bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling of spatial extremes in environmental data science: time to move away from max-stable processes
Authors: Huser Raphaël , Opitz Thomas , Wadsworth Jennifer L. 
Published: January 2025

Abstract
Environmental data science for spatial extremes has traditionally relied heavily on max-stable processes. Even though the popularity of these models has perhaps peaked with statisticians, they are still perceived and considered as the “state of the art” in many applied fields. However, while the asymptotic theory supporting the use of max-stable processes is mathematically rigorous and comprehensive, we think that it has also been overused, if not misused, in environmental applications, to the detriment of more purposeful and meticulously validated models. In this article, we review the main limitations of max-stable process models, and strongly argue against their systematic use in environmental studies. Alternative solutions based on more flexible frameworks using the exceedances of variables above appropriately chosen high thresholds are discussed, and an outlook on future research is given. We consider the opportunities offered by hybridizing machine learning with extreme-value statistics, highlighting seven key recommendations moving forward.
Entire maps with rational preperiodic points and multipliers
Authors: BUFF XAVIER , GORBOVICKIS IGORS , HUGUIN VALENTIN 
Published: January 2025

Abstract
Given a number field

$\mathbb {K} \subset \mathbb {C}$

that is not contained in

$\mathbb {R}$

, we prove the existence of a dense set (with respect to the topology of local uniform convergence) of entire maps

$f \colon \mathbb {C} \rightarrow \mathbb {C}$

whose preperiodic points and multipliers all lie in

$\mathbb {K}$

. This contrasts with the case of rational maps. In addition, we show that there exists an escaping quadratic-like map that is not conjugate to an affine escaping quadratic-like map and whose multipliers all lie in

$\mathbb {Q}$

.
Knowledge, attitudes, and practices towards vector-borne diseases in changing climate in Finland
Authors: Mäkelä Henna , Dub Timothée , Nuorti J. Pekka , Sane Jussi 
Published: January 2025

Abstract
With climate change, the geographic distribution of some VBDs has expanded, highlighting the need for adaptation, and managing the risks associated with emergence in new areas. We conducted a questionnaire survey on the knowledge, attitudes, and practices (KAP) about vector-borne diseases (VBDs) among sample of Finnish residents. The questions were scored and the level of KAP was determined based on scoring as poor, fair, good, or excellent. Binary logistic regression analysis was used to evaluate the associations of different KAP levels with sex, age, education, and possible previous VPD infection. We received 491/1995 (25%) responses across the country and detected generally good knowledge, but only fair practices towards VBDs. Sex and age of the respondents were most often significantly associated with the level of KAP (P > 0.05). Despite the generally good knowledge, we detected major gaps, especially regarding the distinction of tick-borne encephalitis and Lyme borreliosis (LB), risk of disease, and protective measures. Additionally, many respondents thought the vaccination protects against LB or tick bites. This calls for awareness raising on disease risk and prevention measures. With increasing cases and the effects of climate change, surveillance of VBDs communication to the general public should be strengthened.
Teachers’ articulations of digital resources in an upper secondary programme for newly arrived migrants
Authors: Febring Linda , Risenfors Signild 
Published: January 2025

Abstract
The highly digitalised nature of contemporary society has made digital literacy important for newly arrived migrants. However, for teachers, the use of information and communication technologies can be challenging. The aim of the present study is to gain a deeper understanding of how teachers perceive digital resources as useful for teaching migrants language and subject skills. The research question is, In what way do teachers at the language introduction programme for newly arrived migrants in Sweden articulate the use of digital resources in relation to language teaching and in relation to subject teaching? This qualitative study is based on observations of 28 lessons in different subjects in the language introduction programme, as well as interviews with the observed teachers. In analysing the material, we first used the TPACK in situ model (Pareto & Willermark, 2019) to organise the data on the use of digital resources, and thereafter discourse theory (Howarth, 2005) was used to analyse the data. The results show that the teachers limited their students’ use of digital resources during the lessons, which is apparent in two discourses: distrust and dichotomy. In the discourse on distrust, digital technology is seen as an obstacle to teaching, and the discourse dichotomy is about the opposition between the digital and the physical. Moreover, articulations were often expressed in terms of identity; the teachers talked about themselves in relation to digital resources, rather than talking about how they use digital resources in their teaching.
Rural electrification, the credibility revolution, and the limits of evidence-based policy
Authors: Ankel-Peters Jörg , Schmidt Christoph M. 
Published: January 2025

