bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell RNA sequencing identifies molecular biomarkers predicting late progression to CDK4/6 inhibition in patients with HR+/HER2- metastatic breast cancer
Authors: Luo Linjie , Yang Peng , Mastoraki Sofia , Rao Xiayu , Wang Yan , Kettner Nicole M. , Raghavendra Akshara Singareeka , Tripathy Debasish , Damodaran Senthil , Hunt Kelly K. , Wang Jing , Li Ziyi , Keyomarsi Khandan 
Published: February 2025

Abstract

Background
Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) in combination with endocrine therapy are the standard treatment for patients with hormone receptor–positive, HER2–negative metastatic breast cancer (mBC). Despite the efficacy of CDK4/6is, intrinsic resistance occurs in approximately one-third of patients, highlighting the need for reliable predictive biomarkers.

Methods
Single-cell RNA sequencing analyzed metastatic tumors from HR+/HER2- mBC patients pre-CDK4/6i treatment at baseline (BL) and/or at disease progression. BL samples were from CDK4/6i responders (median progression-free survival [mPFS] = 25.5 months), while progressors were categorized as early-progressors (EP, mPFS = 3 months) and late-progressors (LP, mPFS = 11 months). Metastatic sites included liver, pleural effusions, ascites, and bone. InferCNV distinguished tumor cells, and functional analysis utilized the Molecular Signatures Database.

Results
LP tumors displayed enhanced Myc, EMT, TNF-α, and inflammatory pathways compared to those EP tumors. Samples from BL and LP responders showed increased tumor-infiltrating CD8+ T cells and natural killer (NK) cells compared to EP non-responders. Notably, despite a high frequency of CD8+ T cells in responding tumors, a functional analysis revealed significant upregulation of genes associated with stress and apoptosis in proliferative CD4+ and CD8+ T cells in BL tumors compared to in EP and LP tumors. These genes, including HSP90 and HSPA8, are linked to resistance to PD1/PD-L1 immune checkpoint inhibitors. A ligand-receptor analysis showed enhanced interactions associated with inhibitory T-cell proliferation (SPP1-CD44) and suppression of immune activity (MDK-NCL) in LP tumors. Longitudinal biopsies consistently revealed dynamic NK cell expansion and enhanced cytotoxic T cell activity, alongside upregulation of immune activity inhibition, in LP tumors compared to in BL tumors. Notably, the predictive biomarker panel from BL tumor cells was validated in 2 independent cohorts, where it consistently predicted a significant improvement in mPFS duration in signature-high versus -low groups.

Conclusion
This study underscores the significance of molecular biomarkers in predicting clinical outcomes to CDK4/6i. Tumor-infiltration CD8+ T and NK cells may also serve as baseline predictors. These insights pave the way for optimizing therapeutic strategies based on microenvironment-specific changes, providing a personalized and effective approach for managing HR+/HER2- mBC and improving patient outcomes.
Acute compartment syndrome due to skeletal muscle metastases from poorly differentiated upper gastrointestinal adenocarcinoma: a case report
Authors: Gentry Richard , Anand Prince Mohan , Kamal Ahmed I , Alqassieh Ahmad Saleh , Mahmood Ammar Obaid , Ayrapetyan Mesrop , Saud Amer Altiti Monther 
Published: February 2025

Abstract

Background
Acute compartment syndrome (ACS) is characterized by increased pressure within the fascial network of any muscle, leading to impaired circulation and potential myonecrosis. Very rarely, soft tissue infiltration by metastatic disease can cause localized swelling that increases intercompartmental pressures. We report an unusual case of invasive, poorly differentiated upper gastrointestinal adenocarcinoma presented by acute compartment syndrome of the lower extremity and subsequent acute kidney injury (AKI) caused by myonecrosis-induced cast nephropathy.

Case Presentation
A 52-year-old male presented to the hospital with rapid onset unilateral right leg pain and tense edema accompanied by myonecrosis with no explicable etiology complicated by AKI. Surgical fasciotomy and subsequent muscle biopsy yielded poorly differentiated non-small cell adenocarcinoma. CT imaging identified diffuse adenopathy along with abnormal thickening of the distal esophagus, gastroesophageal (GE) junction, and gastric cardia. Further investigation via upper esophagogastroduodenoscopy (EGD) revealed an exophytic mass in the distal esophagus extending into the stomach. This lesion was confirmed via biopsy as primary invasive poorly differentiated upper gastrointestinal (UGI) adenocarcinoma.

