bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational analysis differentiating sporadic carcinomas from colitis-associated colorectal carcinomas
Authors: Dregelies Theresa , Haumaier Franziska , Sterlacci William , Backert Steffen , Vieth Michael 
Published: October 2024

Abstract
Background
Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) that is associated with increased risk of developing colitis-associated carcinoma (CAC). The genetic profile of CACs is fairly similar to the sporadic colorectal carcinomas (sCRCs), although showing certain differences in the timing and sequence of alterations that contribute to carcinogenesis. Also, both cancer types typically show a strong histological resemblance, which complicates the pathologists’ diagnosis. Due to the different clinical consequences, it is of utmost importance to categorize the corresponding cancer type correctly.

Methods
In this study, we determined the mutation profiles of 64 CACs and sCRCs in the hotspot regions of 50 cancer-associated genes and compared them to 29 controls to identify genetic gene variants that can facilitate the pathologists’ diagnosis. Pearson Chi-Square or Fisher’s exact tests were used for statistical analyses.

Results
We found that sCRCs tend to mutate more frequently in APC and PIK3CA genes than CACs and that mainly males were affected. Our CAC cohort identified the KRAS G12D mutation as group-specific variant that was not detected in the sCRCs. When separating conventional from non-conventional CACs, it was discovered that the conventional type shows significantly more mutations for ATM.

Conclusions
Taken together, our data highlights genetic differences between sCRC and CAC and enables the possibility to utilize specific gene alterations to support the pathologist’s diagnosis.
Infrared spectroscopy as a new approach for early fabry disease screening: a pilot study
Authors: Barretto Carolina Teles , Nascimento Márcia Helena Cassago , Brun Bruna Ferro , da Silva Tiago Barcelos , Dias Pedro Augusto Costa , Silva Cassiano Augusto Braga , Singh Maneesh N. , Martin Francis L. , Filgueiras Paulo Roberto , Romão Wanderson , Campos Luciene Cristina Gastalho , Barauna Valerio Garrone 
Published: October 2024

Abstract
Background
Fabry disease (FD) is a rare X-linked lysosomal storage disorder marked by alpha-galactosidase-A (α-Gal A) deficiency, caused by pathogenic mutations in the GLA gene, resulting in the accumulation of glycosphingolipids within lysosomes. The current screening test relies on measuring α-Gal A activity. However, this approach is limited to males. Infrared (IR) spectroscopy is a technique that can generate fingerprint spectra of a biofluid’s molecular composition and has been successfully applied to screen numerous diseases. Herein, we investigate the discriminating vibration profile of plasma chemical bonds in patients with FD using attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy.

Results
The Fabry disease group (n = 47) and the healthy control group (n = 52) recruited were age-matched (39.2 ± 16.9 and 36.7 ± 10.9 years, respectively), and females were predominant in both groups (59.6% and 65.4%, respectively). All patients had the classic phenotype (100%), and no late-onset phenotype was detected. A generated partial least squares discriminant analysis (PLS-DA) classification model, independent of gender, allowed differentiation of samples from FD vs. control groups, reaching 100% sensitivity, specificity and accuracy.

Conclusion
ATR-FTIR spectroscopy harnessed to pattern recognition algorithms can distinguish between FD patients and healthy control participants, offering the potential of a fast and inexpensive screening test.
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
Authors: Bessière Chloé , Xue Haoliang , Guibert Benoit , Boureux Anthony , Rufflé Florence , Viot Julien , Chikhi Rayan , Salson Mikaël , Marchet Camille , Commes Thérèse , Gautheret Daniel 
Published: October 2024

AbstractIndexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbitrary RNA sequences can be quantified in seconds through their decomposition into k-mers, with a precision akin to that of conventional RNA quantification methods. Using an index of the Cancer Cell Line Encyclopedia (CCLE) collection consisting of 1019 RNA-seq samples, we show that k-mer indexing offers a powerful means to reveal non-reference sequences, and variant RNAs induced by specific gene alterations, for instance in splicing factors.
Simple simultaneous analysis of various cardiovascular drug mixtures with vincamine: comparative eco-friendly assessment
Authors: Mourad Sara S. , Barary Magda A. , El-Yazbi Amira F. 
Published: October 2024

