bluuebunny/crossref_metadata_2025_split huggingface dataset:
CT based deep learning model for differentiating primary renal sarcomas from large renal cell carcinomas
Authors: Lin Haishan , Li Shurong , Chen Yuhang , Chen Zhenhua , Wei Jinhuan , Liu Jiumin , Guo Yan , Chen Wei , Wang Huanjun , Luo Junhang , Tian Li , Yao Haohua 
Published: June 2024

Abstract

Background
Due to the prognosis and treatment differences between primary renal sarcomas and renal cell carcinoma, preoperative differentiation between them is important but challenging. This study aims to explore and develop a diagnostic method based on computed tomography (CT) and clinical data for preoperatively differentiating primary renal sarcomas from large renal cell carcinomas.
Methods
Patients pathologically diagnosed with primary renal sarcoma from two center between 2009–2021 were retrospectively included, and large renal cell carcinomas were probably 2:1 compared to renal sarcomas as the control group. Clinical data, standard contrast-enhanced CT images and histological findings were obtained. A clinical model was established with independent indicators based on logistic regression analysis. The region of interest was outlined in each three modal CT images (unenhanced phase [UP], corticomedullary phase [CMP] and nephrographic phase [NP]) and formed 7 modal imaging datasets for deep learning models’ development. Reported performance metrics included accuracy and areas under the receiver operating characteristic curves (AUC).
Results
Totally, 27 renal sarcomas and 58 large RCCs were enrolled. Multivariate logistic regression showed that the independent indicators of renal sarcoma were intratumoral artery and Gerota’s fascia invasion (P < 0.05). The AUC of clinical model was 0.77 (95% confidence interval [CI]: 0.67–0.87), sensitivity 0.74, specificity 0.67, positive predictive value 0.51, and negative predictive value 0.85. The deep learning models yielded effective discrimination. The unenhanced phase model yielded AUC = 0.95±0.09 and accuracy (ACC) = 0.94±0.07, and UP + NP model yielded nearly AUC = 0.95±0.06, and ACC = 0.94±0.07.
Conclusion
The deep learning models based on multimodal CT images show good performance for differentiating renal sarcomas from large renal cell carcinomas, which assist in individualized management.
Unravelling the metagenomic landscape of gut microbiota in endangered proboscis monkey across Malaysian Borneo: Conservation and ecological insight
Authors: Mazlan Norfarhana , Seelan Jaya Seelan Sathiya , Chong Yee Ling , Bernard Henry , Azman Wan Nur Syafinaz Wan , Silang Sundai , Zaini Mohamad Kasyfullah , Khan Faisal Ali Anwarali 
Published: June 2024

Abstract

Numerous research on the gut microbial diversity of non-human primates (NHP) has been done to evaluate the impact of environmental changes on the diversity of gut microbiota and to determine the mutualistic relationship between the animals and gut microbes that aid in their adaptation to living in an altered environment. The metagenomics approach was employed to explore gut microbial diversity and abundance in the endangered and endemic proboscis monkeys of Borneo. The amplicon sequencing of the 16S ribosomal RNA (rRNA) gene from 24 faecal samples successfully generated over two million raw reads of bacteria (98%) and archaea (2%) representing 4030 OTUs. Gut microbial diversity and abundance vary across different populations, i.e.: wild, semi-wild and captivity, suggesting that higher diversity was discovered in individuals inhabiting areas with higher food resource availability in natural habitats. The observed alterations in gut microbial diversity and abundance among proboscis monkey populations inhabiting distinct environmental conditions in this study provide empirical evidence for the impact of environmental changes on the proboscis monkey’s gut microbiota. Besides, the prevalence of pathogenic bacteria identified in the proboscis monkey’s gut highlights the potential hazards associated with human-primate interactions and raises the urgent need for public health management. [197 words]
What is True for the Goose, may not be true for the Gander.
Authors: Gosavi Nachiket 
Published: June 2024

