not located between the genes of an operon. Both datasets, positive and negative, were output as fasta formatted files and were used for neural network training. The fast, adaptive, batch learning algorithm Resilient propagation, exhibits the best overall performance on a 64input-10hidden-1output nodes multi-layer perceptron neural network.
DomainDraw: A Macromolecular Feature Drawing Program
Authors: Fink J. Lynn , Hamilton Nicholas
Published: January 2025

Visualization of functional and structural features of biological macromolecules is an important aspect of communicating and analyzing biological data, for example the presence of a transmembrane domain in relation to a nucleotide binding site or the organization of transcription factor binding sites in a promoter. However, this is not necessarily a trivial task especially when the feature information is complex or lengthy. While there are some tools available that can create these images, none have been implemented for the specific purpose of automating the generation of presentation-quality graphics for displaying feature information. We have implemented DomainDraw, a visualization tool that can be used to generate schematic diagrams of biological macromolecules for the purpose of representing the relative position and range of user-specified domains or motifs. The user specifies the name, position, and range of the domains of interest and DomainDraw generates the image based on these parameters. Optional parameters include domain color and shape, image size, and whether to align multiple proteins using a particular domain. DomainDraw is publicly available as a web server and can be accessed at http://domaindraw.imb.uq.edu.au. The executable may be obtained by contacting the authors.
Deep Metazoan Phylogeny
Authors: Gerlach Daniel , Wolf Matthias , Dandekar Thomas , Müller Tobias , Pokorny Andreas , Rahmann Sven
Published: January 2025

We reconstructed a robust phylogenetic tree of the Metazoa, consisting of almost 1,500 taxa, by profile neighbor joining (PNJ), an automated computational method that inherits the efficiency of the neighbor joining algorithm. This tree supports the one proposed in the latest review on metazoan phylogeny. Our main goal is not to discuss aspects of the phylogeny itself, but rather to point out that PNJ can be a valuable tool when the basal branching pattern of a large phylogenetic tree must be estimated, whereas traditional methods would be computationally impractical.
Efficient Shape Descriptors for Feature Extraction in 3D Protein	Structures
Authors: Ranganath Aruna , Shet K. Chandra Shekar , Vidyavathi Nagardone
Published: January 2025

Structural Genomics initiatives are generating an increasing number of protein structures with very limited biochemical characterization. Characterization of a protein's function and understanding the specific nature of a protein's binding is a critical part of both protein engineering and structure-based drug discovery. The accurate detection of binding site in these protein structures can be valuable in determining its function. As shape plays a crucial role in bimolecular recognition and function, the development of shape analysis techniques is important for understanding protein structure-function relationships. This paper describes the use of the continuous wavelet transforms (CWT) for characterizing shape features of 3D protein structures. The goal is to explore the CWT as a multiscale tool to generate rotation- and translation-invariant shape features.
Constraint-Based Knowledge Discovery from SAGE Data
Authors: Kléma Jiří , Blachon Sylvain , Soulet Arnaud , Crémilleux Bruno , Gandrillon Olivier
Published: January 2025

Current analyses of co-expressed genes are often based on global approaches such as clustering or bi-clustering. An alternative way is to employ local methods and search for patterns – sets of genes displaying specific expression properties in a set of situations. The main bottleneck of this type of analysis is twofold – computational costs and an overwhelming number of candidate patterns which can hardly be further exploited. A timely application of background knowledge available in literature databases, biological ontologies and other sources can help to focus on the most plausible patterns only. The paper proposes, implements and tests a flexible constraint-based framework that enables the effective mining and representation of meaningful over-expression patterns representing intrinsic associations among genes and biological situations. The framework can be simultaneously applied to a wide spectrum of genomic data and we demonstrate that it allows to generate new biological hypotheses with clinical implications.
Influence of C-H…π Hydrogen Bonds in	Interleukins
Authors: Anand Sudha , Anbarasu Anand , Sethumadhavan Rao
Published: January 2025

