bluuebunny/crossref_metadata_2025_split huggingface dataset:
Class I HDAC inhibitor entinostat synergizes with PLK1 inhibitors in MYC-amplified medulloblastoma cells
Authors: Valinciute Gintvile , Ecker Jonas , Selt Florian , Hielscher Thomas , Sigaud Romain , Ridinger Johannes , Thatikonda Venu , Gatzweiler Charlotte , Robinson Sarah , Talbot Julie , Bernardi Flavia , Picard Daniel , Blattner-Johnson Mirjam , Schmid Simone , Jones David T. , van Tilburg Cornelis M. , Capper David , Kool Marcel , Remke Marc , Oehme Ina , Pfister Stefan M. , Roussel Martine F. , Ayrault Olivier , Witt Olaf , Milde Till 
Published: May 2023

Abstract
Purpose
We and others have demonstrated that MYC-amplified medulloblastoma (MB) cells are susceptible to class I histone deacetylase inhibitor (HDACi) treatment. However, single drug treatment with HDACi has shown limited clinical efficacy. We hypothesized that addition of a second compound acting synergistically with HDACi may enhance efficacy.

Methods
We used a gene expression dataset to identify PLK1 as a second target in MB cells and validated the relevance of PLK1 in MB. We measured cell metabolic activity, viability, and cycle progression in MB cells after treatment with PLK1-specific inhibitors (PLK1i). Chou–Talalay synergy calculations were used to determine the nature of class I HDACi entinostat and PLK1i interaction which was validated. Finally, the clinical potential of the combination was assessed in the in vivo experiment.

Results
MYC-amplified tumor cells are highly sensitive towards treatment with ATP-competitive PLK1i as a monotherapy. Entinostat and PLK1i in combination act synergistically in MYC-driven MB cells, exerting cytotoxic effects at clinically relevant concentrations. The downstream effect is exerted via MYC-related pathways, pointing out the potential of MYC amplification as a clinically feasible predictive biomarker for patient selection. While entinostat significantly extended survival of mice implanted with orthotopic MYC-amplified MB PDX, there was no evidence of the improvement of survival when treating the animals with the combination.

Conclusion
The combination of entinostat and PLK1i showed synergistic interaction in vitro, but not in vivo. Therefore, further screening of blood–brain barrier penetrating PLK1i is warranted to determine the true potential of the combination as no on-target activity was observed after PLK1i volasertib treatment in vivo.
Sonodynamic therapy and magnetic resonance-guided focused ultrasound: new therapeutic strategy in glioblastoma
Authors: Bonosi Lapo , Marino Silvia , Benigno Umberto Emanuele , Musso Sofia , Buscemi Felice , Giardina Kevin , Gerardi Rosamaria , Brunasso Lara , Costanzo Roberta , Iacopino Domenico Gerardo , Maugeri Rosario 
Published: May 2023

AbstractGlioblastoma (GB) is one of the most aggressive and difficult-to-treat brain tumors, with a poor prognosis and limited treatment options. In recent years, sonodynamic therapy (SDT) and magnetic resonance focused ultrasound (MRgFUS) have emerged as promising approaches for the treatment of GB. SDT uses ultrasound waves in combination with a sonosensitizer to selectively damage cancer cells, while MRgFUS delivers high-intensity ultrasound waves to precisely target tumor tissue and disrupt the blood–brain barrier to enhance drug delivery. In this review, we explore the potential of SDT as a novel therapeutic strategy for GB. We discuss the principles of SDT, its mechanisms of action, and the preclinical and clinical studies that have investigated its use in Gliomas. We also highlight the challenges, the limitations, and the future perspectives of SDT. Overall, SDT and MRgFUS hold promise as novel and potentially complementary treatment modalities for GB. Further research is needed to optimize their parameters and determine their safety and efficacy in humans, but their potential for selective and targeted tumor destruction makes them an exciting area of investigation in the field of brain cancer therapy.
Separability, Boxicity, and Partial Orders
Authors: Díaz-Báñez José-Miguel , Horn Paul , Lopez Mario A. , Marín Nestaly , Ramírez-Vigueras Adriana , Solé-Pi Oriol , Stevens Alex , Urrutia Jorge 
Published: May 2023