Conclusion
This case highlights the need for clinicians to implement high-risk screening for UGI cancers and consider skeletal muscle metastasis as a cause of nontraumatic ACS. It emphasizes the importance of interdisciplinary collaboration in managing such complex cases and the role of timely surgical and oncological intervention in preventing long-term complications of ACS. Furthermore, it highlights the potential use of more efficient and specific MR imaging techniques to diagnose ambiguous cases of ACS.
Accelerating eucalypt clone selection pipeline via cloned progeny trials and molecular data
Authors: Benatti Thiago Romanos , Ferreira Filipe Manoel , da Costa Rodolfo Manoel Lemes , de Moraes Mario Luiz Teixeira , Aguiar Aurélio Mendes , da Costa Dias Donizete , de Matos José Wilacildo , Fernandes Aline Cristina Miranda , Andrade Mateus Chagas , de Siqueira Leandro , Brum Itaraju Junior Baracuhy , do Nascimento André Vieira , Utsunomiya Yuri Tani , Garcia José Fernando , Tambarussi Evandro Vagner 
Published: February 2025

Abstract
The high productivity of Eucalyptus spp. forest plantations is mainly due to advances in silvicultural techniques and genetic improvement associated with the potential that many species of the genus have for vegetative propagation. However, long reproduction cycles for forest species pose significant challenges for genetic progress via traditional breeding programs. Furthermore, there is often poor correlation between individual (seedling) performance in initial (progeny trials) and final (clonal trials) stages of the breeding program. In this scenario, cloned progeny trials (CPT) offer an alternative to accelerate the eucalypt clone selection pipeline, combining progeny and clonal trials in a single experiment. CPT has the potential to speed up the evaluation process and increase its efficiency by developing new commercial genotypes that were tested as clones from the initial stage of the breeding program. Thus, this study aims to assess the potential of CPT to accelerate eucalypt clone selection programs by estimating the genetic parameters, analyzing responses to selection, and predicting the adequate number of ramets to be used in CPT of Eucalyptus urophylla x Eucalyptus grandis. The results show that when the number of ramets per progeny was decreased from five to one there was a reduction in the estimates of broad-sense heritability and accuracy. However, three ramets/progeny can be used without significant reductions in these estimates. CPT accelerates clonal selection by combining progeny and clonal trial methodologies, enabling an evaluation of performance as both progeny and clone. This capacity is very important for vegetatively propagated crop species such as Eucalyptus. Integrating CPT with SNP markers can offer an alternative to shorten the tree clone selection pipeline, better estimate and decompose the genetic variance components, and improve the correlation between initial and final performance for selected genotypes. This study confirms the potential of CPT to improve selection processes and accelerate genetic gains in the eucalypt clone selection pipeline.
New approach in models for managing the vessel’s unloading process
Authors: Luidmyla L. Nikolaieva , Taras Y. Omelchenko , Oleksandr V. Haichenia 
Published: February 2025

Abstract
New way of formalizing hybrid systems in models for managing the vessel unloading process is caused by the significant increase in container transportation around the world over the past decade. The growth of container traffic is the main reason for the constant modernization of port container terminals and improvement of cargo unloading technology is most promising when using those methods, that allow obtaining maximum results in terms of cargo processing speed. This problem is the subject of an article in which analytical review of container handling technologies existing in world ports is carried out, their key performance indicators are formulated and it is shown how the use of a centralized hybrid control system based on the dynamics of discrete events can lead to increased profitability of the port. Developed concept of a hybrid control system makes possible to consider such features of the vessels unload process that have not been considered until now.
In vivo electrophysiology recordings and computational modeling can predict octopus arm movement
Authors: Gedela Nitish Satya Sai , Radawiec Ryan D. , Salim Sachin , Richie Julianna , Chestek Cynthia , Draelos Anne , Pelled Galit 
Published: February 2025