We have explored the roles played by C-H…π hydrogen bonds in interleukins. Main-chain to side-chain C-H…π interactions are the predominant type of interactions in interleukins. There was an average of 15 C-H…π interactions per protein and also there was an average of one significant C-H…π interaction for every 14 residues in the interleukins investigated. Significant contribution to C-H…π interactions was only from Asp, Gly, His, Lys, Phe, Pro, Ser, Thr, Trp and Tyr in interleukins. Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain 5 member aromatic ring and side-chain to side-chain C-H…π interactions. Short and medium-range C-H…π interactions are the predominant type of interactions in interleukins. More than 50% of C-H…π interacting residues had a conservation score of ⩾ 6. Significant percentage of C-H…π interacting residues had one or more stabilization centers; hence these residues may also contribute additional stability to structure of interleukins.
Specificity and Sensitivity of PROMIR, ERPIN and MIR-ABELA in	Predicting Pre-MicroRNAs in the Chicken Genome
Authors: Sebastian Bram , Aggrey Samuel E.
Published: January 2025

MicroRNAs (miRNAs) are endogenous 21–23 nucleotide molecules that are known to regulate about 30% of protein-coding genes through the RNAi pathway. Low level expression of some miRNA has limited their in-situ discovery. Such limitations could be ameliorated by in-silico methodologies. The efficacies of three major programs (ERPIN, ProMir and miR-abela) in detecting known pre-miRNA were evaluated using chicken pre-miRNA data. The sensitivity of ProMir, miR-abela and ERPIN were 53%, 57% and 93%, respectively. The specificity of the three algorithms using 5,000 random sequences was 98.94%, 99.46%, and 99.10% for ProMir-g, ERPIN and miR-abela, respectively. The sensitivities of the existing programs are low for chicken data and an efficient algorithm may be needed to predict novel chicken pre-miRNAs.
Analysis of Insertional Sites of the SIRE1	Retroelement Family from Glycine Max Using GenBank BAC-end	Sequences
Authors: Flasch Diane A. , Rebman Ellen K. , Olfson Emily H. , Nguyen Khanh K. , Geirut Lucasz E. , Garland Megan C. , Lindorfer Christi M. , Laten Howard M.
Published: January 2025

SIRE1 is a 2,000-copy member of the Ty1/copia retroelement family found in the soybean genome and is closely related to sireviruses found in the genomes of other legumes. Although these elements closely resemble typical plant members of the Ty1/copia family, they are unusual in that they possess an envelope-like coding region immediately downstream of the reverse transcriptase gene. Despite its copy number, very few members of the SIRE1 family are currently present in publicly available genomic assemblies or draft contigs. However, fragments of family members are well-represented as BAC-ends in the GenBank Genome Survey Sequence database. This database was queried using the 5' and 3' ends of SIRE1 in order to catalog sequences into which SIRE1 members have integrated. Seven hundred and eighty-one unique SIRE1 insertions were identified and the majority of insertion sites constituted other repetitive elements, including Class I and Class II transposable elements and satellite DNAs. Ninety-four insertions were in single- or low-copy number sequences and three of these were homologous to characterized protein-coding genes. Examination of the ten bases flanking either side of SIRE1 revealed no clear consensus sequence, but the the distributions of A, C, G, and T at most of the positions were biased with strong statistical significance.
Effects of Misdiagnosis in Input Data on the Identification of	Differential Expression Genes in Incipient Alzheimer Patients
Authors: Joseph Sandeep , Robbins Kelly , Zhang Wensheng , Rekaya Romdhane
Published: January 2025

Gene expression profiles of 16 Alzheimer's (AD) patients, diagnosed as incipient or healthy using Mini-Mental State Examination and Neurofibrillary Tangles scores, were analyzed to validate the reclassification of 4 subjects previously identified as being misdiagnosed. Three datasets were created using original classifications (D1), new classifications, based on a misclassification algorithm (D2), and by removing questionable subjects (D3). Mixed model analysis was used to identify differentially expressed genes. Many genes related to the nervous system and AD were found to be differentially expressed in D2 and D3, while few genes, none related to NS or AD, were found using D1. Several additional relevant genes were found when using D2 versus D3, which were likely due to differences in sample size. These results suggest the 4 questionable subjects were likely misclassified in D1. The similarities between results obtained using D2 and D3 provides further evidence of the adequacy of the misclassification algorithm.
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry
Authors: Dimitrova Z. , Campo D.S. , Ramachandran S. , Vaughan G. , Ganova-Raeva L. , Lin Y. , Forbi J.C. , Xia G. , Skums P. , Pearlman B. , Khudyakov Y.
Published: January 2025