AbstractThe development of two eco-friendly analytical methods for the simultaneous determination of eight cardiovascular drugs; hydrochlorothiazide (HCT), captopril (CPL), lisinopril (LSP), valsartan (VAL), atorvastatin (ATR), bisoprolol (BSL), amlodipine (AML) and carvedilol (CVL); alongside with the nutraceutical vincamine (VIC) is essential for sustainable pharmaceutical analysis. This study explores the application of Micellar Electro Kinetic Chromatography (MEKC) and High-Performance Liquid Chromatography (HPLC) for this purpose. In MEKC method, the separation was done using fused silica capillary (41.5 cm × 50 µm id) and a back ground electrolyte consisting of 50 mM borate buffer (pH 9) containing 50 mM sodium lauryl sulphate (SLS) and 10% organic modifier (Acetonitrile). In HPLC method, separation was performed on a ZORBAX Extend-C18 (4.6 × 250 mm, 5 µm) column, using a gradient mobile phase consisting of 50 mM phosphate buffer pH 3 and methanol. Both methods attained good linearity (r ≥ 0.9996) with low values of LOD and LOQ. Both methods were successfully applied in the determination of co-administered single, binary and ternary dosage form of the studied drugs. Moreover, application of various combinations of co-administered dosage forms was achieved in rat plasma, confirming the applicability of these methods in different matrices. The use of micellar solutions in MEKC enhances separation efficiency while reducing the need for organic solvents, aligning with green chemistry principles. HPLC methods were optimized using environmentally benign solvents, ensuring reduced toxicity and waste production. The methodologies were evaluated through green, white, and blue metrics to ensure comprehensive sustainability, considering ecological impact, safety, and practical efficiency. These methods were not only cost-effective and time-saving but achieved high efficiency, sensitivity, and reproducibility making them ideal for routine use in pharmaceutical analysis.
Impact of virtual reality hypnosedation on perioperative pain and anxiety in port implantation under local anesthesia: a randomized controlled pilot trial (VIP Trial)
Authors: Steinkraus Kira C. , Feldmann Hannah , Hunold Lisa S. , Graf Sandra , Dörr-Harim Colette , Nasir Nadir , Michalski Christoph W. , Hüttner Felix J. 
Published: October 2024

Abstract
Background
This monocentric randomized controlled pilot trial investigates the impact of virtual reality (VR) hypnosedation on perioperative anxiety, pain, patient satisfaction, and medication usage during port implantation under local anesthesia.

Methods
A total of 120 patients undergoing elective port implantation between January 2022 and August 2023 were enrolled and randomized in a 1:1 ratio to either a VR hypnosedation group or a control group. The VR group used a commercially available VR headset with the HypnoVR application, providing various environments, musical backgrounds, and a guiding voice, while the control group underwent the procedure without VR. Patients with ASA > 3, chronic pain, cognitive issues, and contraindications against VR use were excluded. The main outcomes measured were perioperative pain and anxiety scores, with secondary outcomes including perioperative medication usage. Due to the nature of the interventions, blinding of patients and physicians was not feasible. Statistical analysis was primarily descriptive and exploratory, focusing on estimating effect sizes for future trials.

Results
The study found no significant differences in immediate postoperative pain with 1.43 ± 1.63 vs. 1.6 ± 2.05 (p = 0.62) or anxiety scores 30.65 ± 9.13 vs. 31.78 ± 13.34 (p = 0.60) between the no VR and VR group, respectively. Additionally, there was a trend to less usage of certain medications, particularly remifentanil (mean dose of 200 mg vs. 100 mg (p = 0.12)) and novaminsulfon (mean dose of 1250 mg vs. 900 mg (p = 0.26)) in the VR group vs. no VR group, respectively. However, these differences were not statistically significant and therefore no definitive conclusions can be drawn regarding medication usage based on this data.

