bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classifying tumour infiltrating lymphocytes in oral squamous cell carcinoma histopathology using joint learning framework
Authors: Barua Barun , Chyrmang Genevieve , Bora Kangkana , Ahmed Gazi N. , Kakoti Lopamudra , Saikia Manob Jyoti 
Published: January 2025

Abstract
Oral squamous cell carcinoma (OSCC) is the most common form of oral cancer, with increasing global incidence and have poor prognosis. Tumour-infiltrating lymphocytes (TILs) are recognized as a key prognostic indicator and play a vital role in OSCC grading. However, current methods for TILs quantification are based on subjective visual assessments, leading to inter-observer variability and inconsistent diagnostic reproducibility. Only a few studies have been conducted in automating TILs quantification for OSCC, existing methods use score-based systems that focus only on tissue-level spatial analysis, overlooking essential cellular-level information and do not provide TILs infiltration subcategories required for determining OSCC grading. To address these limitations, we propose OralTILs-ViT, a novel joint representation learning framework that integrates cellular and tissue-level information. Our model employs two parallel encoders: one extracts cellular features from cellular density maps, while the other processes tissue features from H&E-stained tissue images. This dual-encoder approach enables OralTILs-ViT to capture complex tissue-cellular interactions, classifying TILs infiltration categories consistent with Broders’ grading system-“Moderate to Marked”, “Slight” and “None to Very Less.” This approach reflects pathology practices and increases TILs classification accuracy. To generate cellular density maps, we introduce TILSeg-MobileViT, a multiclass segmentation model trained using a weakly supervised method, minimizing the need for manual annotation of cellular masks and overcoming the limitations of previous TILs assessment techniques. An extensive evaluation of our methodology demonstrates that OralTILs-ViT with the configuration (Adam,

$$\alpha$$

α

= 0.001) outperforms existing approaches, achieving 96.37% accuracy, 96.34% precision, 96.37% recall, and a 96.35% F1 score. Furthermore, TOPSIS analysis confirms that our method ranks first across all TILs infiltration categories. In summary, our proposed methodology outperforms single modality-representation learning approaches for accurate and automated TILs classification.
Functional genomic insights into Floricoccus penangensis ML061-4 isolated from leaf surface of Assam tea
Authors: Rungsirivanich Patthanasak , Parlindungan Elvina , Mahony Jennifer , Supandee Witsanu , Thongwai Narumol , van Sinderen Douwe 
Published: January 2025

Abstract

Floricoccus penangensis ML061-4 was originally isolated from the leaf surface of an Assam tea plant (Camellia sinensis var. assamica) from Northern Thailand. To assess the functions encoded by the F. penangensis ML061-4 genome, gene identification and annotation were undertaken by in silico analysis. The complete genome of F. penangensis ML061-4 consists of single chromosome of 2,159,127 base pairs, containing a GC content of 33.2% and encompassing 2049 predicted protein-encoding genes. A total of 1195 genes (58.0%) in the F. penangensis ML061-4 genome have assignable functions based on BlastKOALA analysis. Furthermore, 1235 genes (59.9%) were classified into six KEGG functional categories with 187 associated pathways, while 1419 genes (68.8%) were assigned a putative function by the Clusters of Orthologous Groups (COGs) database. The ML061-4 genome was evaluated for genes associated with complex carbohydrate metabolism, bacterial adhesion, virulence factors, pathogenicity, bacteriophages, antiviral defence systems as well as toxin- and antibiotic-resistance associated genes, and genes involved in toxin production, secondary metabolite biosynthesis and xenobiotics biodegradation. The obtained results support the notion of F. penangensis ML061-4 being safe for biotechnological and food industry purposes. This is the first report outlining functional genomic insights regarding a member of the genus Floricoccus.
Novel relatives of Mecsek Mountains mammarenavirus (family Arenaviridae) in hedgehogs living in different sampling areas in Hungary
Authors: Takáts Károly , Pankovics Péter , Balázs Benigna , Boros Ákos , Mátics Róbert , Reuter Gábor 
Published: January 2025