AbstractA collection $$S=\{S_i, \ldots , S_n\}$$

S
=
{

S
i

,
…
,

S
n

}

of disjoint closed convex sets in $$\mathbb {R}^d$$

R

d

is separable if there exists a direction (a non-zero vector) $$ \overrightarrow{v}$$

v
→

of $$\mathbb {R}^d$$

R

d

such that the elements of S can be removed, one at a time, by translating them an arbitrarily large distance in the direction $$ \overrightarrow{v}$$

v
→

without hitting another element of S. We say that $$S_i \prec S_j$$

S
i

≺

S
j

if $$S_j$$

S
j

has to be removed before we can remove $$S_i$$

S
i

. The relation $$\prec $$
≺
defines a partial order $$P(S,\prec )$$

P
(
S
,
≺
)

on S which we call the separability order of S and $$ \overrightarrow{v}$$

v
→

. A partial order $$P(X, \prec ')$$

P
(
X
,

≺
′

)

on $$X=\{x_1, \ldots , x_n\}$$

X
=
{

x
1

,
…
,

x
n

}

is called a separability order if there is a collection of convex sets S and a vector $$ \overrightarrow{v}$$

v
→

in some $$\mathbb {R}^d$$

R

d

such that $$x_i \prec ' x_j$$

x
i

≺
′

x
j

in $$P(X, \prec ')$$

P
(
X
,

≺
′

)

if and only if $$S_i \prec S_j$$

S
i

≺

S
j

in $$P(S,\prec )$$

P
(
S
,
≺
)

. We prove that every partial order is the separability order of a collection of convex sets in $$\mathbb {R}^4$$

R

4

, and that any poset of dimension 2 is the separability order of a set of line segments in $$\mathbb {R}^3$$

R

3

. We then study the case when the convex sets are restricted to be boxes in d-dimensional spaces. We prove that any partial order is the separability order of a family of disjoint boxes in $$\mathbb {R}^d$$

R

d

for some $$d \le \lfloor \frac{n}{2} \rfloor +1$$

d
≤
⌊

n
2

⌋
+
1

. We prove that every poset of dimension 3 has a subdivision that is the separability order of boxes in $$\mathbb {R}^3$$

R

3

, that there are partial orders of dimension 2 that cannot be realized as box separability in $$\mathbb {R}^3$$

R

3

and that for any d there are posets with dimension d that are separability orders of boxes in $$\mathbb {R}^3$$

R

3

. We also prove that for any d there are partial orders with box separability dimension d; that is, d is the smallest dimension for which they are separable orders of sets of boxes in $$\mathbb {R}^d$$

R

d

.
Assessing the validity and responsiveness of a generic preference quality of life measure in the context of posttraumatic stress disorder
Authors: Matthews Sheradyn R. , Elizabeth Marja , Roberts Larissa N. , Kaambwa Billingsley , Wade Tracey D. , Nixon Reginald D. V. 
Published: May 2023

Abstract
Purpose
There is limited research exploring the usefulness of generic preference-based quality of life (GPQoL) measures used to facilitate economic evaluation in the context of posttraumatic stress disorder (PTSD). The aim of the current study was to explore the validity and responsiveness of a common GPQoL measure (Assessment of Quality of Life 8 Dimension [AQoL-8D]) in relation to a PTSD condition-specific outcome measure (Posttraumatic Stress Disorder Checklist for the DSM-5 [PCL-5]).

Method
This aim was investigated in a sample of individuals (N = 147) who received trauma-focused cognitive-behavioural therapies for posttraumatic stress disorder. Convergent validity was investigated using spearman’s correlations, and the level of agreement was investigated using Bland–Altman plots. Responsiveness was investigated by exploring the standardised response means (SRM) from pre-post-treatment across the two measures, which allow the comparison of the magnitude of change between the measures over time.

Results
Correlations between the AQoL-8D (dimensions, utility and summary total scores) and the PCL-5 total score ranged from small to large and agreement between the measures was considered moderate to good. While SRMs were large for the AQoL-8D and PCL-5 total scores, the SRM for the PCL-5 was nearly double that of the AQoL-8D.

