bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of bulk RNA sequencing data and single-cell RNA sequencing analysis on the heterogeneity in patients with colorectal cancer
Authors: Zhang Jiawei , Wu Yangsheng , Shen Zhong 
Published: June 2023

AbstractThe cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway has emerged as a critical innate immune pathway that could virtually impact nearly all aspects of tumorigenesis including colorectal cancer. This work aimed to develop and validate molecular subtypes related to cGAS-STING pathways for colorectal cancer using Bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data. Bulk RNA-seq data were acquired from The Cancer Genome Atlas dataset (training dataset) and Gene Expression Omnibus dataset (validation dataset). Univariate COX survival analysis was utilized to identify prognostic differentially expressed genes (DEGs) from 6 immune pathways related to cGAS-STING. ConsensusClusterPlus package was used to classify different subtypes based on DEGs. scRNA-seq data were used to validate differences in immune status between different subtypes. Two clusters with distinct prognosis were identified based on 27 DEGs. The six cGAS-STING-related pathways had different levels of significance between the two clusters. Clust1 had most number of amplified CNVs and clust2 had the most number of loss CNVs. TP53 was the top mutated gene of which missense mutations contributed the most of single-nucleotide variants. Immune score of clust1 was higher than that in clust2, as reflected in macrophages, T cells, and natural killer cells. Three unfavorable genes and 31 protection factors were screened between the two clusters in three datasets. ScRNA-seq data analysis demonstrated that macrophages were more enriched in clust1, and tumor cells and immune cells had close interaction. We classified two distinct subtypes with different prognosis, mutation landscape, and immune characteristics.
Model-Guided Design and Optimization of CPA Perfusion Protocols for Whole Organ Cryopreservation
Authors: Han Zonghu , Rao Joseph Sushil , Ramesh Srivasupradha , Hergesell Jan , Namsrai Bat-Erdene , Etheridge Michael L. , Finger Erik B. , Bischof John C. 
Published: June 2023

AbstractVitrification could enable long-term organ preservation, but only after loading high-concentration, potentially toxic cryoprotective agents (CPAs) by perfusion. In this paper, we combine a two-compartment Krogh cylinder model with a toxicity cost function to theoretically optimize the loading of CPA (VMP) in rat kidneys as a model system. First, based on kidney perfusion experiments, we systematically derived the parameters for a CPA transport loading model, including the following: Vb = 86.0% (ra = 3.86 μm), Lp = 1.5 × 10–14 m3/(N·s), ω = 7.0 × 10–13 mol/(N·s), σ = 0.10. Next, we measured the toxicity cost function model parameters as α = 3.12 and β = 9.39 × 10–6. Combining these models, we developed an improved kidney-loading protocol predicted to achieve vitrification while minimizing toxicity. The optimized protocol resulted in shorter exposure (25 min or 18.5% less) than the gold standard kidney-loading protocol for VMP, which had been developed based on decades of empirical practice. After testing both protocols on rat kidneys, we found comparable physical and biological outcomes. While we did not dramatically reduce toxicity, we did reduce the time. As our approach is now validated, it can be used on other organs lacking defined toxicity data to reduce CPA exposure time and provide a rapid path toward developing CPA perfusion protocols for other organs and CPAs.
Big data optimisation and management in supply chain management: a systematic literature review
Authors: Alsolbi Idrees , Shavaki Fahimeh Hosseinnia , Agarwal Renu , Bharathy Gnana K , Prakash Shiv , Prasad Mukesh 
Published: June 2023

AbstractThe increasing interest from technology enthusiasts and organisational practitioners in big data applications in the supply chain has encouraged us to review recent research development. This paper proposes a systematic literature review to explore the available peer-reviewed literature on how big data is widely optimised and managed within the supply chain management context. Although big data applications in supply chain management appear to be often studied and reported in the literature, different angles of big data optimisation and management technologies in the supply chain are not clearly identified. This paper adopts the explanatory literature review involving bibliometric analysis as the primary research method to answer two research questions, namely: (1) How to optimise big data in supply chain management? and (2) What tools are most used to manage big data in supply chain management? A total of thirty-seven related papers are reviewed to answer the two research questions using the content analysis method. The paper also reveals some research gaps that lead to prospective future research directions.
Automated market maker inventory management with deep reinforcement learning
Authors: Vicente Óscar Fernández , Fernández Fernando , García Javier 
Published: June 2023