Hepatitis C Virus sequence studies mainly focus on the viral amplicon containing the Hypervariable region 1 (HVR1) to obtain a sample of sequences from which several population genetics parameters can be calculated. Recent advances in sequencing methods allow for analyzing an unprecedented number of viral variants from infected patients and present a novel opportunity for understanding viral evolution, drug resistance and immune escape. In the present paper, we compared three recent technologies for amplicon analysis: (i) Next-Generation Sequencing; (ii) Clonal sequencing using End-point Limiting-dilution for isolation of individual sequence variants followed by Real-Time PCR and sequencing; and (iii) Mass spectrometry of base-specific cleavage reactions of a target sequence. These three technologies were used to assess intra-host diversity and inter-host genetic relatedness in HVR1 amplicons obtained from 38 patients (subgenotypes 1a and 1b). Assessments of intra-host diversity varied greatly between sequence-based and mass-spectrometry-based data. However, assessments of inter-host variability by all three technologies were equally accurate in identification of genetic relatedness among viral strains. These results support the application of all three technologies for molecular epidemiology and population genetics studies. Mass spectrometry is especially promising given its high throughput, low cost and comparable results with sequence-based methods.
In Silico Analysis of Voltage-gated Sodium	Channel in Relation to DDT Resistance in Vector Mosquitoes
Authors: Rajesh Rengaraj , Gunasekaran Kasinathan , Muthukumaravel Subramanian , Balaraman Kothandapani , Jambulingam Purusothaman
Published: January 2025

The voltage-gated sodium channel (VGSC) is the target site for insecticides such as DDT and synthetic pyrethroids. A single base (A-T) change in the knock-down resistance (kdr) allele leads to an amino acid substitution at position 267 that confers the target-mediated resistance to DDT and synthetic pyrethroids in Anopheles gambiae. A theoretical model of the VGSC domain II that contains the site of mutation was constructed using the K $^+$ channel protein of Aeropyrum pernix as a template. The validated model with 88.6% residues in the favored region was subjected to the CASTp program that predicted 30 pockets in the modeled domain II for ligand interaction. In the model, at position 267, leucine was manually replaced with phenylalanine. When this altered model was subjected to the CASTp program, the search results showed the same number of pockets. The docking results indicate that DDT interacts with the modeled VGSC domain II at position 275 in the presence of leucine or in the presence of phenylalanine (binding energy =−5.32 kcal/mol, −6.21 kcal/mol). It appears from the results that the mutation at position 267 has no direct influence on the interaction of DDT with the target protein. Therefore, to understand the interaction affinity of DDT with the target and influence of the mutation on the existence of active sites/pockets in relation to ligand binding, a whole VGSC model is necessary.
Clustering Gene Expression Data Using Graph Separators
Authors: Kaba Bangaly , Pinet Nicolas , Lelandais Gaëlle , Sigayret Alain , Berry Anne
Published: January 2025

Recent work has used graphs to modelize expression data from microarray experiments, in view of partitioning the genes into clusters. In this paper, we introduce the use of a decomposition by clique separators. Our aim is to improve the classical clustering methods in two ways: first we want to allow an overlap between clusters, as this seems biologically sound, and second we want to be guided by the structure of the graph to define the number of clusters. We test this approach with a well-known yeast database (Saccharomyces cerevisiae). Our results are good, as the expression profiles of the clusters we find are very coherent. Moreover, we are able to organize into another graph the clusters we find, and order them in a fashion which turns out to respect the chronological order defined by the the sporulation process.
Clustering Formal Concepts to Discover Biologically Relevant	Knowledge from Gene Expression Data
Authors: Blachon Sylvain , Pensa Ruggero G. , Besson Jérémy , Robardet Céline , Boulicaut Jean-François , Gandrillon Olivier
Published: January 2025