Conclusion
Our findings demonstrate that the AQoL-8D has good construct validity but present preliminary evidence that economic evaluations using only GPQoL measures may not fully capture the effectiveness of PTSD treatments.
Contribution of area-based fisheries management measures to fisheries sustainability and marine conservation: a global scoping review
Authors: Petza Dimitra , Anastopoulos Panagiotis , Kalogirou Stefanos , Coll Marta , Garcia Serge , Kaiser Michel , Koukourouvli Nikoletta , Lourdi Irene , Rice Jake , Sciberras Marija , Katsanevakis Stelios 
Published: May 2023

AbstractArea-based fisheries management measures (ABFMs) are commonly related to the sustainable use of resources but are increasingly considered broader conservation measures. This Scoping Review (ScR) identified and mapped the evidence base regarding the contribution of ABFMs to fisheries sustainability and marine conservation. The ScR was conducted following the JBI methodology and the PRISMA statement. A total of 2,391 documents were identified, and following a two-stage screening process, 151 documents were eventually included in the ScR for full review and data extraction. Most of the documents were published during the last 12 years. Studies had a wide geographical distribution (mainly located in Europe and North America), were primarily conducted at the subnational level, concerned fishing restrictions of towed gears, and assessed ABFMs from a single stock’s perspective. ABFMs identified were of various types, and the use of terminology was not consistent in the literature. Multiple combinations of data collection (primarily experimental surveys/sampling and open data sources) and analysis methods (most commonly, fisheries and ecological analyses and modelling) were applied (often in combination), using a variety of different metrics. Various knowledge gaps emerged, mainly related to the study of ABFMs networks and the application of an interdisciplinary and ecosystem-based approach for assessing ABFMs. The social, economic, and environmental impact of ABFMs was positive in most cases (56%) and in less cases negative (22%) or mixed (14%). This ScR is a valuable source of information for the contribution of ABFMs to rebuilding marine ecosystems and attaining CBD conservation targets through the lens of the OECM concept.
Graphical abstract
A diachronic perspective on citation latency in Wikipedia articles on CRISPR/Cas-9: an exploratory case study
Authors: Schmidt Marion , Kircheis Wolfgang , Simons Arno , Potthast Martin , Stein Benno 
Published: May 2023

AbstractThis paper analyzes Wikipedia’s representation of the Nobel Prize winning CRISPR/Cas9 technology, a method for gene editing. We propose and evaluate different heuristics to match publications from several publication corpora against Wikipedia’s central article on CRISPR and against the complete Wikipedia revision history in order to retrieve further Wikipedia articles relevant to the topic and to analyze Wikipedia’s referencing patterns. We explore to what extent the selection of referenced literature of Wikipedia’s central article on CRISPR adheres to scientific standards and inner-scientific perspectives by assessing its overlap with (1) the Web of Science (WoS) database, (2) a WoS-based field-delineated corpus, (3) highly-cited publications within this corpus, and (4) publications referenced by field-specific reviews. We develop a diachronic perspective on citation latency and compare the delays with which publications are cited in relevant Wikipedia articles to the citation dynamics of these publications over time. Our results confirm that a combination of verbatim searches by title, DOI, and PMID is sufficient and cannot be improved significantly by more elaborate search heuristics. We show that Wikipedia references a substantial amount of publications that are recognized by experts and highly cited, but that Wikipedia also cites less visible literature, and, to a certain degree, even not strictly scientific literature. Delays in occurrence on Wikipedia compared to the publication years show (most pronounced in case of the central CRISPR article) a dependence on the dynamics of both the field and the editor’s reaction to it in terms of activity.
Improving conformance checking in process modelling: a multiperspective algorithm
Authors: Calheno Rui , Carvalho Paulo , Rito Lima Solange , Rangel Henriques Pedro , Ramos Merino Mateo 
Published: May 2023

AbstractBusiness process model and notation (BPMN) is a popular notation used for process modelling mainly due to its high expressiveness. However, BPMN has shortcomings when dealing with specific domains (namely Hazard Analysis and Critical Control Points systems), struggling to model activity duration, quality control points, activity effects and monitoring nature. To tackle these limitations, the business process model and notation extended expressiveness (BPMN-E2) was proposed. In this paper, a multiperspective conformance checking algorithm is developed focusing on detecting non-conformity between an event log and a process model, regarding the information provided by the new elements within BPMN-E2. The proposed algorithm follows a two-step approach that starts by converting the model into a directly follows model (annotated with conformance rules), which is then used in a second phase to perform conformance checking effectively. This modular approach allows to apply the proposed algorithm to other process model notations than BPMN-E2. An event log clustering technique was also developed to downsize large-event logs without compromising data relevance. In this way, both the multiperspective algorithm and the log-downsize clustering technique here proposed are a key contribution to improve conformance checking in process modelling, as evinced in the proof-of-concept provided.
Hematopoietic stem cells on the crossroad between purinergic signaling and innate immunity
Authors: Franczak Stephanie , Ulrich Henning , Ratajczak Mariusz Z. 
Published: May 2023

