bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary explants of the postnatal thymus allow the expansion of clonogenic thymic epithelial cells that constitute thymospheres
Authors: Ocampo-Godinez Juan M. , Gonzalez-Quiroz Jose L. , Cote-Palafox Hector , George Elizabeth , Vergara-Lope Nuñez Jael A. , Villagomez-Olea Guillermo , Vazquez-Vazquez Febe C. , Lopez-Villegas Edgar O. , Leon-Avila Gloria , Dominguez-Lopez Maria L. , Alvarez-Perez Marco A. 
Published: October 2023

Abstract
Background
Thymic epithelial cells (TECs) are responsible for shaping the repertoires of T cells, where their postnatal regeneration depends on a subset of clonogenic TECs. Despite the implications for regenerative medicine, their cultivation and expansion remain challenging. Primary explant cell culture is a technique that allows the seeding and expansion of difficult-to-culture cells. Here, we report a reliable and simple culture system to obtain functional TECs and thymic interstitial cells (TICs).

Methods
To establish primary thymic explants, we harvested 1 mm cleaned fragments of thymus from 5-week-old C57/BL6 mice. Tissue fragments of a complete thymic lobe were placed in the center of a Petri dish with 1 mL of DMEM/F-12 medium supplemented with 20% fetal bovine serum (FBS) and 1% penicillin‒streptomycin. To compare, thymic explants were also cultivated by using serum-free DMEM/F-12 medium supplemented with 10% KnockOut™.

Results
We obtained high numbers of functional clonogenic TECs and TICs from primary thymic explants cultivated with DMEM/F-12 with 20% FBS. These cells exhibited a highly proliferative and migration profile and were able to constitute thymospheres. Furthermore, all the subtypes of medullary TECs were identified in this system. They express functional markers to shape T-cell and type 2 innate lymphoid cells repertoires, such as Aire, IL25, CCL21 and CD80. Finally, we also found that ≥ 70% of lineage negative TICs expressed high amounts of Aire and IL25.

Conclusion
Thymic explants are an efficient method to obtain functional clonogenic TECs, all mTEC subsets and different TICs Aire+IL25+ with high regenerative capacity.
Autologous mesenchymal stromal cells embedded with Tissucol Duo® for prevention of air leak after anatomical lung resection: results of a prospective phase I/II clinical trial with long-term follow-up
Authors: Jiménez Marcelo F. , Gómez-Hernández María Teresa , Villarón Eva M. , López-Parra Miriam , Sánchez-Guijo Fermín 
Published: October 2023

Abstract
Background
Prolonged air leak (PAL) is the most frequent complication after pulmonary resection. Several measures have been described to prevent the occurrence of PAL in high-risk patients, however, the potential role of mesenchymal stem cells (MSCs) applied in the parenchymal suture line to prevent postoperative air leak in this setting has not been fully addressed.

Objective
To analyse the feasibility, safety and potential clinical efficacy of the implantation of autologous MSCs embedded in Tissucol Duo® as a prophylactic alternative to prevent postoperative prolonged air leak after pulmonary resection in high-risk patients.

Study design
Phase I/II single-arm prospective clinical trial.

Methods
Six patients with high risk of PAL undergoing elective pulmonary resection were included. Autologous bone marrow-derived MSCs were expanded at our Good Manufacturing Practice (GMP) Facility and implanted (embedded in a Tissucol Duo® carrier) in the parenchymal suture line during pulmonary resection surgery. Patients were monitored in the early postoperative period and evaluated for possible complications or adverse reactions. In addition, all patients were followed-up to 5 years for clinical outcomes.

Results
The median age of patients included was 66 years (range: 55–70 years), and male/female ratio was 5/1. Autologous MSCs were expanded in five cases, in one case MSCs expansion was insufficient. There were no adverse effects related to cell implantation. Regarding efficacy, median air leak duration was 0 days (range: 0–2 days). The incidence of PAL was nil. Radiologically, only one patient presented pneumothorax in the chest X-ray at discharge. No adverse effects related to the procedure were recorded during the follow-up.

Conclusions
The use of autologous MSCs for prevention of PAL in patients with high risk of PAL is feasible, safe and potentially effective.
Trial registration No. EudraCT: 2013-000535-27. Clinicaltrials.gov idenfier: NCT02045745.
Principal component analysis: development and initial validation of the mirror effects inventory
Authors: Ho Wing W. Y. 
Published: October 2023

Abstract
Background
Mirroring is a specific phenomenon that occurs in groups. People observe others enacting different roles in given situations, whereby concretizing the role of the observing aspect of their self as if looking in a mirror. Individuals could acquire emotional, cognitive, imaginative, behavioral, and interpersonal experiences through this process of mirroring; that is, “mirror effects.” Given that there are very few comprehensive scales capable of evaluating mirror effects, the Mirror Effects Inventory (MEI) was developed to measure experiences after participating in counseling education. This study describes the development of the MEI based on an interpersonal perspective and aimed to validate this scale.

