bluuebunny/crossref_metadata_2025_split huggingface dataset:
Queen reflections: a modification of Wythoff Nim
Authors: Fokkink Robbert , Rust Dan 
Published: November 2022

Abstract
Wythoff Nim is a classical combinatorial game of queen moves on a chessboard. There are many ways to describe its P-positions (safe positions to move to). One way is to code them by the Fibonacci word 010010100100101..., which is the unique fixed point of the substitution of 0 by 01, and of 1 by 0. The coordinates of the n-th P-position are encoded by the location of the n-th zero and the n-th one in the Fibonacci word. We show that a minor modification of the rules of Wythoff Nim leads to a game with P-positions that are coded by 010010010010100100... This word can be derived by deleting all 2’s from the Tribonacci word, which is the unique fixed point of the substitution of 0 by 01, of 1 by 02, and of 2 by 0.
Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
Authors: Kuswanto Wilson , Nolan Garry , Lu Guolan 
Published: November 2022

AbstractMultiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.
Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness
Authors: Šimon Martin , Mikec Špela , Morton Nicholas M. , Atanur Santosh S. , Konc Janez , Horvat Simon , Kunej Tanja 
Published: November 2022

AbstractAlternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.
Influence of convective processes on weather research and forecasting model precipitation biases over East Asia
Authors: Sugimoto Shiori , Xue Yongkang , Sato Tomonori , Takahashi Hiroshi G. 
Published: November 2022

AbstractDynamical downscaling with a 20 km horizontal resolution was undertaken over East Asia for the period May–August in 1991–2015 using the Weather Research and Forecasting (WRF) model with Grell-3D ensemble cumulus parameterization as a product of the Impact of Initialized Land Temperature and Snowpack on Sub-Seasonal to Seasonal Prediction (LS4P) program. Simulated climatological precipitation biases were investigated over land during June when heavy precipitation occurred. Simulations underestimated precipitation along the Meiyu/Baiu rainband, while overestimating it farther north. Dry and wet biases expanded to south and north of the Yangtze River in China, respectively, marking years with poor precipitation simulations. Model biases in synoptic-scale circulation patterns indicate a weakened clockwise circulation over the western North Pacific in the model due to active convection there, and suppressed northward moisture transport to the Meiyu/Baiu rainband. Moisture convergence was slightly enhanced over central China due to an apparent anticyclonic circulation bias over northern China. In years with large biases, positive feedback between reduced moisture inflow and inactive convection occurred over southern China, while moisture transport to central China intensified on regional scales, with amplification of dry and wet biases over China. The Kain–Fritch scheme was used to test the influence of cumulus parameterization, improving the dry bias over southern China due to the modification of synoptic-scale circulation patterns in the lower troposphere. However, precipitation was further overestimated over central China, with the accuracy of precipitation distribution deteriorating.
Heterogeneity of persisting symptoms after sport-related concussion (SRC): exploring symptom subtypes and patient subgroups
Authors: Langdon S. , Goedhart E. , Inklaar M. , Oosterlaan J. , Königs M. 
Published: November 2022

AbstractThis study aimed to explore the heterogeneity of persisting symptoms after sport-related concussion (SRC). We examined the structure of symptom subtypes within 163 patients with SRC (M = 16.7 weeks post-injury). Subsequently, we investigated the existence of subgroups of patients based on comparable configuration of co-occurring symptom subtypes. To explore factors that may contribute to the emergence of SRC patient subgroups, subgroups were compared on pre-injury (i.e., demographics and medical history), personality (Severity Indices of Personality Problems Short Form) and SRC characteristics (i.e., history of prior concussions, loss of consciousness and post-traumatic amnesia). To investigate the relevance of SRC subgrouping for clinical outcome, subgroups were compared on symptom severity (Sport Concussion Assessment Tool 5). The results provide empirical evidence for the existence of symptom subtypes, characterized as a: neurocognitive, fatigue, emotional, migraine and vestibular-ocular symptom subtype in patients with persisting SRC. Study results also showed evidence for the existence of SRC subgroups of patients with a comparable configuration of co-occurring prevailing symptom subtypes, including a neurocognitive-migraine, fatigue, migraine-emotional and neurocognitive-emotional subgroup. The subgroups differed on pre-injury, personality and SRC characteristics, suggesting that these factors may contribute to the emergence of specific SRC patient subgroups. The subgroups also differed in the severity of persisting symptoms, highlighting the clinical relevance of SRC subgrouping. These results support the idea that patient subgroups with persisting SRC with a comparable pattern of co-occurring symptom subtypes exists, which may require targeted prognosis, clinical management and treatment to optimize recovery.
Plasma cell neoplasms and related entities—evolution in diagnosis and classification
Authors: Fend Falko , Dogan Ahmet , Cook James R. 
Published: November 2022