The production of high-throughput gene expression data has generated a crucial need for bioinformatics tools to generate biologically interesting hypotheses. Whereas many tools are available for extracting global patterns, less attention has been focused on local pattern discovery. We propose here an original way to discover knowledge from gene expression data by means of the so-called formal concepts which hold in derived Boolean gene expression datasets. We first encoded the over-expression properties of genes in human cells using human SAGE data. It has given rise to a Boolean matrix from which we extracted the complete collection of formal concepts, i.e., all the largest sets of over-expressed genes associated to a largest set of biological situations in which their over-expression is observed. Complete collections of such patterns tend to be huge. Since their interpretation is a time-consuming task, we propose a new method to rapidly visualize clusters of formal concepts. This designates a reasonable number of Quasi-Synexpression-Groups (QSGs) for further analysis. The interest of our approach is illustrated using human SAGE data and interpreting one of the extracted QSGs. The assessment of its biological relevancy leads to the formulation of both previously proposed and new biological hypotheses.
Correlation Between Gene Silencing Activity and Structural	Features of Antisense Oligodeoxynucleotides and Target RNA
Authors: Liao Li , Li Zhongwei
Published: January 2025

Antisense oligonucleotides inactivate mRNA targets, providing a tool for post-transcriptional gene silencing and a potential novel treatment for many diseases. Reliable design of active antisense depends on better understanding of the mechanism of antisense-target RNA interaction. We have studied the correlation between activity of antisense oligodeoxynucleotides (ASO) and structural features of both antisense and target RNAs. A total of 348 ASOs with known activities and their target RNA sequences are classified into categories according to their predicted secondary structural features. Statistical analysis showed that higher activity is more likely to happen at RNA stem-loops than at other RNA structural categories. The data suggest a weak correlation between the stability of ASO structure and activity. Remarkably, a structural fit between ASO and target seems important for antisense activity. Significantly higher antisense activity is achieved with stem-loop ASOs on stem-loop or linear RNA targets.
Self-Alignments to Detect Mutually Exclusive Exon Usage
Authors: Stephan Martin , Möller Friedrich , Wiehe Thomas , Kleffe Jürgen
Published: January 2025

The surprisingly low number of about 25,000 genes in the human genome [1] confirmed a fairly accurate estimate given by King and Jukes in 1969 based on population genetical arguments [2]. On the other hand, the number of different transcripts vastly exceeds gene number. This fact intensified the search for alternatively spliced genes. Recent results [1,3,4-7] suggest that more than 60% of the human genes are alternatively spliced, some of them with a myriad of different splice forms. Alternative splicing is found in all higher eukaryotic species in varying frequency. In this paper we focus on a particular form of alternative splicing, the so-called mutually exclusive exon usage (MEEU). In most known examples mutually exclusive exons are arranged in cassettes of highly similar exons suggesting that they have been derived by exon duplication [8-10]. Since classical gene-finding programs may fail to correctly predict such genes [11-16], we present a method, which is based on local similarity of exons, to detect gene candidates with mutually exclusive exon usage. We have screened the entire genome of D. melanogaster and found five new genes with MEEU in addition to eight previously described cases. Additional 1703 candidate regions of putative mutually exclusive exons were identified.
MODIFIED LOW-DOSE FORMALIN PRESERVATION: IN THE ANATOMICAL-SURGICAL DISSECTION & PROSECTED ANATOMICAL MODELS: A CASE REPORT
Authors: Veronica Fifi , Gradia Resti , Fitri Lulu L.
Published: January 2025

The development of cadaver preservation has been fast-paced. The subtraction of formalin dose in embalming has been used since many negative factors were found in long-term usage. Preventing putrefaction progress on the cadavers, ensuring no risk of infection when in contact with a dead body, preventing hardening and retention of color tissue and organs, preventing desiccation, inhibit fungal or bacterial growth are the main goals of embalming for anatomical purposes. The new formula has been developed by using low-dose formalin, ethanol, phenol, and sodium chloride (Modified Low-Dose Formalin). This method can be used in practical anatomical-surgical dissection using either cadavers or anatomical models with low-cost maintenance.
THE QUALITY OF SLEEP IN BRAIN TUMOR PATIENTS
Authors: Diansari Yunni , Handayani Sri , Mukhlisa  , Marisdina Selly , Syahputri Rizka Aprillia , Susanty Tri , Irfannuddin
Published: January 2025

