bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive value of m6A regulators in prognosis and immunotherapy response of clear cell renal cell carcinoma: a bioinformatics and radiomics analysis
Authors: Chen Wanqi , Lin Tuanyu , Wang Zhenshan , Zeng Liting , Lin Haitao , Yang Guisheng , Huang Weipeng 
Published: June 2024

Aim: This study aimed to develop an m6A-related gene signature for predicting the prognosis of clear cell renal cell carcinoma (ccRCC) patients and explore its value in predicting the immunotherapy response.
Methods: In total, 530 ccRCC patients with gene expression data in the TCGA cohort were included and classified into the training (n = 371) and validation (n = 159) sets. Differential expression analyses of 23 m6A regulators between survivors and non-survivors were performed. Subsequently, an m6A-related gene signature was developed via LASSO Cox regression. All patients were categorized into two groups of m6A subtypes, i.e., low or high m6A score group. The Kaplan-Meier survival curves and Tumor Immune Dysfunction and Exclusion (TIDE) scores of the two m6A subtype groups were compared to measure the gene signature’s predictive value in prognosis and potential immunotherapy response, respectively.
Results : Eighteen m6A regulators were significantly differentially expressed between the survivors and non-survivors, and were also related to overall survival (OS). A gene signature containing five selected m6A methylation regulators (KIAA1429 , METTL14 , IGF2BP2 , IGF2BP3 , and SRSF2 ) was developed and showed favorable discrimination in the training (C-index 0.708) and validation (C-index 0.689) sets. Patients with low m6A scores had significantly better OS and lower TIDE scores than those with high m6A scores. Moreover, a robust MRI-based radiomic signature was developed to noninvasively predict the m6A subtype for each patient.
Conclusion : We demonstrated the prognostic value of five m6A regulators and constructed a gene signature for prognosis and immunotherapy response prediction among ccRCC patients. In addition, a radiomic signature was developed for noninvasive prediction of the m6A subtype. These findings may promote precision medicine and provide novel insights into the regulation of tumor immune microenvironment.
Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model
Authors: Klaassens Eline Suzanne , Baak Mirna Lilian , Mekkes Nienke Jacobine , Bongoni Radhika , Schaubeck Monika 
Published: June 2024

Aim: Microbial colonization of the neonatal gut is pivotal in priming the infant’s immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant’s microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem.
Methods: By using an ex-vivo infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [Limosilactobacillus fermentum (L. fermentum ) CECT 5716 (Lf) and Bifidobacterium breve (B. breve ) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking.
Results: Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem.
Conclusion: Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.
Kesesuaian Realisasi Program Pemanfaatan Ruang dengan Indikasi Program dalam Rencana Detail Tata Ruang (RDTR) Kawasan Perkotaan Mbay
Authors: Hamid Nevi Vilianty 
Published: June 2024