Abstract
Stock markets are the result of the interaction of multiple participants, and market makers are one of them. Their main goal is to provide liquidity and market depth to the stock market by streaming bids and offers at both sides of the order book, at different price levels. This activity allows the rest of the participants to have more available prices to buy or sell stocks. In the last years, reinforcement learning market maker agents have been able to be profitable. But profit is not the only measure to evaluate the quality of a market maker. Inventory management arises as a risk source that must be under control. In this paper, we focus on inventory risk management designing an adaptive reward function able to control inventory depending on designer preferences. To achieve this, we introduce two control coefficients, AIIF (Alpha Inventory Impact Factor) and DITF (Dynamic Inventory Threshold Factor), which modulate dynamically the behavior of the market maker agent according to its evolving liquidity with good results. In addition, we analyze the impact of these factors in the trading operative, detailing the underlying strategies performed by these intelligent agents in terms of operative, profitability and inventory management. Last, we present a comparison with other existing reward functions to illustrate the robustness of our approach.

Graphic Abstract
Safety, feasibility, and hemodynamic response of regadenoson for stress perfusion CMR
Authors: Muñiz-Sáenz-Diez Javier , Ezponda Ana , Caballeros Meylin , de la Fuente Ana , Gavira Juan J. , Bastarrika Gorka 
Published: June 2023

AbstractOwing to its pharmacodynamics and posology, the use of regadenoson for stress cardiac magnetic resonance (CMR) has potential advantages over other vasodilators. We sought to evaluate the safety, hemodynamic response and diagnostic performance of regadenoson stress-CMR in routine clinical practice. All regadenoson stress-CMR examinations performed between May 2017 and July 2020 at our institution were retrospectively reviewed. A total of 698 studies were included for the final analysis. A conventional stress/rest protocol was performed using a 1.5T MRI scanner (Magnetom Aera, Siemens Healthineers, Erlangen, Germany). Adverse events, clinical symptoms, and hemodynamic response were assessed. Diagnostic accuracy of the test was evaluated in patients who underwent invasive coronary angiography. Nearly half of patients (48.5%) remained asymptomatic. Most common clinical symptoms included dyspnea (137, 19.6%), chest pain (116, 16.6%) and flushing (44, 6.3%). Two patients (0.28%) could not complete the examination due to severe hypotension or unbearable chest pain. Overall, an increase in heart rate (HR) response (36.2% [IQR: 22.5?50.9]) and a decrease in systolic and diastolic blood pressure (BP) (median systolic BP response of -5% [IQR: -11.5-0.6]; median diastolic BP response of -6.3 mmHg [IQR: -13.4-0]) was observed. Patients with symptoms induced by regadenoson showed higher HR response (40.3%, IQR: 26.4?56.1 vs. 32.4%, IQR: 19-45.6, p < 0.001), whereas a blunted HR response was observed in diabetic (29.6%, IQR: 18.4?42 p < 0.001), obese (31.7%, IQR: 20.7?46.2 p = 0.005) and patients aged 70 years or older (32.9%, IQR: 22.6?43.1 p < 0.001). Overall, regadenoson stress-CMR showed 95.65% (IQ 91.49?99.81) sensitivity, 54.84% (IQ 35.71?73.97) specificity, 86.99% (IQ 82.74?94.68) positive predictive value, and 77.27% (IQ 57.49?97.06) negative predictive value for detecting significant coronary stenosis as compared with invasive coronary angiography. Regadenoson is a well-tolerated vasodilator that can be safely employed for stress perfusion CMR, with high diagnostic performance.
Exploring fish functional trait assemblages in Eastern Mediterranean rivers: a study across multiple scales using network analysis
Authors: Tachos Vassilis , Koutsikos Nicholas , Dimitrakopoulos Panayiotis G. , Zogaris Stamatis 
Published: June 2023

