bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the hair detectability of prohibited substances in sports: an in vivo-in silico-clinical approach and analytical implications compared with plasma, urine, and faeces
Authors: Hung Shao-Hsin , Kan Hung-Lin , Tung Chun-Wei , Lin Yi-Ching , Chen Ting-Ting , Tian Ciao , Chang William Chih-Wei 
Published: January 2024

AbstractHair analysis is a crucial method in forensic toxicology with potential applications in revealing doping histories in sports. Despite its widespread use, knowledge about detectable substances in hair is limited. This study systematically assessed the detectability of prohibited substances in sports using a multifaceted approach. Initially, an animal model received a subset of 17 model drugs to compare dose dependencies and detection windows across different matrices. Subsequently, hair incorporation data from the animal experiment were extrapolated to all substances on the World Anti-Doping Agency’s List through in-silico prediction. The detectability of substances in hair was further validated in a proof-of-concept human study involving the consumption of diuretics and masking agents. Semi-quantitative analysis of substances in specimens was performed using ultra-performance liquid chromatography–tandem mass spectrometry. Results showed plasma had optimal dose dependencies with limited detection windows, while urine, faeces, and hair exhibited a reasonable relationship with the administered dose. Notably, hair displayed the highest detection probability (14 out of 17) for compounds, including anabolic agents, hormones, and diuretics, with beta-2 agonists undetected. Diuretics such as furosemide, canrenone, and hydrochlorothiazide showed the highest hair incorporation. Authentic human hair confirmed diuretic detectability, and their use duration was determined via segmental analysis. Noteworthy is the first-time reporting of canrenone in human hair. Anabolic agents were expected in hair, whereas undetectable compounds, such as peptide hormones and beta-2 agonists, were likely due to large molecular mass or high polarity. This study enhances understanding of hair analysis in doping investigations, providing insights into substance detectability.
Drug-drug interaction perpetrators of oxycodone in patients with cancer: frequency and clinical relevance
Authors: Hulskotte L. M. G. , Töpfer W. , Reyners A. K. L. , Taxis K. , Jansman F. G. A. 
Published: January 2024

Abstract
Aim
Oxycodone is known to have numerous drug-drug interactions (DDIs) that can potentially decrease efficacy or lead to adverse drug reactions (ADRs). However, there is limited research on the frequency of DDIs associated with oxycodone, which is important in optimising pharmacovigilance and the need for additional research on certain DDIs. In this study, the frequency of pharmacologically and clinically relevant DDI perpetrators was studied in patients with cancer.

Methods
This was a cross-sectional study using hospital pharmacy records of patients with cancer who were prescribed oxycodone between September 2021 and September 2022. Medication records of patients prescribed oxycodone during a period of ≥ 5 consecutive days (= oxycodone treatment episodes) were reviewed to identify the concomitant use of pharmacologically relevant perpetrators, based on reference sources (Lexicomp®, Micromedex®, the Dutch Kennisbank and the Dutch Commentaren Medicatiebewaking). The clinical relevance was examined by a clinical pharmacologist and a medical oncologist. Additionally, the frequency of double interactions—concomitant oxycodone use with two CYP3A4 and / or CYP2D6 perpetrators—was studied.

Results
Overall, 254 oxycodone treatment episodes were included, of which 227 (89.4%) were found to contain at least one pharmacologically relevant DDI perpetrator. Of these, 210 (82.7%) were considered to be clinically relevant. A total of 80 different pharmacologically relevant perpetrators were identified, with 65 (81.3%) being considered clinically relevant. Double interactions were observed in 21 (8.3%) oxycodone treatment episodes.

Conclusion
A high frequency of pharmacologically and clinically relevant perpetrators of oxycodone was observed in our cohort. Moreover, a high number of double interactions involving oxycodone was registered. More intense monitoring of DDIs may be needed to improve medication safety of patients with cancer taking oxycodone.
Characterization of a novel aspartic protease from Trichoderma asperellum for the preparation of duck blood peptides
Authors: Xue Yibin , Yan Qiaojuan , Li Xue , Jiang Zhengqiang 
Published: January 2024

