bluuebunny/crossref_metadata_2025_split huggingface dataset:
Le cohérentisme en systématique
Authors: Rieppel Olivier , Deleporte Pierre , Lecointre Guillaume 
Published: December 2024

L’école de pensée de « l’évidence totale » en systématique biologique est comparée à l’école de pensée de « l’évidence pertinente ». L’histoire et la signification de l’approche d’évidence totale pour l’inférence inductive sont passées en revue, et il en découle que le principe d’évidence totale ne peut pas être relié au réfutationisme poppérien, comme cela est fait dans la systématique contemporaine. On montre que le « test de congruence » pratiqué en systématique est enraciné dans une épistémologie cohérentiste, ce qui est une condition nécessaire mais non suffisante pour la reconstruction phylogénétique. Les conditions suffisantes pour l’étude des relations évolutives nécessitent, en plus de la cohérence des énoncés de caractères ( character statements ), leur fondement expérientiel. De tels fondements expérientiels permettent de distinguer entre évidence « totale » et « pertinente ».
Les deux biogéographies : biogéographie historique vs histoire géographique
Authors: Zaragüeta-Bagils René 
Published: December 2024

Dans cet article, je montre que la discipline connue sous le nom de biogéographie correspond à deux problématiques distinctes, ce qui est probablement lié au faible nombre de laboratoires de biogéographie et de biogéographes non principalement taxonomistes. Ces deux biogéographies dérivent de deux traditions bien distinctes. La première biogéographie, que l’on peut appeler chorologie, dérive d’une tradition remontant à Linné et dont la justification, purement métaphysique, se trouve dans un essai de mise en cohérence de légendes religieuses et de résultats empiriques. Malgré le fait d’être une théorie fondée sur des croyances religieuses, qui a échoué à tous les tests empiriques initiaux et qui a été modifiée pour faire des prédictions non testables, la chorologie, c’est-à-dire l’étude de l’histoire géographique des taxons, est restée très majoritairement pratiquée. La deuxième tradition remonte à Candolle. Elle commence par la découverte de régions délimitées et caractérisées par des distributions de plantes et non par des structures administratives (géographie politique) ou des accidents géographiques (géographie physique) : il s’agit d’une nouvelle géographie, la géographie botanique. La découverte de régions zoologiques similaires permettra de parler de biogéographie. Croizat, un siècle et demi plus tard, découvrit que lorsqu’il reliait des aires de distributions de taxons apparentés, il trouvait de la congruence entre ces liens : la Terre et la vie évoluent ensemble. Nelson, Platnick et Rosen montrèrent que si les relations de parenté entre taxons renseignent sur les relations de parenté entre aires biogéographiques, le problème des relations entre aires biogéographiques est un problème cladistique. Je montre l’équivalence formelle qui existe entre la phylogénétique et la biogéographie si l’on accepte que l’interprétation propre à l’analyse à trois éléments constitue l’interprétation phylogénétique correcte. Cette équivalence formelle montre aussi le manque de pertinence de la chorologie, qui est fondée sur les équivalents de la paraphylie (centre d’origine) et de l’homoplasie (explication ad hoc par dispersion).
Les paléoanthropologues sont-ils en meilleure position que les autres pour se permettre d’ignorer les règles de la systématique ? Un bref historique
Authors: Zeitoun Valéry 
Published: December 2024

La propagation d’analyses à sensation ou incomplètes, de même que l’interprétation erronée de données, ont conduit à une série de consensus paléoanthropologiques qui, pour l’essentiel, relève de la répétition de conjectures. Ces pratiques sont associées à une absence de maîtrise des règles de la classification dont il résulte un discours paléoanthropologique phylogénétique le plus souvent découplé des règles de la systématique. À partir des années 1960, les travaux paléoanthropologiques s’intéressent plus spécifiquement à la nomenclature et la taxinomie des Hominidés en rendant compte explicitement des travaux de Dobzhansky et Mayr. De nos jours, le discours paléoanthropologique ressemble à un discours phylogénétique mais les paléoanthropologues n’emploient ni les outils ni les méthodes de la phylogénie et ne connaissent que rarement les règles de la systématique. Ce phénomène a été décrit par Bonde (1977), à une période où l’école cladiste commençait tout juste à influencer quelques paléoanthropologues. Dans les années suivantes ont suivi des discussions sur la valeur et la polarité des caractères observés, se substituant aux débats antérieurs fondés sur la ressemblance globale. Des auteurs ont, ensuite, proposé des listes d’espèces fondées sur la présence de caractères autapomorphes. Enfin, des cladogrammes ont été produits. Cependant, après deux décennies, des discussions portant sur la constitution des unités taxinomiques opérationnelles (UTO), sur la définition des caractères et sur la prise en compte de la variabilité, de la surreprésentation ou de la redondance de certains caractères conduisirent au rejet de la cladistique en paléoanthropologie. En dépit du fait que Barriel (1994) et Tassy (1996) aient répondu à ces objections dans les années 1990, ces réponses ont été ignorées ou incomprises des paléoanthropologues et, dans les années 2000, la cladistique a été presque complétement abandonnée au profit d’un retour à la systématique évolutionniste classique ou d’un engouement pour la phénétique ; deux approches quantitatives. Se pose ainsi la question formulée récemment par Bonde (2012) : « Est-il vraiment impossible de transmettre une telle méthode (la systématique phylogénétique) si simple et logique aux anthropologues ou bien n’en n’ont-ils cure ? »
Signal phylogénétique
Authors: Cubo Jorge 
Published: December 2024