Abstract
Mammarenaviruses (genus Mammarenavirus, family Arenaviridae) are rodent-borne zoonotic viruses consisting of 52 viral species, including ten that are pathogenic to humans. Currently, only two endemic mammarenavirus species are known in Europe: the human pathogenic Mammarenavirus choriomeningitidis (LCMV) and the recently discovered hedgehog-origin Mammarenavirus mecsekense (MEMV). In this study, 59 faecal specimens from Northern white-breasted hedgehogs (Erinaceus roumanicus) from different geographic regions in Hungary were investigated for mammarenavirus presence and complete genome characterization using newly designed screening primers by RT-semi-nested PCR and sequencing methods. Five (8.5%) of the 59 samples tested positive for mammarenavirus RNA (ER8, ER15, ER27, ER33, and ER39, GenBank accession numbers PQ441959-PQ441968). The L- and S-segments of these strains showed 66–93% and 73–92% nt identity to the closest known mammarenavirus, MEMV, respectively. The NP protein exhibited 86–97% aa sequence identity compared to the corresponding protein of MEMV. Notably, the S-segment intergenic region (S-IGR) of strains ER8, ER15, ER27 and ER33 exceeded the average nt length among known mammarenaviruses and contained two, highly similar stem-loop structures with conserved self-complementary nucleotide motifs. Based on the sequence- and phylogenetic analysis these strains (ER8, ER15, ER27 and ER33) potentially represent a novel mammarenavirus species, tentatively named Pannonia mammarenavirus (PANV).
AHNAK2: a potential diagnostic biomarker for pancreatic cancer related to cellular motility
Authors: Zardab Mohamed ,   Barts Pancreas Tissue Bank, Roberts Rhiannon , Hughes Christine , Imrali Ahmet , Saad Amina , Chelala Claude , Grose Richard P. , Kocher Hemant M. 
Published: January 2025

Abstract
Pancreatic ductal adenocarcinoma lacks suitable biomarkers for early diagnosis of disease. In gene panels developed for early diagnosis of pancreatic cancer, high AHNAK2 mRNA expression was one possible biomarker. In silico analysis of published human sample datasets (n = 177) and ex vivo analysis of human plasma samples (n = 30 PDAC with matched 30 healthy control) suggested AHNAK2 could be a diagnostic biomarker. At a plasma level of 421.47 ng/ml, AHNAK2 could potentially diagnose PDAC with a specificity and sensitivity of 83.33% and 86.67%. In vitro analysis suggests that in cell lines with diffuse cytoplasmic distribution of AHNAK2, there was colocalization of AHNAK2 with Cortactin in filipodia. This colocalization increased when cells were cultured on substrates such as Fibronectin and Collagen, as well as in hypoxia, and resulted in an augmented invasion of cancer cells. However, in cell lines with a vesicular AHNAK2 staining, such changes were not observed. Our study posits AHNAK2 as a valuable diagnostic biomarker in PDAC, now demanding prospective validation. Determination of mechanisms regulating AHNAK2 subcellular localisation may help explain its biological role.
Novel euthanasia technique for zebrafish using electric shock in standard group housing aquaria
Authors: Saarinen Ulla , Sundell Erika , Sneddon Lynne , Gräns Albin 
Published: January 2025

Abstract
Zebrafish are widely used in research, accounting for approximately 50% of all laboratory fish across Europe. Due to their rapid reproduction and aging, effective and practical euthanasia methods are necessary for managing large stocks. This study investigated whether adult zebrafish can be euthanised by delivering an electrical current directly via the water in their housing aquaria. For this, portable plate electrodes were developed for 3.5 and 8.0 L Tecniplast™ housing aquaria. Our results show that adult zebrafish can be euthanised in groups (5 fish per litre) with electrical fields and current densities of at least 6 or 7 VRMS cm−1, and 0.7 or 0.8 ARMS dm−2 in 3.5–8 L aquaria, respectively, when delivered for 30 s in water at 28 °C with a conductivity of 800 µS cm−1 at 50 Hz. If widely implemented, this technique could improve the welfare of the vast number of zebrafish used across the world.
Analytical protocol for measuring micro-molar quantities of sulfur volatile species in experimental high pressure and temperature fluids
Authors: Secchiari Arianna , Toffolo Luca , Recchia Sandro , Tumiati Simone 
Published: January 2025