Abstract
The so-called credibility revolution dominates empirical economics, with its promise of causal identification to improve scientific knowledge and ultimately policy. By examining the case of rural electrification in the Global South, this opinion paper exposes the limits of this evidence-based policy paradigm. The electrification literature boasts many studies using the credibility revolution toolkit, but at the same time, several systematic reviews demonstrate that the evidence is divided between very positive and muted effects. This bifurcation presents a challenge to the science-policy interface, where policymakers, lacking the resources to sift through the evidence, may be drawn to the results that serve their (agency's) interests. The interpretation is furthermore complicated by unresolved methodological debates circling around external validity as well as selective reporting and publication decisions. These features, we argue, are not particular to the electrification literature but inherent to the credibility revolution toolkit.
Can abatement efforts in a common pool resource promote overexploitation of the resource?
Authors: Surve Aditi A. , Espinola-Arredondo Ana 
Published: January 2025

Abstract
We examine a common pool resource (CPR) where appropriations deteriorate the quality of the resource and, thus, its impact on the exploitation of the CPR. We focus on two settings: (i) firms use the CPR without abatement efforts, and (ii) abatement is allowed. We provide comparisons between these two settings and identify socially optimal appropriation levels. We find that (i) higher quality of the CPR could induce firms to overuse the resource, and (ii) first-period appropriations with abatement decrease in the regeneration rate. However, abatement induces an overuse of the resource when the quality of the CPR improves.
Fast Inference for Probabilistic Answer Set Programs Via the Residual Program
Authors: AZZOLINI DAMIANO , RIGUZZI FABRIZIO 
Published: January 2025

AbstractWhen we want to compute the probability of a query from a probabilistic answer set program, some parts of a program may not influence the probability of a query, but they impact on the size of the grounding. Identifying and removing them is crucial to speed up the computation. Algorithms for SLG resolution offer the possibility of returning the residual program which can be used for computing answer sets for normal programs that do have a total well-founded model. The residual program does not contain the parts of the program that do not influence the probability. In this paper, we propose to exploit the residual program for performing inference. Empirical results on graph datasets show that the approach leads to significantly faster inference. The paper has been accepted at the ICLP2024 conference and under consideration in Theory and Practice of Logic Programming (TPLP).
Dominating Set Reconfiguration with Answer Set Programming
Authors: KATO MASATO , BANBARA MUTSUNORI , SCHAUB TORSTEN , SOH TAKEHIDE , TAMURA NAOYUKI 
Published: January 2025

AbstractThe dominating set reconfiguration problem is defined as determining, for a given dominating set problem and two among its feasible solutions, whether one is reachable from the other via a sequence of feasible solutions subject to a certain adjacency relation. This problem is PSPACE-complete in general. The concept of the dominating set is known to be quite useful for analyzing wireless networks, social networks, and sensor networks. We develop an approach to solve the dominating set reconfiguration problem based on answer set programming (ASP). Our declarative approach relies on a high-level ASP encoding, and both the grounding and solving tasks are delegated to an ASP-based combinatorial reconfiguration solver. To evaluate the effectiveness of our approach, we conduct experiments on a newly created benchmark set.
A novel wearable device integrating ECG and PCG for cardiac health monitoring
Authors: Zang Junbin , An Qi , Li Bo , Zhang Zhidong , Gao Libo , Xue Chenyang 
Published: January 2025