<p><em><span lang="IN">Kawasan Perkotaan Mbay merupakan ibu kota Kabupaten Nagekeo yang merupakan pusat berbagai aktivitas masyarakat. Pelaksanaan pemanfaatan ruang di Kawasan Perkotaan Mbay diatur dalam Peraturan Daerah Kabupaten Nagekeo Nomor 4 Tahun 2017 tentang Rencana Detail Tata Ruang dan Peraturan Zonasi Kawasan Perkotaan Mbay Tahun 2017-2037. Di Kawasan Perkotaan Mbay, terdapat permasalahan banjir di kawasan permukiman akibat tidak tersedianya saluran drainase dan meluapnya air sungai. Berdasarkan data indikasi program untuk jangka lima tahun, terdapat program pembangunan saluran drainase dan normalisasi sungai. Akan tetapi, kondisi aktual berbeda dengan rencana. Pembangunan drainase belum tuntas terlaksana dan program normalisasi sungai tidak terlaksana. Penelitian ini bertujuan untuk mengetahui kesesuaian realisasi program pemanfaatan ruang dengan indikasi program yang terdapat dalam RDTR Kawasan Perkotaan Mbay antara tahun 2018-2021. Metode penelitian yang digunakan adalah metode kualitatif. Data yang dikumpulkan adalah data sekunder berupa data realisasi program pemanfaatan ruang dan indikasi program tahun 2018-2021 yang bersumber dari instansi/dinas terkait. Teknik pengumpulan data dilakukan melalui telaah dokumen Laporan Penyelenggaraan Pemerintah Daerah (LPPD) untuk data realisasi program dan dokumen RDTR Kawasan Perkotaan Mbay untuk data indikasi program. Teknik analisis menggunakan analisis deskriptif dengan membuat matriks persandingan program pemanfaatan ruang yang mengacu pada matriks persandingan program dalam Peraturan Menteri ATR/BPN Nomor 9 Tahun 2017 tentang Pedoman Pemantauan dan Evaluasi Pemanfaatan Ruang. Hasil penelitian menemukan nilai kesesuaian program pemanfaatan ruang sebesar 54,39% yang termasuk dalam klasifikasi tingkat kesesuaian kurang berkualitas. Hal tersebut berarti bahwa pelaksanaan program pemanfaatan ruang tahun 2018-2021 belum sesuai dengan Rencana Pola Ruang dan Rencana Struktur Ruang dalam indikasi program RDTR Kawasan Perkotaan Mbay Tahun 2017-2037.</span></em></p>
Preferensi Bermukim Buruh Industri Besar di Kecamatan Grogol, Kabupaten Sukoharjo
Authors: Octavia Fiki , Mukaromah Hakimatul , Andini Isti 
Published: June 2024

<em><span lang="IN">Hinterland Kota Surakarta merupakan wilayah yang strategis dalam pengembangan sektor industri, dimana salah satunya adalah di Kabupaten Sukoharjo. Menurut Rencana Pembangunan Industri Kabupaten Sukoharjo Tahun 2018-2038, di Kabupaten Sukoharjo terdapat kawasan yang perkembangannya sangat pesat, yaitu Kecamatan Grogol. Perkembangan pesat di Kecamatan Grogol ini ini mengundang banyak pendatang untuk bekerja sebagai buruh industri yang kemudian tidak dapat mengakses perumahan formal sebagai akibat kurangnya penyediaan rumah formal bagi buruh industri. Dengan latar belakang dan karakteristik yang berbeda-beda, para pendatang mengakses perumahan dengan preferensi yang berbeda sesuai dengan kebutuhan dan keinginan mereka. Penelitian ini memiliki tujuan untuk mengetahui faktor-faktor yang menjadi pengaruh dalam preferensi untuk bermukim pada buruh industri besar di Kecamatan Grogol. Penelitian ini merupakan penelitian kuantitatif dengan pengumpulan data primer melalui observasi dan kuesioner, serta pengumpulan data sekunder melalui pengumpulan data instansional dan studi literatur. Teknik analisis yang dipakai adalah analisis faktor. Hasil analisis yang mendapatkan bahwa faktor yang mempengaruhi buruh industri dalam menentukan lokasi bermukim adalah faktor kondisi rumah dan kualitas lingkungan, faktor kenyamanan lingkungan dan jarak tempat kerja, faktor keamanan mengakses layanan umum, serta yang terakhir adalah faktor sarana dasar. Faktor dominan yang mempengaruhi buruh industri besar di Kecamatan Grogol dalam memilih tempat tinggal adalah faktor kondisi rumah dan kualitas lingkungan.</span></em>
Confluence of Preoperative high levels of C-Reactive Protein and Visceral Fat index as Potential Contributor to Postoperative Complications in Colorectal Cancer: a Randomized Clinical Trial Incorporating Parenteral Nutrition
Authors: López-Rodríguez-Arias Francisco , Sánchez-Guillén Luis , Sanchís-López Antonio , Aranaz-Ostáriz Verónica , Sánchez-Romero Ana , Alcaide Maria José , Soler-Silva Álvaro , Lacueva Francisco Javier , Arroyo Antonio 
Published: June 2024