Abstract
A novel aspartic protease gene (TaproA1) from Trichoderma asperellum was successfully expressed in Komagataella phaffii (Pichia pastoris). TaproA1 showed 52.8% amino acid sequence identity with the aspartic protease PEP3 from Coccidioides posadasii C735. TaproA1 was efficiently produced in a 5 L fermenter with a protease activity of 4092 U/mL. It exhibited optimal reaction conditions at pH 3.0 and 50 °C and was stable within pH 3.0–6.0 and at temperatures up to 45 °C. The protease exhibited broad substrate specificity with high hydrolysis activity towards myoglobin and hemoglobin. Furthermore, duck blood proteins (hemoglobin and plasma protein) were hydrolyzed by TaproA1 to prepare bioactive peptides with high ACE inhibitory activity. The IC50 values of hemoglobin and plasma protein hydrolysates from duck blood proteins were 0.105 mg/mL and 0.091 mg/mL, respectively. Thus, the high yield and excellent biochemical characterization of TaproA1 presented here make it a potential candidate for the preparation of duck blood peptides.

Key points
• An aspartic protease (TaproA1) from Trichoderma asperellum was expressed in Komagataella phaffii.
• TaproA1 exhibited broad substrate specificity and the highest activity towards myoglobin and hemoglobin.
• TaproA1 has great potential for the preparation of bioactive peptides from duck blood proteins.
LL-37_Renalexin hybrid peptide exhibits antimicrobial activity at lower MICs than its counterpart single peptides
Authors: Narh Julius Kwesi , Casillas-Vega Nestor G. , Zarate Xristo 
Published: January 2024

Abstract
An alarming global public health and economic peril has been the emergence of antibiotic resistance resulting from clinically relevant bacteria pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species constantly exhibiting intrinsic and extrinsic resistance mechanisms against last-resort antibiotics like gentamycin, ciprofloxacin, tetracycline, colistin, and standard ampicillin prescription in clinical practices. The discovery and applications of antimicrobial peptides (AMPs) with antibacterial properties have been considered and proven as alternative antimicrobial agents to antibiotics. In this study, we have designed, produced, and purified a recombinant novel multifunctional hybrid antimicrobial peptide LL-37_Renalexin for the first time via the application of newly designed flexible GS peptide linker coupled with the use of our previously characterized small metal-binding proteins SmbP and CusF3H+ as carrier proteins that allow for an enhanced bacterial expression, using BL21(DE3) and SHuffle T7(DE3) Escherichia coli strains, and purification of the hybrid peptide via immobilized metal affinity chromatography. The purified tag-free LL-37_Renalexin hybrid peptide exhibited above 85% reduction in bacteria colony-forming units and broad-spectrum antimicrobial effects against Staphylococcus aureus, Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), and Klebsiella pneumoniae bacteria clinical isolates at a lower minimum inhibition concentration level (10–33 μM) as compared to its counterpart single-AMPs LL-37 and Renalexin (50–100 μM).

Key points
• The hybrid antimicrobial peptide LL-37_Renalexin has been designed using a GS linker.
• The peptide was expressed with the carrier proteins SmbP and CusF3H+.
• The hybrid peptide shows antibacterial potency against clinical bacterial isolates.
The potency of mitochondria enlargement for mitochondria-mediated terpenoid production in yeast
Authors: Yanagibashi So , Bamba Takahiro , Kirisako Takayoshi , Kondo Akihiko , Hasunuma Tomohisa 
Published: January 2024

Abstract
Terpenoids are widely used in the food, beverage, cosmetics, and pharmaceutical industries. Microorganisms have been extensively studied for terpenoid production. In yeast, the introduction of the mevalonate (MVA) pathway in organelles in addition to the augmentation of its own MVA pathway have been challenging. Introduction of the MVA pathway into mitochondria is considered a promising approach for terpenoid production because acetyl-CoA, the starting molecule of the MVA pathway, is abundant in mitochondria. However, mitochondria comprise only a small percentage of the entire cell. Therefore, we hypothesized that increasing the total mitochondrial volume per cell would increase terpenoid production. First, we ascertained that the amounts of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the final molecules of the MVA pathway, were 15-fold higher of the strain expressing the MVA pathway in mitochondria than in the wild-type yeast strain. Second, we found that different deletion mutants induced different mitochondrial volumes by measuring the mitochondrial volume in various deletion mutants affecting mitochondrial morphology; for example,Δmdm32 increased mitochondrial volume, and Δfzo1 decreased it. Finally, the effects of mitochondrial volume on amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) were investigated using mutants harboring large or small mitochondria expressing the MVA pathway in mitochondria. Amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) increased when the mitochondrial volume expanded. Introducing the MVA pathway into mitochondria for terpenoid production in yeast may become more attractive by enlarging the mitochondrial volume.