Abstract
The octopus has many features that make it advantageous for revealing principles of motor circuits and control and predicting behavior. Here, an array of carbon electrodes providing single-unit electrophysiology recordings were implanted into the octopus anterior nerve cord. The number of spikes and arm movements in response to stimulation at different locations along the arm were recorded. We observed that the number of spikes occurring within the first 100 ms after stimulation were predictive of the resultant movement response. Machine learning models showed that temporal electrophysiological features could be used to predict whether an arm movement occurred with 88.64% confidence, and if it was a lateral arm movement or a grasping motion with 75.45% confidence. Both supervised and unsupervised methods were applied to gain streaming measurements of octopus arm movements and how their motor circuitry produces rich movement types in real time. For kinematic analysis, deep learning models and unsupervised dimensionality reduction identified a consistent set of features that could be used to distinguish different types of arm movements. The neural circuits and the computational models identified here generated predictions for how to evoke a particular, complex movement in an orchestrated sequence for an individual motor circuit. This study demonstrates how real-time motor behaviors can be predicted and distinguished, contributing to the development of brain-machine interfaces. The ability to accurately model and predict complex movement patterns has broad implications for advancing technologies in robotics, neuroprosthetics, and artificial intelligence, paving the way for more sophisticated and adaptable systems.
Health benefits of okra (Abelmoschus esculentus) against diabetes mellitus and cognitive dysfunction: a review
Authors: Ahmad Nazir , Lesa Kaisun Nesa , Ikawati Zullies , Fakhrudin Nanang 
Published: February 2025

Abstract
Diabetes mellitus (DM), both type 1 and type 2, has been linked to decreased performance across a number of cognitive function categories, with more recent studies emphasizing the contribution of DM mediated dementia. Despite the therapeutic advantages of antidiabetic medications for the management of DM mediated cognitive dysfunction (CD), the majority of these pharmaceuticals are linked to a number of negative side effects, raising questions about their long-term advantages. Botanical medicines, which often have low toxicity and adverse effects, are supported by some latter research. These medicines are attracting increased interest from researchers studying traditional herbal remedies owing to the minimal side effects for prevention and managing DM and CD in developing and developed countries. To emphasize the health benefits of okra (Abelmoschus esculentus) against DM and CD. Different databases, including PubMed, Google Scholar, and Scopus, were searched with a combination of keywords. The available research on the health benefits of okra against DM and CD is compiled in this study which indicates that okra has the ability to manage DM and CD. It will serve as a base for further investigation into the okra preparation for its potential commercial production as a therapeutic agent for DM and CD.

Graphical Abstract
Epidemiological factors affecting post-COVID-19 acute invasive fungal rhinosinusitis incidence and prognosis
Authors: Ayad Mostafa Mohammed , Aglan Yasser Ibrahim , Hamad Mohamed Hisham Aly , Ebeid Kamal Abdelmonem 
Published: February 2025

Abstract

Background
Acute invasive fungal rhinosinusitis (AIFR) is a life-threatening disease that presents usually in immune-compromised patients with impaired neutrophilic response.

Aim
To study and statistically analyze the epidemiological factors leading to the observed increased incidence of invasive fungal rhinosinusitis in coronavirus disease-19 (COVID-19) diseased patients and identify the prognostic factors that may affect the course and outcome of the disease.

Methods
This case–control study was carried out on 23 patients diagnosed with acute invasive fungal sinusitis patients, patients with positive coronavirus or recently recovered from coronavirus infection admitted to tertiary or secondary centers in El-Gharbia governorate, and 46 participants as a control. The study was focused on the epidemiological predisposing factors that may affect the incidence of the disease.

Results
COVID-19 reporting and data system (CORAD), level of O2 saturation, PH, steroid therapy dose and duration, duration of O2 therapy, and anterior septal deviation were insignificantly different between the two studied groups. Random blood sugar (RBS), neutropenia, and type O2 therapy were significantly different between the two studied groups. Steroid therapy dose and duration were significantly higher in the patients’ group than control group (P < 0.05). In the total number of 23 patients, 16 (69.6%) patients had their middle turbinate as the first site to be affected by the pathology, 3 (13%) patients in the right maxilla, 1 (4.3%) patient in the left maxilla, 2 (8.7%) patients in the right sphenoid sinus, and 1 (4.3%) patient in the hard palate.