Methods
The development and validation of the MEI involved a seven-stage process that utilized both qualitative and quantitative methods. Former students who studied counseling (N = 24) were surveyed via semi-structured telephone interviews. A subjective perceived scale (the MEI) was then constructed. The MEI was administered to part-time university students (N = 221) studying counseling courses. Psychometric tests were performed to examine its validity and reliability. Validation of the MEI included examining correlations between three types of mirror effects and age differences and educational attainment.

Results
The PCA revealed three types of mirror effects: general, positive, and negative. These components accounted for 53.82% of the total variance. Reliability estimates measured using Cronbach’s alpha of .88 indicated that the items were internally consistent. The findings showed that as the general mirror effect increased, there was a corresponding increase in the positive mirror effect and a decrease in the negative mirror effect. However, an increase in positive mirror effects was associated with an increase in negative mirror effects.

Conclusions
The development of a reliable and valid measure of mirror effects has benefits and implications for counseling education and clinical practice. Further empirical research could contribute to resolving the controversies concerning the basic conceptual understanding of MEI.
The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves
Authors: Si Hongyang , Zhou Kun , Zhao Tingyi , Cui Bing , Liu Fang , Zhao Mingqin 
Published: October 2023

AbstractFermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.
Graphical Abstract
Harmonization of brain PET images in multi-center PET studies using Hoffman phantom scan
Authors: Shekari Mahnaz , Verwer Eline E. , Yaqub Maqsood , Daamen Marcel , Buckley Christopher , Frisoni Giovanni B. , Visser Pieter Jelle , Farrar Gill , Barkhof Frederik , Gispert Juan Domingo , Boellaard Ronald ,   the AMYPAD Consortium
Published: October 2023

Abstract
Background
Image harmonization has been proposed to minimize heterogeneity in brain PET scans acquired in multi-center studies. However, standard validated methods and software tools are lacking. Here, we assessed the performance of a framework for the harmonization of brain PET scans in a multi-center European clinical trial.

Method
Hoffman 3D brain phantoms were acquired in 28 PET systems and reconstructed using site-specific settings. Full Width at Half Maximum (FWHM) of the Effective Image Resolution (EIR) and harmonization kernels were estimated for each scan. The target EIR was selected as the coarsest EIR in the imaging network. Using “Hoffman 3D brain Analysis tool,” indicators of image quality were calculated before and after the harmonization: The Coefficient of Variance (COV%), Gray Matter Recovery Coefficient (GMRC), Contrast, Cold-Spot RC, and left-to-right GMRC ratio. A COV% ≤ 15% and Contrast ≥ 2.2 were set as acceptance criteria. The procedure was repeated to achieve a 6-mm target EIR in a subset of scans. The method’s robustness against typical dose-calibrator-based errors was assessed.

Results
The EIR across systems ranged from 3.3 to 8.1 mm, and an EIR of 8 mm was selected as the target resolution. After harmonization, all scans met acceptable image quality criteria, while only 13 (39.4%) did before. The harmonization procedure resulted in lower inter-system variability indicators: Mean ± SD COV% (from 16.97 ± 6.03 to 7.86 ± 1.47%), GMRC Inter-Quartile Range (0.040–0.012), and Contrast SD (0.14–0.05). Similar results were obtained with a 6-mm FWHM target EIR. Errors of ± 10% in the DRO activity resulted in differences below 1 mm in the estimated EIR.

Conclusion
Harmonizing the EIR of brain PET scans significantly reduced image quality variability while minimally affecting quantitative accuracy. This method can be used prospectively for harmonizing scans to target sharper resolutions and is robust against dose-calibrator errors. Comparable image quality is attainable in brain PET multi-center studies while maintaining quantitative accuracy.
Histology and morphometry of the skin of purple spaghetti-eel Moringua raitaborua (Anguilliformes, Moringuidae)
Authors: Kim Hyun-Tae 
Published: October 2023

AbstractThe purple spaghetti-eel Moringua raitaborua lives on the sandy or muddy bottoms of estuaries, which are subject to rapid and wide changes in salinity, pH, and osmoregulatory and hypoxic conditions due to the influx of organic materials from sources of freshwater. The species has adapted to hypoxic environments by developing a thicker epidermis with stratified polygonal cells, club cells, two types of mucous cells (goblet and, oval cells), stratified cuboidal cells and dermis with abundant blood capillaries. Among them, histological modification of thinner dorsal, lateral, and ventral body skin to include abundant capillaries and well-developed dermal vascularization may provide cutaneous respiration, permitting survival in brackish waters with low levels of oxygen and variable environmental parameters.
Association of IL-1β rs16944 and IL-1RN rs2234663 gene polymorphisms with graft function in renal transplant recipients
Authors: Issac Marianne Samir Makboul , El Nahid Maggie S. 
Published: October 2023