Abstract
The alarming prevalence and mortality rates associated with cardiovascular diseases have emphasized the urgency for innovative detection solutions. Traditional methods, often costly, bulky, and prone to subjectivity, fall short of meeting the need for daily monitoring. Digital and portable wearable monitoring devices have emerged as a promising research frontier. This study introduces a wearable system that integrates electrocardiogram (ECG) and phonocardiogram (PCG) detection. By ingeniously pairing a contact-type PZT heart sound sensing structure with ECG electrodes, the system achieves the acquisition of high-quality ECG and PCG signals. Notably, the signal-to-noise ratios (SNR) for ECG and PCG signals were measured at 44.13 dB and 30.04 dB, respectively, demonstrating the system’s remarkable stability across varying conditions. These collected signals were subsequently utilized to derive crucial feature values, including electromechanical delay (EMD), left ventricular ejection time (LVET), and pre-ejection period (PEP). Furthermore, we collected a dataset comprising 40 cases of ECG and PCG signals, enabling a comparative analysis of these three feature parameters between healthy individuals and coronary heart disease patients. This research endeavor presents a significant step forward in the realm of early, non-invasive, and intelligent monitoring of cardiovascular diseases, offering hope for earlier detection and more effective management of these life-threatening conditions.
Mast cells: key players in digestive system tumors and their interactions with immune cells
Authors: Shu Feihong , Yu Jie , Liu Youjia , Wang Fang , Gou Guoyou , Wen Min , Luo Chen , Lu Xianmin , Hu Yanxia , Du Qian , Xu Jingyu , Xie Rui 
Published: January 2025

Abstract
Mast cells (MCs) are critical components of both innate and adaptive immune processes. They play a significant role in protecting human health and in the pathophysiology of various illnesses, including allergies, cardiovascular diseases and autoimmune diseases. Recent studies in tumor-related research have demonstrated that mast cells exert a substantial influence on tumor cell behavior and the tumor microenvironment, exhibiting both pro- and anti-tumor effects. Specifically, mast cells not only secrete mediators related to pro-tumor function such as trypsin-like enzymes, chymotrypsin, vascular endothelial cell growth factor and histamine, but also mediators related to anti-tumor progression such as cystatin C and IL-17F. This dual role of mast cells renders them an under-recognized but very promising target for tumor immunotherapy. Digestive system tumors, characterized by high morbidity and associated mortality rates globally, are increasingly recognized as a significant healthcare burden. This paper examines the influence of mast cell-derived mediators on the development of tumors in the digestive system. It also explores the prognostic significance of mast cells in patients with various gastrointestinal cancers at different stages of the disease. Additionally, the article investigates the interactions between mast cells and immune cells, as well as the potential relationships among intratumoral bacteria, immune cells, and mast cell within digestive system microenvironment. The aim is to propose new strategies for the immunotherapy of digestive system tumors by targeting mast cells.
Cyclodehydrogenation of molecular nanographene precursors catalyzed by atomic hydrogen
Authors: Zuzak Rafal , Dabczynski Pawel , Castro-Esteban Jesús , Martínez José Ignacio , Engelund Mads , Pérez Dolores , Peña Diego , Godlewski Szymon 
Published: January 2025

Abstract
Atomically precise synthesis of graphene nanostructures on semiconductors and insulators has been a formidable challenge. In particular, the metallic substrates needed to catalyze cyclodehydrogenative planarization reactions limit subsequent applications that exploit the electronic and/or magnetic structure of graphene derivatives. Here, we introduce a protocol in which an on-surface reaction is initiated and carried out regardless of the substrate type. We demonstrate that, counterintuitively, atomic hydrogen can play the role of a catalyst in the cyclodehydrogenative planarization reaction. The high efficiency of the method is demonstrated by the nanographene synthesis on metallic Au, semiconducting TiO2, Ge:H, as well as on inert and insulating Si/SiO2 and thin NaCl layers. The hydrogen-catalyzed cyclodehydrogenation reaction reported here leads towards the integration of graphene derivatives in optoelectronic devices as well as developing the field of on-surface synthesis by means of catalytic transformations. It also inspires merging of atomically shaped graphene-based nanostructures with low-dimensional inorganic units into functional devices.
Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex
Authors: Bernhard Harald , Petržílková Hana , Popelářová Barbora , Ziemkiewicz Kamil , Bartosik Karolina , Warmiński Marcin , Tengo Laura , Gröger Henri , Dolce Luciano G. , Mackereth Cameron D. , Micura Ronald , Jemielity Jacek , Kowalinski Eva 
Published: January 2025

