bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-invasive imaging techniques for diagnosis of pelvic deep endometriosis and endometriosis classification systems: an International Consensus Statement,
Authors: Condous G , Gerges B , Thomassin-Naggara I , Becker C , Tomassetti C , Krentel H , van Herendael B J , Malzoni M , Abrao M S , Saridogan E , Keckstein J , Hudelist G ,   Intersociety Consensus Group §, Aas-Eng K , Alcazar J L , Bafort C , Bazot M , Bielen D , Bokor A , Bourne T , Carmona F , Di Giovanni A , Djokovic D , Egekvist A , English J , Exacoustos C , Ferreira H , Ferrero S , Forstner R , Freeman S , Goncalves M , Grimbizis G , Guerra A , Guerriero S , Jansen F W , Jurkovic D , Khazali S , Leonardi M , Maciel C , Manganaro L , Mueller M , Nisolle M , Noe G , Reid S , Roman H , Rousset P , Seyer Hansen M , Singh S , Thomas V , Timmerman D , Ulrich U A , Van den Bosch T , Van Schoubroeck D , Wattiez A 
Published: May 2024

Abstract
The International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) and International Deep Endometriosis Analysis (IDEA) group, the European Endometriosis League (EEL), the European Society for Gynaecological Endoscopy (ESGE), ESHRE, the International Society for Gynecologic Endoscopy (ISGE), the American Association of Gynecologic Laparoscopists (AAGL) and the European Society of Urogenital Radiology (ESUR) elected an international, multidisciplinary panel of gynecological surgeons, sonographers, and radiologists, including a steering committee, which searched the literature for relevant articles in order to review the literature and provide evidence-based and clinically relevant statements on the use of imaging techniques for non-invasive diagnosis and classification of pelvic deep endometriosis. Preliminary statements were drafted based on review of the relevant literature. Following two rounds of revisions and voting orchestrated by chairs of the participating societies, consensus statements were finalized. A final version of the document was then resubmitted to the society chairs for approval. Twenty statements were drafted, of which 14 reached strong and three moderate agreement after the first voting round. The remaining three statements were discussed by all members of the steering committee and society chairs and rephrased, followed by an additional round of voting. At the conclusion of the process, 14 statements had strong and five statements moderate agreement, with one statement left in equipoise. This consensus work aims to guide clinicians involved in treating women with suspected endometriosis during patient assessment, counselling, and planning of surgical treatment strategies.
Hackflex library preparation enables low-cost metagenomic profiling
Authors: Goldman Samantha L , Sanders Jon G , Sprockett Daniel D , Landers Abigail , Yan Weiwei , Moeller Andrew H 
Published: May 2024

Abstract
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations &lt;1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
Toward reciprocal feedback between computational design, engineering, and fabrication to co-design coreless filament-wound structures
Authors: Kannenberg Fabian , Zechmeister Christoph , Gil Pérez Marta , Guo Yanan , Yang Xiliu , Forster David , Hügle Sebastian , Mindermann Pascal , Abdelaal Moataz , Balangé Laura , Schwieger Volker , Weiskopf Daniel , Gresser Götz T , Middendorf Peter , Bischoff Manfred , Knippers Jan , Menges Achim 
Published: May 2024

Abstract
Fiber-reinforced composites offer innovative solutions for architectural applications with high strength and low weight. Coreless filament winding extends industrial processes, reduces formwork, and allows for tailoring of fiber layups to specific requirements. A previously developed computational co-design framework for coreless filament winding is extended toward the integration of reciprocal design feedback to maximize design flexibility and inform design decisions throughout the process. A multi-scalar design representation is introduced, representing fiber structures at different levels of detail to generate feedback between computational design, engineering, and fabrication. Design methods for global, component, and material systems are outlined and feedback generation is explained. Structural and fabrication feedback are classified, and their integration is described in detail. This paper demonstrates how reciprocal feedback allows for co-evolution of domains of expertise and extends the existing co-design framework toward design problems. The developed methods are shown in two case studies at a global and component scale.
Carotid artery dissection and non-aneurysmal subarachnoid hemorrhage following carotid endarterectomy
Authors: Kaoutzani Lydia , Garcia Klepper Alfredo , Rahimi Scott Y 
Published: May 2024