Key points
• IPP/DMAPP content increased in the strain expressing the MVA pathway in mitochondria
• IPP/DMAPP and terpenoid contents are positively correlated with mitochondrial volume
• Enlarging the mitochondria may improve mitochondria-mediated terpenoid production
Production of antiviral “OP7 chimera” defective interfering particles free of infectious virus
Authors: Pelz Lars , Dogra Tanya , Marichal-Gallardo Pavel , Hein Marc Dominique , Hemissi Ghada , Kupke Sascha Young , Genzel Yvonne , Reichl Udo 
Published: January 2024

Abstract
Defective interfering particles (DIPs) of influenza A virus (IAV) are suggested for use as broad-spectrum antivirals. We discovered a new type of IAV DIP named “OP7” that carries point mutations in its genome segment (Seg) 7 instead of a deletion as in conventional DIPs (cDIPs). Recently, using genetic engineering tools, we generated “OP7 chimera DIPs” that carry point mutations in Seg 7 plus a deletion in Seg 1. Together with cDIPs, OP7 chimera DIPs were produced in shake flasks in the absence of infectious standard virus (STV), rendering UV inactivation unnecessary. However, only part of the virions harvested were OP7 chimera DIPs (78.7%) and total virus titers were relatively low. Here, we describe the establishment of an OP7 chimera DIP production process applicable for large-scale production. To increase total virus titers, we reduced temperature from 37 to 32 °C during virus replication. Production of almost pure OP7 chimera DIP preparations (99.7%) was achieved with a high titer of 3.24 log10(HAU/100 µL). This corresponded to an 11-fold increase relative to the initial process. Next, this process was transferred to a stirred tank bioreactor resulting in comparable yields. Moreover, DIP harvests purified and concentrated by steric exclusion chromatography displayed an increased interfering efficacy in vitro. Finally, a perfusion process with perfusion rate control was established, resulting in a 79-fold increase in total virus yields compared to the original batch process in shake flasks. Again, a very high purity of OP7 chimera DIPs was obtained. This process could thus be an excellent starting point for good manufacturing practice production of DIPs for use as antivirals.

Key points
• Scalable cell culture-based process for highly effective antiviral OP7 chimera DIPs
• Production of almost pure OP7 chimera DIPs in the absence of infectious virus
• Perfusion mode production and purification train results in very high titers
Structural and functional characterization of a new thermophilic-like OYE from Aspergillus flavus
Authors: Li Na , Wang Yuan , Meng Yinyin , Lv Yangyong , Zhang Shuaibing , Wei Shan , Ma Pingan , Hu Yuansen , Lin Hui 
Published: January 2024

Abstract
Old yellow enzymes (OYEs) have been proven as powerful biocatalysts for the asymmetric reduction of activated alkenes. Fungi appear to be valuable sources of OYEs, but most of the fungal OYEs are unexplored. To expand the OYEs toolbox, a new thermophilic-like OYE (AfOYE1) was identified from Aspergillus flavus strain NRRL3357. The thermal stability analysis showed that the T1/2 of AfOYE1 was 60 °C, and it had the optimal temperature at 45 °C. Moreover, AfOYE1 exhibited high reduction activity in a wide pH range (pH 5.5–8.0). AfOYE1 could accept cyclic enones, acrylamide, nitroalkenes, and α, β-unsaturated aldehydes as substrates and had excellent enantioselectivity toward prochiral alkenes (> 99% ee). Interestingly, an unexpected (S)-stereoselectivity bioreduction toward 2-methylcyclohexenone was observed. The further crystal structure of AfOYE1 revealed that the “cap” region from Ala132 to Thr182, the loop of Ser316 to Gly325, α short helix of Arg371 to Gln375, and the C-terminal “finger” structure endow the catalytic cavity of AfOYE1 quite deep and narrow, and flavin mononucleotide (FMN) heavily buried at the bottom of the active site tunnel. Furthermore, the catalytic mechanism of AfOYE1 was also investigated, and the results confirmed that the residues His211, His214, and Tyr216 compose its catalytic triad. This newly identified thermophilic-like OYE would thus be valuable for asymmetric alkene hydrogenation in industrial processes.