AbstractFunctional traits of river fish assemblages have rarely been studied in the Eastern Mediterranean region. A dataset of 254 Greek electrofished near-natural sites (427 samples) was analyzed to explore native fish functional structure across three spatial scales: (a) among six ecoregions, (b) within a single ecoregion, and (c) in a river basin. Overall, 76 native fish species were assigned eight functional categories, involving 24 different traits. Bipartite networks were used to interpret spatial patterns of species trait data. Two major trait assemblage types were detected in all three spatial scales: the upland type, dominated by insectivorous, benthic, rheophilic, intolerant species, and the lowland type, incorporating omnivorous, limnophilic, phytophilic, and tolerant species. In order to provide further insights between traits and key environmental variables, redundancy analysis (RDA) was employed. The RDA depicted a strong upstream–downstream environmental gradient. Upland and lowland assemblage types form two distinct functional zones along the upstream and downstream river stretches, respectively. Yet, no consistent boundary criteria seem to exist between them. Notably, within a region of high fish assemblage heterogeneity such as the Eastern Mediterranean, functional patterns follow well-established phenomena along the upstream–downstream longitudinal profile of temperate lotic waters.
Whole genome sequencing and disease pattern in patients with juvenile polyposis syndrome: a nationwide study
Authors: Jelsig Anne Marie , van Overeem Hansen Thomas , Gede Lene Bjerring , Qvist Niels , Christensen Lise-Lotte , Lautrup Charlotte Kvist , Ljungmann Ken , Christensen Louise Torp , Rønlund Karina , Tørring Pernille Mathiesen , Bertelsen Birgitte , Sunde Lone , Karstensen John Gásdal 
Published: June 2023

AbstractJuvenile polyposis syndrome (JPS) is a hereditary hamartomatous polyposis syndrome characterized by gastrointestinal juvenile polyps and increased risk of gastrointestinal cancer. Germline pathogenic variants are detected in SMAD4 or BMPR1A, however in a significant number of patients with JPS, the etiology is unknown. From Danish registers, and genetic department and laboratories, we identified all patients in Denmark with a clinical diagnosis of JPS and/or a pathogenic variant in BMPR1A or SMAD4. In patients where no variant had been detected, we performed genetic analysis, including whole genome sequencing. We collected clinical information on all patients to investigate the phenotypic spectrum. Sixty-six patients (mean age 40 years) were included of whom the pathogenic variant was unknown in seven patients. We detected a pathogenic variant in SMAD4 or PTEN in additional three patients and thus ≈ 95% of patients had a pathogenic germline variant. Endoscopic information was available in fifty-two patients (79%) and of these 31 (60%) fulfilled the clinical criteria of JPS. In 41 patients (79%), other types of polyps than juvenile had been removed. Our results suggest that almost all patients with a clinical diagnosis of JPS has a pathogenic variant in mainly BMPR1A, SMAD4, and more rarely PTEN. However, not all patients with a pathogenic variant fulfil the clinical criteria of JPS. We also demonstrated a wide clinical spectrum, and that the histopathology of removed polyps varied.
Firewood and Energy Sovereignty on Navajo Nation
Authors: Magargal Kate , Yellowman Jonah , Chee Shaniah , Wabel Molly , Macfarlan Shane , Codding Brian F. 
Published: June 2023

AbstractClimate-induced drought jeopardizes future access to sufficient energy sources for many people reliant on firewood, especially those underrepresented in forest management decision-making. To identify where interventions might be most effective in facilitating self-determination and sustained firewood harvest, we investigate the case of Diné firewood harvesters. Using data from surveys, interviews and participant observations, we articulate who uses firewood and why, what the costs of firewood are, and who imposes those costs. Reducing both the cost and need for firewood for the Diné and others would support energy sovereignty by facilitating sustained access to firewood.
The Accessibility of Moral Virtue in the Context of Depressive Episodes
Authors: Neijzen Mara 
Published: June 2023