Abstract
Stroke continues to be a major public health issue resulting in high mortality and severe long-term disability. Carotid endarterectomy (CEA) plays an important role in the prevention of ischemic stroke. Complications associated with CEA can be life threatening and prompt recognition is crucial. In this report, we present a patient who presented to the hospital with progressive headache, 2 weeks following CEA. He was neurologically intact and hypertensive. Non-contrast head computed tomography (CT) scan showed convexity subarachnoid hemorrhage (SAH). He was found to have a left internal carotid artery dissection. Patients who present to the hospital following CEA with headache and hypertension benefit from a non-contrast head CT scan. The presence of SAH can be a warning sign of cerebral hyperperfusion syndrome. Carotid artery dissection is also a disease entity that can occur in the post-operative period. Prompt recognition and treatment is crucial for the management of these disease entities.
Optimizing aesthetic results in Asian women with giant phyllodes tumors over 10 cm: the periareolar mastopexy approach
Authors: Chen Kun-Han , Hsu Yu-Chen 
Published: May 2024

Abstract
Giant phyllodes tumors, typically exceeding 10 cm in size, are neoplastic lesions with malignant potential. Surgical excision in small-breasted Asian women presents unique challenges where expected poor aesthetic outcomes may delay timely medical intervention. The periareolar mastopexy technique offers a comprehensive solution, enabling complete tumor removal alongside mastopexy to achieve optimal breast contouring. This approach consistently delivers favorable aesthetic outcomes, enhancing symmetry and contour. Additionally, the periareolar approach minimizes visible scarring, thereby enhancing patient satisfaction with the cosmetic outcome. Herein, we present a case report of Asian women with giant phyllodes tumors exceeding 10 cm, successfully managed using the periareolar mastopexy technique, emphasizing the importance of optimizing aesthetic outcomes in these challenging cases.
Patient-derived reference intervals for alkaline phosphatase to support appropriate utility for isoenzymes determinations and hypophosphatasia
Authors: Joseph Jonathan , Hashim Ibrahim A 
Published: May 2024

Abstract

Background
Appropriate age- and sex-specific reference intervals for alkaline phosphatase (ALP) are essential to identify patients with hypophosphatasia (low ALP) and to avoid unnecessary ALP isoenzymes analysis (elevated ALP). This study used patient ALP historical data to statistically derive sex- and age-specific reference intervals.

Methods
The ALP values reported as part of clinical management during an 18 month period (from July 2021 to March 2023) were obtained. Following logarithmic transformation of ALP data and repeated removal of outliers, cumulative frequency plots were generated using a modified Hoffmann approach to derive age- and sex-specific reference intervals.

Results
Age-specific ALP reference intervals ranged from 110 to 250 and 120 to 295 U/L for males and females &lt;15 days old, 80 to 400 and 90 to 380 U/L for males and females 15 days to 1 year old, 105 to 280 and 90 to 290 U/L for males and females 1 to 10 years old, 75 to 300 and 90 to 300 U/L for males and females 10 to 13 years old, 80 to 300 and 60 to 175 U/L for males and females 13 to 15 years old, 55 to 150 and 60 to 180 U/L for males and females 15 to 18 years old, and 55 to 140 and 60 to 147 U/L for male and female adults, respectively (&gt;18 years old).

Conclusion
By applying derived ranges, a retrospective review of ALP isoenzymes would eliminate 24.5% of requests. Additionally, 9 neonates would have required investigation for possible hypophosphatasia.
90 years of Gödel’s incompleteness theorems: Logic and computation
Authors: Baaz Matthias , Ertel Marcel , Kahle Reinhard , Piecha Thomas , von Plato Jan 
Published: May 2024

Abstract
This volume is one of two special issues collecting articles by invited speakers of the conference ‘Celebrating 90 Years of Gödel’s Incompleteness Theorems’ held in Nürtingen (Germany) in July 2021. The conference was organized by the Carl Friedrich von Weizsäcker Center at the University of Tübingen with support by the ERC-funded project Gödel Enigma: Rediscovering Kurt Gödel through his unpublished works at the University of Helsinki and by the Kurt Gödel Society in Vienna.
Management of disseminated histoplasmosis in a high-complexity clinic in Cali, Colombia
Authors: Ramos-Ospina Natalia , Carolina Lambertinez-Álvarez Indira , Johanna Hurtado-Bermúdez Leidy , Patricia Muñoz-Lombo Jenny , Diego Vélez-Londoño Juan , Andrés Valencia-Montagut Jorge , Andrés Moncada-Vallejo Pablo 
Published: May 2024