Abstract

Background: Visceral fat and inflammatory conditions are risk factors in patients undergoing colorectal cancer (CRC) surgery. This study was conducted to evaluate the effect of early peripheral parenteral nutrition (PPN) in patients with an elevated inflammatory state and/or an increase in their visceral fat on the anastomotic leak of patients undergoing CRC surgery within an enhanced recovery program.
Methods: A clinical trial was performed in patients undergoing CRC surgery between October 2016 and September 2019. Patients were randomized into two groups: PPN with periOlimel N4-E and conventional fluid therapy (FT). With C-reactive protein (CRP) values prior to surgery and visceral fat analysis of preoperative computer tomography, patients were stratified according to their risk of anastomotic leakage (AL). AL rates was obtained in each risk group differentiating whether they had received PPN or FT.
Results: A total of 116 patients were analyzed; 63 received PPN and 53 FT. Patients with high visceral fat index (VFI) had higher mean postoperative CRP values, especially on the 2nd postoperative day (p<0.05).
CRP values prior to surgery ≥5 mg/L and high VFI were associated with an AL rate of 28% (30% FT group vs. 23.5% PPN group): OR (95% CI) of 4.8 (p=0.003), and CRP values ≥10.2 mg/L showed an AL rate of 25.7% (30.8% FT group vs. 22.7% PPN group): OR (95% CI) of 6.6 (p= 0.001).
Conclusions: Analysis of visceral fat and the inflammatory state of patients with CRC allows us to evaluate the risk of anastomotic leakage, and PPN should be considered to improve AL rates.
Trial registration number: NCT03606863
Comparison of several salt water concentrations on salivary flora
Authors: alkhaled abdulrhman , Kouchaji Chaza 
Published: June 2024

Abstract

Objective :Mouth washing involves soaking the mouth's mucosa, gums, and teeth in a solution. Its objectives include treating certain oral diseases and enhancing oral hygiene. Examining the impact of salt water mouthwashes on oral flora in vitro is the goal of this study.
Methodology : in the Bacteriology Division of the Central Laboratory of Tishreen university Hospital, we carried out a cross-over clinical trial. From January 2021to July 2022, this study has a 6-month duration. We performed convenience sampling throughout this work.
In our article, the same mouthwash was given to every participant at the same time, and the results were tracked throughout time (H1–H5). In order to prevent carry-over effects, a wash-out time of 3 days was observed between the interventions (mouthwashes with various saline solutions: 0.9%; 2%; 5.8% and 23%). To identify the bacterial species impacted by the mouthwashes, gram staining was done before and seven hours after the mouthwashes . We selected 10 subjects, from whom we collected 240 samples of saliva. There was a 1:1 sex ratio.
Results :Our findings demonstrated that all solutions reduced the oral flora 2 minutes after rinsing (e.g., 5.8% saline reduced the original flora by half). The handmade saline (2%) exhibited an antibacterial impact on the oral flora that lasted for 3 hours, but the action of the 0.9% saline was only present for this period. However, only the 5.8% and 23% concentrations significantly reduced the oral flora as the sampling process went on. 5.8% salt content exhibited a 5-hour bactericidal effect, while 23% salt concentration had a 7-hour effect. We also observed a more pronounced action on gram positive bacteria.
Conclusion: the 5.8% saline is more well-tolerated by the subjects and has long-lasting efficacy. Since the prepared saline in home has an antibacterial effect that lasts for three hours, it can be recommended for short-term purposes. Since the 23% saline has a strong, unpleasant taste, it should be avoided.
A bidirectional two-sample Mendelian randomization using the gut microbiota to reveal potential therapeutic targets for acute pancreatitis
Authors: He Lin , Luo Haojun , Li Yu , Lu Jing , Li Jinzhi , Peng Li , Xu Yan , Liu Hang 
Published: June 2024

