bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithms and Complexity on Indexing Founder Graphs
Authors: Equi Massimo , Norri Tuukka , Alanko Jarno , Cazaux Bastien , Tomescu Alexandru I. , Mäkinen Veli 
Published: July 2022

AbstractWe study the problem of matching a string in a labeled graph. Previous research has shown that unless theOrthogonal Vectors Hypothesis(OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example,Wheeler graphs(Gagie et al. Theor. Comp. Sci.2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced frommultiple sequence alignments().Elastic degenerate strings(Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization:elastic founder graphs. We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless , and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general . Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time.
Exploring clinically relevant risk profiles in patients undergoing lumbar spinal fusion: a cohort study
Authors: Janssen Esther R. C. , Prestigiacomo F. G. , van Leent E. A. P. , van Meeteren N. L. U. , Hulsbosch M. 
Published: July 2022

Abstract
Purpose
To explore risk profiles of patients scheduled for lumbar spinal fusion (LSF) and their association with short-term recovery of patient after surgery.

Methods
Forty-nine patients scheduled for elective 1–3 level LSF between March 2019 and June 2020 were included. Patients underwent a preoperative risk screening, consisting of an anamnesis, questionnaires and physical performance tests. A latent profile analysis (LPA) was used to identify possible risk profiles within this population.

Results
Two risk profiles could be established: a fit and deconditioned risk profile. A significant between-profile difference was found in smoking status (p = 0.007), RAND36-PCS (p < 0.001), Timed Up and Go (TUG) (p < 0.001), de Morton Morbidity Index (DEMMI) (p < 0.001), finger floor distance (p = 0.050), motor control (p = 0.020) and steep ramp test (p = 0.005). Moreover, the fit risk profile had a significant shorter time to functional recovery (3.65 days versus 4.89 days, p = 0.013) and length of hospital stay (5.06 days versus 6.00 days, p = 0.008) compared to the deconditioned risk profile. No differences in complication rates between both risk profiles could be established. Allocation to a risk profile was associated with the functional recovery rate (p = 0.042), but not with LOS or complications.

Conclusion
This study found a fit and deconditioned risk profile. The patients with a fit risk profile perceived a better quality of life, performed better in mobility, motor control, cardiopulmonary tests and showed also a significant shorter stay in the hospital and a shorter time to functional recovery. Preoperatively establishing a patient’s risk profile could aid in perioperative care planning and preoperative decision-making.
The virtualization of human–robot interactions: a user-centric workload assessment
Authors: Nenna Federica , Orso Valeria , Zanardi Davide , Gamberini Luciano 
Published: July 2022

AbstractInterest in the virtualization of human–robot interactions is increasing, yet the impact that collaborating with either virtual or physical robots has on the human operator’s mental state is still insufficiently studied. In the present work, we aimed to fill this gap by conducting a systematic assessment of a human–robot collaborative framework from a user-centric perspective. Mental workload was measured in participants working in synergistic co-operation with a physical and a virtual collaborative robot (cobot) under different levels of task demands. Performance and implicit and explicit workload were assessed as a function of pupil size variation and self-reporting questionnaires. In the face of a similar self-reported mental demand when maneuvering the virtual or physical cobot, operators showed shorter operation times and lower implicit workload when interacting with the virtual cobot compared to its physical counterpart. Furthermore, the benefits of collaborating with a virtual cobot most vividly manifested when the user had to position the robotic arm with higher precision. These results shed light on the feasibility and importance of relying on multidimensional assessments in real-life work settings, including implicit workload predictors such as pupillometric measures. From a broader perspective, our findings suggest that virtual simulations have the potential to bring significant advantages for both the user's mental well-being and industrial production, particularly for highly complex and demanding tasks.
In silico development and experimental validation of a novel 7-gene signature based on PI3K pathway-related genes in bladder cancer
Authors: Wang Linhui , Wang Yutao , Bi Jianbin 
Published: July 2022