Abstract
Histoplasmosis presents a substantial clinical challenge globally, with a particular prevalence in South America, especially among patients with concurrent Human Immunodeficiency Virus (HIV) infection. Despite itraconazole's established efficacy, investigating alternative therapeutic approaches remains imperative. This is the largest study in our region to date, assessing the effectiveness of the less explored posaconazole treatment. This observational study, conducted at Fundación Valle del Lili (FVL) from 2016 to 2022, encompassed adults with disseminated histoplasmosis. Patients (n = 31) were treated with liposomal amphotericin B as an initial treatment, followed by consolidation treatment with posaconazole or itraconazole. Patients with single-organ cases, those lacking microbiological diagnosis, those who received initial treatment with antifungals other than liposomal Amphotericin B and those with &lt; 6 months follow-up were excluded (Figure 1). Analyses considered population characteristics, treatments, and outcomes. Patients (average age: 45.6; 58.1% female) had common comorbidities (HIV 38.7%, solid organ transplantation 29% and oncologic disease 12.9%). Lungs (48.4%) and lymph nodes (16.1%) were commonly affected. Biopsy (64.5%) was the primary diagnostic method. Initial treatment with liposomal amphotericin B (100%) was given for 14 days on average. Follow-up indicated 71% completion with 19.4% requiring treatment modifications. Notably, 70.9% completed a posaconazole consolidation regimen over 350 days on average. Drug interactions during consolidation (80.6%) were common. No relapses occurred, and three deaths unrelated to histoplasmosis were reported. Traditionally, itraconazole has been the prevalent initial treatment; however, in our cohort, 55.9% of patients received posaconazole as the primary option. Encouragingly, posaconazole showed favorable tolerance and infection resolution, suggesting its potential as an effective and well-tolerated alternative for consolidation treatment. This finding prompts further exploration of posaconazole, potentially leading to more effective patient care and better outcomes.
Deciphering the association between biopsy-confirmed systemic small vessel vasculitis and Epstein–Barr virus-positive polymorphic B-cell lymphoproliferation
Authors: Sunaga Atsuhiko , Seno Takahiro , Omura Satoshi , Inoue Takuya , Miyagawa-Hayashino Aya , Omatsu Ikoi , Wada Makoto , Kohno Masataka , Kawahito Yutaka 
Published: May 2024

ABSTRACT
The Epstein-Barr virus (EBV) is associated with various lymphoproliferative disorders (LPDs). Additionally, EBV infection has correlated with diverse autoimmune diseases. However, the association between EBV and systemic small vessel vasculitis (SVV) remains controversial. Here, we report a case of SVV with pauci-immune glomerulonephritis accompanied by an EBV-positive polymorphic B-cell LPD, not otherwise specified. The intricate distinction between EBV-positive B-cell LPD and SVV was difficult, as both diseases demonstrated similar clinical presentations. Lymph node and kidney biopsies facilitated the accurate diagnosis of these two conditions. The administration of high-dose prednisolone, combined with rituximab, proved efficacious, with no instances of relapse over the subsequent 2-year period. This case indicates an association between EBV-positive B-cell LPD and SVV. The diligent execution of biopsies is a crucial diagnostic and interpretive strategy, generating precise comprehension of this condition and guiding its appropriate therapeutic management.
Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization
Authors: Behrmann Megan S , Perera Himasha M , Welikala Malisha U , Matthews Jacquelynn E , Butterworth Lauren J , Trakselis Michael A 
Published: May 2024