Conclusions
The prognostic factors favoring bad prognosis are uncontrolled co-morbidities, high CORAD grade, high grade of fungal invasion, serum neutropenia, the use of ventilators as an O2 delivery method, and medical treatment alone without surgical treatment.
Tenascin-C Potentiates Wnt Signaling in Thyroid Cancer
Authors: Hartmann Heather A , Loberg Matthew A , Xu George J , Schwarzkopf Anna C , Chen Sheau-Chiann , Phifer Courtney J , Caroland Kailey , Chen Hua-Chang , Diaz Diana , Tigue Megan L , Hesterberg Amanda B , Gallant Jean-Nicolas , Shaddy Sophia M , Sheng Quanhu , Netterville James L , Rohde Sarah L , Solórzano Carmen C , Bischoff Lindsay A , Baregamian Naira , Hurley Paula J , Murphy Barbara A , Choe Jennifer H , Huang Eric C , Ye Fei , Lee Ethan , Weiss Vivian L 
Published: February 2025

Abstract
Tenascin-C (TNC) is a secreted extracellular matrix protein that is highly expressed during embryonic development and re-expressed during wound healing, inflammation, and neoplasia. Studies in developmental models suggest that TNC may regulate the Wnt signaling pathway. Our laboratory has shown high levels of Wnt signaling and TNC expression in anaplastic thyroid cancer (ATC), a highly lethal cancer with an abysmal approximately 3- to 5-month median survival. Here, we investigated the role of TNC in facilitating ligand-dependent Wnt signaling in thyroid cancer. We used bulk RNA-sequencing from 3 independent multi-institutional thyroid cancer patient cohorts. TNC expression was spatially localized in patient tumors with RNA in situ hybridization. The role of TNC was investigated in vitro using Wnt reporter assays and in vivo with a NOD.PrkdcscidIl2rg–/− mouse ATC xenograft tumor model. TNC expression was associated with aggressive thyroid cancer behavior, including anaplastic histology, extrathyroidal extension, and metastasis. Spatial localization of TNC in patient tissue demonstrated a dramatic increase in expression within cancer cells along the invasive edge, adjacent to Wnt ligand–producing fibroblasts. TNC expression was also increased in areas of intravascular invasion. In vitro, TNC bound Wnt ligands and potentiated Wnt signaling. Finally, in an ATC mouse model, TNC increased Wnt signaling, tumor burden, invasion, and metastasis. Altogether, TNC potentiated ligand-driven Wnt signaling and promotes cancer cell invasion and metastasis in a mouse model of thyroid cancer. Understanding the role of TNC and its interaction with Wnt ligands could lead to the development of novel biomarkers and targeted therapeutics for thyroid cancer.
Materializing Metafiction: Embedded Media and Embodied Reading in Ruth Ozeki's A Tale for the Time Being
Authors: Manis Karl 
Published: February 2025

Abstract
The term metafiction is widely used to describe fiction that foregrounds its own narrative and linguistic construction. It also has historically specific roots in reflexive postmodernist literary experimentation. This article asks how contemporary metafiction inherits postwar traditions of self-conscious narration within the context of twenty-first-century social and technological mediation. At a time when digital media compels written literature to take stock of its print lineage, this article argues that narrative reflexivity is accompanied by a reflexive materiality: an ethical concern with the material conditions of reading and writing. It examines how Ruth Ozeki's novel A Tale for the Time Being tethers reflexive narration to material media, drawing attention to the collaborative exchanges and fleshly encounters that inflect and animate any act of reading. Told partly through handwritten diary entries and partly through the online searches, emails, and editorial efforts of a fictionalized version of Ozeki, the novel blends multiple modes and media into its depiction of intimately embodied reading practices. At the same time, its depiction of gendered and racialized violence shows how bodies are often read in cruel and undesirable ways. In effect, the novel materializes metafiction, embedding within textual self-awareness an ethical attunement to the materialities that complicate and exceed written inscription. It thereby resists the involuted loops of postmodern linguistic self-reference, instead deploying a feminist insistence that fiction choreographs a constant torsion between discursive structures and fleshly bodies and enticing readers to imaginatively enact fictional meaning in whatever postures are particular to their own bodies.
Myopia as a problem of the modern world. Methods of treatment and prevention
Authors: Szewczyk Marcelina , Ufnal Julia , Rosińska-Lewandoska Dominika , Lewandowska Dominika , Kożuchowska Klaudia , Pilarz Dawid , Morawska Maria , Wolff Anna , Gruszka Szymon , Jarosz Kinga 
Published: February 2025

Introduction and objective
Sight is one of the most important human senses, which enables proper coordination of the entire body. Short-sightedness is increasingly being called the “scourge” of our time. Prognosis in early 2024 predict that people with myopia problems may represent as much as 35% of humanity. In the research, we want to present the possibilities of treating and preventing short-sightedness, collect those that seem most relevant and effective against the background of today's knowledge.