Conclusion
While VR hypnosedation did not significantly reduce perioperative pain or anxiety in this pilot trial, the observed trends in reduced medication usage suggest potential benefits. These findings warrant further investigation in larger, confirmatory trials to better understand the role of VR in enhancing patient comfort and potentially reducing reliance on pharmacological interventions during surgical procedures.

Trial registration
German Clinical Trials Register: DRKS00028508; registration date 15 March 2022; Universal Trial Number: U1111-1275–4995.
How to interpret Jiangnan gardens: a study of the spatial layout of Jiangnan gardens from the perspective of fractal geometry
Authors: Sun Ce , Jiang Zhenyu , Yu Bingqin 
Published: October 2024

Abstract
This study contributes to design studies by offering a novel approach to understanding the spatial layout of Jiangnan gardens through the lens of fractal geometry. Analyzing 106 gardens, we found that the ideal fractal dimension range for Jiangnan gardens is 1.148 ~ 1.276, with gardens in the 2500 ~ 7200 m2 range exhibiting the highest complexity (1.238 ~ 1.276). Additionally, for gardens ranging from 2500  ~ 20,000 m2, the maximum spacious space area stabilizes, no longer expanding indefinitely with overall area. This suggests a design principle of spatial proportion and balance. By quantifying spatial complexity and the contrast between spacious and profund spaces, the study provides a new method for evaluating garden design and can help students and designers better apply the principles of Jiangnan garden design.
A review of geopolymer binder as a grouting material
Authors: Sierra Karla , An Jinwoo , Shamet Ryan , Chen Jiannan , Kim Yong Je , Nam Boo Hyun , Park Philip 
Published: October 2024

AbstractThe utilization of geopolymer as a grouting material has gained significant attention in research and construction applications. Geopolymer grout is a type of binding material that differs from traditional grouts, typically based on Portland cement. Researchers have explored its effectiveness and potential applications in grouting processes, considering its unique properties and characteristics. In this paper, various studies employing and utilizing geopolymer as a grouting material are reviewed. The emphasis is on mixture design of geopolymer grout, physical property, chemical composition of geopolymer grout, rheological behavior of geopolymer grout such as yield stress (in case of Bingham fluid) and viscosity, and engineering properties such as compressive strength, expansion, shrinkage, etc.
A proof-of-concept study of a prototype needle that mitigates intraocular pressure rise following intravitreal injection
Authors: Sverstad Alexander , Kristianslund Olav , Petrovski Goran , Moe Morten Carstens , Jørstad Øystein Kalsnes 
Published: October 2024

Abstract
Purpose
To determine the feasibility of a prototype needle that enhances vitreous reflux (VR) to control intraocular pressure (IOP) in intravitreal injection (IVI).

Methods
We created an eye model to compare IVI using a standard 30-G needle with four different versions of a 30-G prototype needle with one to four surface grooves that enhanced VR. We injected 50, 70, and 100 µl saline through porcine sclera or 460-µm-thick rubber and measured the peak and 3-second pressure before we extracted the needle and measured the 10-second pressure.

Results
50-µl injection through sclera with the standard needle resulted in mean (SD) pressure of 58.6 (3.8) mmHg at peak, 52.8 (4.7) mmHg at 3 s, and 39.6 (18.0) mmHg at 10 s. The prototype needle lowered the pressure; four grooves resulted in mean (SD) pressure of 29.4 (5.6) mmHg at peak, 22.0 (3.7) mmHg at 3 s, and 7.2 (6.6) mmHg at 10 s. 70-µl and 100-µl injections through sclera with the standard needle resulted in mean (SD) pressure of 68.8 (3.6) and 86.0 (6.0) mmHg at peak. Similar to 50-µl injection, the prototype needle lowered the pressure for 70-µl and 100-µl injections. At 10 s, we observed varying leakage at the injection site for sclera but not for rubber.

