bluuebunny/crossref_metadata_2025_split huggingface dataset:
CPclus: Candecomp/Parafac Clustering Model for Three-Way Data
Authors: Vicari Donatella , Giordani Paolo 
Published: June 2023

AbstractA novel clustering model, CPclus, for three-way data concerning a set of objects on which variables are measured by different subjects is proposed. The main aim of the proposal is to simultaneously summarize the objects through clusters and both variables and subjects through components. The object clusters are found by adopting a K-means-based strategy where the centroids are reduced according to the Candecomp/Parafac model in order to exploit the three-way structure of the data. The clustering process is carried out in order to reveal between-cluster differences in mean. Least-squares fitting is performed by using an iterative alternating least-squares algorithm. Model selection is addressed by considering an elbow-based method. An extensive simulation study and some real-life applications show the effectiveness of the proposal, also in comparison with its potential competitors.
Changes in atmospheric moisture transport over tropical South America: an analysis under a climate change scenario
Authors: Arias Paola A. , Rendón Maria Lizeth , Martínez J. Alejandro , Allan Richard P. 
Published: June 2023

AbstractWarming induced by increased greenhouse gas emissions is intensifying the global water cycle and increasing the water vapor content of the global atmosphere. However, there is a lack of scientific literature assessing how regional atmospheric moisture transport and recycling will change in a warming climate. This work analyzes the projections of atmospheric moisture transport and recycling over tropical South America by the end of the twenty-first century (2070–2100) under a climate change scenario (RCP8.5). We used the Dynamic Recycling Model to estimate atmospheric moisture contributions to the region considering input data from the European Centre for Medium-Range Weather Forecasts ERA5 reanalysis and 11 models included in the Fifth Phase of the Coupled Model Intercomparison Project. Projected increases of precipitable water in tropical South America are linked with increased evaporation from the oceans. However, those projections also indicate (1) reductions in the precipitation contributed by the main atmospheric moisture sources to the continental regions of tropical South America, (2) reductions of total precipitation, and (3) reductions of recycled precipitation over the region. The largest reductions of precipitation recycling are projected over the southern Amazon during the dry-to-wet transition season (about 31%) and the northern Amazon during its dry season (about 25%). This is particularly relevant since the southern Amazon has experienced the occurrence of longer dry seasons during the recent decades and has been highlighted as a hotspot of climate change.
Validation of the Subjective Spine Value: A new single item score for the assessment of spine-specific function
Authors: Leopold Vincent J. , Warminski Nikolas , Löchel Jannis , Labbus Kirsten , Pumberger Matthias , Zahn Robert K. 
Published: June 2023

Abstract
Background
Spinal function can be assessed through different patient reported outcome measures (PROMs). Purpose: The aim of the present study was to evaluate a novel single-item score for the assessment of spinal function: The Subjective Spine Value (SSpV). It was hypothesized that the SSpV correlates with the established scores Oswestry disability index (ODI) and Core Outcome Measures Index (COMI).

Methods
Between 08/2020 and 11/2021 151 consecutive patients were prospectively enrolled and completed a questionnaire with the ODI, COMI as well as the SSpV. Patients were divided into 4 groups depending on their specific pathology (Group 1: Degenerative pathologies, Group 2: Tumor, Group 3: Inflammatory / Infection, Group 4: Trauma). Pearson correlation coefficient was used to evaluate correlation between the SSpV and the ODI and COMI separately. Floor and ceiling effects were evaluated.

Results
Overall, the SSpV correlated significantly with both ODI (p =  < 0.001; r = − 0.640) and COMI (p =  < 0.001; r = − 0.640). This was also observed across all investigated groups (range − 0.420–0.736). No relevant floor or ceiling effects were noticed.

Conclusions
The SSpV is a valid single-item score for the assessment of spinal function. The SSpV offers a useful tool to efficiently assess spinal function in a variety of spinal pathologies.