Abstract
Validating thermodynamic models is essential in experimental geosciences for exploring increasingly complex systems and developing analytical protocols. However, investigating solid–fluid equilibria in mm3-sized experimental capsules poses several challenges, particularly in sulfur-bearing chemical systems. These include maintaining bulk fluid composition and performing quantitative analysis with extremely low amounts of synthesized fluid. We present an innovative methodology for measuring ultra-low amounts of sulfur volatiles (H2S and SO2) generated during experimental runs at high pressure and temperature conditions of 3 GPa and 700 °C. Using solid sulfides (FeS + FeS2) and water as reactants, we performed redox-controlled syntheses employing a piston cylinder apparatus. We demonstrate that ex-situ measurements of these fluids by quadrupole mass spectrometry ensure accurate and precise analysis, confirming predicted thermodynamic compositions. This methodology allows in-depht investigation of sulfide solid–fluid equilibria, shedding light on sulfur volatiles behavior and geochemical cycles under high P–T conditions characteristic of the Earth’s interior.
Investigating the redshift evolution of lensing galaxy density slopes via model-independent distance ratios
Authors: Geng S. , Grespan M. , Thuruthipilly H. , Harikumar S. , Pollo A. , Biesiada M. 
Published: January 2025

Context. Strong-lensing systems are expected to be discovered in great numbers by next-generation surveys. They provide a powerful tool for studying cosmology and the galaxy evolution. The coupling of the galaxy structure and cosmology through distance ratios means that it is essential for advancing both fields to examine the evolution of the lensing galaxy mass density profiles.
Aims. We introduce a novel method that is independent of the dark energy assumed in the model to investigate the mass density slopes of lensing galaxies and their redshift evolution using an extended power-law (EPL) model.
Methods. We adopted a nonparametric approach based on artificial neural networks trained on type Ia supernovae data to reconstruct the distance ratios of strong-lensing systems. These reconstructed ratios were compared with theoretical predictions to estimate the evolution of EPL model parameters.
Results. A negative evolutionary trend of the mass density power-law exponent with increasing redshift is observed across different analysis levels. Assuming a triangular prior for the anisotropy of lensing galaxies, we find evidence for a redshift evolution of the mass density slope, quantified as ∂γ/∂z = −0.20 ± 0.12.
Conclusions. This study confirms that the redshift evolution of the matter density slopes in lensing galaxies can be determined independent of dark energy models at the population level. The Legacy Survey of Space and Time (LSST) Rubin Observatory forecasts are expected to identify 100 000 strongly lensed galaxies. We show based on simulations with data from the LSST that spectroscopic follow up of just 10% of these systems can reduce the uncertainty in the redshift evolution coefficient of the total mass density slope (Δ∂γ/∂z) to 0.021. This precision would be able to distinguish between evolving and nonevolving scenarios for lensing galaxies.
Single-Session Surgical Intervention with Resection of a Primary Cranial Osteosarcoma and Cranioplasty using a 3D-Printed Craniotomy Template and Cranioplasty Molds
Authors: Duda Sven , Ivanyi Philipp , Omar Mohamed , Hartmann Christian , Musienko Eugen , Wessling Heinrich 
Published: January 2025

AbstractAlthough osteosarcomas are the most frequent primary malignant bone tumors, the primary cranial manifestation of this condition is very rare with only a limited number of cases presented in the literature.We present the case of a 20-year-old male patient who underwent single-session surgical intervention for resection of right frontal osteosarcoma with a tailor-made craniotomy and cranioplasty using virtually designed 3D-printed templates and molds. Subsequently, the patient was treated according to the EURAMOS protocol and received adjuvant systemic chemotherapy.At 18-month follow-up, the patient was clinically asymptomatic, and both the magnetic resonance imaging scan of the head and the staging computed tomography showed no signs of tumor recurrence or metastases. The case presented shows that the use of 3D-printed molds facilitate a safe preoperative planning of the resection area and a single-session surgery including a custom-made cranioplasty responding to the highest esthetical standards.
Endoscopic Orbital Clearance/Debridement: A Potential Substitute for Orbital Exenteration in Rhino-orbital Mucormycosis
Authors: Sweed Ahmed Hassan , Anany Ahmed Mohammad , Hussein Atef , Nada Waleed , Eesa Mohamed , Elnashar Ismail , Mobashir Mohamed , Ibrahim Enas Moustafa , Elmaghawry Mohammed Elsayed 
Published: January 2025