Conclusions
The study provides proof of concept for a needle design for which surface grooves enhance VR and counteract the effect of IVI on IOP. The safety and efficacy of the prototype needle must be studied further in a clinical trial.
Anesthetic management of a patient with mandibular hypoplasia, deafness, progeroid features, lipodystrophy syndrome: a case report
Authors: Sekiguchi Ryo , Kinoshita Michiko , Sakai Yoko , Tanaka Katsuya 
Published: October 2024

Abstract
Background
Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy (MDPL) syndrome is a rare autosomal dominant disorder that presents unique challenges for anesthetic management due to its multisystemic manifestations. This report outlines the anesthetic considerations for MDPL patients based on our case experience.

Case presentation
A 15-year-old male with MDPL syndrome underwent testicular extraction under general anesthesia. Insertion of a peripheral venous catheter was challenging due to scleroderma-like skin. Although the facial features of MDPL syndrome suggested a difficult airway, intubation with a McGrath™ Mac video laryngoscope was successful. Despite MDPL syndrome’s association with hypertriglyceridemia due to lipodystrophy, this patient’s triglyceride levels were normal. Thiamylal and sevoflurane were used without issues such as delayed emergence from anesthesia.

Conclusions
MDPL syndrome requires careful preoperative assessment and tailored anesthetic management due to potential airway challenges arising from its distinctive facial features and the possibility of altered anesthetic pharmacokinetics associated with lipodystrophy.
Efficient gene editing with an Arg-tRNA promoter-driven CRISPR/Cas9 in the rice blast fungus Pyricularia oryzae
Authors: Wang Rui-Jin , Zhao Jianhui , Bhadauria Vijai , Peng You-Liang 
Published: October 2024

AbstractCRISPR/Cas9 technology has been widely adopted for genome editing in a wide range of organisms, including many fungi. Pyricularia oryzae is a filamentous fungal pathogen that causes the devastating rice blast disease. However, an efficient and cost-effective CRISPR/Cas9 system for the rice blast fungus has yet to be established. Here, we report an 84-bp arginyl (Arg)-tRNA promoter-driven CRISPR/Cas9 system, which enables efficient and cost-effective gene editing in P. oryzae. Preliminary screening of three tRNAs from the 179 predicted tRNAs in P. oryzae showed that two Arg-tRNA CRISPR/Cas9 cassettes reproducibly generated MoB56 disruption efficiently. Further, five genes located on distinct chromosomes, including two previously uncharacterized genes, were randomly picked up to test the efficiency of the Mo_tRNAArg24-gRNA-Cas9 cassette. Ppg1 is a gene essential to the pathogenicity and important for mycelial growth and conidiation of P. oryzae, which is located at chromosome 2 and exhibited a relatively low gene replacement rate (< 1/500) by the traditional gene replacement approach. By using the Mo_tRNAArg24-gRNA-Cas9 cassette, Ppg1 gene disruption rate was increased up to 75.9%. In addition, Bip2, an uncharacterized genes located close to the centromere of chromosome 4, was disrupted at 66.7%. For all the five tested genes, our Mo_tRNAArg24-gRNA-Cas9 cassette showed high gene disruption efficiency in P. oryzae, ranging from 66.7% to 100%. Importantly, it rarely induces Cas9 toxicity to P. oryzae. The Mo_tRNAArg24-gRNA-Cas9 cassette described in this study can be adopted as an alternative for functional genomics study in P. oryzae.
The third-generation anticoagulants: factors XI, XII, and XIII inhibitors
Authors: Prajapathi Sudesh , Pradhan Akshyaya , Mohta Aditi , Sethi Rishi 
Published: October 2024

Abstract
Background
Arterial or venous thromboembolic events are responsible for one-fourth of all deaths worldwide. Anticoagulants are the mainstay for the prevention and treatment of venous thromboembolic events (VTE). Heparin and vitamin K antagonists were the first non-specific medications used in anticoagulant therapy, followed by safer alternatives, such as fondaparinux, argatroban, and direct oral anticoagulants. However, the latter bear the risk of potentially lethal internal bleeding. Novel drugs inhibiting various coagulation factors, such as factors XIa, XIIa, and XIIIa, appear to have a lesser risk of bleeding and are in the spotlight. This review aims to consolidate findings from published clinical trials of newer drugs inhibiting factors XIa, XIIa, and XIIIa.