Toute espèce choisie aléatoirement a tendance à ressembler plus à une espèce étroitement apparentée qu’à une troisième espèce moins proche. Cette observation a été formalisée sous le nom de signal phylogénétique. Dans cet article, je décris la succession de méthodes qui ont été utilisées au fil des années dans mon aire d’expertise, l’ostéohistologie, pour tester et quantifier le signal phylogénétique : les Random Tree-Length Distributions , les régressions sur des matrices de distance, les Phylogenetic Eigenvector Regressions , le C mean d’Abouheif, le λ de Pagel et le K de Blomberg. L’utilisation de méthodes avec modèle permet de préciser le concept intuitif de signal phylogénétique évoqué cidessus. Dans le cas du λ de Pagel et du K de Blomberg, le signal phylogénétique pourrait être défini comme une distribution de valeurs phénotypiques qui ne diffère pas de celle attendue sous un modèle d’évolution brownien. Ces méthodes permettent de tester des hypothèses concernant les mécanismes d’évolution à partir des patrons de variation phénotypique observés
Systemic artery aneurysms – A marker of high-risk Kawasaki disease
Authors: Kadiyani Lamk , Mohankumar Shivaprasad P , Arumugam Praveen , Gupta Saurabh Kumar , Bagri Narendra Kumar , Pandey Niraj , Kumar Sanjeev 
Published: December 2024

ABSTRACT
Kawasaki disease, traditionally classified as medium vessel vasculitis, is known for the preferential involvement of coronary arteries. Infrequently, large systemic arteries might be involved and may affect the prognosis. Here, we present an infant with Kawasaki disease who had extensive involvement of large vessels such as the abdominal aorta and medium vessels of the extremities, along with giant coronary artery aneurysms.
Generalized arterial calcification of infancy – Fetal diagnosis to postnatal management
Authors: Kadiyani Lamk , Shivaprasad PM , Ramakrishnan Sivasubramanian , Rana Anubhuti , Pandey Niraj 
Published: December 2024

ABSTRACT
Generalized arterial calcification of infancy is a rare entity with poor fetal and postnatal outcomes and high morbidity in survivors. Half of the cases are diagnosed intrauterine due to hemodynamic compromise, and the associated manifestations pose unique management challenges. We hereby report an account of a fetal diagnosis in a referral for hydrops with postnatal evaluation and management.
Prevalence of Vitamin D deficiency among individuals with Fontan palliation: A systematic review and meta-analysis
Authors: Khansa Firyal , Ichwan Chairul , Ghifari Muhammad Haneef , Daffa Muhammad Brilliant , Nadia Farah Rizky , Zulfa Putri Oktaviani , Rampengan Derren David Christian Homenta , Yufika Amanda , Gusti Naufal , Iqhrammullah Muhammad 
Published: December 2024

ABSTRACT

Background:
Children with one functional ventricle might receive the Fontan procedure as palliative management to prolong their lives. However, the heart remains functionally univentricular, which may result in disrupted absorption of nutrients, including Vitamin D. Individuals with Fontan circulation have limited physical activity and sun exposure, which might further contribute to Vitamin D deficiency.

Objective:
This study aimed to estimate the prevalence of Vitamin D deficiency among individuals with Fontan circulation and analyze probable contributing factors to it through meta-regression analysis.

Methods:
A predetermined search strategy was applied on PubMed, Scopus, Scilit, Web of Science, Europe PMC, and Google Scholar to identify relevant literature as of July 2024. In general, studies reporting the prevalence or incidence of Vitamin D deficiency (<20 ng/mL) among Fontan patients were eligible for inclusion. Only cohort and cross-sectional studies were included. The pooled estimates were carried out using a restricted maximum-likelihood model and Freeman–Tukey double-arcsine transformation (FTT).