Key points

A new thermophilic-like OYE AfOYE1 was identified from Aspergillus flavus, and the T1/2of AfOYE1 was 60 °C

AfOYE1 catalyzed the reduction of 2-methylcyclohexenone with (S)-stereoselectivity

The crystal structure of AfOYE1 was revealedv
A novel, robust peptidyl-lys metalloendopeptidase from Trametes coccinea recombinantly expressed in Komagataella phaffii
Authors: Ahmed Uzair , Stadelmann Tobias , Heid Daniel , Würtz Berit , Pfannstiel Jens , Ochsenreither Katrin , Eisele Thomas 
Published: January 2024

Abstract
A novel peptidyl-lys metalloendopeptidase (Tc-LysN) from Tramates coccinea was recombinantly expressed in Komagataella phaffii using the native pro-protein sequence. The peptidase was secreted into the culture broth as zymogen (~38 kDa) and mature enzyme (~19.8 kDa) simultaneously. The mature Tc-LysN was purified to homogeneity with a single step anion-exchange chromatography at pH 7.2. N-terminal sequencing using TMTpro Zero and mass spectrometry of the mature Tc-LysN indicated that the pro-peptide was cleaved between the amino acid positions 184 and 185 at the Kex2 cleavage site present in the native pro-protein sequence. The pH optimum of Tc-LysN was determined to be 5.0 while it maintained ≥60% activity between pH values 4.5—7.5 and ≥30% activity between pH values 8.5—10.0, indicating its broad applicability. The temperature maximum of Tc-LysN was determined to be 60 °C. After 18 h of incubation at 80 °C, Tc-LysN still retained ~20% activity. Organic solvents such as methanol and acetonitrile, at concentrations as high as 40% (v/v), were found to enhance Tc-LysN’s activity up to ~100% and ~50%, respectively. Tc-LysN’s thermostability, ability to withstand up to 8 M urea, tolerance to high concentrations of organic solvents, and an acidic pH optimum make it a viable candidate to be employed in proteomics workflows in which alkaline conditions might pose a challenge. The nano-LC-MS/MS analysis revealed bovine serum albumin (BSA)’s sequence coverage of 84% using Tc-LysN which was comparable to the sequence coverage of 90% by trypsin peptides.

Key points
•A novel LysN from Trametes coccinea (Tc-LysN) was expressed in Komagataella phaffii and purified to homogeneity
•Tc-LysN is thermostable, applicable over a broad pH range, and tolerates high concentrations of denaturants
•Tc-LysN was successfully applied for protein digestion and mass spectrometry fingerprinting
Outcome and complication rate of total hip arthroplasty in patients younger than twenty years: which bearing surface should be used?
Authors: Kang Sang Yoon , Ko Young-Seung , Kim Hong Seok , Yoo Jeong Joon 
Published: January 2024

Abstract
Purpose
Total hip arthroplasty (THA) in younger patients remains controversial due to concerns regarding long-term implant survival and potential complications. This study aimed to evaluate long-term clinical outcomes, complications, differences in complication and revision rates by bearing surfaces, and Kaplan–Meier survival curves for THA in patients under 20 years old.

Methods
A retrospective review was conducted for 65 patients (78 hips) who underwent THA between 1991 and 2018. Their mean age was 18.9 years. Their clinical outcomes were assessed using the Harris Hip Score (HHS). Radiological outcomes were evaluated based on the presence of loosening, osteolysis, and heterotopic ossification. Complications such as dislocation, periprosthetic fractures, and infections were assessed. The mean follow-up period was 13.2 years (range, 5.0–31.2 years).

Results
The mean HHS improved from 44.6 to 90.1. There were two cases of dislocation. However, no periprosthetic fracture, deep infection, or ceramic component fracture was noted. There were 19 revisions of implants. Eighteen of 19 hips were operated with hard-on-soft bearings in the index surgery (p < 0.01). The 23-year survivorship was 97.8% for THA using ceramic-on-ceramic bearings, while the 31-year survivorship was 36.7% using hard-on-soft bearings.

Conclusion
THA in patients under 20 years old yielded promising clinical and radiological outcomes, although polyethylene-bearing-related concerns persisted. Previously operated patients with hard-on-soft bearing should be meticulously examined during the follow-up. As ceramic-on-ceramic bearing showed excellent survivorship in this particular cohort, we recommend the use of this articulation as the bearing of choice.
Automated MRI liver segmentation for anatomical segmentation, liver volumetry, and the extraction of radiomics
Authors: Gross Moritz , Huber Steffen , Arora Sandeep , Ze’evi Tal , Haider Stefan P. , Kucukkaya Ahmet S. , Iseke Simon , Kuhn Tom Niklas , Gebauer Bernhard , Michallek Florian , Dewey Marc , Vilgrain Valérie , Sartoris Riccardo , Ronot Maxime , Jaffe Ariel , Strazzabosco Mario , Chapiro Julius , Onofrey John A. 
Published: January 2024

Abstract
Objectives
To develop and evaluate a deep convolutional neural network (DCNN) for automated liver segmentation, volumetry, and radiomic feature extraction on contrast-enhanced portal venous phase magnetic resonance imaging (MRI).