The Quality of Sleep in Brain Tumors Patients. Sleep quality is often compromised in patients with brain tumors. The underlying factors contributing to sleep quality disturbances in this patient population are multifaceted, and investigating these factors remains scarce. Sixty-eight patients with brain tumors, aged ≥ 18 years, were selected consecutively, and data was recorded in the form of sociodemographic characteristics (gender and age), clinical characteristics (clinical manifestations, tumor type, location, comorbid diseases) and therapy characteristics (management and types of drugs). Sleep quality was assessed using the Pittsburgh Sleep Quality Index (PSQI) questionnaire. Data were analyzed bivariate with chi-square and multivariate with logistic regression. Around 45.6% experienced poor sleep quality. Age, gender, systemic malignancies, pain, type of primary brain tumor, tumor location, operation, radiotherapy, and steroid have a significant relationship with sleep quality in patients with brain tumors (p-value <0.05). Multivariate analysis shows that age is the factor that most strongly influences the sleep quality of patients with brain tumors. Age, gender, systemic malignancies, pain, type of primary brain tumor, tumor location, operative treatment, radiotherapy, and steroids influence the quality of sleep in patients with brain tumors, but age has the most decisive influence.
Utilization Trends of Glucose-Lowering Medications Among Adult Kidney Transplant Recipients with Type 2 Diabetes in the United States
Authors: Hansrivijit Panupong , Tesfaye Helen , Wexler Deborah , Abdi Reza , Patorno Elisabetta , Paik Julie
Published: January 2025

Background: To date, there are limited studies describing the use of glucose-lowering medications (GLMs) in adult kidney transplant recipients (KTRs), and the uptake of sodium glucose cotransporter-2 inhibitors (SGLT2is) and glucagon-like peptide-1 receptor agonists (GLP1RAs). Thus, we aimed to evaluate the use of GLMs, including SGLT2i and GLP1RA, among adult KTRs with type 2 diabetes (T2D). Methods: This is an ecologic study of adult KTR with T2D. Data were sourced from two large U.S. health insurance claim databases from 2014 to 2023. The proportions of any user and incident use of GLMs were reported in percentage. Any use of GLM was defined through prescription claims, and incident use was further defined as the absence of any prior dispensing within the preceding 365 days. Results: From 2014 to 2023, we identified 33,913 adult KTRs with T2D who were prescribed any GLMs. Any use of SGLT2i and GLP1RA increased throughout the study period (0.4% to 14.4% for SGLT2i, and 2.8% to 12.5% for GLP1RA). While insulin was the most frequently used GLM, ranging from 58% to 74%, the usage gradually declined over time. By 2023, SGLT2i and GLP1RA were initiated nearly as frequently as insulin (5.1% for SGLT2i, 5.7% for GLP1RA, and 5.7% for insulin). Compared with insulin initiators, SGLT2i initiators (n = 1009) had a higher prevalence of cardiovascular comorbidities and proteinuria, while GLP1RA initiators (n = 2149) had a higher prevalence of obesity. Conclusions: Any use of both SGLT2i and GLP1RA among KTRs with T2D increased over time with the incident use of SGLT2i and GLP1RA as high as insulin by 2023. Our findings emphasize the need for the effectiveness and safety analysis of SGLT2i and GLP1RA among KTRs with T2D.
Investigation of electric double layer effects at Li3PO4 Li+ solid electrolyte thin film interfaces using a field-effect transistor with Al-doped SiC (0001) single crystal
Authors: Shibata Kaoru , Namiki Wataru , Nishioka Daiki , Terabe Kazuya , Tsuchiya Takashi
Published: January 2025