AbstractHematopoiesis is regulated by several mediators such as peptide-based growth factors, cytokines, and chemokines, whose biological effects have been studied for many years. However, several other mediators have been identified recently that affect the fate of hematopoietic stem/progenitor cells (HSPC) as well as non-hematopoietic cells in the bone marrow microenvironment. These new mediators comprise members of purinergic signaling pathways and are active mediators of the soluble arm of innate immunity, the complement cascade (ComC). In this review, we will discuss the coordinated effects of these pathways in regulating the biology of HSPC. Importantly, both purinergic signaling and the ComC are activated in stress situations and interact with specific receptors expressed on HSPC. Evidence has accumulated indicating that some of the purinergic as well as ComC receptors could also be activated intracellularly by intrinsically expressed ligands. To support this recent evidence, our work indicates that the major mediator of purinergic signaling, adenosine triphosphate, and the cleavage product of the fifth component of the ComC (C5), C5a anaphylatoxin, can activate their corresponding receptors expressed on the outer mitochondrial membrane in an autocrine manner. We will also discuss recent evidence that these responses, mediated by purinergic signaling and the ComC network, are coordinated by activation of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 2 - reactive oxygen species - NLR family pyrin domain containing 3 (NLRP3) inflammasome (Nox2-ROS-NLRP3) axis.
Performance comparison of IHACRES, random forest and copula-based models in rainfall-runoff simulation
Authors: Nazeri Tahroudi Mohammad , Ahmadi Farshad , Mirabbasi Rasoul 
Published: May 2023

AbstractIn this study, two models of Random Forest and copula-based simulation were used to evaluate the accuracy and efficiency of the IHACRES rainfall-runoff model in simulating the daily discharge of the Siminehroud River in the south of Lake Urmia basin, Iran. A trivariate copula-based model was created using discharge, rainfall and temperature data on a daily scale in the period 1992–2018. Vine family models and their conditional densities were used to implement the copula-based model. By calibrating the IHACRES model and also selecting the tree sequence in accordance with the data, rainfall-runoff simulations were performed in the study area. The accuracy and efficiency of the studied models were evaluated using RMSE and NSE criteria, and also violin plot and Taylor diagram. The results of comparing the error rate of rainfall-runoff simulation in the study area showed that the vine-based model reduces the RMSE statistics by about 14.5 and 16.5%, respectively, compared to the IHACRES and Random Forest models. According to the presented diagrams, the efficiency and certainty of IHACRES and copula-based simulation models are acceptable. While the Random Forest model does not have acceptable accuracy and efficiency in the study area. The copula-based simulation model has a good performance due to the unique tree sequence as well as involving the marginal distributions fitted to the data. Although the copula-based simulation model has increased the efficiency of the model in simulating the daily discharge by about 5% compared to the IHACRES model, it is not significant compared to the mathematical complexity of the copula-based model.
Ultrasonic-assisted removal of cationic and anionic dyes residues from wastewater using functionalized triptycene-based polymers of intrinsic microporosity (PIMs)
Authors: Amin Mohamed O. , Al-Hetlani Entesar , Antonangelo Ariana R. , Zhou Haoli , Carta Mariolino 
Published: May 2023