Level of evidence
I, prospective cohort study.
Multiple Correspondence Analysis and HLA-Associations of Organ Involvement in a Large Cohort of African-American and European-American Patients with Sarcoidosis
Authors: Rasmussen Astrid , Dawkins Bryan A. , Li Chuang , Pezant Nathan , Levin Albert M. , Rybicki Benjamin A. , Iannuzzi Michael C. , Montgomery Courtney G. 
Published: June 2023

AbstractSarcoidosis is a systemic granulomatous disease with predominant pulmonary involvement and vast heterogeneity of clinical manifestations and disease outcomes. African American (AA) patients suffer greater morbidity and mortality. Using Multiple Correspondence Analysis, we identified seven clusters of organ involvement in European American (EA; n = 385) patients which were similar to those previously described in a Pan-European (GenPhenReSa) and a Spanish cohort (SARCOGEAS). In contrast, AA (n = 987) had six, less well-defined and overlapping clusters with little similarity to the cluster identified in the EA cohort evaluated at the same U.S. institutions. Association of cluster membership with two-digit HLA-DRB1 alleles demonstrated ancestry-specific patterns of association and replicated known HLA effects.These results further support the notion that genetically influenced immune risk profiles, which differ based on ancestry, play a role in phenotypic heterogeneity. Dissecting such risk profiles will move us closer to personalized medicine for this complex disease.
Neurological update: non-motor symptoms in atypical parkinsonian syndromes
Authors: Ananthavarathan Piriyankan , Patel B. , Peeros S. , Obrocki R. , Malek N. 
Published: June 2023

AbstractAmong people with Parkinson’s disease (PD), non-motor symptoms (NMS) are a well-recognised cause of significant morbidity and poor quality of life. Yet, it is only more recently that NMS have been recognised to affect the lives of patients with atypical parkinsonian syndromes in a similar fashion. The aim of this article is to highlight and compare the relative prevalence of NMS among patients with atypical parkinsonian syndromes in the published literature, which largely remain underreported and unaddressed in routine clinical practice. All NMS that are recognised to occur in PD are also found to commonly occur in atypical parkinsonian syndromes. In particular, excessive daytime sleepiness is more prevalent among atypical parkinsonian syndromes (94.3%) compared to PD (33.9%) or normal controls (10.5%) (p < 0.001). Urinary dysfunction (not limited to urinary incontinence) is not only found to occur in MSA (79.7%) and PD (79.9%), but has also been reported in nearly half of the patients with PSP (49.3%), DLB (42%) and CBD (53.8%) (p < 0.001). Apathy is significantly more common among the atypical parkinsonian syndromes [PSP (56%), MSA (48%), DLB (44%), CBD (43%)] compared to PD (35%) (p = 0.029). Early recognition and addressing of NMS among atypical parkinsonian syndromes may help improve the holistic patient care provided and may encompass a range of conservative and pharmacotherapeutic treatments to address these symptoms.
Hospital-to-home transitions for children with medical complexity: part 1, a systematic review of reported outcomes
Authors: de Lange Annemieke , Alsem Mattijs W. , Haspels Heleen N. , van Karnebeek Clara D. M. , van Woensel Job B. M. , Etten–Jamaludin Faridi S. , Maaskant Jolanda M. 
Published: June 2023

AbstractOutcome selection to evaluate interventions to support a successful transition from hospital to home of children with medical complexity (CMC) may be difficult due to the variety in available outcomes. To support researchers in outcome selection, this systematic review aimed to summarize and categorize outcomes currently reported in publications evaluating the effectiveness of hospital-to-home transitional care interventions for CMC. We searched the following databases: Medline, Embase, Cochrane library, CINAHL, PsychInfo, and Web of Science for studies published between 1 January 2010 and 15 March 2023. Two reviewers independently screened the articles and extracted the data with a focus on the outcomes. Our research group extensively discussed the outcome list to identify those with similar definitions, wording or meaning. Consensus meetings were organized to discuss disagreements, and to summarize and categorize the data. We identified 50 studies that reported in total 172 outcomes. Consensus was reached on 25 unique outcomes that were assigned to six outcome domains: mortality and survival, physical health, life impact (the impact on functioning, quality of life, delivery of care and personal circumstances), resource use, adverse events, and others. Most frequently studied outcomes reflected life impact and resource use. Apart from the heterogeneity in outcomes, we also found heterogeneity in designs, data sources, and measurement tools used to evaluate the outcomes. Conclusion: This systematic review provides a categorized overview of outcomes that may be used to evaluate interventions to improve hospital-to-home transition for CMC. The results can be used in the development of a core outcome set transitional care for CMC.

