bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 896: Predicting metastatic transcriptomes of patient tumors with deep learning
Authors: Li Gang , Béal Evan , Sumner Dean , Galli Giorgio G. , Cremasco Viviana , Korn Joshua M. , Dondelinger Frank , Ruddy David , Kauffmann Audrey , Dimitrieva Slavica 
Published: March 2024

Abstract
Metastases are the primary cause of cancer-related death, and improving the means of predicting and targeting their development is one of the major goals in cancer research. While surgical resection and neo-adjuvant therapy can cure well-confined primary tumors, our ability to effectively treat cancer is largely dependent on our capacity to interdict the process of metastasis. The recent accumulation of ‘omics data from metastatic tumors provides an unprecedented opportunity to develop machine learning models to predict the molecular changes during metastasis and explore the patterns of metastasis formation. With this in mind, we developed MetMapper, a deep learning model trained on primary and metastatic tumors from &gt; 13 000 patients integrating data from 11 published data resources. MetMapper can predict the transcriptomic changes of a primary tumor when it metastasizes to different distant organs. The results were extensively validated using transcriptomics data from matched primary and metastatic tumor biopsies extracted from the same patients. Furthermore, MetMapper’s predictions revealed that the non-random patterns of cancer metastases can be partly explained by the degree of transcriptome reprogramming needed during metastasis: primary tumors tend to metastasize to organs that require minimal changes to their transcriptomes. Using MetMapper, we derived a metastatic potential score for patient tumors and demonstrate that this score can be used to stratify patients into high and low survival groups across different indications. The predicted metastatic potential of patient tumors significantly correlates with experimentally characterized metastatic potential of cancer cell lines. Additionally, by performing in-silico perturbations of genes and oncogenic pathways that can alter the metastatic potential of patient tumors, we identified genomic features that are highly associated with metastases to specific organs, some of which were reported by existing pan-cancer clinical sequencing studies. Our results demonstrate the utility of MetMapper as a novel AI-powered methodology for investigating mechanisms and patterns of metastatic dissemination, as well as forecasting metastatic outcomes of patient tumors.
Citation Format: Gang Li, Evan Béal, Dean Sumner, Giorgio G. Galli, Viviana Cremasco, Joshua M. Korn, Frank Dondelinger, David Ruddy, Audrey Kauffmann, Slavica Dimitrieva. Predicting metastatic transcriptomes of patient tumors with deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 896.
Abstract 928: Real-world comparison of first-line treatments for metastatic clear cell renal cell carcinoma (mccRCC)
Authors: Yazdanpanah Omid , Dwabe Sami , Harada Garrett , Seyedin Steven , Mar Nataliya 
Published: March 2024

Abstract
Multiple regimens are available for management of mccRCC including either immuno-oncology doublet (IO/IO) or combinations of IO and tyrosine kinase inhibitors (TKI). Clinical trials have compared these regimens to sunitinib, with no direct comparison between them. As such, there is ambiguity among physicians about preferred first-line for mccRCC. We performed a single-institution retrospective study of adults treated in first-line for mccRCC between 1/1/2017 and 1/1/2023. Regimens included IO/IO (ipilimumab/nivolumab [I/N]) or IO/TKI (pembrolizumab/axitinib [P/A], nivolumab/cabozantinib [N/C], or pembrolizumab/lenvatinib [P/L]). We compared efficacy and toxicity endpoints, using Kruskal-Wallis test for medians and Chi-square for categorical variables. 42 patients with median age of 61 (range: 36-95) were included. Patient distribution in IO/IO vs IO/TKI group was 20.0% vs 30.8% in International Metastatic Database Consortium (IMDC) favorable risk, 46.7% vs 38.5% in intermediate-risk, and 33.3% vs 30.8% in poor-risk group. 78.6% vs 66.6% of patients had WHO grade 3/4 ccRCC, 18.8% vs 15.4% had sarcomatoid features in the IO/IO vs IO/TKI, respectively. 38% (16/42) received I/N, 7% (3/42) N/C, 52% (22/42) P/A, and 2% (1/42) P/L. Median follow-up was 109 weeks. Table-1 compares the efficacy of IO/IO vs IO/TKI. IO-related toxicity, TKI-related toxicity, treatment interruptions, dose reductions, and need for steroids were not significantly different between IO/IO and IO/TKI (p= 0.240, p=0.372, p=0.923, p=1.00, and p=0.248, respectively). Genomic characteristics will be reported in poster.
Despite small sample size, our real-world data showed that patients treated with IO/IO had significantly worse outcomes compared to those treated with IO/TKI. While this difference may stem from a more aggressive disease in IO/IO group but further insights needs to be obtained through future prospective studies comparing IO/IO and IO/TKI regimens.
Variable IO/IO IO/TKI p-value Median treatment duration (weeks) 8.3 59.4 &lt;0.001 Disease control rate (complete response + partial response + stable disease) (%) 50.0 91.7 0.024 Time from 1st line to 2nd line therapy (weeks) 14.6 57.1 0.001 Median overall survival (weeks) 63.6 Not reached 0.001
Citation Format: Omid Yazdanpanah, Sami Dwabe, Garrett Harada, Steven Seyedin, Nataliya Mar. Real-world comparison of first-line treatments for metastatic clear cell renal cell carcinoma (mccRCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 928.
Immersive and Interactive 3D Visualization of Large-Scale Geoscientific Data
Authors: Flatken Markus , Schneegans Simon , Fellegara Riccardo , Gerndt Andreas 
Published: March 2024