Abbreviated description of the state of knowledge
Short-sightedness (myopia) is a visual defect in which light rays do not focus properly on the retina, but in front of it. Among the methods of treating and slowing down the progression of myopia, we can identify environmental, pharmacological, optical and surgical methods. Intracular lenses and soft contact lenses are the most frequently used forms of correction. However, at high values of the defect, they may not be effective enough. The choice in such situation is hard contact lenses, which are not always well tolerated by patients. Among the methods confirmed by numerous studies of slowing the progression of myopia still include atropine and orthocorrection. More innovative techniques include DIMS lenses, HAL and red light therapy. However, they require more research to confirm their long-term effectiveness and safety.

Summary
In recent years, myopia has become a worldwide problem. Promising results are provided by recent studies on HAL spectacle lenses, DIMS, MiSight contact lenses and RLRL. Thanks to the large number of treatment methods, the doctor can adjust the treatment that seems to be best for the patient. The development of current therapies, as well as an appropriate lifestyle, are important aspects for the treatment of myopia.
Disease trajectory and competing risks of patients with cirrhosis in the US
Authors: Mohammadi Mohsen , Hasjim Bima J. , Balbale Salva N. , Polineni Praneet , Huang Alexander A. , Paukner Mitchell , Banea Therese , Dentici Oriana , Vitello Dominic J. , Obayemi Joy E. , Duarte-Rojo Andrés , Nadig Satish N. , VanWagner Lisa B. , Zhao Lihui , Mehrotra Sanjay , Ladner Daniela P. 
Published: February 2025

Background
Cirrhosis is a dynamic disease process leading to liver-related death, which has increased by over 65% over the last decade. Unpredictable hepatic decompensation complications are a major source of morbidity and mortality. Thus, accurately characterizing disease progression through discrete stages of cirrhosis is critical towards implementing timely intervention and liver transplant (LT) waitlisting.

Methods
A retrospective, longitudinal, population-cohort study of adult patients with cirrhosis from a US metropolitan area (2006–2012) was conducted. Clinical diagnoses were defined by ICD-9 and CPT codes. Cirrhosis stages were defined as: compensated without portal hypertension (Stage 1), compensated with portal hypertension (Stage 2), variceal bleeding (Stage 3), hepatic encephalopathy (Stage 4a), ascites (Stage 4b), and ≥2 different decompensating complications (Stage 5). Multivariate Fine-Gray competing risk survival analysis adjusted for clinicodemographic covariates.

Results
Among 12,196 patients with cirrhosis, the mean (±SD) age was 56.8 (±11.7) years with a follow-up time of 2.35 (±1.81) years. A novel 5-stage disease progression framework was used. The 1-year mortality rates for each stage were 7.3% for Stage 1, 5.4% for Stage 2, 11.4% for Stage 3, 10.0% for Stage 4a, 20.2% for Stage 4b, and 43.8% for Stage 5. Compared to those in Stage 1, Stage 3 (sHR:1.83, 95% CI:1.36–2.48, P<0.001), Stage 4b (sHR:1.45, 95% CI:1.23–1.70, P<0.001), and Stage 5 (sHR:1.95, 95% CI:1.71–2.23, P<0.001) patients had higher risks of mortality. Additional disease progression rates were identified.

Conclusion
Even among patients with compensated cirrhosis, the 1-year mortality rate was as high as 7.3% and subsequently increases with each decompensation complication. This one-year mortality rate is higher than 5-years mortality rate reported in previously known non-US studies. The highest associated risk of death was observed among patients with ≥2 different decompensating complications (95.2%), variceal bleeding (83.2%) and ascites (44.9%). Overall, patients in advanced stages of cirrhosis were more likely to die than they were to receive a LT, suggesting that patients should be referred and waitlisted for LT earlier in the disease process.