We developed a Li+ electrolyte-gated electric double-layer transistor (EDLT) using Al-doped SiC (0001) single crystal as the channel material. Thanks to the high tolerance of SiC single crystal to plasma irradiation, the Al-doped SiC EDLT was successfully fabricated with RF-sputtered Li3PO4 Li+ solid electrolyte thin film, which was previously difficult due to plasma-induced damage to the semiconductor channel. The EDLT operation of the device was confirmed by observing a 75% resistance change in the transfer characteristics. Hall measurements were employed to evaluate carrier density changes and directly investigate the behavior of the EDL at the interface. The calculated capacitance revealed contributions from both the EDL capacitance and depletion layer capacitance, indicating that the depletion layer formed on the SiC channel surface prevented accurate evaluation of EDL capacitance. For accurate EDL capacitance measurement, generating an accumulation layer on the surface of the semiconductor channel is found to be essential.
خــطط النجــــف الأشرف في فــــكر الأمـــــــام الصادق عليه السلام
Authors: الحكيم حسن عيسى
Published: January 2025

ساعدت فترة الانتقال السياسي في الدولة الإسلامية من الأمويين إلى العباسيين الإمام جعفر الصادق عليه السلام على نشر علوم أهل البيت سلام الله عليهم بحرية واطمئنان وكانت الحقبة الزمنية التي عاشها الأمام الصادق تمثل جانب النضج الفكري والسياسي وكان قد عاصر تيارات فكرية مختلفة وأراء ابتعدت عن مبادئ الإسلام وأحكامه، وقد تصدى لها بالقوة الفكرية، وأبطل دعاتها وفند اضاليلها فيقول الشيخ محمد أبو زهرة:(إن الأمام الصادق وقف في وجه أولئك  الذين كانوا ينحرفون في اعتقادهم أو يهاجمون الاعتقاد الصحيح) (1) كالزنادقة والملحدين والغلاة والمجسمة والقدرية والجبرية والمرجئة وغيرها وأراد عليه السلام  تثبيت الفكر والأمامي عن طريق الأئمة سلام الله عليهم، وفق التسلسل المعروف بالإمامة وبذلك دحض جميع الآراء المتفرعة من التسلسل وتصدى للفرق المتشعبة عن الأمامية كالكيسانية والزيدية والواقفةوالناووسية وغيرها، وكانت مدرسته في المدينة المنورة والكوفة من أوسع المدارس الفكرية في العالم الإسلامي، وكانت هاتان المدرستان ملتقى الفقهاء والمفسرين والمحدثين، ويقول الأستاذ احمد أمين (أن الأمام الصادق أوسع الناس علما واطلاعا وأقواله تدل على حكمته، وبعد نظرة وسعة علمه)(2) وقد قصد الأمام الصادق عليه السلام مدينتي الحيرة والكوفة في عهدي السفاح والمنصور، واستدعاه أبو جعفر المنصور إلى بغداد عدة مرات، وفــــــــــــــــــي أثنـــــــاء وجوده في العراق زار مرقدي الإمامين علي والحسين عليهما السلام، وتتلمذ عليه جمع من علماء الكوفة، وعند عودته إلــى المدينة بقي الكوفيون علــى صلة به، ويقـول يحيى بن عبدا لله بن الحســن: (سمعت الصادق يقول وعنده أناس من أهل الكوفة)(3)  وروى إسماعيل بن أبي الازدي- وهو من الكوفيين- عن الأمام الصادق عليه السلام كتاب (القضايا) وسمع منه مقرئ القران الكريم في مسجد الكوفة عبد الله بن أبي يعفور(4) وبقي اثر الأمام الصادق عليه السلام في مدينة الكوفة بعد وفاته عام  148 هـ فكان العلماء يتناقلون آراءه جيل بعد جيل، فيقول الحسن بن علي بن زياد الوشــاء البجلي:(أدركت في المسجد تسعمائة شيخ كل يقول: حدثني جعفر بن محمد عليه السلام) (5).
مكانة المرأة في العصر الجاهلي والإسلامي
Authors: التميمي منى عبد الحسن أحمد , الزاملي أ.د. بلاسم عزيز
Published: January 2025