Abstract
Virtual reality (VR) technology has great potential in supporting planetary scientists and the field of geosciences by offering immersive and interactive experiences for data exploration and analysis. This paper shows the opportunities presented by the use of VR technology in the geosciences domain while also identifying the open challenges associated with this integration. Our focus is on highlighting the several benefits that VR brings, including stereo vision, head tracking, and collaborative capabilities. These features can foster knowledge exchange and interdisciplinary research. Nevertheless, the adoption of VR presents certain challenges that need to be addressed. These include maintaining high refresh rates, handling large heterogeneous datasets, and striking a balance between visualization fidelity and performance. Fortunately, significant advancements have been made in high-performance data analysis, progressive data streaming, and real-time visualization, enabling interactive exploration of large-scale datasets within VR environments. To support a broader adoption among domain experts, we propose a visualization approach that scales both with display and with data size. As such, the system can be used to interactively explore large-scale datasets in immersive environments like CAVEs or powerwalls, on HMDs, or on traditional desktop setups. This approach allows for seamless transitions between desktop and VR experiences, leveraging immersive environments for collaboration and outreach activities. In this paper, we present an architectural framework, hardware environments, use cases, lessons learned, and the future potential of VR in this field. Through this scalable system, we anticipate transformative advancements in scientific exploration, collaboration, and knowledge dissemination.
Newly Found South Slavic Manuscripts of the Fourteenth and Fifteenth Centuries with the Pseudo-Athanasian Questions and Answers to Antiochus the Duke
Authors: Gritsevskaya Irina M. , Lytvynenko Viacheslav V. 
Published: March 2024

Abstract
This paper addresses the problem of an insufficient base of manuscript material for the study of the Slavonic translation of the Pseudo-Athanasian Questions and Answers to Antiochus the Duke (QAD). It begins with a brief survey of the two existing approaches to identifying the main groups of manuscripts and versions of the text (Lara Sels and William R. Veder) and alerts researchers to the fact that the number of examined witnesses today is too small to establish the real textual tradition of QAD. In the second part of the article, the authors present three newly found manuscripts as a way of partly responding to this problem and also suggest a new way of grouping them with those that have been previously studied.
Loanwords in Basic Vocabulary as an Indicator of Borrowing Profiles
Authors: de Heer Mervi , Blokland Rogier , Dunn Michael , Vesakoski Outi 
Published: March 2024

Abstract
Loanwords carry information on linguistic interactions, and can also reveal (pre-)historical population contacts. The contact history of a particular language family is an essential component of historical linguistics, but it is also illuminating for integrative studies of the human past. However, data availability and the time-consuming nature of etymology mean that comprehensive research on loanword layers exists for relatively few languages, forcing us to rely on limited material for others. This paper compares the loanword layers in the basic and total vocabulary of six well-studied Uralic languages, assessing how accurately the borrowing profile in basic vocabulary reflects the full profile of a language. We define “borrowing profile” as the known contact history of a language reflected by its loanword layers. We demonstrate that the loanword layers in basic vocabulary provide an adequate cross-section of the full borrowing profile, although basic vocabulary manifests prehistoric contacts more strongly than more recent contacts.
Diabetes in Trauma Patients: A Potential Gateway to a Medical Home
Authors: Hart Kaylee , Thames Margaret A. , Massey Ashley Caroline , Capasso Thomas , Lee Yannlei L. , Mbaka Maryann , Kinnard Christopher M. , Bright Andrew C. , Williams Ashley Y. , Polite Nathan M. , Simmons Jon D. , Butts C. Caleb 
Published: March 2024