Abstract
Introduction Mucormycosis is an aggressive, lethal fungal infection affecting the nasal and paranasal territory in immunocompromised patients. Orbital involvement is not uncommon and may require orbital exenteration.
Objectives The management of orbital involvement in invasive fungal sinusitis is challenging, ranging from conservative retrobulbar amphotericin B injection in the early stages to orbital exenteration in late stages. Endoscopic endonasal debridement is a minimally invasive technique used to manage orbital fungal involvement in the late stages.
Methods Endoscopic endonasal orbital clearance was performed to manage late-stage orbital invasive fungal infection (≥ stage 3c) or after failure of retrobulbar amphotericin B injection with no light perception. Removal of the lamina papyracea (LP) and incision of the periorbita were done to expose all the necrotic intraorbital content in the extra and intraconal spaces. A microdebrider was utilized to debride necrotic fungal infected tissue until a healthy vascularized plane was reached. Gelfoam (Pfizer Inc., New York, NY, United States) soaked in amphotericin B was applied as an adjunctive step to deliver antifungal medication to the orbital content.
Results Fourteen patients were included in the study, 9 of whom were male and 5 female, with a mean age of 58.5 years. Eleven patients showed no evidence of disease progression (complete recovery and cessation of medical treatment). Two patients died 15 days after the surgery. The last patient developed frontal lobe abscess but has been treated with double antifungal medication.
Conclusion Endoscopic endonasal orbital debridement could be an effective method to treat late-stage orbital fungal infection without jeopardizing the patient's life.
Level of Evidence: 4.
A Retrospective Study on the Imaging Spectrum of Functional Single Ventricle and Its Associations
Authors: Niva B. , Rajeshkannan Ramiah 
Published: January 2025

Abstract
Objective The aim of the study was to identify the various spectrum of single ventricle (SV) physiology and to correlate the anatomical variants.
Design and Methods All congenital heart disease cases with computed tomography/magnetic resonance imaging during the period from 2008 to 2023 were retrospectively assessed. Among these, we identified those corresponding to the definition of SV (n = 160). In each case, we described the situs, looping, atrioventricular (AV)/ventriculoarterial (VA) connections, and associated anomalies. Descriptive statistics of each parameter were obtained and compared with similar parameters of other published studies.
Results Among the 160 cases, there were 93 males (58.1%) and 67 females (41.9%). The mean age was 8.41 ± 8.84 years. The most common defects were tricuspid atresia (TA) at 28%, double inlet left ventricle (DILV) at 23%, and AV canal defect (AVCD) at 22%. Other conditions include double outlet right ventricle, large ventricular septal defect, dextro-transposition of great arteries, levo-transposition of great arteries, mitral atresia, pulmonary atresia, hypoplastic left heart syndrome, and crisscross heart. There were 123 situs solitus, 28 right isomerism, 4 left isomerism, and 5 situs inversus cases. Among the patients with right isomerism, the most common defect was AVCD (86%). Sixty-five percent of DILV had discordant VA connections, while only 14% showed concordance. Sixty-three percent of TA cases showed VA concordance. Knowing the underlying anatomy in detail helps the physician to anticipate the wide array of problems unique to SV circulation and treat them accordingly.
Conclusion The conditions coming under the SV spectrum can be classified based on AV and VA connections. The incidence of each condition and observed associations were described.
Gynecomastia Surgery: Liposuction Alone versus Liposuction with Endoscope-Assisted Glandular Excision—A Comparative Study
Authors: Ali Sheikh Sarfraz , Ahmed Imran , Khurram Mohammed Fahud , Rehman Noha , Abhishek Rupraj 
Published: January 2025

Abstract
Background Gynecomastia, affecting around 30% of young males, has seen evolving surgical treatments, transitioning from traditional excision methods to contemporary techniques like liposuction. Emotional distress persists when glandular tissue is inadequately addressed, prompting exploration of combined liposuction and glandular excision procedures.
Materials and Methods Patients undergoing gynecomastia surgery over a period of 2 years were assessed, considering their demographics, medical history, and gynecomastia grade. Surgical procedures involved liposuction alone or with glandular excision. Endoscopy was used to assess the presence of fibroglandular tissue and the need for glandular excision. Postoperative assessments, clinical photography, and patient questionnaires spanned a 6-month follow-up.
Results Thirty-two breasts (17 in liposuction alone and 15 in liposuction with glandular excision groups) were included. Liposuction alone led to bruising and two hematomas, and “puffy nipples” necessitating one redo surgery. Glandular excision resulted in four cases of crater deformity and one case each of superficial skin necrosis, hematoma, and seroma. Cosmetic evaluations showed similar outcomes, with the liposuction alone group having higher redo surgery rates.
Conclusion This study finds that combining liposuction with glandular excision delivers comparable cosmetic results to liposuction alone for gynecomastia. Despite added complexity, the combined approach proves effective and helps in decision-making, emphasizing the need for tailored techniques and ongoing research to optimize treatment strategies.
Automated bail-in: eliminating regulatory restraints
Authors: Lendermann Urs B. 
Published: January 2025