Abstract

This essay focuses on the Delhi National Capital Region (NCR) as a case study of a rural-urban mega area. It analyses and compares commuting patterns in the region using digitized district boundaries, transport networks, and commute distances. The study also explores the impact of transport infrastructure and nodes on the economic influence area. In contrast to earlier assumptions, the findings reveal similar commute patterns in rural and urban areas within the NCR. Many individuals seeking wage employment travel distances of less than five kilometre for their daily commute. These short distances can be covered using sustainable modes like walking and cycling. To promote a sustainable mega area, it is crucial to reassess existing policies. Rather than solely focusing on connecting distant areas to an urban core or central business district, priority should be given to local worker circulation and addressing urban-rural disparities in transport planning. Implementing such policies can foster the development of self-sustaining mega areas that promote balanced regional growth. These research findings provide valuable insights for policymakers and urban planners, especially in developing countries facing similar conditions as India, by creating more equitable and resilient regions that support sustainable and balanced growth. They emphasize the importance of considering local commuting patterns and prioritizing sustainable development in shaping the future of transportation and regional growth.
Single-cell transcriptome analysis of low-dose radiotherapy-mediated alleviation of LPS-induced acute lung injury
Authors: Lee Sung Eun , Seo Sang Hoon , Kim Yeon Joo , Kim Yeeun , Cho Junhun , Jeong Jun-Gi , Kim Hyung-Yong , Choi Changhoon , Oh Dongryul 
Published: June 2024

Abstract

Background
Acute lung injury (ALI), a condition with a high incidence and mortality rate worldwide, is a type of acute respiratory failure characterized by infiltrative lesions in the lungs. Low-dose radiation therapy (LDRT), which uses less than 1 Gy X-ray per session, has been tested for its clinical feasibility in suppressing lung inflammation in conditions that cause ALI. However, a mechanistic understanding of how LDRT alleviates inflammation in the lungs and restores balance in the immune environment is still lacking.
Methods
In this study, we assessed the immunomodulatory effects of LDRT using single-cell RNA sequencing (scRNA-seq) and flow cytometry in a lipopolysaccharide (LPS)-induced ALI mouse model.
Results
LDRT with 1 Gy X-rays reduced the lung inflammation, immunostimulatory cells such as M1 macrophages, and pro-inflammatory cytokines such as interleukin 6 in the bronchoalveolar lavage fluid, while increasing the levels of immunosuppressive cells such as M2 macrophages and the anti-inflammatory cytokine TGF-β. Furthermore, scRNA-seq analysis of whole lung tissues confirmed that LDRT reduced the number of macrophages and neutrophils and downregulated the genes involved in inflammatory response pathways. Flow cytometry showed that LDRT effectively eliminated pro-inflammatory immune cells via apoptosis.
Conclusions
Our findings underscore the potential utility of LDRT in ALI treatment by rebalancing immune homeostasis.
Molecular detection of Dengue virus from febrile patient cases in Ghana
Authors: Bonney Joseph Humphrey , Pratt Deborah , Ofori Magdalene , Hayashi Takaya , Awuku-Larbi Yaw , Abankwa Abigail , Kumordjie Selassie , Agbodzi Bright , Salisu Musah , Mante Ama Amankwa , Bour Stella , Eshun Miriam , Amaning Juliana Naa Dedei Acquah , Ketorwoley Prince , Enimil Nancy , Koomson Joel , Stephens Gertrude , Asiedu-Bekoe Franklin , Laryea Dennis , Dadzie Samuel , Suzuki Toshihiko 
Published: June 2024