Abstract
Kinetoplastids are a clade of eukaryotic protozoans that include human parasitic pathogens like trypanosomes and Leishmania species. In these organisms, protein-coding genes are transcribed as polycistronic pre-mRNAs, which need to be processed by the coupled action of trans-splicing and polyadenylation to yield monogenic mature mRNAs. During trans-splicing, a universal RNA sequence, the spliced leader RNA (SL RNA) mini-exon, is added to the 5’-end of each mRNA. The 5’-end of this mini-exon carries a hypermethylated cap structure and is bound by a trypanosomatid-specific cap-binding complex (CBC). The function of three of the kinetoplastid CBC subunits is unknown, but an essential role in cap-binding and trans-splicing has been suggested. Here, we report cryo-EM structures that reveal the molecular architecture of the Trypanosoma brucei CBC (TbCBC) complex. We find that TbCBC interacts with two distinct features of the SL RNA. The TbCBP20 subunit interacts with the m7G cap while TbCBP66 recognizes double-stranded portions of the SL RNA. Our findings pave the way for future research on mRNA maturation in kinetoplastids. Moreover, the observed structural similarities and differences between TbCBC and the mammalian cap-binding complex will be crucial for considering the potential of TbCBC as a target for anti-trypanosomatid drug development.
CPK1 activates CNGCs through phosphorylation for Ca2+ signaling to promote root hair growth in Arabidopsis
Authors: Zhu Meijun , Du Bo-Ya , Tan Yan-Qiu , Yang Yang , Zhang Yang , Wang Yong-Fei 
Published: January 2025

Abstract
Cyclic nucleotide-gated channel 5 (CNGC5), CNGC6, and CNGC9 (CNGC5/6/9 for simplicity) control Arabidopsis root hair (RH) growth by mediating the influx of external Ca2+ to establish and maintain a sharp cytosolic Ca2+ gradient at RH tips. However, the underlying mechanisms for the regulation of CNGCs remain unknown. We report here that calcium dependent protein kinase 1 (CPK1) directly activates CNGC5/6/9 to promote Arabidopsis RH growth. The loss-of-function mutants cpk1-1, cpk1-2, cngc5-1 cngc6-2 cngc9-1 (shrh1/short root hair 1), and cpk1 shrh1 show similar RH phenotypes, including shorter RHs, more RH branching, and dramatically attenuated cytosolic Ca2+ gradients at RH tips. The main CPK1-target sites are identified as Ser20, Ser27, and Ser26 for CNGC5/6/9, respectively, and the corresponding alanine substitution mutants fail to rescue RH growth in shrh1 and cpk1-1, while phospho-mimic versions restore the cytosolic Ca2+ gradient at RH apex and rescue the RH phenotypes in the same Arabidopsis mutants. Thus we discover the CPK1-CNGC modules essential for the Ca2+ signaling regulation and RH growth in Arabidopsis.
Syntalos: a software for precise synchronization of simultaneous multi-modal data acquisition and closed-loop interventions
Authors: Klumpp Matthias , Embray Lee , Heimburg Filippo , Alves Dias Ana Luiza , Simon Justus , Groh Alexander , Draguhn Andreas , Both Martin 
Published: January 2025

Abstract
Complex experimental protocols often require multi-modal data acquisition with precisely aligned timing, as well as state- and behavior-dependent interventions. Tailored solutions are mostly restricted to individual experimental setups and lack flexibility and interoperability. We present an open-source, Linux-based integrated software solution, called ‘Syntalos’, for simultaneous acquisition and synchronization of data from an arbitrary number of sources, including multi-channel electrophysiological recordings and different live imaging devices, as well as closed-loop, real-time interventions with different actuators. Precisely matching timestamps for all inputs are ensured by continuous statistical analysis and correction of individual devices’ timestamps. New data sources can be integrated with minimal programming skills. Data is stored in a comprehensively structured format to facilitate pooling or sharing data between different laboratories. Syntalos enables precisely synchronized multi-modal recordings as well as closed-loop interventions for multiple experimental approaches. Preliminary neuroscientific experiments on mice with different research questions show the successful performance and easy-to-learn structure of the software suite.
Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)
Authors: Krawczyk Katarzyna , Szablińska-Piernik Joanna , Paukszto Łukasz , Maździarz Mateusz , Sulima Paweł , Przyborowski Jerzy Andrzej , Szczecińska Monika , Sawicki Jakub 
Published: January 2025