AbstractAlthough bladder cancer (BLCA) is the 10th most common tumor worldwide, particularly practical markers and prognostic models that might guide therapy are needed. We used a non-negative matrix factorization algorithm to classify PI3K pathway-related genes into molecular subtypes. A weighted gene co-expression network analysis (WGCNA) was generated to identify co-expression modules. Univariate Cox regression, least absolute shrinkage sum selection operator-Cox regression, and multivariate Cox regression were utilized to develop a prognostic score model. Kaplan–Meier analysis and receiver operating characteristics were utilized to measure the model’s effectiveness. A nomogram was constructed to improve the predictive ability of the model based on clinical parameters and risk. Decision curve analysis (DCA) was used to evaluate the nomogram. To evaluate the immune microenvironment, an estimate algorithm was used. Drug sensitivity was identified using the R package “pRRophetic.” UM-UC-3 cell line was used to measure the effect of CDK6 in Western blotting, proliferation assay, and 5-ethynyl-20-deoxyuridine assay. Based on PI3K pathway-related genes, The Cancer Genome Atlas (TCGA)-BLCA and GSE32894 patients were divided into two subtypes. Twenty-five co-expression modules were established using the WGCNA algorithm. A seven-gene signature (CDK6, EGFR, IGF1, ITGB7, PDGFRA, RPS6, and VWF) demonstrated robustness in TCGA and GSE32894 datasets. Expression levels of CDK6 and risk positively correlated with M2 macrophages and IgG. Cisplatin, gemcitabine, methotrexate, mitomycin C, paclitaxel, and vinblastine are sensitive to different groups based on the expression of CDK6 and risk. Functional experiments suggested that CDK6 promotes the proliferation of UM-UC-3 cells. We constructed a seven-gene prognostic signature as an effective marker to predict the outcomes of BLCA patients and guide individual treatment.
Modeling ATP-mediated endothelial cell elongation on line patterns
Authors: Roselli Nicole , Castagnino Alessia , Pontrelli Giuseppe , Natalini Roberto , Barakat Abdul I. 
Published: July 2022

AbstractEndothelial cell (EC) migration is crucial for a wide range of processes including vascular wound healing, tumor angiogenesis, and the development of viable endovascular implants. We have previously demonstrated that ECs cultured on 15-μm wide adhesive line patterns exhibit three distinct migration phenotypes: (a) “running” cells that are polarized and migrate continuously and persistently on the adhesive lines with possible spontaneous directional changes, (b) “undecided” cells that are highly elongated and exhibit periodic changes in the direction of their polarization while maintaining minimal net migration, and (c) “tumbling-like” cells that migrate persistently for a certain amount of time but then stop and round up for a few hours before spreading again and resuming migration. Importantly, the three migration patterns are associated with distinct profiles of cell length. Because of the impact of adenosine triphosphate (ATP) on cytoskeletal organization and cell polarization, we hypothesize that the observed differences in EC length among the three different migration phenotypes are driven by differences in intracellular ATP levels. In the present work, we develop a mathematical model that incorporates the interactions between cell length, cytoskeletal (F-actin) organization, and intracellular ATP concentration. An optimization procedure is used to obtain the model parameter values that best fit the experimental data on EC lengths. The results indicate that a minimalist model based on differences in intracellular ATP levels is capable of capturing the different cell length profiles observed experimentally.
Tumor response and survival outcomes of salvage concurrent chemoradiotherapy with three-dimensional conformal radiotherapy and 5-fluorouracil/platinum-based chemotherapy for postoperative locoregional recurrence of esophageal squamous cell carcinoma
Authors: Ito Renma , Nakamura Yoshiaki , Sunakawa Hironori , Fujiwara Hisashi , Hojo Hidehiro , Nakamura Naoki , Fujita Takeo , Yano Tomonori , Daiko Hiroyuki , Akimoto Tetsuo , Yoshino Takayuki , Kojima Takashi 
Published: July 2022

Abstract
Background
Salvage concurrent chemoradiotherapy is effective against locoregional recurrence after curative resection of esophageal squamous cell carcinoma. However, there is no consensus on its application. We investigated the outcomes of salvage concurrent chemoradiotherapy (60 Gy in 30 fractions) with three-dimensional conformal radiotherapy and 5-fluorouracil/platinum-based chemotherapy.