Main body
Factor XI inhibitors have been researched more extensively as compared to factor XII and factor XIII inhibitors. Phase 2 study results of factor XI inhibitors indicated their superiority over enoxaparin for reduction of VTE incidence and better safety profile in terms of bleeding. Factor XII inhibitors also hold the promise of lowering the risk of bleeding, as indicated in animal studies. Further human studies would ensure their safety and applicability in the human population. Numerous laboratory researches have revealed, the potent antithrombotic profile of factor XIII inhibition with limited bleeding risks.

Conclusion
Larger statistically powered studies could supplement data to establish the role of FXI inhibitors in the prevention of both arterial and venous thromboembolic events in high-risk populations. While early results of factor XII and factor XIII inhibitors look promising, they still have a long road ahead before their therapeutic efficacy in humans is established.
Effect of continuous inhaled corticosteroids on glycated hemoglobin in asthmatic children: a pilot study
Authors: Fawzy Erini Farid , Attar Mona Mohsen El , Badry Mahmoud Ahmed El , Al Khashab Khaled Mohammed 
Published: October 2024

Abstract
Background
Asthma is a prevalent chronic disease with significant impact on patients, families, and communities. Inhaled corticosteroids (ICS) are the mainstay of treatment for persistent and uncontrolled asthma. However, concerns remain about the potential adverse effects of ICS, including HbA1c level. This study aims to evaluate the influence of ICS on Hemoglobin A1c (HbA1c) levels in children with bronchial asthma.

Methods
This prospective cohort study included 48 pediatric asthma patients aged 2 to 15 years who had been using ICS for at least 6 months. Comprehensive clinical assessments and measurements of HbA1c levels were conducted at the start of recruitment and after 6 months of ICS use. The types and doses of ICS used followed the guidelines provided by the Global Initiative for Asthma (GINA).

Results
The initial HbA1c levels ranged from 4.46 to 6.11, with a mean of 5.32 ± 0.35. Three patients (6.3%) had persistent prediabetes status after 6 months. There was no significant relationship between glycemic status and the characteristics of ICS. The duration of ICS therapy and the doses used did not significantly affect HbA1c levels. A weak positive correlation was observed between initial and subsequent HbA1c levels.

Conclusion
The study found no significant difference in HbA1c levels among asthmatic children using ICS after six months of treatment. Additionally, there was no significant difference in HbA1c levels between patients using different types of ICS. Regular monitoring of HbA1c levels is recommended, particularly for children on high doses or prolonged use of inhaled Fluticasone.
Resistant inflammatory breast lesions: can AI exclude malignancy?
Authors: El-nasr Safaa Ibrahim Saif , ElSayed Norhan Mohamed Samy , Badawy Eman , Taha Sherif Nasser , Hegazy Rania Mohamed A. 
Published: October 2024

Abstract
Background
Numerous underlying causes can lead to inflammatory breast disorders. A wide range of non-specific symptoms may be presenting symptoms, which could cause a delay in diagnosis and thus improper therapy. Studies on artificial intelligence (AI) are rapidly developing and offer a wide range of possible uses in breast imaging. Artificial intelligence-based computer-assisted diagnosis (AI-CAD) holds promise in the field of mammography. It demonstrated diagnostic performances that are equivalent to or even better than those achieved by stand-alone methods. The current work aimed to identify whether AI can improve the performance of mammography in diagnosing inflammatory breast diseases and excluding the underlying malignancy in cases resistant to treatment that may reduce the need for interventional procedures such as biopsy.

Methods
Our study was a retrograde one done on 34 patients with pathologically proven inflammatory breast lesions.

Results
Suppurative breast lesions gave high false positive results. This was also the case with granulomatous mastitis; while simple inflammatory lesions gave true negative results on AI interrogation.

Conclusions
Artificial intelligence can be of great value in diagnosing simple inflammatory breast lesions thus following up on such lesions can usually be sufficient without asking for unneeded biopsies. On the other hand, our study showed that AI had high false positive results in suppurative lesions and granulomatous mastitis. Consequently, ultrasonography can be more reliable in their diagnosis.