Results:
Six studies were included, comprising 255 individuals with the Fontan circulation. The prevalence of Vitamin D deficiency was 51% (95% confidence interval: 35%– 67%) with noticeable heterogeneity (I
2 = 84.38%; p-Het <0.001). Extracardiac conduit/lateral tunnel (P = 0.003) was the main contributor to the heterogeneity.

Conclusion:
Vitamin D deficiency is highly prevalent among individuals with Fontan palliation, highlighting the need for active monitoring and investigation into the benefits of Vitamin D supplementation.
PROSPERO registration: CRD42024574724.
Transcatheter salvage of dying Glenn – An innovative strategy for postGlenn thrombosis
Authors: Jain Shantanu , Gangopadhyay Debasree , Paulraj Sabharisundaravel , Roy Mahua , Mazumdar Jayitri , Dutta Joyeeta 
Published: December 2024

ABSTRACT
PostGlenn thrombosis is an infrequent, serious complication requiring immediate attention, which is not uncommon in a resource-limited setting where patients are often lost to follow-up and have poor compliance with medications. This rare complication has infrequently been reported in the past. We describe a case of a massive thromboembolic event in a patient presenting acutely in a decompensated state 14 years after initial palliation by Glenn shunt. We report an innovative strategy of using transcatheter mechanical thrombectomy using a rotational thrombectomy device and chemical thrombolysis for the successful salvation of the Glenn circuit.
Effect of Two Different Penetration Depths of Micro-osteoperforation on the Rate of Orthodontic Tooth Movement: A Prospective Clinical Study
Authors: Jain Abhay Kumar , Singh Shresthaa , Priya Parul , Garg Nishita , Kumar Abhishek , Goswami Monalisa 
Published: December 2024

Objective:
The objective is to evaluate the effectiveness of two different penetration depths of micro-osteoperforations (MOPs) on the rate of orthodontic tooth movement over 60 days. In addition, the amount of pain and discomfort caused by the MOP was evaluated.

Materials and Methods:
A total of 22 patients (18–30 years) who need fixed orthodontic treatment were recruited and randomly assigned into two groups. Randomization for determination of the experimental side and depth of perforations was done using sealed envelopes. On each patient, the other side of the mouth worked as control side with no MOPs. Patients in group 1 (MOP-5) received 3MOPs on the buccal surface of the alveolar bone each at 5 mm depth, whereas patients in group 2 (MOP-7) received 3MOPs on the buccal surface of the alveolar bone each at 7 mm depth. The amount of canine retraction was measured every 30 days at two intervals on both sides of the mouth. Pain perception was measured after 1 h, 24 h, 72 h, 7 days, and 28 days of procedure. MOP-related pain was measured using a visual analog scale. The level of statistical significance was P ≤ 0.05.

Results:
The result of the intra-examiner reliability using intraclass correlation coefficient more than 0.97 (P < 0.001), indicating excellent repeatability and reliability of the measurements. The baseline characteristics between groups were similar (P > 0.05). Both the groups demonstrated a significantly higher canine movement than the control group. No significant difference was seen between the MOP-5 and MOP-7 groups (P > 0.05) in terms of canine retraction. Mild-to-moderate pain was experienced only in the first 24 h of the procedure.

Conclusion:
Three MOPs with a depth of 5 mm can be performed as an effective method to increase the rate of tooth movement. However, increasing the depth of perforation beyond 5 mm does not additionally enhance tooth movement.
Assessment of the TGF-β gene and its target miR-1908-5p gene expression and its role in the treatment of beta-thalassemia in Iraqi patients
Authors: Abdulhassn Manal Lafta , Al-Khafaji Hiba Muneer Abdel Hassan , Mohammed Maryam Qasim 
Published: December 2024

Abstract

BACKGROUND:
Thalassemia is potentially inherited fatal anemia and can cause health problems when left untreated. Beta-thalassemia is the most severe formula of the illness. Transforming growth factor-beta (TGF-β) is a cytokine that has multicellular functions. The miRNAs have been confirmed to play important roles in gene expression regulation during the development of a variety of human diseases. In a variety of hematological diseases, miRNAs influence the TGF-β signaling pathway. The etiology of the disease may be supported by the dysregulation of this interaction.

OBJECTIVES:
This study aimed to estimate the role of TGF-β and its target miR-1908-5p expression and its effect on the prognosis and treatment of beta-thalassemia (β-thal) in Iraqi patients.