Methods
We retrospectively investigated the outcomes and prognostic factors in 51 patients with esophageal squamous cell carcinoma treated with salvage concurrent chemoradiotherapy.

Results
The median follow-up was 17.5 (range, 2.8–116.1) months. The overall response, complete response, and partial response rates were 74.5%, 49.0%, and 25.5%, respectively. The median progression-free survival was 8.2 months; the 3-year progression-free survival rate was 22.9%. The median overall survival was 23.1 months; the 3-year overall survival rate was 40.7%. Overall survival was significantly longer in patients with a complete response than in those without (median overall survival: not reached vs. 15.3 months); 3-year overall survival rate: 62.5% vs. 20.3% (hazard ratio: 0.222; P < 0.001). Multivariate analysis showed that the independent prognostic factor for overall survival was < 25 mm longest diameter of metastatic lymph nodes (hazard ratio: 3.71).

Conclusions
Salvage concurrent chemoradiotherapy (60 Gy in 30 fractions) with three-dimensional conformal radiotherapy and 5-fluorouracil/platinum-based chemotherapy was an effective and safe treatment for locoregional recurrence after curative resection of esophageal squamous cell carcinoma, especially in those approaching a complete response. Additionally, a shorter longest diameter of metastatic lymph nodes may be associated with better long-term survival.
Renal resistance index independently predicts worsening of renal function after coronary angiography
Authors: Barone Roberta , Goffredo Giovanni , Di Terlizzi Vito , Alcidi Gianmarco , Tabella Erika , Centola Antonio , Campanale Giulio , Ruggiero Antonio , Cuculo Andrea , Di Biase Matteo , Brunetti Natale Daniele , Iacoviello Massimo 
Published: July 2022

AbstractThe renal resistance index (RRI) has been demonstrated to be a useful parameter that can detect patients at a high risk of worsening of renal function (WRF). This study was designed to evaluate the role of the RRI in predicting WRF mediated by the intravascular administration of contrast media. We enrolled patients who were referred for coronary angiography. Renal arterial echo-color Doppler was performed to calculate the RRI. WRF was defined as an increase of > 0.3 mg/dL and at least 25% of the baseline value in creatinine concentration 24–48 h after coronary angiography. Among the 148 patients enrolled in this study, 18 (12%) had WRF. In the multivariate logistic analysis, the RRI was independently associated with WRF (odds ratio [OR]: 1.22; 95% confidence interval [CI]: 1.09–1.36; p = 0.001). After angiography, the RRI significantly increased in both patients with and without WRF. In the receiver operating characteristic curve analyses for WRF, the RRI at baseline and after angiography showed similar accuracy, and the best cutoff value for predicting WRF was 70%. In patients undergoing coronary angiography, the RRI is independently associated with WRF, probably because it provides more accurate information about cardiorenal pathophysiological factors and reflects kidney hemodynamic status and flow reserve.
Saponins as cytotoxic agents: an update (2010–2021). Part II—Triterpene saponins
Authors: Podolak Irma , Grabowska Karolina , Sobolewska Danuta , Wróbel-Biedrawa Dagmara , Makowska-Wąs Justyna , Galanty Agnieszka 
Published: July 2022

AbstractSaponins make up an important group of natural glycosidic compounds which are distinguished by triterpene or steroidal aglycone. Although widely distributed in terrestrial flora, especially higher plants, they can also be found in some marine organisms. Cytotoxic activity is one of the most frequently reported from a wide array of pharmacological activities known for these metabolites. The current review is an update of our previous paper—Saponins as cytotoxic agents(Podolak et al. Phytochem Rev 9:425–474, 2010), and covers studies that were since published (2010–2021). This part refers to triterpene saponins and complements the first, which was devoted solely to steroidal saponins (Sobolewska et al. Phytochem Rev 19:139–189, 2020). Cytotoxic activities in vitro and in vivo are presented with a main focus on structure-activity relationships and molecular mechanisms of action.
Unbiased proteomic analysis of extracellular vesicles secreted by senescent human vascular smooth muscle cells reveals their ability to modulate immune cell functions
Authors: Głuchowska Agata , Cysewski Dominik , Baj-Krzyworzeka Monika , Szatanek Rafał , Węglarczyk Kazimierz , Podszywałow-Bartnicka Paulina , Sunderland Piotr , Kozłowska Ewa , Śliwińska Małgorzata A. , Dąbrowski Michał , Sikora Ewa , Mosieniak Grażyna 
Published: July 2022