Abstract

Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with a cosmopolitan distribution among a wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into the genetic aspects of this species is limited. In this study, the chromosome-scale telomere-to-telomere genome of R. sorocarpa was assembled exclusively by Oxford Nanopore long-read sequencing and Pore-C technology. A high-quality chromosomal-scale assembly was obtained with a final genome size of 376.690 Mbp, contig N50 of 49.132 Mbp and 97.02% of the assembled contigs associated with the eight chromosomes. Genome assembly completeness was confirmed by BUSCO analysis accounting 91.8%. Among 27,626 total genes, 23,562 (85.29%) were functionally annotated. Moreover, collinearity of Marchantiales was analyzed as well as gene family evolution and DNA methylation profile. The availability of this genome, which is the second telomere-to-telomere liverwort assembly, opens up new avenues for in-depth analysis of R. sorocarpa genetic diversity and genomic characteristics.
Comprehensive genome-scale CRISPR knockout screening of CHO cells
Authors: Shin Sung Wook , Kim Su Hyun , Gasselin Aghiles , Lee Gyun Min , Lee Jae Seong 
Published: January 2025

Abstract
Chinese hamster ovary (CHO) cells play a pivotal role in the production of recombinant therapeutics. In the present study, we conducted a genome-scale pooled CRISPR knockout (KO) screening using a virus-free, recombinase-mediated cassette exchange-based platform in CHO-K1 host and CHO-K1 derived recombinant cells. Genome-wide guide RNA (gRNA) amplicon sequencing data were generated from cell libraries, as well as short- and long-term KO libraries, and validated through phenotypic assessment and gRNA read count distribution. Additionally, we obtained gRNA amplicon sequencing data from the highly productive recombinant cell populations. By analyzing these datasets, essential genes involved in cell fitness as well as functional target genes associated with therapeutic protein production can be identified. Collectively, our next-generation sequencing datasets, derived from a robust and reliable CRISPR screening method, provide valuable insights into CHO genomic functions, advancing the development of next-generation CHO factories.
A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples
Authors: Bai Xiangning , Rayner Simon , Skuggen Linda Ellevog , Engseth Kine Kragl , Bjørnstad Pål Marius , Dalland Marianne , Gilfillan Gregor D. , Bjørås Magnar , Matussek Andreas 
Published: January 2025

Abstract
The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation of respiratory microbiota. Here, we performed a pilot study to assess the suitability of the NAxtra nucleic acid extraction protocol for profiling bacterial microbiota in respiratory samples. A small number of nasopharyngeal aspirate (n = 8), nasal swab (n = 8), and saliva samples (n = 8) were collected, nucleic acids were isolated using the NAxtra protocol, and 16 S rRNA gene sequencing was performed to characterize bacterial microbiota, which were compared to the same sample types from previous studies using other protocols. The bacterial composition in nasal and saliva samples were consistent with previous reports. Saliva microbiota was significantly richer than nasal microbiota and varied less among individual samples than nasal microbiota. Bacterial composition in nasal samples was distinct from nasopharyngeal aspirates, but closer to saliva samples. A sequencing depth of 50,000 reads/sample was sufficient for microbiota profiling in low biomass respiratory samples. Our pilot study indicates the potential of the NAxtra protocol for bacterial microbiota characterization of low-microbial biomass samples and supports a more comprehensive study to fully evaluate the value of the NAxtra protocol in microbiota research and clinical diagnostics of respiratory pathogens.