Materials and methods
This retrospective study included hepatocellular carcinoma patients from an institutional database with portal venous MRI. After manual segmentation, the data was randomly split into independent training, validation, and internal testing sets. From a collaborating institution, de-identified scans were used for external testing. The public LiverHccSeg dataset was used for further external validation. A 3D DCNN was trained to automatically segment the liver. Segmentation accuracy was quantified by the Dice similarity coefficient (DSC) with respect to manual segmentation. A Mann-Whitney U test was used to compare the internal and external test sets. Agreement of volumetry and radiomic features was assessed using the intraclass correlation coefficient (ICC).

Results
In total, 470 patients met the inclusion criteria (63.9±8.2 years; 376 males) and 20 patients were used for external validation (41±12 years; 13 males). DSC segmentation accuracy of the DCNN was similarly high between the internal (0.97±0.01) and external (0.96±0.03) test sets (p=0.28) and demonstrated robust segmentation performance on public testing (0.93±0.03). Agreement of liver volumetry was satisfactory in the internal (ICC, 0.99), external (ICC, 0.97), and public (ICC, 0.85) test sets. Radiomic features demonstrated excellent agreement in the internal (mean ICC, 0.98±0.04), external (mean ICC, 0.94±0.10), and public (mean ICC, 0.91±0.09) datasets.

Conclusion
Automated liver segmentation yields robust and generalizable segmentation performance on MRI data and can be used for volumetry and radiomic feature extraction.

Clinical relevance statement
Liver volumetry, anatomic localization, and extraction of quantitative imaging biomarkers require accurate segmentation, but manual segmentation is time-consuming. A deep convolutional neural network demonstrates fast and accurate segmentation performance on T1-weighted portal venous MRI.

Key Points
• This deep convolutional neural network yields robust and generalizable liver segmentation performance on internal, external, and public testing data.
• Automated liver volumetry demonstrated excellent agreement with manual volumetry.
• Automated liver segmentations can be used for robust and reproducible radiomic feature extraction.
Pathways to paediatric urology subspecialisation: a study of casemix, incumbent attitudes and opinions
Authors: O’Kelly F. , t’Hoen L. A. , Banuelos Marco B. , Lammers R. J. M. , Sforza S. , Hiess M. , Bindi E. , Baydilli N. , Donmez M. I. , Paraboschi I. , Atwa A. , Spinoit A. F. , Haid B. , Silay S. ,   The EAU-YAU Paediatric Urology Working Group
Published: January 2024

Abstract
Objective
To identify any self-reported differences or attitudes towards certification, publication, or practice patterns between adult urology and paediatric general surgery-trained paediatric urology providers. There are no known published differences in clinical/operative/research outcomes in either group.

Methods
An 18-item cross-sectional survey was compiled through the EAU Young Academic Urologists (YAU) office and disseminated to a trans-Atlantic convenience sample of current practising paediatric urologists. This was created using a mini-Delphi method to provide current semi-quantitative data relating to current opinions and attitudes of this cohort.

Results
A total of 228 respondents completed the survey, with female respondents representing 37% and 34% for urology and paediatric general surgery, respectively. Nearly 90% overall respondents felt that a full 2-year paediatric fellowship program was very important and 94% endorsed a collaborative dedicated paediatric urology on call service, with 92% supporting the joint development of transitional care. Urology managed higher numbers of bedwetting (p = 0.04), bladder bowel dysfunction (p = 0.02), endourological procedures (p = 0.04), and robotics (p = 0.04). Paediatric general surgery managed higher numbers of laparoscopic reconstruction (p = 0.03), and posterior urethral valve ablation (p = 0.002).

Conclusion
This study represents the first time that a cross-sectional cohort of paediatric urologists from different training backgrounds were compared to assess their productivity, practice patterns and attitudes. Paediatric urology is in a unique position to have two contributing specialities, with the ability to provide optimal transitional and lifelong care. We believe that there should be a strong emphasis on collaboration and to remove any historically-created barriers under policies of equity, diversity and inclusivity.