What is Known:• Studies on the effectiveness of interventions to support the hospital-to-home transition of CMC are numerous.•Heterogeneity in outcomes hamper comparisons across studies and therewith the ability to move research forward.

What is New:•This systematic review summarizes and categorizes outcomes reported in publications that evaluated interventions to improve the hospital-to-home transition for CMC.•In total 172 reported outcomes were summarized to 25 unique outcomes that were assigned to six outcome domains.
Cuproptosis-related gene SERPINE1 is a prognostic biomarker and correlated with immune infiltrates in gastric cancer
Authors: Feng Leiran , Li Guixin , Li Dongbin , Duan Guoqiang , Liu Jin 
Published: June 2023

Abstract
Purpose
The serine protease inhibitor clade E member 1 (SERPINE1) has been studied as a potential biomarker in a variety of cancers, but poorly studied in gastric cancer (GC). The purpose of this study was to explore the prognostic value of SERPINE1 in GC and primarily analyze its functions.

Methods
We analyzed the the prognostic value of SERPINE1 and studied the relationship with clinicopathologic biomarkers in gastric cancer. The expression of SERPINE1 was analyzed by GEO and TCGA databases. Moreover, we validated the results by immunohistochemistry. Next, the correlation analysis between SERPINE1 and the cuproptosis-related genes was analyzed by the “Spearman” method. CIBERSORT and TIMER algorithms were used to analyze the correlation of SERPINE1 with immune infiltration. Furthermore, GO and KEGG gene enrichment analyses were used to study the functions and pathways that SERPINE1 might be involved in. Then, drug sensitivity analysis was performed using CellMiner database. Finally, a cuproptosis-immune-related prognostic model was constructed using genes related to immune and cuproptosis, and verified against external datasets.

Results
SERPINE1 was up-regulated in gastric cancer tissues, which tends toward poor prognosis. Using immunohistochemistry experiment, the expression and prognostic value of SERPINE1 were verified. Then, we found that SERPINE1 was negatively correlated with cuproptosis-related genes FDX1, LIAS, LIPT1, and PDHA1. On the contrary, SERPINE1 was positively correlated with APOE. This indicates the effect of SERPINE1 on the cuproptosis process. Furthermore, by conducting immune-related analyses, it was revealed that SERPINE1 may promote the inhibitory immune microenvironment. The infiltration level of resting NK cells, neutrophils, activated mast cells, and macrophages M2 was positively correlated with SERPINE1. However, B cell memory and plasma cells were negatively correlated with SERPINE1. Functional analysis showed that SERPINE1 was closely related to angiogenesis, apoptosis, and ECM degradation. The KEGG pathway analysis showed that SERPINE1 may be associated with P53, Pi3k/Akt, TGF-β, and other signaling pathways. Drug sensitivity analysis showed that SERPINE1 could be also seen as a potential treatment target. The risk model based on SERPINE1 co-expression genes could better predict the survival of GC patients than SERPINE1 alone. We also verified the prognostic value of the risk score by GEO external datasets.

Conclusion
SERPINE1 is highly expressed in gastric cancer and related to poor prognosis. SERPINE1 may regulate cuproptosis and the immune microenvironment by a series of pathways. Therefore, SERPINE1 as a prognostic biomarker and potential therapeutic target deserves further study.
Prognostic factors in refractory metastatic colorectal cancer patients treated with Trifluridine/Tipiracil
Authors: Koper Agnieszka , Wileński Sławomir , Śledzińska Paulina , Bebyn Marek , Koper Krzysztof 
Published: June 2023

Abstract
Purpose
The systemic treatment options for metastatic colorectal cancer (mCRC) are unsatisfactory, and the disease recurs despite the use of numerous medications and their combinations. Trifluridine/Tipiracil is a relatively new drug used in refractory mCRC. Little is known about its real-world effectiveness and prognostic and predictive factors. Therefore, this study aimed to develop a prognostic model for refractory mCRC treated with Trifluridine/Tipiracil.