Background Diabetes is a major determinant of health outcomes. Trauma patients are disproportionately from lower socioeconomic status, where lack of access to health care prevents timely treatment. Trauma centers could play a role in identifying patients in need of improved glucose management, but the current burden of disease is not known. We assessed the incidence of patients in need of intervention that presented to a level 1 trauma center over a 6-month period. Methods A retrospective chart review over 6 months of all trauma patients admitted to a level 1 trauma center was performed. Patients’ past medical history (PMH), medication reconciliation, and hemoglobin A1c (HbA1c) were recorded on initial assessment; patients <18 years old, lacking an HbA1c, or missing PMH were excluded. Patients with PMH of diabetes or antihyperglycemic use were classified by HbA1c: well-controlled ≤8.0% or poorly controlled >8.0%. Patients with no history of diabetes or antihyperglycemic use were classified based on their HbA1c: non-diabetic <5.7%, pre-diabetic 5.7-6.4%, and undiagnosed diabetic ≥6.5%. Results Overall, 1377 patients were identified. After exclusion criteria, 903 patients were classified as follows: 593 (66%) non-diabetics, 160 (18%) pre-diabetics, and 150 (17%) diabetics. Fifteen diabetics were undiagnosed; 39 of the diagnosed diabetics were poorly controlled. Including pre-diabetics, a total of 214 (24%) trauma patients were in need of improved glycemic control. Discussion One in four trauma patients would benefit from improved outpatient glycemic management, representing a missed opportunity for preventative health care. Trauma centers should develop strategies to meet this need as part of their post-discharge care.
Weight-Based Dosing for Low-Molecular-Weight Heparin (Enoxaparin) Administration to Achieve Optimal VTE Prophylaxis in Trauma Patients
Authors: Thind Tarendeep , Heye Thomas , Henson Curran , Reif Rebecca , Jensen Hanna K. , Kalkwarf Kyle J. , Bhavaraju Avi , Robertson Ronald , Jenkins Allison 
Published: March 2024

Introduction Patients admitted after traumatic injuries are at high risk for developing venous thromboembolism (VTE). Low-molecular-weight heparin (LMWH) is commonly used to prevent VTE in this patient population; however, the optimal dosing strategy has yet to be determined. To address this question, a fixed-dosing strategy of LMWH was compared to a weight-based dosing strategy of LMWH for VTE prophylaxis. Methods A retrospective, pre-post implementation cohort study compared a fixed vs a weight-based dosing strategy of LMWH for VTE prophylaxis. Patients admitted to our level 1 trauma center were included if they had an estimated glomerular filtration rate >30 mL/min/1.73 m2, received at least 3 doses of LMWH, and had an appropriately drawn anti-Xa level on their initial dosing regimen. Patients in the pre-cohort received 30 mg LMWH subcutaneously twice daily as the initial dosing regimen. Patients in the post-cohort received .5 mg/kg (max 60 mg) LMWH subcutaneously every 12 h as the initial dosing regimen. A goal anti-Xa of .2-.4 IU/mL was targeted for prophylaxis. Results There were 817 patients in the fixed-dosing group (FDG) and 874 patients in the weight-based dosing group (WBDG). In the FDG, 42.8% of the patients achieved the goal initial anti-Xa level, with 54.1% and 3.1% reaching sub- and supratherapeutic doses, respectively. In the WBDG, 66.5% of patients reached goal initial anti-Xa levels, with 23.5% and 10.1% at sub- and supratherapeutic levels. The distribution of dose ranges was significantly different between the dosing strategies ( P-value <.001). There was no difference in the number of patients who received blood products (39.1% vs 41.7%. P-value = .299). Conclusions In our study, weight-based dosing of LMWH yielded a significantly higher proportion of patients who achieved goal prophylactic anti-Xa levels than fixed-dosing of LMWH. Larger-scale studies are needed to assess the risk of VTE events and bleeding with these dosing strategies.
Opioid Use in Pelvic Fractures: The Impact of Opioid Prescribing Laws in Pennsylvania
Authors: Villa Nicole Ann E. , Shum Kristina , Atkinson Allison , Ong Adrian , Muller Alison , Espiridion Eduardo 
Published: March 2024