AbstractAtherosclerosis, a common age-related disease, is characterized by intense immunological activity. Atherosclerotic plaque is composed of endothelial cells, vascular smooth muscle cells (VSMCs), lipids and immune cells infiltrating from the blood. During progression of the disease, VSMCs undergo senescence within the plaque and secrete SASP (senescence-associated secretory phenotype) factors that can actively modulate plaque microenvironment. We demonstrated that senescent VSMCs secrete increased number of extracellular vesicles (senEVs). Based on unbiased proteomic analysis of VMSC-derived EVs and of the soluble fraction of SASP (sSASP), more than 900 proteins were identified in each of SASP compartments. Comparison of the composition of VMSC-derived EVs with the SASP atlas revealed several proteins, including Serpin Family F Member 1 (SERPINF1) and Thrombospondin 1 (THBS1), as commonly upregulated components of EVs secreted by senescent VSMCs and fibroblasts. Among soluble SASP factors, only Growth Differentiation Factor 15 (GDF15) was universally increased in the secretome of senescent VSMCs, fibroblasts, and epithelial cells. Bioinformatics analysis of EV proteins distinguished functionally organized protein networks involved in immune cell function regulation. Accordingly, EVs released by senescent VSMCs induced secretion of IL-17, INFγ, and IL-10 by T cells and of TNFα produced by monocytes. Moreover senEVs influenced differentiation of monocytes favoring mix M1/M2 polarization with proinflammatory characteristics. Altogether, our studies provide a complex, unbiased analysis of VSMC SASP and prove that EVs derived from senescent VSMCs influence the cytokine milieu by modulating immune cell activity. Our results strengthen the role of senescent cells as an important inducer of inflammation in atherosclerosis.
Virtual Reality to Support Inpatient Addiction Treatment: Patients Are Ready, What About Therapists? A Feasibility Study
Authors: Arissen Clemence , van der Helm Laura , Dijkstra Boukje , Markus Wiebren 
Published: July 2022

AbstractThis study aimed to identify facilitators and barriers for implementation of virtual reality therapy (VRT), used to train communication and problem-solving skills aiding relapse prevention, when integrated with addiction treatment (Treatment as Usual; TAU). Mixed methods were used in an observational, partly prospective, design. A total of 21 therapists and 113 patients from three inpatient addiction clinics were assessed. Therapists filled in questionnaires to gauge expectancies and experiences regarding facilitators and barriers at baseline, after a try-out period, halfway, and at the end of the pilot lasting 6–12 months. They also participated in focus-group interviews. Patients filled in similar questionnaires before an initial, and after they finished a third, VRT session. In addition, nine patients were interviewed. All VRT sessions were logged, with patients answering additional questions. Acceptability of VRT was high in both groups. It was feasible to integrate VRT with TAU and integration showed potential effectiveness. Barriers included incidental motion sickness, technical difficulties, costs, and device setup time. Both therapists and patients advocated VRT use to augment addiction treatment. Findings suggest a clinical effectiveness study is warranted.
Effects of Difficulty in Handling Emotions and Social Interactions on Nomophobia: Examining the Mediating Role of Feelings of Loneliness
Authors: Valenti Giusy D. , Bottaro Rossella , Faraci Palmira 
Published: July 2022