كانت المرأة قبل الإسلام تُعامل كممتلكات للرجل ومحرومة من حقوقها الأساسية، مثل الإرث والمشاركة الاجتماعية. في المجتمعات الآشورية والسومرية، كانت خاضعة لتبعية تامة، بينما في الجاهلية، عانت من ظلم شديد، كما كان الزواج والطلاق يتمان دون تنظيم، والمرأة تابعة للرجل، وفي المجتمعات المتحضرة كالهند والصين، ورغم التحضر النسبي، ظلت المرأة مهمشة، حيث تُحرق في الهند مع جثة زوجها بعد وفاته وتُعتبر في الصين مملوكة. جاء الإسلام ليغير هذا الواقع، فأعطى المرأة حقوقاً متساوية مع الرجل، مثل حق الإرث والاستقلال المالي، ووضع ضوابط للزواج والطلاق، وقد أكد القرآن على مكانة المرأة، مستشهداً بقصص مثل مريم التي اصطفاها الله.
Вплив колійності на покритті автомобільної дороги на безпеку руху під час виконання маневрів автомобілями
Authors: Смолянюк Р.В.
Published: January 2025

В результаті впливу різних чинників на автомобільних дорогах утворюються колії. Колії не тільки погіршують естетичний вигляд покриття дороги, а й становлять небезпеку для автомобілів. Очевидно, що під час опадів в коліях накопичується вода, що може привезти до аквапланування і втрати стійкості автомобілем. На сухих покриттях колійність також може становити небезпеку, коли автомобіль виїжджає зі своєї смуги для виконання маневру обгону чи іншого маневру. Колії призводять до додаткових коливань підвіски, розхитування кузова, втрати контакту колеса з покриттям, що негативно позначається на безпеці руху. В статті наведено результати дослідження щодо оцінки такого впливу. Також наведено рекомендації щодо врахування цього впливу.
Визначення місця розміщення павільйону та рекомендації з проєктування зупинок маршрутного пасажирського транспорту
Authors: Тімкіна С.Ю.
Published: January 2025

Стаття присвячена аналізу та розробці рекомендацій щодо оптимального розміщення павільйонів і проєктування зупинок маршрутного пасажирського транспорту. Дослідження показали, що місце розташування павільйону суттєво впливає на ефективність використання зупинкового майданчика, пропускну спроможність зупинок та зручність обслуговування пасажирів. Проаналізовано взаємодію пішоходів і пасажирів, що очікують транспорт, з транспортними засобами, які прибувають на зупинку.
На основі експериментальних даних встановлено, що транспортний засіб, як правило, зупиняється навпроти павільйону, незалежно від його місця розташування. Це спричиняє нерівномірне використання довжини зупинкового майданчика, особливо за відсутності заїзної кишені.
Аналіз снігоочисної техніки та заходи, направлені на покращення зимового утримання автомобільних доріг
Authors: Шимчук О.П. , Процюк В.О. , Талах Л.О. , Панчук Ю.М.
Published: January 2025

У статті проведено аналіз існуючої снігоочисної техніки для зимового утримання автомобільних доріг та міських вулиць. Запропоновано шнековий снігоочисник, який забезпечить видалення снігу з проїзної частини, завантаження його в кузови автомобілів та вивезення за межі дороги.
Detecting Land Use Changes in Ordos City Using the Google Earth Engine Remote Sensing Cloud Platform
Authors: Ye Zhigang , Yin Shan , Wang Yong
Published: January 2025

This study leverages Google Earth Engine's remote sensing cloud platform to examine land use changes in Ordos City between 2000 and 2017. The analysis focuses on the quantitative shifts, intensity, and spatial structure of land use dynamics. Findings indicate significant land use transformation over the period, with woodland increasing by 56% at a rapid annual growth rate of 3.29%, while grassland, water areas, and unused land decreased. The development pace of various land types accelerated between 2010 and 2015, particularly for woodland, cultivated land, and construction land. Spatial disparities were evident among different types of land use changes, with more significant variations observed in the southeast compared to the northwest. Despite less noticeable differences from 2010 to 2017, land use diversity grew gradually. These results offer valuable data-driven insights for promoting sustainable land use and development strategies in the region.
Psychological Mechanism of Outdoor Physical Exercise in Polluted Weather Based on Social Cognitive Theory
Authors: Ma Wentao
Published: January 2025