Methods
We retrospectively evaluated the data from 163 patients who had received Trifluridine/Tipiracil as a third or fourth line of treatment for refractory mCRC.

Results
After starting Trifluridine/Tipiracil, 21.5% of patients survived one year, and the median overall survival after Trifluridine/Tipiracil initiation was 251 days (SD: 17.855; 95%CI: 216–286). Median progression-free survival after Trifluridine/Tipiracil initiation was 56 days (SD: 4.826; 95%CI 47–65). Moreover, the median overall survival from diagnosis was 1333 days (SD: 82.84; 95%CI: 1170–1495). In forward stepwise multivariate Cox regression analysis, initial radical treatment (HR = 0.552, 95% CI 0.372–0.819, p < 0.003), the number of cycles of first-line chemotherapy (HR = 0.978, 95% CI 0.961–0.995, p < 0.011), the number of cycles of second-line chemotherapy (HR = 0.955, 95% CI 0.931–0.98, p < 0.011), BRAF mutation (HR = 3.016, 95% CI = 1.207–7.537, p = 0.018), and hypertension (HR = 0.64, 95% CI = 0.44–0.931, p = 0.02) were all associated with survival after Trifluridine/Tipiracil initiation. Our model and model-based nomogram displayed an AUC of 0.623 for one-year survival estimation in the testing cohort. The C-index for the prediction nomogram was 0.632.

Conclusion
We have developed a prognostic model for refractory mCRC treated with Trifluridine/Tipiracil based on five variables. Moreover, we reported a nomogram which could be used by oncologists in clinic visits on a daily basis.

Graphical abstract
Osteopontin is a prognostic circulating biomarker in patients with neuroendocrine neoplasms
Authors: Kidess Evelyn , Giesecke Yvonne , Eichhorn Ines , Mohr Raphael , Jann Henning , Fischer Christian , Wiedenmann Bertram , Roderburg Christoph , Tacke Frank , Sigal Michael 
Published: June 2023

Abstract
Purpose
Osteopontin (OPN), also called secreted phosphoprotein 1 (SPP1) is a matricellular glycoprotein whose expression is elevated in various types of cancer and which has been shown to be involved in tumorigenesis and metastasis in many malignancies. Its role in neuroendocrine neoplasms (NEN) remains to be established. The aim of the study was to analyze plasma concentrations of OPN in patients with NEN and to explore its diagnostic and prognostic value as a clinical biomarker.

Methods
OPN plasma concentrations were measured in a total of 38 patients with histologically proven NEN at three different time points during the course of disease and therapy (at the start of the study, after 3 and 12 months, respectively) as well as in healthy controls. Clinical and imaging data as well as concentrations of Chromogranin A (CgA) and Neuron Specific Enolase (NSE) were assessed.

Results
OPN levels were significantly higher in patients with NEN compared to healthy controls. High-grade tumors (grade 3) showed the highest OPN levels. OPN levels were neither different between male and female patients nor between different primary tumor sites. OPN correlated significantly with corresponding NSE levels, while there was no correlation with Chromogranin A. High OPN levels above a cutoff value of 200 ng/ml at initial analysis predicted a worsened prognosis with significantly shorter progression-free survival of patients with NEN, which also held true within the subgroup of well-differentiated G1/G2 tumors.

Conclusion
Our data indicate that high baseline OPN levels in patients with NEN are predictive of an adverse outcome with shorter progression-free survival, even within the group of well differentiated G1/G2 tumors. Therefore, OPN may be used as a surrogate prognostic biomarker in patients with NEN.
The efficacy and safety of short-course neoadjuvant denosumab for en bloc spondylectomy in spinal giant cell tumor of bone: a preliminary report
Authors: Tang Qinglian , Lu Jinchang , Zhu Xiaojun , Song Guohui , Wu Hao , Xu Huaiyuan , Wang Anqi , Wang Jin 
Published: June 2023

Abstract
Purpose
This study aimed to investigate whether short course of neoadjuvant denosumab treatment for spinal GCTB could (1) Induce radiological and histological response? (2) Facilitate en bloc resection? (3) Achieve satisfactory oncological and functional outcomes?