Abstract
Background
After renal transplantation, renal graft function affects both patient and graft survival. There is growing evidence of the genetic association between interleukin-1β (IL-1β) or its receptor antagonist (IL-1RN) and graft function in renal transplantation. The objective of this study is to investigate the role of the recipient IL-1β and IL-1RN gene polymorphisms and their haplotypes on renal graft outcome.

Methods
Using PCR, IL-1β (− 511C/T) and IL-1RN (86 bp VNTR) gene polymorphisms were determined in 31 renal allograft recipients; eight cases with stable allograft function and 23 cases with early renal dysfunction as well as 26 age- and gender-matched healthy controls.

Results
A statistically significant difference in IL-1 β (− 511C/T) gene polymorphisms and IL-1RN/IL-1β haplotypes was observed on comparing renal allograft recipients with stable allograft function and those with early renal allograft dysfunction. However, the difference in the frequency distribution of IL-1RN gene polymorphisms, between these two groups, did not reach statistical significance. Also, no statistically significant difference was observed in comparing these two gene polymorphisms and their haplotypes between renal allograft recipients and healthy controls.

Conclusion
The IL-1β − 511 CT/TT polymorphic genotypes and IL-1RN/IL-1β polymorphic haplotypes are associated with early renal allograft dysfunction. These are observational data that can be repeated in larger studies. If the results obtained are consistent, this might open doors to personalized medicine where clinicians can take necessary measures to identify the renal transplant recipients’ genotypes at risk of mounting an increased inflammatory response and hence administer the appropriate immunosuppressive protocol.
Evaluation of a Natural Language Processing Model to Identify and Characterize Patients in the United States With High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Narayan Vikram M. , Siolas Despina , Meadows Eric S. , Turzhitsky Vladimir , Sillah Arthur , Imai Kentaro , McMurry Andrew J. , Li Haojie 
Published: October 2023

PURPOSE Treatment of non–muscle-invasive bladder cancer (NMIBC) is guided by risk stratification using clinical and pathologic criteria. This study aimed to develop a natural language processing (NLP) model for identifying patients with high-risk NMIBC retrospectively from unstructured electronic medical records (EMRs) and to apply the model to describe patient and tumor characteristics. METHODS We used three independent EMR-derived data sets including adult patients with a bladder cancer diagnosis in 2011-2020 for NLP model development and training (n = 140), validation (n = 697), and application for the retrospective cohort analysis (n = 4,402). Deep learning methods were used to train NLP recognition of medical chart terminology to identify seven high-risk NMIBC criteria; model performance was assessed using the F1 score, weighted across features. An algorithm was then used to classify each patient as high-risk NMIBC (yes/no). Manually reviewed records served as the gold standard. RESULTS The F1 scores after model training were >0.7 for all but one uncommon feature (prostatic urethral involvement). The highest area under the receiver operating curves (AUC) was observed for Ta (0.897) and T1 (0.897); the lowest AUC was for carcinoma in situ (CIS; 0.617). For high-risk NMIBC classification, positive predictive value was 79.4%, negative predictive value was 93.2%, and false-positive rate was 8.9%. Sensitivity and specificity were 83.7% and 91.1%, respectively. Of 748 patients manually confirmed as having high-risk NMIBC, 196 (26%) had CIS (of whom 19% also had T1 and 23% also had Ta disease); 552 tumors (74%) had no associated CIS. CONCLUSION The NLP model, combined with a rule-based algorithm, identified high-risk NMIBC with good performance and will enable future work to study real-world treatment patterns and clinical outcomes for high-risk NMIBC.
NOTCH3 signalling controls human trophoblast stem cell expansion and differentiation
Authors: Dietrich Bianca , Kunihs Victoria , Lackner Andreas I. , Meinhardt Gudrun , Koo Bon-Kyoung , Pollheimer Jürgen , Haider Sandra , Knöfler Martin 
Published: October 2023