Abstract

Background: Numerous studies have indicated a correlation between the gut microbiota (GM) and acute pancreatitis (AP), yet the precise causal relationship between them remains ambiguous.
Methods: A two-sample Mendelian randomization (MR) study was conducted utilizing aggregated data from genome-wide association studies (GWASs) of 471 taxa (11 phyla, 19 orders, 24 orders, 62 families, 146 genera, and 209 species) and AP patients. Various methods, including inverse variance weighting (IVW), MR‒Egger, weighted medians, simple mode, and weighted mode, were employed to assess the causal association between the GM and AP. Sensitivity analyses were conducted utilizing Cochran's Q test, MR-Egger regression intercept analysis, and MR-PRESSO, followed by reverse MR analysis to evaluate the potential reverse causality between AP and GM.
Results: Three gut microbial taxa were found to have significant associations with acute pancreatitis (AP). The inverse variance weighted (IVW) results revealed that Coprobacillus (OR 1.19, 95% CI 1.01 to 1.40, p=0.035) and Holdemania sp900120005 (OR 1.18, 95% CI 1.02 to 1.35, p=0.023) were identified as risk factors for the development of AP, while Megamonas (OR: 0.87, 95% CI: 0.77 to 0.98, p=0.023) was found to be a protective factor against the occurrence of AP. A thorough sensitivity analysis confirmed the reliability of our findings. Reverse Mendelian randomization (MR) analysis did not indicate any causal relationship between AP and the gut microbiota (GM).
Conclusions: This study revealed a complex causal relationship between 3 GM taxa and AP, providing new evidence for the development of AP from a genetic perspective.
Urodynamic Evaluation of Neurogenic Bladder in Patients with Spinal Cord Injury within 6 months Post-Injury: A Retrospective Cross-sectional Study
Authors: Lee Byung Chan , Kim Onyoo , An Lyekyung 
Published: June 2024

Abstract

Study Design Retrospective cross-sectional survey of Korean patients with spinal cord injury (SCI) within 6 months post-injury. Objective To evaluate urodynamic parameters and identify unfavorable urodynamic findings in patients with neurogenic bladder due to spinal cord injury (SCI) during the acute to subacute stages of the disease based on the post-injury time interval. Setting National Rehabilitation Center, Seoul, Korea Methods Data from urodynamic tests performed on SCI patients within 6 months post-injury were collected. Based on the time interval from injury to testing, the recruited patients were divided into three groups: 0–90 days, 91–135 days, and 136–180 days. Based on these groups, urodynamic test parameters and incidence of unfavorable urodynamic findings (detrusor overactivity [DO], high detrusor pressure exceeding 40 cmH2O during the filling phase, low compliance of the bladder, underactive or acontractile bladder, and detrusor-sphincter dyssynergia [DSD]) were compared. Results Analysis of urodynamic study (UDS) findings in 191 patients with acute to subacute SCI, revealed that unfavorable urodynamic findings were observed within 3 months after injury in both complete and incomplete SCI. The UDS test results and incidence of unfavorable outcomes based on the interval between injury and examination showed no significant statistical differences over time. Conclusion The urodynamics of SCI patients suggest that unfavorable urodynamic results are common in the acute to subacute stages of SCI.
Prediction of dike seepage pressure based on ISSA-BiLSTM
Authors: Chen Shoukai , Liu Beiying , Xing Chunpeng , Zhao Mengdie , Zhou Jiayang 
Published: June 2024

Abstract

Seepage behavior is one of the critical factor in the operational safety of dams, and predicting dam seepage is the key content in dam monitoring and safety assessment research. The existing traditional dam seepage pressure prediction models have problems such as easy to fall into local optimum and limited predictive efficiency. The sparrow search algorithm(SSA) was improved as ISSA using both methods nonlinear Sine Cosine optimization algorithm and adaptive producer and scrounger ratio. We combined the Bidirectional Long Short-Term Memory (BiLSTM) neural network model with ISSA to develop the ISSA-BiLSTM seepage pressure prediction model. And the critical feature factors were extracted based on LightGBM to construct the input layer for seepage pressure prediction. The results show that the ISSA-BiLSTM model's fitting outcomes are generally consistent with the observed changes in seepage pressure observations, achieving an R2 of 0.987. In comparison to SSA-BiLSTM and BiLSTM, the model exhibits a substantial reduction in errors, decreasing by approximately 20% and 30%, respectively. This model can provide technical support and insights for accurately predicting dam seepage, contributing to the advancement of this field.
Buccolingual inclination of posterior dentition in maxillary impacted canine patients using quadrant analysis - A cone-beam computed tomographic study
Authors: Sökmen Tevhide , Bagcı Nuray , Tuncer Burcu Balos 
Published: June 2024