AbstractIn this work, a series of hypercrosslinked polymers of intrinsic microporosity (HCP-PIMs), namely nitro-triptycene (TRIP-NO2), amino-triptycene (TRIP-NH2), sulfonated-triptycene (TRIP-SO3H) and hydrocarbon-triptycene (TRIP-HC), are employed for the adsorption of organic dyes from wastewater. The materials show the efficient removal of cationic (malachite green, MG) and anionic (methyl orange, MO) dyes. The adsorption parameters herein investigated include the initial pH, the adsorbate concentration and the contact time, with the aim to elucidate their effect on the adsorption process. Furthermore, the adsorption kinetic and isotherms are studied, and the findings suggest the results fit well with pseudo-second-order kinetics and Langmuir model. The reported maximum adsorption capacity is competitive for all the tested polymers. More specifically, TRIP-SO3H and TRIP-HC exhibit adsorptions of ~ 303 and ~ 270 mg g−1 for MG and MO, respectively. The selectivity toward cationic and anionic dyes is assessed by mixing the two dyes, and showing that TRIP-HC completely removes both species, whereas TRIP-NO2, TRIP-NH2 and TRIP-SO3H show an enhanced selectivity toward the cationic MG, compared to the anionic MO. The effect of the type of water is assessed by performing ultrasonic-assisted adsorption experiments, using TRIP-SO3H and TRIP-HC in the presence of either tap or seawater. The presence of competing ions and their concentrations is evaluated by ICP-MS. Our study shows that tap water does not have a detrimental effect on the adsorption of both polymers, whereas, in the presence of seawater, the performance of TRIP-HC toward MO proved to be more stable than MG with TRIP-SO3H, which is probably due to a larger concentration of competing ions. Comparison between ultrasonic-assisted and magnetic stirring adsorption demonstrates that the former exhibits a greater efficiency. This seems due to a more rapid mass transfer, driven by the formation of high velocity micro-jets, acoustic microstreaming and shock waves, at the polymer surface. Reusability studies show a good stability up to five adsorption–desorption cycles.
Spatial evaluation of climate change-induced drought characteristics in different climates based on De Martonne Aridity Index in Iran
Authors: Jafarpour Mohammad , Adib Arash , Lotfirad Morteza , Kisi Özgur 
Published: May 2023

AbstractIn recent years, greenhouse gas emissions have caused extensive changes in the global climate. Climate change leads to extreme events, such as droughts. The present study investigates precipitation and temperature variations and the past and future drought characteristics in Iran through data from 40 synoptic stations and 33 general circulation models (GCMs) under RCP4.5 and RCP8.5 scenarios. As a first step, the country of Iran was classified into different climatic regions based on De Martonne aridity index. The GCMs were ranked using TOPSIS in four climatic regions and an ensemble of top ten GCMs was used in each region. Furthermore, the homogeneity of monthly precipitation was studied in the baseline and future periods. Meteorological drought was calculated through the standardized precipitation index (SPI), deriving drought severity, peak, and duration based on run theory. The results revealed that precipitation will reduce in future periods in the majority of Iran and temperature will reduce in the south and southeast and will increase in the northwest and north of Iran. Furthermore, the highest drought severity and peaks will occur in semi-arid and arid regions, while the longest drought duration will happen in the southeast and west of Iran. Overall, future droughts are found to have higher severity, duration, peaks, and standard deviation than the baseline period. Also, the results showed a reducing trend of the SPI values in northwestern regions, while the other stations indicated no significant trend.
Combined effects of freeze–thaw cycles and chemical corrosion on triaxial mechanical properties of sandstone
Authors: Wu Jing , Lu Yani , Wang Kaibin , Cai Yang , Xiao Cong 
Published: May 2023

AbstractTo study the combined effects of freeze–thaw cycles and chemical corrosion on deterioration mechanism of triaxial mechanical properties of sandstone in cold regions, triaxial compression tests were carried out on homologous sandstone specimens after corrosion action of acidic, alkaline or neutral solution and cyclic freeze–thaw action, by taking the pH value of the hydrochemical solution and the number of freeze–thaw cycles as control parameters. The failure mode of triaxial compression is shear-slip failure, and the deviatoric stress–strain curves can be divided into four stages of compaction, linear elastic, yield, and failure. The stress–strain curves and deterioration law of triaxial mechanical properties were analyzed. With the increase of freeze–thaw cycles, the peak stress, peak strain and modulus all decrease, the deterioration degree of the rock specimens increases, and the yield plateau and plastic characteristics in the yield stage become weaker. The strong acid solution shows the largest degree of damage, and the peak stress, peak strain and modulus decreased significantly. The precipitates produced by the reaction between the strong alkaline solution and the specimens adhere to the specimen surface, pores, and fissures, thereby inhibiting further damage and deterioration. Confining pressure is an essential factor affecting the rock mechanical properties. As confining pressure increases, the strength and deformation-resistant ability of specimens increase, and the yield stage on the stress–strain curve is more obvious. The sensitivity of acidic solution to the deterioration of mechanical properties of sandstone is obviously greater than that of alkaline solution. These results provide a theoretical basis for the construction of geotechnical engineering structures in cold regions.