Abstract

Background
Viral hemorrhagic fevers (VHFs) are any group of viral infectious diseases that interfere with the blood’s ability to clot. Viruses that cause these hemorrhagic fevers are found in a variety of hosts including bats, rodents or arthropods like mosquitoes and ticks. Most VHFs are characterized or identified as outbreaks which makes it difficult to monitor or predict. As a result of the danger these infectious pathogens pose, the Noguchi Memorial institute for Medical Research (NMIMR) as part of its mandate in providing high end molecular and genomic laboratory diagnostics in support of national public health programs runs a test for suspected VHFs collected from health facilities across the country.
Methods
This a cross-sectional study where suspected viral hemorrhagic fever patients were recruited between January 2022 to December 2023. During the period, 2586 suspected serum and plasma samples were transported under cold chain to the NMIMR for testing. These samples were subjected to molecular amplification with the Real time polymerase chain reaction assay for potential VHFs including yellow fever, Ebola/Marburg, Lassa fever and Dengue viruses.
Results
We detected Dengue virus RNA from eight patient samples and subtyped into serotypes 1, 2 and 3 respectively, using the Johnson B. W. et al., 2005 protocol. All DENV cases were resident in the Greater Accra region. Phylogenetic analysis revealed that the DENV-1 strain detected shared similarity with circulating strains in West Africa. Whole genome sequencing was conducted using Illumina Next Generation Sequencing Technology. Using IQ-TREE, a maximum likelihood phylogenetic analysis was carried out.
Conclusion
Until the emergence of recent cases, the circulating subtype has been serotyped Dengue two. With the detection of serotype one, it increases the possibility of multiple infections in individuals and may have worse or increased risk of severe dengue fever. There is therefore the need to intensify surveillance and also to control the mosquito vectors which can transmit these DENV in Ghana.
Neutrophils Aggravate Inflammation and NEC-like Lesions in NEC Intestinal Organoids
Authors: Vincent Deirdre , Heuer Kim , Raluy Laia Pagerols , Hagens Johanna , Kolman Jan , Bunders Madeleine , Wesche Jasmin , Knopf Jasmin , Herrmann Martin , Reinshagen Konrad , Boettcher Michael 
Published: June 2024

Abstract

Necrotizing enterocolitis (NEC) is a leading cause of neonatal death and long-term morbidity, involving complex pathophysiology including prematurity, abnormal bacterial colonization, and ischemia-reperfusion injury, partially mediated by neutrophils. However, development of targeted therapies for NEC is hindered by the limitations of current animal models. Thus, this study aimed to develop a human intestinal organoid model for NEC to investigate its pathophysiology, understand neutrophil involvement, and bridge animal and human research. Organoid cultures were established from human neonatal intestinal samples with NEC (n = 7) and without gut inflammation (controls, n = 7), treated with lipopolysaccharide (LPS), and/or cocultured with neutrophils. Flow cytometry quantified neutrophil survival (PI/Annexin), activation (CD11b/CD66b), and TLR-4 expression, as well as organoid TLR-4 expression and apoptosis markers. NEC status and neutrophil recruitment were analyzed using immunofluorescence. After LPS administration, NEC organoids showed significantly increased TLR-4 expression, intestinal apoptosis markers, and NEC scores compared to controls, with more pronounced differences after neutrophil addition. Neutrophil activation markers were elevated when cocultured with both NEC and control organoids, but TLR-4 expression increased only with NEC organoids. The findings suggest that epithelial cells from NEC patients have a heightened innate TLR-4 expression upon LPS stimulation, potentially contributing to NEC development. LPS stimulation resulted in more pronounced NEC-like lesions in NEC organoids, which was exacerbated by neutrophils. This model demonstrates that neutrophils might contribute to NEC manifestation and maintenance, and that NEC organoids can reflect disease aspects, potentially aiding in the development of targeted therapies.
Fostering Participatory Action Research in Higher Degree Research Settings through a Transdisciplinary Peer-mentoring Collaborative
Authors: Pratt Susanne , Heggart Keith , Christensen Pernille H. , Sankaran Shankar 
Published: June 2024

Abstract

In this paper we take inspiration from Levin’s (2003) provocation “can universities ever become a greenhouse for education in action research?” His assertion that creating action research learning opportunities within universities is possible becomes particularly relevant in the context of a changing Higher Degree Research (HDR) landscape, notably in Australia. The increasing emphasis on industry-focused doctorates and the demand for post-doctoral career pathways beyond academia necessitates a deeper understanding of supporting engaged and impact-oriented research training. To address these challenges, we present a reflexive discussion centred around the HDR Participatory Action Research (PAR) Collaborative—a year-long peer-learning initiative designed to cultivate a community of practice on transdisciplinary participatory research among graduate researchers at the [Institution]. This was conducted as a participatory action research project, with a systems-thinking orientation. We articulate lessons learned around the blockers and enablers for training HDR candidates engaged in participatory research to tackle wicked problems and ways to enhance HDR researcher development in this area, including the prototyping of new peer learning and mentoring approaches. Through aligning with Levin's emphasis on practical and useful knowledge, we highlight the importance of curriculum design for synchronous and asynchronous hybrid delivery, collective peer learning practices, and transdisciplinary orientations to research as crucial factors for success in action research programs within the academic context. By addressing the evolving needs of HDR training and research cultures, our study contributes to the ongoing dialogue on holistic and integrative research approaches and ways to support them within higher education.
A Deep Investigation of the Poorly Studied Open Cluster King 18 Using CCD VRI, Gaia DR3 and 2MASS
Authors: Ahmed Nasser M. , Bendary R. , Samir R. M. , Elhosseiny E. G. 
Published: June 2024