Pennsylvania’s Prescription Drug Monitoring Program (PDMP) was established in 2016, but its impact on opioid use for pelvic fractures is understudied. We compared opioid use in 277 pelvic fracture cases between two periods: 2015-2017 (T1) and 2018-2020 (T2). Outcomes included daily inpatient morphine milligram equivalents (MME), long-term opioid use (LOU) 60-90 days post-discharge, and intermediate-term opioid use (IOU) 30-60 days post-discharge. T1 and T2 had comparable baseline characteristics. T2 was associated with a decrease in average daily inpatient MME (58.6 vs 78.5, P = .02), particularly in younger patients. Regression analyses showed age and Injury Severity Score (ISS) were significant predictors for daily inpatient MME, while time period was not. Geriatric patients in T2 had significantly decreased IOU (30% vs 9%, P = .05). Pelvic fracture type and daily MME predicted IOU, while pelvic fracture type predicted LOU. This study suggests a modest impact of these laws, but further study is needed.
Urbanisation and Economic Growth: Some Insights from the Himalayan State of Sikkim
Authors: Singha Komol , Sherpa Lakpa Doma , Jaman Md. Samsur 
Published: March 2024

Sikkim has experienced rapid urbanisation and industrialisation, particularly since the implementation of the North East Industrial and Investment Promotion Policy in 2007 (NEIIPP 2007). Though urbanisation and economic growth are inextricably linked, previous research findings on their causal relationships appear to be contradictory. Increased urbanisation/industrialisation seemed to enrage the Sikkimese, not because of revenue generation or environmental concerns, but because of their disproportionate share of employment opportunities in comparison to outsiders. Using secondary data, this article investigated two critical research questions: (a) Whether urbanisation is a result of or a cause of economic growth; and (b) Has Sikkim’s industrialisation, largely fuelled by the NEIIPP 2007, benefited locals? The causality test revealed a unidirectional relationship between the two, with urbanisation causing economic growth. Despite attracting migrant labour, Sikkim’s increased industrialisation/urbanisation has significantly reduced poverty and unemployment. JEL Codes: H20, L59, O10, O15, O25, R23
Association of iron overload with infectious complications in liver transplant recipients: a systematic review and meta-analysis
Authors: Zhang Jingpo , Yan Bingzheng , Shi Xin 
Published: March 2024

Objective This study was performed to examine the possible association of iron overload with infectious complications and survival among liver transplant recipients. Methods We conducted a systematic review and meta-analysis of studies published in the PubMed, Embase, Web of Science, and Cochrane Library databases up to September 2022. Hazard ratios (HRs) and 95% confidence intervals (CIs) were extracted to estimate the association of iron overload with infectious outcomes and overall survival after liver transplantation. Results Eight studies involving 2817 recipients met the inclusion criteria. Iron overload was strongly associated with an increased risk of infection after liver transplantation (HR, 1.66; 95% CI, 1.03–2.68). An increase in the serum ferritin level was associated with an increased risk of infection after liver transplantation (HR, 1.44; 95% CI, 1.09–1.91). Iron overload was a significant predictor of worse overall survival (HR, 1.35; 95% CI, 1.11–1.64). In addition, a high serum ferritin level was significantly associated with an increased risk of death (HR, 1.34; 95% CI, 1.10–1.64). Conclusion Iron overload may be associated with a higher risk of infectious complications and a worse prognosis among liver transplant recipients.
Bone involvement in the early stages of Parkinson’s disease: a case–control study
Authors: Liguori Sara , Moretti Antimo , Paoletta Marco , Gargiulo Fiorinda , Barra Giuseppe , Gimigliano Francesca , Iolascon Giovanni 
Published: March 2024