Abstract
This study was addressed to assess nomophobia in an Italian sample (N = 456, 53.1% men, Mage = 31.8, SD = 11.1), also providing a deeper knowledge about how it is distributed across demographics, as well as identifying its best predictors. The main goal was to investigate the direct and indirect effects of difficulty in emotion regulation and social interaction anxiety on nomophobia through loneliness. Our findings indicated that loneliness explained the effect of the expressive suppression strategy (fully) and social interaction anxiety (partially) on nomophobia, whereas it was not a significant mediator when the cognitive reappraisal strategy was taken into account. Our study suggests that loneliness during the pandemic plays a crucial role in explaining the associations between the investigated predictors and the outcome variable, offering a deeper understanding of the underlying mechanisms of this emerging construct. Theoretical and practical implications are discussed, and shortcomings and suggestions for future works are presented.
A tale of two stations: a note on rejecting the Gumbel distribution
Authors: Rydén Jesper 
Published: July 2022

AbstractThe existence of an upper limit for extremes of quantities in the earth sciences, e.g. for river discharge or wind speed, is sometimes suggested. Estimated parameters in extreme-value distributions can assist in interpreting the behaviour of the system. Using simulation, this study investigated how sample size influences the results of statistical tests and related interpretations. Commonly used estimation techniques (maximum likelihood and probability-weighted moments) were employed in a case study; the results were applied in judging time series of annual maximum river flow from two stations on the same river, but with different lengths of observation records. The results revealed that sample size is crucial for determining the existence of an upper bound.
Brain Prehabilitation for Oncologic Surgery
Authors: Daksla Neil , Nguyen Victoria , Jin Zhaosheng , Bergese Sergio D. 
Published: July 2022

AbstractPurpose of ReviewThis review aims to summarize the current research on postoperative cognitive complications, such as delirium and cognitive dysfunction. This includes discussion on preoperative preventive strategies, such as physical and nutritional prehabilitation as well as up-to-date information on neuroprehabilitation.Recent FindingsCurrent recommendations for prevention of postoperative delirium have focused on multicomponent interventions. The optimal composition of surgical prehabilitation programs targeting exercise and nutrition has not yet been established. The Neurobics Trial shows that cognitive prehabilitation improves cognitive reserve and may be a useful addition to multimodal surgical prehabilitation.SummaryPerioperative management of oncologic patients is often associated with a myriad of challenges, such as the management of tumor-related pathologies, adverse events from neoadjuvant therapy, and chronic metabolic and immunological changes associated with malignancy. In addition, oncologic patients are at increased risk of developing frailty, which adversely affects postoperative recovery and further cancer treatment. As a result, oncologic patients are at considerable risk of developing postoperative cognitive complications, such as delirium and cognitive dysfunction. In this review, we discuss the effect of prehabilitation on postoperative cognitive outcomes.
Understanding manufacturing repurposing: a multiple-case study of ad hoc healthcare product production during COVID-19
Authors: Ho Wan Ri , Maghazei Omid , Netland Torbjørn H. 
Published: July 2022

AbstractThe repurposing of manufacturing facilities has provided a solution to the surge in demand for healthcare products during the COVID-19 pandemic. Despite being a widespread and important phenomenon, manufacturing repurposing has received scarce research. This paper develops a grounded understanding of the key factors that influence manufacturing repurposing at the macro and micro levels. We collected rich qualitative data from 45 case studies of firms’ repurposing initiatives during COVID-19. Our study focuses on four types of healthcare products that experienced skyrocketing demand during the first months of the COVID-19 pandemic: face shields, facemasks, hand sanitizers, and medical ventilators. Based on the case studies, we identify and generalize driving factors for manufacturing repurposing and their relationships, which are summarized in causal loop diagrams at both macro and micro levels. Our research provides practitioners, policymakers, and scholars with a conceptual understanding of the phenomenon of manufacturing repurposing. It helps manufacturing managers understand why, when, and how they should engage in manufacturing repurposing and informs policymakers when and how to tailor incentive policies and support schemes to changing situations. Scholars can build on our work to develop and test dynamic system–behavior models of the phenomenon or to pursue other research paths we discover. The world stands to benefit from improved manufacturing repurposing capabilities to be better prepared for future disruptions.