Despite improved living standards, many individuals continue to engage in outdoor physical exercise despite air pollution. This study explores the psychological mechanisms that facilitate this behavior in adverse environmental conditions. Using Social Cognitive Theory as a framework, we investigate the reasons individuals choose to exercise outdoors in polluted weather compared to those who prefer cleaner conditions. Our research includes a statistical analysis of demographic data and an examination of psychological and social factors influencing exercise habits. We distributed a structured questionnaire to 300 participants, receiving 290 responses, of which 280 were valid. By analyzing these responses, we aim to uncover the psychological drivers that sustain commitment to outdoor exercise despite pollution challenges. The findings provide valuable insights into the motivations and mechanisms that encourage individuals to maintain their physical activity in less-than-ideal conditions.
In vivo Evaluation of Saccharomyces-Modified Tempeh as Potential Prebiotic and Probiotic Food using Mus musculus as an Animal Model
Authors: Kustyawati Maria Erna , Suryawan Tegar , Rizal Samsul , Fadhallah Esa Ghanim , Berawi Khairun Nisa
Published: January 2025

Saccharomyces-modified tempeh (SM tempeh), which is produced by adding Saccharomyces cerevisiae during soybean fermentation, is considered to have the potential as a source of prebiotics. The research aims to determine the prebiotic activity score (PAS) of SM tempeh extract against the probiotics S. cerevisiae and Lactobacillus casei, as well as to evaluate the resistance of S. cerevisiae and Escherichia coli in the intestines of mice fed tempeh. The PAS evaluation was carried out using a factorial complete randomized block design with three replications and one-way ANOVA for data analysis followed by the least significant difference test (5%). Meanwhile, microbial survivability was carried out in vivo using male Mus musculus strain mice fed standard feed, and standard feed with tempeh extract supplementation. The results showed that the supplemetation of either SM or commercial tempeh extract to the growth media significantly affected on the microbial load of S. cerevisiae, L. casei and E. coli, but the concentrations of tempeh extract had no significant effect. Apart from that, the concentrations of tempeh extract had no effect on the PAS of S. cerevisiae and L. casei, meaning that it was able to promote the growth of probiotics in the amount added to the media in the range of 2–10%. In addition, the feeding type had a significant effect on the survival of S. cerevisiae and E. coli in the intestines. S. cerevisiae carried on SM tempeh was detected surviving in the mice intestine at a rate of 6.12 log CFU/g, indicating that the tempeh was a probiotic food. Most likely SM tempeh is a synbiotic food.
Small approximately 2-absorbing submodules and modules
Authors: Shyaa Farhan Dakhil
Published: January 2025

In this paper, we introduce new classes of submodules and modules named small approximately 2-absorbing submodules and modules which are new generalization of small prime submodule and small prime module. A proper submodule N of M is said to be small approximately 2-absorbing submodules (res Small approximately 2-absorbing Module) if when a, b ∈ R and < m > ≪M, abm ∈ N implies that a2 ∈N or b2 m∈N or a2 b2∈ (N : M) (res if < 0 > is a small approximately 2-absorbing submodule of M, such that if abm ∈ <0> and ≪M, then a2 m = 0 or b2 m = 0 or (ab)2 ∈ annM). Also, give various results and properties of this concepts.
New results for a subclass of analytic functions with integral operator appling differential subordination and superordination
Authors: Mihsin Bassim Kareem
Published: January 2025

We have closed this article, for deriving new superordination and subordination results for analytic functions in open unit disk Ʋ by using an integral operator Lυ ξ,ϱ,τ,ζ f(z).
Many conclusions will be obtained for differential superordination and subordination to the new formula linked by integral operator and conclude several sandwich-type results are also acquired.
Inside of nano topological spaces : A novel generalized open and closed nano operator
Authors: Hamd Hawraa Sahib Abu , Hameed Abdulaziz S , Aziz Nabila I.
Published: January 2025

In this study, a novel class of operators in Nano topological spaces is defined a novel Open and Closed Nano operators (briefly, (Ɲ ̂ (Ᾱ) and Ɲ ̂ (Ᾱ)), proved properties and theorems in Nano topological spaces.