Objective To evaluate the qualitative and quantitative alterations of bone tissue in patients with early-stage Parkinson’s disease (PD) and to measure the associations between bone mineral density (BMD), trabecular bone score (TBS) and physical performance. Methods This case–control study enrolled patients with early-stage PD and age-matched controls. BMDs for the left femoral neck (L-FN) and lumbar spine (LS) were measured. Bone microarchitecture for the LS was determined using TBS. Muscle performance was assessed using the short physical performance battery (SPPB). Patients and controls were stratified in two groups based on the SPPB score: a poor performance group (SPPB score ≤8) and high performance group (SPPB > 8). Results This study included 26 patients: 13 in the PD group and 13 age-matched controls. The mean ± SD BMD results in the PD group were: L1–L4 BMD = 0.935 ± 0.183 g/cm2; L-FN BMD = 0.825 ± 0.037 g/cm2; with bone microarchitecture degraded in four patients and partially degraded in three patients. TBS was significantly different in the patients with PD stratified according to SPPB. Among the controls, there was a significant difference in body mass index between the two SPPB groups. Conclusion TBS might identify bone involvement earlier than BMD in the initial stages of PD.
Triclosan, an antimicrobial drug, induced reproductive impairment in the freshwater fish, Anabas testudineus (Bloch, 1792)
Authors: Chokki Veettil Priyatha , Nikarthil Sidhick Jeena , Kavungal Abdulkhader Sajeela , MS Siva Prasad , Kumari Chidambaran Chitra 
Published: March 2024

Triclosan (TCS), an antimicrobial drug, is known to occupy different compartments in aquatic ecosystems. The present study focused to evaluate the reproductive toxicity of triclosan, at environmentally relevant (0.009 and 9 μg L−1) and sublethal (176.7 μg L−1) concentrations for 90 days in the pre-spawning phase of the fish, Anabas testudineus. The reproductive biomarkers, namely, gonadal steroidogenic enzymes, expression of aromatic genes, levels of serum gonadotropins, sex hormones, and histology of gonads were analyzed. The weight of the animal, brain weights along with gonadosomatic index decreased while mucus deposition increased significantly at all concentrations of triclosan as the primary defensive mechanism to prevent the entry of toxicants. Triclosan disrupted gonadal steroidogenesis as evidenced by a reduction in the activities of gonadal steroidogenic enzymes. The expressions of cyp19a1a and cyp19a1b genes were up-regulated in the brain of both sexes and testis, while down-regulated in the ovary indicating estrogenic effects of the compound. The endocrine-disrupting effects of triclosan were confirmed. The current results suggest that chronic exposure to triclosan altered reproductive endpoints thereby impairing normal reproductive functions in fish.
Pilot Study to Assess the Effectiveness of the Sustainable Culturally Adaptive Nutrition Program (SCAN) to Improve Adherence to the National Diabetes Prevention Program
Authors: Perkison William B. , Fwelo Pierre , Velasco-Huerta Fernanda , Heredia Natalia I. , Yang James J. , Beg Sidra S. , Reininger Belinda M. , Rodriguez Serena A. , Almohamad Maha , Pulicken Catherine , Garza Ella , White Grace E. , Fernandez Maria E. 
Published: March 2024

Purpose The Sustainable Culturally Adapted Nutrition Program (SCAN) is a novel adaptation to the National Diabetes Prevention Program (NDPP) that aims to improve attendance and effectiveness. This paper presents its feasibility and impact through the initial 6-month outcomes. Design A pragmatic quasi-experimental pilot study with intervention (DPP plus SCAN) and control (DPP only) groups. Samples and Inclusion Criteria Sustainable Culturally Adapted Nutrition Program participants were recruited from federally qualified health center (FQHC) clinic patients enrolled in a NDPP in Houston, Texas. Participants needed to be (1) ≥18 years old, (2) body mass index >25, (3) no prior diagnosis of diabetes, and (4) not pregnant. Intervention Sustainable Culturally Adapted Nutrition Program cooking classes were designed to teach skills to prepare fresh produce, and utilized Motivational Interviewing (MI) techniques to encourage participants to adapt these skills for foods that were culturally important to them. Outcome Measures (1) National Diabetes Prevention Program attendance, (2) BMI and (3) percent weight loss. Analysis We used linear mixed models to test the association between weights and NDPP attendance. Results 22 intervention and 15 control participants completed the program to the 6-month point. Intervention participants had increased DPP attendance over controls (7.14 vs 6.87 session). Intervention participants also demonstrated on average, 1.5% weight loss for each additional SCAN class attended ( P = .144). Conclusions The SCAN adaptation shows promising results for effectively increasing both NDPP attendance and weight loss.