Abstract

In this paper, we re-estimate the astrometric and photometric parameters of the young open star cluster King 18 based on Gaia Data Release 3 (DR3) and 2Mass, then compare them with the results from VRI CCD observations using the f/4.9 Newtonian focus of 74-inch telescope at Kottamia Astronomical Observatory (KAO) in Egypt. King 18 is a poorly studied open star cluster, for which new results are found in the current study. In order to estimate the membership and determine all the astrophysical parameters of the cluster, we use data from Gaia DR3 and KAO. The center, cluster radius, radial density distribution, color-magnitude diagrams, distance, age, and reddening of King 18 are calculated. Also, the luminosity and mass functions, the total mass and the relaxation time of the cluster are estimated.
The slope value of the mass function of King 18 is found to be 2.27± 0.17, comparable with Salpeter value. Our estimates for the average cluster age and the relaxation time are 224 ± 6.3 and 28.92 Myrs, respectively. This indicates that the King 18 is dynamically stable and a relaxed cluster. The cluster distance modulus from Gaia, 2Mass and VRI observation has been determined to be 12.38±1.32, 12.32 ±0.107 and 12.28 ±0.29 mag respectively. This results are in good agreement within the error. Moreover the color excesses E(V-I), E(J-K s) and E(G BP-G RP) are 0.85±0.087, 0.38±0.091 and 0.98 ± 0.13 respectively. Finally, the proper motions (µ α cosδ , µ δ), and parallaxes ϖ are-2.603 ± 0.018,-2.106 ± 0.013 and 0.324 ± 0.04 respectively.
Should the one-stage hepatectomy be performed for hepatitis B virus-related hepatocellular carcinoma patients with liver fibrosis or cirrhosis when the RLV/SLV is between 30% to 40%?
Authors: Gao Junping , Yang Haojie , Lu Zhan , Zhan Guohua , Huang Juntao , Gong Wenfeng , xiang bangde 
Published: June 2024

Abstract

Background
Currently, it is known whether associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) or one-stage hepatectomy (OSH) be applied as a treatment for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients with liver fibrosis or cirrhosis when the remnant liver volume (RLV) to standard liver volume (SLV) ratio is between 30–40% and the liver function is normal.
Methods
In this study, consecutive HBV-related HCC patients with liver fibrosis or cirrhosis who underwent right hepatectomy, with RLV/SLV between 30–40% and normal liver function (Child-pugh A and ICG-R15 < 10%) were enrolled from November 2014 to November 2022. The clinical datas of patients were recorded. Primary endpoints was post-hepatectomy liver failure (PHLF), while secondary endpoints were severe complication and mortality. The postoperative datas of patients were compared between OSH group and ALPPS group.
Results
Forty-two patients who underwent OSH were enrolled in our study. No significant difference was obtained in the incidence of PHLF between the OSH group (59.5%) and the ALPPS group (52.3%) (P = 0.411). The mortality within 90 days of the OSH group (0%) post-surgery was significantly lower compared with that of the ALPPS group (13.2%) (P = 0.006). Moreover, there was no significant difference in the incidence of severe complication (Clavien-Dindo classification ≥Ⅲa) between the OSH group (26.2%) and the ALPPS group (36.8%) (P = 0.199).
Conclusion
OSH may be an effective treatment option for patients with liver fibrosis or cirrhosis when the RLV/SLV is between 30–40% with normal liver function (Child-pugh A and ICG-R15 < 10%).
Cerebral small vessel disease may not critically influence familial Parkinson’s disease
Authors: Marhat Bigyan , Bimala Malla , Foddis Marco , Holtgrewe Manuel , Beule Dieter , Bras Jose , Guerreiro Rita , Kola Vasilis , Schmitt Hans-Michael , Endres Matthias , Sassi Celeste 
Published: June 2024