Methods
The clinical information of ten consecutive patients between 2018 and 2022 with spinal GCTB treated with short course of neoadjuvant denosumab (≤ 5 doses) and en bloc spondylectomy was retrospectively reviewed. The radiological and histological response, operative data, oncological and functional outcomes were analyzed.

Results
The mean doses of neoadjuvant denosumab were 4.2 (range 3–5 doses). After neoadjuvant denosumab, there were 9 cases showing new ossification and 5 cases with reappearance of cortical integrity. The values of Hounsfield units (HU) of the soft tissue component were increased by > 50% in 7 cases. The signal intensity (SI) ratios of tumor/muscle in T2WI of plain MRI were decreased by > 10% in 60% of the cases. Shrinkage of soft tissue mass by > 10% was observed in 4 cases. The mean duration of operation was 575 ± 174 min, and the mean estimated blood loss (EBL) was 2790 ± 1934 ml. No obvious adhesion to dura mater or major vessels was encounter intraoperatively. There is no tumor collapse or breakage during surgery. Multinucleated giant cells were decreased in 6 cases (60%) with the remaining 4 cases showing absence of multinucleated giant cells. Mononuclear stromal cells existed in most of the cases (8 cases, 80%). New bone formation was noticed in 8 cases (80%). No patient had a worsening of neurologic function after surgery. No tumor recurrence was noticed within the mean follow-up of 24 ± 20 months.

Conclusion
Short-term neoadjuvant denosumab could yield radiological and histological responses and might facilitate en bloc spondylectomy by hardening the tumor and causing less adhesion to segmental vessels, major vessels and nerve roots, which was beneficial to achieve the optimal oncological and functional outcomes.
How I do it — asleep DBS placement for Parkinson’s disease
Authors: Roldan Pedro , Mosteiro Alejandra , Valldeoriola Francesc , Rumià Jordi 
Published: June 2023

Abstract
Background
Traditionally, functional neurosurgery relied in stereotactic atlases and intraoperative micro-registration in awake patients for electrode placement in Parkinson’s disease. Cumulative experience on target description, refinement of MRI, and advances in intraoperative imaging has enabled accurate preoperative planning and its implementation with the patient under general anaesthesia.

Methods
Stepwise description, emphasising preoperative planning, and intraoperative imaging verification, for transition to asleep-DBS surgery.

Conclusion
Direct targeting relies on MRI anatomic landmarks and accounts for interpersonal variability. Indeed, the asleep procedure precludes patient distress. A particular complication to avoid is pneumocephalus; it can lead to brain-shift and potential deviation of electrode trajectory.
ORKG-Leaderboards: a systematic workflow for mining leaderboards as a knowledge graph
Authors: Kabongo Salomon , D’Souza Jennifer , Auer Sören 
Published: June 2023

AbstractThe purpose of this work is to describe theorkg-Leaderboard software designed to extractleaderboardsdefined astask–dataset–metrictuples automatically from large collections of empirical research papers in artificial intelligence (AI). The software can support both the main workflows of scholarly publishing, viz. as LaTeX files or as PDF files. Furthermore, the system is integrated with the open research knowledge graph (ORKG) platform, which fosters the machine-actionable publishing of scholarly findings. Thus, the systemsss output, when integrated within the ORKG’s supported Semantic Web infrastructure of representing machine-actionable ‘resources’ on the Web, enables: (1) broadly, the integration of empirical results of researchers across the world, thus enabling transparency in empirical research with the potential to also being complete contingent on the underlying data source(s) of publications; and (2) specifically, enables researchers to track the progress in AI with an overview of the state-of-the-art across the most common AI tasks and their corresponding datasets via dynamic ORKG frontend views leveraging tables and visualization charts over the machine-actionable data. Our best model achieves performances above 90% F1 on theleaderboardextraction task, thus provingorkg-Leaderboards a practically viable tool for real-world usage. Going forward, in a sense,orkg-Leaderboards transforms theleaderboardextraction task to an automated digitalization task, which has been, for a long time in the community, a crowdsourced endeavor.