PATIENTS, MATERIALS, AND METHODS:
The case–control study encompassed 100 Iraqi individuals, categorized into two groups: Fifty patients diagnosed with β-thal and fifty apparently healthy controls. Blood samples were collected from Baghdad Teaching Hospital at the Medical City in Baghdad from December 2023 to February 2024. Hematological and biochemical parameters were measured. Total RNA was extracted and converted into complementary DNA, finally, to assess the levels of TGF-β and miR-1908-5p gene expression by the reverse transcription-polymerase chain reaction.

RESULTS:
The results showed that a decrease in the hemoglobin (Hb) level was significantly correlated with a significant increase in the ferritin level and the white blood cell (WBC) count in thalassemia patients in comparison to healthy controls, with a significant difference (P < 0.01). The expression of the TGF-β gene was notably lower in thalassemia patients (0.783) compared with control, with an increase in the miR-1908-5p gene expression level (1.431); furthermore, the correlation between them using Spearman’s coefficient was negative with a significant difference of 0.04.

CONCLUSION:
A low level of Hb in patients acts as a pointer to increase the level of the ferritin and the WBC count. A low level of gene expression of the TGF-β gene targeted by high-level miR-1908-5p gene expression in Iraqi patients with β-thal is considered a good biomarker according to the ROC curve test. It might be possible to regulate TGF-β expression by modifying miR-1908-5p, therefore could improve the effectiveness of gene-based therapies in hematological therapies.
Oculodermal melanocytosis in Asian Indian patients: Prevalence, clinical presentation, and association with choroidal melanoma
Authors: Chheda Prapti , Ramamurthy Srishti , Raval Vishal , Kaliki Swathi 
Published: December 2024

Objective:
To study the prevalence, clinical presentation, treatment, and follow-up of ocular (dermal) melanocytosis (ODM) and its association with choroidal melanoma (CM) in Asian Indian patients.

Methods:
This was a retrospective case series of patients with ODM conducted in a quaternary eye care center.

Results:
Of the total 1.48 million patients during the study period, we identified 213 patients with ODM with a prevalence rate of 0.014%. Median age at presentation was 13 years (range 0–76 years). Unilateral presentation of ODM was noted in 87% cases. ODM involved the sclera in 100% cases, the iris in 23%, the choroid in 20%, the eyelid in 29%, and V1 and V2 dermatomes in 53% cases. Nineteen patients (9%) were found to have CM, with 1.3 times increased risk of CM compared to the Caucasian population. The most common tumor location was in the inferior quadrant (n = 8, 44%). The mean tumor thickness was 8.3 ± 2.8 mm with a mean basal diameter of 14.0 ± 4.3 mm. Primary treatment of CM included plaque brachytherapy (n = 6), enucleation (n = 9), and few patients refused for treatment (n = 3). During a mean follow-up period of 21 months, one patient died because of lung metastasis.

Conclusion:
Although rare, choroidal melanoma does occur in the presence of ODM with an increased risk in Asian Indians compared to the Caucasian population. Patients with ODM should be examined periodically for early detection of CM.
Predicting macular hole surgery outcomes: Integrating preoperative OCT features with supervised machine learning statistical models
Authors: Venkatesh Ramesh , Gandhi Priyanka , Choudhary Ayushi , Sehgal Gaurang , Godani Kanika , Darade Shubham , Kathare Rupal , Hande Prathiba , Prabhu Vishma , Chhablani Jay 
Published: December 2024

Purpose:
To evaluate various supervised machine learning (ML) statistical models to predict anatomical outcomes after macular hole (MH) surgery using preoperative optical coherence tomography (OCT) features.

Methods:
This retrospective study analyzed OCT data from idiopathic MH eyes at baseline and at 1-month post-surgery. The dataset was split 80:20 between training and testing. XLSTAT® statistical software (Lumivero, USA) was used to train different ML models on 10°CT parameters: prefoveal posterior cortical vitreous status, epiretinal membrane, intraretinal cysts, foveal retinal pigment epithelium hyperreflectivity, MH basal diameter, MH area (MHA), hole-forming factor, MH index, tractional hole index, and diameter hole index. The most effective statistical model was identified and was further assessed for accuracy, sensitivity, and specificity on a separate testing dataset.

Results:
Six ML statistical models were trained on 33,260°CT data points from 3326°CT images of 308 operated MH (300 patients) eyes. Following training and internal validation, the random forest (RF) model achieved the highest accuracy (0.92), precision (0.94), recall (0.97), and F-score (0.96), and lowest misclassification rate. RF model identified the MHA index as the best predictor of post-surgical anatomical success. Following external testing, the RF model confirmed the highest accuracy and lowest misclassification rate (8.8%).