Abstract

Familial Parkinson’s disease (PD) and vascular parkinsonism (VP) overlap in their clinical, neuroradiologic and neuropathologic features. To investigate whether PD and VP may share a pathogenic link, we used the modified Scheltens scale and assessed the classic neuroradiological features of cerebral small vessel disease in the axial T2 MRI flair sequences in a cohort of 58 familial PD patients, 46 familial PD prodromal patients and 48 age-matched controls from the PPMI publicly available database. We next examined the protein coding variability in the main PD-causing genes and genetic risk factors in a cohort of 96 patients with familial cerebral small vessel disease (cSVD) and 243 elderly healthy individuals from the HEX database. Patients with familial and prodromal PD have a moderate but still significant burden of superficial white matter hyperintensities compared to age-matched controls (Wilcox Test p-value = 4.335e-07, OR = 4.1, 95% CI = 1.8–9.23), with moderate motor impairment and minimal and non-pathological cognitive decline (UPDRS and MoCa up to 25 and 26,respectively). In contrast, 100% of patients carrying SNCA p.A53T and 25% of patients carrying LRRK2 p.G2019S, p.R1441C or GBA p.N409S, p.E365K and p.L483P had moderate to very severe dementia (average MoCa Score = 21) and mild motor impairment (mean UPDRS III score = 20) and only very modest white matter lesions. Finally, we report no known pathogenic coding variant in the PD genes studied in cSVD patients. Our study shows that familial PD and small vessel disease likely have distinct not necessarily mutually exclusive, pathogenic mechanisms.
Telehealth to increase healthcare access; perspectives of people who use drugs
Authors: Papalamprakopoulou Zoi , Ntagianta Elisavet , Triantafyllou Vasiliki , Kalamitsis George , Dharia Arpan , Dickerson Suzanne S. , Hatzakis Angelos , Talal Andrew H. 
Published: June 2024

Abstract

Background: People who use drugs (PWUD) often face restricted healthcare access despite their heightened healthcare needs. Factors such as stigma, mistrust of the healthcare system, competing priorities, and geographical barriers pose significant challenges to accessing healthcare services for PWUD. Telehealth offers an innovative solution to expand healthcare access for better inclusion of underserved populations in healthcare. We aimed to explore PWUDs’ perceptions of telehealth as a healthcare delivery modality.
Methods: We utilized purposive sampling to recruit participants (N = 57) for nine focus group discussions (FGDs) in Athens, Greece. Eligibility criteria required participants to be at least 18 years old, with a history of injection drug use, and current internet access. The FGDs followed a semi-structured interview guide, were audio recorded, transcribed verbatim, translated into English, and de-identified. We applied thematic analysis to analyze FGD transcripts.
Results: Participants’ mean (standard deviation) age was 47.9 (8.9) years, 89.5% (51/57) were male, 91.2% (52/57) were of Greek origin, and 61.4% (35/57) had attended at least 10 years of school. Three main themes emerged from the FGDs: (1) high internet utilization for healthcare-related purposes among PWUD, (2) highlighting telehealth benefits despite access obstacles and PWUDs’ concerns about diagnostic accuracy, and (3) approaches to overcome access obstacles and build digital trust. Participants extensively used the internet for healthcare-related processes such as accessing healthcare information and scheduling provider appointments. Despite being telehealth-inexperienced, most participants expressed a strong willingness to embrace telehealth due to its perceived convenience, time-saving nature, and trusted digital environment. Some participants perceived the inability to conduct a physical examination during telehealth encounters as limiting its diagnostic accuracy, while others expressed concerns about digital literacy and technological infrastructure accessibility. To build trust in telehealth and promote patient-centeredness, participants recommended an initial in-person visit, virtual eye contact during telehealth encounters, patient education, and partnerships with PWUD-supportive community organizations equipped with appropriate infrastructure.
Conclusions: PWUD frequently use the internet for health-related purposes and suggested several approaches to enhance virtual trust. Their insights and suggestions are practical guidance for policymakers seeking to enhance healthcare access for underserved populations through telehealth.
Clintrials.gov registration number: NCT05794984