Abstract
The Credit Suisse default in 2023 sparked considerable discourse about the absence of bank resolution procedures. Instead of resolution, public guarantees and unconventional emergency liquidity assistance (ELA) were provided. Of course, this occurred nearly two decades after the global financial crisis of 2007–2009, and evidently, there are still lessons to be learned. This study explores the bail-in tool and the total loss-absorbing capacity (TLAC) introduced by the G20 Financial Stability Board to eliminate the need for public bailouts of global systemically important banks in case of failure. Acknowledging the pragmatic standpoint, it is essential to recognise that banks hold divergent perspectives concerning their resolution planning while policymakers continue to grapple with the ‘too-big-to-fail’ dilemma without a discernible pathway for resolution. Thus, this study proposes contractual approaches to enhance the TLAC framework, incorporating a market-based trigger design. These improvements aim to create conditions that enable central banks to provide ELA, thereby averting systemic disruptions during a financial crisis.
The discursive representation of migrants, refugees and asylum seekers in Austrian news coverage:
2010–2015–2020
Authors: Goldberger Marie-Antoinette , Janík Miroslav 
Published: January 2025

Abstract
is paper traces the terminological shifts in the media representation of immigrants from 2010 to 2020. Using a
corpus-based approach to Critical Discourse Analysis, we examine the terms “migrant(s),” “refugee(s),” and “asylum seeker(s)” in
the Austrian daily newspaper Der Standard during the refugee crisis (2015) and five years before (2010) and after
(2020). Our research, which employs collocation analysis complemented by critical discourse analysis, reveals significant shifts
in the connotations of all three terms. The notion of “migrant” evolves from a positive and individualizing portrayal in 2010 to a
more negative, stereotypical one by 2020. Conversely, “asylum seekers” shift from being viewed with suspicion in 2010 to being
recognized as legitimate beneficiaries of protection in 2020. Only “refugees” remain relatively featureless. We interpret these
changes as a reflection of the balancing act between the left-liberal stance of Der Standard and the rising
right-wing extremism in society.
The metapragmatic act of debating in the media
Authors: Jacobsen Ronald R. 
Published: January 2025

Abstract
The aim of this paper is to lay the theoretical foundation of the metapragmatic act of debating, and to present
evidence that it provides a better approach to mediated debate than existing theoretical notions of metapragmatic acts and
intertextuality in the media. To achieve this goal, it contrasts its notion with Bublitz’
(2015) metapragmatic act of quoting, and analyses a simple and a complex exchange from the First 2004 US presidential
debate. The theory proposed and data analyzed suggest two things: (1) that the metapragmatic act of debating is best conceived of
as a combination of Caffi’s (2006) third sense of metapragmatics and Mey’s (2001) notion of pragmatic act, (2) operationalizing the theoretical notion of a
metapragmatic act means adapting it to a specific context, for example, there is no such thing as a general metapragmatic act.
A hydrostatic comparator for the density determination of solid objects
Authors: McLinden Mark O , Bernardini Luca , Richter Markus 
Published: January 2025

Abstract
We describe a hydrostatic comparator optimized for the determination of the density (or equivalently volume) of the sinkers used in magnetic suspension densimeters. The hydrostatic comparator is a modification of the traditional hydrostatic weighing technique for the determination of the density of solid objects: by weighing a density standard as well as the unknown object (with both immersed in a fluid) the density information of the standard is transferred to the unknown, and the density of the hydrostatic bath fluid need not be known. Our instrument makes use of two density standards of single-crystal silicon and a high-density, fluorinated-ether bath fluid; it can weigh objects as large as 100 g four-at-a-time (one or more standards and up to three unknowns). We discuss weighing designs and demonstrate a new method that employs an additional standard to eliminate the need for the usual empty-pan weighings. Uncertainties are reduced by the use of compensation and sensitivity masses. As a demonstration of the instrument’s capabilities, results are presented for a set of 12 objects with masses from 33 g to 99 g and densities from 2.33 g⋅cm–3–16.7 g⋅cm–3. The expanded (k = 2) uncertainty in volume averaged 0.000 041 cm–3, with relative uncertainties ranging from 1.1 × 10–6 for a 99 g/42.3 cm3 silicon object to 7.5 × 10–6 for a 60 g/7.5 cm3 gold-plated stainless steel object.