Conclusion:
ML-based statistical models can be used to predict MH status after surgery. The RF model was the most accurate ML model, and the MHA index was the best predictor of postoperative hole closure after surgery based on preoperative OCT parameters. These predictions may help with future surgical planning for MH patients.
Liquid chromatography/tandem mass spectrometric characterization of Rhodotorula mucilaginosa GMM natural pigment and its synergistic antitumor effect with γ-radiation: in-vitro and in-vivo study
Authors: Ibrahim Ghada S. , Hassan Amal I. , Mahmoud Manal G. , Asker Mohsen M.S. , Marzouk Mohamed 
Published: December 2024

Background/aim
Recently, there has been a marked increase in interest toward using microbial resources, especially yeast, to synthesize carotenoids. Ovarian cancer is a major health problem worldwide, as it is the most frequently diagnosed form of cancer in women and contributes significantly to cancer-related deaths. Yeast carotenoids are currently under evaluation for cost-effective and nonhazardous drugs derived from natural products. The principal objective of this study is to evaluate the natural pigment produced from Rhodotorula and characterize it by liquid chromatography-mass spectrometric and to evaluate the ability of its synergistic antitumor effect with γ-radiation.

Materials and methods
A new pigmented yeast was isolated from yogurt and identified. The pigment was characterized and studies of its biological activities were conducted. The isolate was defined as Rhodotorula mucilaginosa GMM with accession number OQ120277 by 18 S rDNA, and the pigment was characterized by liquid chromatography-mass spectrometric. Combining γ-radiation with a carotenoid pigment was also tested for its synergistic anticancer properties in CAOV-3 and HEK-293 cell lines and in experimental mice bearing solid tumors. BAX, BCL2, P53, MMP2, MMP9, caspase-3, and caspase-9 were measured using ELISA techniques.

Results
The maximum production of total carotenoids was 2.99 g/l. Pigment extract constituents exhibited 12 major compounds during its identification. Their structures can be sorted as 8 tetra, and 3 triterpenoidal carotenes (astaxanthin, 4,4’-E-diapophytoene, torularhodin, 1,2,1’,2’-tetrahyroxylycopene, E-β-apo-8’-carotenal, 10’-apo-E-β-caroten-10’-ol, β-carotene, torulene, echinenone, 1,2,1’,2’-tetrahyroxy dihydrolycopene, and α-canthaxanthin). The pigment exhibited DPPH scavenging activity, and the combination of natural pigment and radiation therapy showed a significant reduction (P<0.05) in the levels of matrix metalloproteinases (MMP2, MMP9), and significant increases (P<0.05) in the levels of tumor protein p53, Bax and caspases-3 and caspases-9 in CAOV-3 cell lines and mice bearing solid tumors.

Conclusion
The natural pigment produced by yeast fermentation in this study exhibited a potential antitumor efficacy when combined with radiation in cell lines and against Ehrlich solid tumors.
Tibial scoring as a predictor for amputation-free survival in critical limb ischemic patients
Authors: Sadek Yehia K. , El Emam Sameh El Sayed , Mohamed Ahmed K. 
Published: December 2024

Background/aim
Evaluating the risk of amputation in patients with peripheral arterial disease (PAD) is essential. A critical Limb Ischemic patient (CLI) is known as end stage of PAD. Creating novel approaches to pinpoint high-risk patients would allow for targeted treatments and support specialized clinical trials focused on limb preservation. This study’s objective is to evaluate tibial adversity and scoring for risk of lower extremity amputation in critical limb ischemic patients (CLI).

Patients and methods
This study is a prospective study carried out on 30 patients with symptomatic lower extremity PAD in Al-Zahraa University Hospital from February 2023 to January 2024 interval. All patients were assessed by hemodynamics study and multislice noncontrast CT and tibial angioplasty according to inclusion and exclusion criteria. The patients followed up at day 1 and 3 and 6 months.

Results
Patients with CLI exhibited significant high (p < 0.05) tibial artery calcification scores, which were linked to increased limb ischemia levels, with high risk for amputation compared to traditional risk factors. 26 patients were amputation free rate and only 4 patients were done major amputation. Nonmodifiable risk factors correlated with elevated tibial artery calcification scores.

Conclusions
The present study indicated that tibial scoring independently predicts the risk of lower extremity amputation, even when considering other risk factors in patient with CLI. Increasing calcium scores are associated with greater PAD severity.