ABSTRACT
Failures in growth and differentiation of the early human placenta are associated with severe pregnancy disorders such as pre-eclampsia and fetal growth restriction. However, regulatory mechanisms controlling development of placental epithelial cells, the trophoblasts, remain poorly elucidated. Using trophoblast stem cells (TSCs), trophoblast organoids (TB-ORGs) and primary cytotrophoblasts (CTBs) of early pregnancy, we herein show that autocrine NOTCH3 signalling controls human placental expansion and differentiation. The NOTCH3 receptor was specifically expressed in proliferative CTB progenitors and its active form, the nuclear NOTCH3 intracellular domain (NOTCH3-ICD), interacted with the transcriptional co-activator mastermind-like 1 (MAML1). Doxycycline-inducible expression of dominant-negative MAML1 in TSC lines provoked cell fusion and upregulation of genes specific for multinucleated syncytiotrophoblasts, which are the differentiated hormone-producing cells of the placenta. However, progenitor expansion and markers of trophoblast stemness and proliferation were suppressed. Accordingly, inhibition of NOTCH3 signalling diminished growth of TB-ORGs, whereas overexpression of NOTCH3-ICD in primary CTBs and TSCs showed opposite effects. In conclusion, the data suggest that canonical NOTCH3 signalling plays a key role in human placental development by promoting self-renewal of CTB progenitors.
Energetics of collective movement in vertebrates
Authors: Zhang Yangfan , Lauder George V. 
Published: October 2023

ABSTRACT
The collective directional movement of animals occurs over both short distances and longer migrations, and is a critical aspect of feeding, reproduction and the ecology of many species. Despite the implications of collective motion for lifetime fitness, we know remarkably little about its energetics. It is commonly thought that collective animal motion saves energy: moving alone against fluid flow is expected to be more energetically expensive than moving in a group. Energetic conservation resulting from collective movement is most often inferred from kinematic metrics or from computational models. However, the direct measurement of total metabolic energy savings during collective motion compared with solitary movement over a range of speeds has yet to be documented. In particular, longer duration and higher speed collective motion must involve both aerobic and non-aerobic (high-energy phosphate stores and substrate-level phosphorylation) metabolic energy contributions, and yet no study to date has quantified both types of metabolic contribution in comparison to locomotion by solitary individuals. There are multiple challenging questions regarding the energetics of collective motion in aquatic, aerial and terrestrial environments that remain to be answered. We focus on aquatic locomotion as a model system to demonstrate that understanding the energetics and total cost of collective movement requires the integration of biomechanics, fluid dynamics and bioenergetics to unveil the hydrodynamic and physiological phenomena involved and their underlying mechanisms.
Can we revolutionize diagnostic imaging by keeping Pandora’s box closed?
Authors: Kwee Thomas C , Yakar Derya , Sluijter Tim E , Pennings Jan P , Roest Christian 
Published: October 2023

Abstract
Incidental imaging findings are a considerable health problem, because they generally result in low-value and potentially harmful care. Healthcare professionals struggle how to deal with them, because once detected they can usually not be ignored. In this opinion article, we first reflect on current practice, and then propose and discuss a new potential strategy to pre-emptively tackle incidental findings. The core principle of this concept is to keep the proverbial Pandora’s box closed, i.e. to not visualize incidental findings, which can be achieved using deep learning algorithms. This concept may have profound implications for diagnostic imaging.
Assessment of weed species composition and diversity in tomato (Solanum lycopersicum L.) farms in Ethiopia
Authors: Geremew Dereje , Dechassa Nagassa , Bedada Shashitu , Bekele Getachew , Hundessa Niguse , Abdisa Tesfaye , Gella Desalegn , Duguma Mosisa 
Published: October 2023

Background: Weeds compete for vital nutrients and water with the tomato plants and serve as an alternative host for other pests. Although there is limited information on the weed species composition in major tomato-growing areas in Ethiopia, this study was conducted to identify the economically important weed species in tomato fields in the East Wollega, Shewa, West Shewa, Arsi, and Sidama zones. Methods: The weed flora assessment was conducted in major tomato growing zones of the country, such as East Shewa, Wollega, West Shewa, Arsi, and Sidama zones, in the 2018–2019 cropping season during the off-season. In each tomato field a 1 m x 1 m quadrat was thrown following an inverted X pattern, and weed species were recorded. Weed species composition was calculated using standard formulas. Results: The results revealed that 63 weed species under 23 families were identified at the surveyed locations. Portulaca oleracea was the most abundant and dominant, with 50% of the dominance value. Weed frequency values ranged from 0.06 to 72% in the studied areas. The weed similarity index was also different among the surveyed locations. The results of farmers perceptions on weed management in tomato fields showed that 61% of respondents practiced hoeing followed by hand weeding, and Tuta absoluta was the most significant constraint to tomato production in the surveyed areas. Conclusions: This assessment showed that there are differences in the composition and distribution of weed species in tomato fields in Ethiopia, which aid in predicting the population dynamics of weed flora. Farmers perceptions of weed management practices in tomato fields were also different. Therefore, different environmentally friendly weed management options such as good crop husbandry, biological control, and integrated management should be designed to increase tomato production and productivity.