AbstractDespite efforts to make virtue-acquisition more accessible, neo-Aristotelian accounts of virtue currently exclude those who occasionally experience depressive episodes from potentially possessing moral virtue. This problem of accessibility is especially relevant given the increased prevalence of depression due to, e.g., the COVID19 pandemic. Through an interdisciplinary analysis, I argue that one’s ability to adequately recognise and respond to virtuous possibilities for action is impoverished during a depressive episode. This is illustrated through the depressed agent’s field of affordances: the collection of possible actions an agent perceives. As moral virtues are conceptualised as stable dispositions, even a temporary yet significant decrease in moral competence excludes the agent from possessing the relevant virtue. To solve this problem of accessibility, I argue that, similar to Aristotle’s discussion of sleep, depressive episodes can be conceptualised as temporary states that cause one’s virtues to be inactive, rather than absent.
Military Training and Revisionist Just War Theory’s Practicability Problem
Authors: Surber Regina Sibylle 
Published: June 2023

AbstractThis article presents an analytic critique of the predominant revisionist theoretical paradigm of just war (henceforth: revisionism). This is accomplished by means of a precise description and explanation of the practicability problem that confronts it, namely that soldiers that revisionism would deem “unjust” are bound to fail to fulfil the duties that revisionism imposes on them, because these duties are overdemanding. The article locates the origin of the practicability problem in revisionism’s overidealized conception of a soldier as an individual rational agent analogous to the aggressor or defender in a case of lethal self-defense, who is capable of reflecting on the morality of his status in war and of the killing he performs and thus of recognizing his revisionist duties. Revisionism, however, ignores the following fact: Killing in war is not a natural human behavior. This is why training soldiers to kill is—and arguably always has been—a necessity for the existence of war and the killing that occurs in it. Moreover, this training involves a certain level of moral desensitization to violence whose goal is to prevent soldiers from thoroughly reflecting on the morality of the killing they engage in. Hence, war and killing can only exist if soldiers are trained in such a way that they do not reflect on whether they could be addressees of revisionist duties in the first place. This means that military training is a “constitutive condition” of soldiers and war, which is why it cannot excuse their noncompliance with revisionist duties, thus making these duties categorically overdemanding. The argument here draws on the paradigmatic example of modern US military killing conditioning (MC), but embeds it into a broader military-historical perspective that describes how soldiers have always needed to be mentally and morally influenced in order to enable war and killing. The article’s explanation of revisionism’s practicability problem has a constructive consequence for future theory-building in the ethics of war: It implies that a potentially revised ethical theory of war must necessarily analyze the institutions that allocate belligerent resources, if it aims to morally assess battlefield behavior in a practicable manner.
The effects of climate change on the timing of peak fall foliage in Acadia National Park
Authors: Spera Stephanie A. , Spangler Keith R. , Hubert M. Olivia , Gorman Marc G. 
Published: June 2023

AbstractContextIn recent decades, most United States’ National Parks have experienced extreme temperature and precipitation regimes outside of their historical ranges of variability with unknown effects on fall phenology.ObjectivesWe determine 1) how seasonal climate in Acadia National Park, Maine and the timing of peak fall foliage have changed between 1950 and 2021; 2) how changes in seasonal climate have affected fall foliage; and 3) how we might expect the timing of fall foliage to change given future climate projections.MethodsWe use ERA5-Land data to analyze changes in climate. We couple remotely sensed data with archival research to determine changes in the timing of peak fall foliage. We use multivariate regressions to understand the relationship between climate and fall foliage. We use CESM2 data to predict the timing of peak fall foliage coloration through 2060.ResultsMinimum temperatures, maximum temperatures, precipitation, and the number of warm nights, hot nights, warm days, hot days, and downpour days have all significantly increased (p ≤ 0.05). The timing of peak fall foliage is now occurring almost two weeks later (p ≤ 0.05). September temperature and precipitation and May precipitation were positively correlated with delayed peak fall foliage. Early October precipitation was negatively correlated. Future climate projections predict the timing of peak fall foliage to occur between October 30 and November 2 by 2060.ConclusionUnderstanding how climate is affecting leaf senescence both is crucial in a national park where fall tourism brings large gains to the local economy and provides key information to park managers planning for a resilient, sustainable future.
Treatment of Perinatal Depression and Correlates of Treatment Response Among Pregnant Women Living with HIV in Uganda
Authors: Faherty Laura J. , Gwokyalya Violet , Dickens Akena , McBain Ryan , Ngo Vicky , Nakigudde Janet , Nakku Juliet , Mukasa Barbara , Beyeza-Kashesya Jolly , Wanyenze Rhoda K. , Wagner Glenn J. 
Published: June 2023