Abstract

Background
To examine the buccolingual inclination of maxillary posterior teeth, curve of Wilson, and transversal dimensions in palatally impacted maxillary canine patients, compared to controls by cone-beam computed tomography (CBCT).
Materials and Methods:
Pre-treatment images of 22 bilateral, 32 unilateral impacted maxillary canine patients and 30 controls were included. All patients had palatally impacted canines, with no posterior cross-bite. Data were reclassified in quadrants according to the presence of impaction, as the impaction quadrant (right and left quadrants of 22 bilateral impacted cases, and quadrants presenting impaction of 32 unilateral cases, n = 76), unaffected quadrant (quadrant without impaction in 32 unilateral cases, n = 32) and the control quadrant (right and left quadrants of 30 controls, n = 60) to evaluate the buccolingual inclination angle, transversal width, and arch perimeter. Additionally, comparisons were made regarding curve of Wilson and total arch perimeter among bilateral and unilateral impaction groups with the control group. Statistical analysis was performed by one-way ANOVA and Kruskal Wallis tests. Tukey or Dunn tests were used for comparisons between groups in pairs.
Results
No significant difference was found for the buccolingual inclination of maxillary posterior teeth and curve of Wilson among groups. The buccolingual inclination of canines in the impaction quadrant was significantly lower than the other quadrants (p < 0,001). Basal bone width at the level of second premolars, and alveolar width at both premolars were significantly narrower in the impaction quadrant than in the unaffected quadrant (p < 0,05). Dental arch width at the level of first premolar was significantly decreased in the impaction quadrant compared to other quadrants (p < 0,05). Arch perimeter was significantly reduced in the impaction quadrant than in the unaffected quadrant (p < 0,05).
Conclusion
The presence of bilateral or unilateral palatally impacted maxillary canines did not effect the buccolingual inclination of posterior teeth, and curve of Wilson. Transverse discrepancy was evident in the impaction quadrant even in the absence of posterior cross-bite. Quadrant analysis was particularly useful in evaluating asymmetry for basal bone and alveolar bone widths in the premolar region in patients with unilateral palatally impacted maxillary canine patients.
Single-cell atlas comparison across vertebrates reveals evolution of auditory cell types and mechanisms for hair cell regeneration
Authors: Li Jun 
Published: June 2024

Abstract

The loss of auditory hair cell in mammals including humans results in permanent hearing impairment, as they lack the inherent capacity for regeneration. In contrast, the lower vertebrates exhibit remarkable capacity for hair cell regeneration and hearing restoration, however, the mechanisms remain unclear. In this work, we characterized the first single-cell atlas of inner ear from the high regenerative species Xenopus laevis and further performed a comprehensive comparison with mouse model. An exceptionally conserved inner ear neuronal cell type was discovered and confirmed across species. Comprehensive characterization of the auditory hair cell across species revealed that the outer hair cells (OHCs) represent a newly evolved subtype, existing exclusively in mammals. Importantly, our analyses revealed an orchestrated gene expression program of the highly regenerative capacity in Xenopus, characterized by upregulation of genes associated with hair cell regeneration, coupled with downregulation of proliferation inhibitory genes. These findings unveil a natural feature of the highly regenerative capacity in Xenopus, and provide molecular and evolutionary evidences for the regulatory mechanisms for differential regenerative capacities across vertebrates. This work offers novel insights from amphibian into developing strategies to solve the challenges of hair cell regeneration and hearing repair in humans.