Abstract
The replicative helicase, DnaB, is a central component of the replisome and unwinds duplex DNA coupled with immediate template-dependent DNA synthesis by the polymerase, Pol III. The rate of helicase unwinding is dynamically regulated through structural transitions in the DnaB hexamer between dilated and constricted states. Site-specific mutations in DnaB enforce a faster more constricted conformation that dysregulates unwinding dynamics, causing replisome decoupling that generates excess ssDNA and induces severe cellular stress. This surplus ssDNA can stimulate RecA recruitment to initiate recombinational repair, restart, or activation of the transcriptional SOS response. To better understand the consequences of dysregulated unwinding, we combined targeted genomic dnaB mutations with an inducible RecA filament inhibition strategy to examine the dependencies on RecA in mitigating replisome decoupling phenotypes. Without RecA filamentation, dnaB:mut strains had reduced growth rates, decreased mutagenesis, but a greater burden from endogenous damage. Interestingly, disruption of RecA filamentation in these dnaB:mut strains also reduced cellular filamentation but increased markers of double strand breaks and ssDNA gaps as detected by in situ fluorescence microscopy and FACS assays, TUNEL and PLUG, respectively. Overall, RecA plays a critical role in strain survival by protecting and processing ssDNA gaps caused by dysregulated helicase activity in vivo.
PHF2 regulates genome topology and DNA replication in neural stem cells via cohesin
Authors: Feng Jia , Chuah You Heng , Liang Yajing , Cipta Nadia Omega , Zeng Yingying , Warrier Tushar , Elfar Gamal Ahmed Rashed Elsayed , Yoon Jeehyun , Grinchuk Oleg V , Tay Emmy Xue Yun , Lok Ker-Zhing , Zheng Zong-Qing , Khong Zi Jian , Chong Zheng-Shan , Teo Jackie , Sanford Emma May , Neo Cheryl Jia Yi , Chiu Hsin Yao , Leung Jia Yu , Wang Loo Chien , Lim Yan Ting , Zhao Tianyun , Sobota Radoslaw M , Crasta Karen Carmelina , Tergaonkar Vinay , Taneja Reshma , Ng Shi-Yan , Cheok Chit Fang , Ling Shuo-Chien , Loh Yuin-Han , Ong Derrick Sek Tong 
Published: May 2024

Abstract
Cohesin plays a crucial role in the organization of topologically-associated domains (TADs), which influence gene expression and DNA replication timing. Whether epigenetic regulators may affect TADs via cohesin to mediate DNA replication remains elusive. Here, we discover that the histone demethylase PHF2 associates with RAD21, a core subunit of cohesin, to regulate DNA replication in mouse neural stem cells (NSC). PHF2 loss impairs DNA replication due to the activation of dormant replication origins in NSC. Notably, the PHF2/RAD21 co-bound genomic regions are characterized by CTCF enrichment and epigenomic features that resemble efficient, active replication origins, and can act as boundaries to separate adjacent domains. Accordingly, PHF2 loss weakens TADs and chromatin loops at the co-bound loci due to reduced RAD21 occupancy. The observed topological and DNA replication defects in PHF2 KO NSC support a cohesin-dependent mechanism. Furthermore, we demonstrate that the PHF2/RAD21 complex exerts little effect on gene regulation, and that PHF2’s histone-demethylase activity is dispensable for normal DNA replication and proliferation of NSC. We propose that PHF2 may serve as a topological accessory to cohesin for cohesin localization to TADs and chromatin loops, where cohesin represses dormant replication origins directly or indirectly, to sustain DNA replication in NSC.
Imaging meningioma biology: Machine learning predicts integrated risk score in WHO grade 2/3 meningioma
Authors: Kertels Olivia , Delbridge Claire , Sahm Felix , Ehret Felix , Acker Güliz , Capper David , Peeken Jan C , Diehl Christian , Griessmair Michael , Metz Marie-Christin , Negwer Chiara , Krieg Sandro M , Onken Julia , Yakushev Igor , Vajkoczy Peter , Meyer Bernhard , Zips Daniel , Combs Stephanie E , Zimmer Claus , Kaul David , Bernhardt Denise , Wiestler Benedikt 
Published: May 2024

Abstract

Background
Meningiomas are the most common primary brain tumors. While most are benign (WHO grade 1) and have a favorable prognosis, up to one-fourth are classified as higher-grade, falling into WHO grade 2 or 3 categories. Recently, an integrated risk score (IRS) pertaining to tumor biology was developed and its prognostic relevance was validated in a large, multicenter study. We hypothesized imaging data to be reflective of the IRS. Thus, we assessed the potential of a machine learning classifier for its noninvasive prediction using preoperative magnetic resonance imaging (MRI).