Abstract
Introduction
Perinatal depression is common among women living with HIV, but depression care is limited in low-resource settings. We examined (1) characteristics of women receiving Problem Solving Therapy (PST) versus antidepressant therapy (ADT), (2) treatment response by modality, and (3) correlates of treatment response.

Methods
This analysis used data from 191 Ugandan women in the intervention arm of a cluster randomized controlled trial of task-shifted, stepped-care depression treatment for pregnant women living with HIV (PWLWH). Treatment response was defined as scoring < 5 on the nine-item Patient Health Questionnaire (PHQ-9). Bivariate analysis and multivariable logistic regression were used to examine characteristics of women by treatment group and correlates of treatment response.

Results
Of 134 participants with depression, 129 (96%) were treated: 84 (65%) received PST and 45 (35%) received ADT. Severe depression at treatment initiation was more common in those receiving ADT (28.9% versus 4.8%, Fischer’s Exact Test < 0.001). Treatment response was higher for PST (70/84; 83.3%) than ADT (30/45; 66.7%; p = .03). ADT side effects were rare and minor; no infants had serious congenital defects. Of 22 participants (19%) who did not respond to treatment, only five received intensified management. Social support and interpersonal violence were associated with treatment response (adjusted odds ratio, [aOR] = 3.06, 95% CI = 1.08–8.66 and aOR = 0.64, 95% CI = 0.44–0.93).

Discussion
Both depression treatment modalities yielded high response rates in Ugandan PWLWH; ADT was well-tolerated. Our results highlight a need to build capacity to implement the stepped-care protocol for non-responders and screen for social support and interpersonal violence.
What we know when we act
Authors: Kearl Timothy 
Published: June 2023

AbstractTwo traditions in action theory offer different accounts of what distinguishes intentional action from mere behavior. According to the causalist tradition, intentional action has certain distinguished causal antecedents, and according to the Anscombian tradition, intentional action has certain distinguished epistemological features. I offer a way to reconcile these ostensibly conflicting accounts of intentional action by way of appealing to “ability-constituting knowledge”. After explaining what such knowledge is, and in particular its relationship to inadvertent virtue and knowledge-how, I suggest that, among other things, appealing to ability-constituting knowledge can help us flesh out what it is for an agent’s reasons to non-deviantly cause and sustain her purposive behavior.
Near term algorithms for linear systems of equations
Authors: Pellow-Jarman Aidan , Sinayskiy Ilya , Pillay Anban , Petruccione Francesco 
Published: June 2023

AbstractFinding solutions to systems of linear equations is a common problem in many areas of science and engineering, with much potential for a speed up on quantum devices. While the Harrow–Hassidim–Lloyd (HHL) quantum algorithm yields up to an exponential speed up over classical algorithms in some cases, it requires a fault-tolerant quantum computer, which is unlikely to be available in the near-term. Thus, attention has turned to the investigation of quantum algorithms for noisy intermediate-scale quantum (NISQ) devices where several near-term approaches to solving systems of linear equations have been proposed. This paper focuses on the Variational Quantum Linear Solvers (VQLS), and other closely related methods and adaptions. Several contributions are made in this paper, which include: the first application of the Evolutionary Ansatz to the VQLS (EAVQLS), the first implementation of the Logical Ansatz VQLS (LAVQLS), based on the Classical Combination of Quantum States (CQS) method, a proof of principle demonstration of the CQS method on real quantum hardware and a method for the implementation of the Adiabatic Ansatz on the VQLS (AAVQLS). These approaches are implemented and contrasted. The CQS method is run with moderate success on a real quantum device. The EAVQLS and AAVQLS show promise as possible improvements to the standard VQLS algorithm once refined.