Methods
In total, 160 WHO grade 2 and 3 meningioma patients from 2 university centers were included in this study. All patients underwent surgery with histopathological workup including methylation analysis. Preoperative MRI scans were automatically segmented, and radiomic parameters were extracted. Using a random forest classifier, 3 machine learning classifiers (1 multiclass classifier for IRS and 2 binary classifiers for low-risk and high-risk prediction, respectively) were developed in a training set (120 patients) and independently tested in a hold-out test set (40 patients).

Results
Multiclass IRS classification had a test set area under the curve (AUC) of 0.7, mostly driven by the difficulties in clearly separating medium-risk from high-risk patients. Consequently, a classifier predicting low-risk IRS versus medium-/high-risk showed a very high test accuracy of 90% (AUC 0.88). In particular, “sphericity” was associated with low-risk IRS classification.

Conclusion
The IRS, in particular molecular low-risk, can be predicted from imaging data with high accuracy, making this important prognostic classification accessible by imaging.
Childhood dyslipidemia: Clinician management practices in the primary care setting
Authors: Tom Katherine N , Polack Alicia M , De Silva Natasha D , Wong Jonathan P , Keown-Stoneman Charles D G , Maguire Jonathon L , Birken Catherine S , Wong Peter D 
Published: May 2024

Abstract

Objectives
To describe clinician management practices for childhood dyslipidemia in the community setting.

Methods
A descriptive study was conducted for children aged 2 to 10 years with dyslipidemia as defined by the National Cholesterol Education Program Expert Panel on Cholesterol in Children criteria. A convenience sample of participants from the TARGet Kids! cohort study (Toronto, Canada) was used. Trained research assistants reviewed participant medical records to document clinician management practices of abnormal lipid levels. The study outcome was the proportion of clinicians engaging in each management practice. Descriptive statistics were completed, reporting the proportion of clinician engagement in management practices.

Results
All 768 children were seen by primary paediatric care providers after lipid levels identified dyslipidemia. Medical history regarding lifestyle behaviours and cardiovascular risk factors were frequently obtained (n = 565, 73.6%). Physicians rarely informed families about abnormal lipid levels (n = 11, 1.43%). Management plans for abnormal lipid levels were rarely documented (n = 4, 0.5%). Clinicians did not refer to paediatric lipid specialists or initiate statin therapy.

Conclusions
Paediatric care providers rarely identified and initiated early management for abnormal lipid levels. Our results may inform the need for improved knowledge translation of the recently published Canadian clinical practice update for the detection and management of childhood dyslipidemia.
ContinUNet: fast deep radio image segmentation in the Square Kilometre Array era with U-Net
Authors: Stewart Hattie , Birkinshaw Mark , Yeung Siu-Lun , Maddox Natasha , Maughan Ben , Thiyagalingam Jeyan 
Published: May 2024

Abstract
We present a new machine learning (ML)-driven source-finding tool for next-generation radio surveys that performs fast source extraction on a range of source morphologies at large dynamic ranges with minimal parameter tuning and post-processing. The construction of the Square Kilometre Array (SKA) radio telescope will revolutionize the field of radio astronomy. However, accurate and automated source-finding techniques are required to reach SKA science goals. We have developed a novel source-finding method, ContinUNet, powered by an ML segmentation algorithm, U-Net, that has proven highly effective and efficient when tested on SKA precursor data sets. Our model was trained and tested on simulated radio continuum data from SKA Science Data Challenge 1 and proved comparable with the state-of-the-art source-finding methods, PyBDSF and ProFound. ContinUNet was then tested on the MeerKAT International GHz Tiered Extragalactic Exploration Early Science data without retraining and was able to extract point-like and extended sources with equal ease; processing a 1.6 deg$^2$ field in $\lt $13 s on a supercomputer and $\approx$2 min on a personal laptop. We were able to associate components of extended sources without manual intervention with the powerful inference capabilities learnt within the network, making ContinUNet a promising tool for enabling science in the upcoming SKA era.