Abstract
Plasma cell neoplasms including multiple myeloma (MM) and related terminally differentiated B-cell neoplasms are characterized by secretion of monoclonal immunoglobulin and stepwise development from a preneoplastic clonal B and/or plasma cell proliferation called monoclonal gammopathy of undetermined significance (MGUS). Diagnosis of these disorders requires integration of clinical, laboratory, and morphological features. While their classification mostly remains unchanged compared to the revised 2016 WHO classification and the 2014 International Myeloma Working Group consensus, some changes in criteria and terminology were proposed in the 2022 International Consensus Classification (ICC) of mature lymphoid neoplasms. MGUS of IgM type is now divided into IgM MGUS of plasma cell type, precursor to the rare IgM MM and characterized by MM-type cytogenetics, lack of clonal B-cells and absence of MYD88 mutation, and IgM MGUS, NOS including the remaining cases. Primary cold agglutinin disease is recognized as a new entity. MM is now formally subdivided into cytogenetic groups, recognizing the importance of genetics for clinical features and prognosis. MM with recurrent genetic abnormalities includes MM with CCND family translocations, MM with MAF family translocations, MM with NSD2 translocation, and MM with hyperdiploidy, with the remaining cases classified as MM, NOS. For diagnosis of localized plasma cell tumors, solitary plasmacytoma of bone, and primary extraosseous plasmacytoma, the importance of excluding minimal bone marrow infiltration by flow cytometry is emphasized. Primary systemic amyloidosis is renamed immunoglobulin light chain amyloidosis (AL), and a localized AL amyloidosis is recognized as a distinct entity. This review summarizes the updates on plasma cell neoplasms and related entities proposed in the 2022 ICC.

Key points
• Lymphoplasmacytic lymphoma can be diagnosed with lymphoplasmacytic aggregates in trephine biopsies < 10% of cellularity and evidence of clonal B-cells and plasma cells.
• IgM MGUS is subdivided into a plasma cell type and a not otherwise specified (NOS) type.
• Primary cold agglutinin disease is recognized as a new entity.
• The term “multiple myeloma” replaces the term “plasma cell myeloma” used in the 2016 WHO classification.
• Multiple myeloma is subdivided into 4 mutually exclusive cytogenetic groups and MM NOS.
• Minimal bone marrow infiltration detected by flow cytometry is of major prognostic importance for solitary plasmacytoma of bone and to a lesser extent for primary extraosseous plasmacytoma.
• Localized IG light chain amyloidosis is recognized as a separate entity, distinct from systemic immunoglobulin light chain (AL) amyloidosis.
Remarkably high blue ring occurrence in Estonian Scots pines in 1976 reveals wood anatomical evidence of extreme autumnal cooling
Authors: Greaves Ciara , Crivellaro Alan , Piermattei Alma , Krusic Paul J. , Oppenheimer Clive , Potapov Aleksei , Hordo Maris , Metslaid Sandra , Kask Regino , Kangur Ahto , Büntgen Ulf 
Published: November 2022

Abstract
Key message
An exceptionally high number of blue rings were formed within and between Scots pine trees from Estonia in 1976: a year that is well known for its outstanding summer heatwave over Western Europe, but its extreme autumnal cooling over Eastern Europe has so far been neglected in scientific literature.

Abstract
‘Blue rings’ (BRs) are visual indicators of less lignified cell walls typically formed towards the end of a tree’s growing season. Though BRs have been associated with ephemeral surface cooling, often following large volcanic eruptions, the intensity of cold spells necessary to produce BRs, as well as the consistency of their formation within and between trees still remains uncertain. Here, we report an exceptionally high BR occurrence within and between Scots pine (Pinus sylvestris L.) trees at two sites in Estonia, including the first published whole-stem analysis for BRs. Daily meteorological measurements from a nearby station allowed us to investigate the role temperature has played in BR formation since the beginning of the twentieth century. The single year in which BRs were consistently formed within and amongst most trees was 1976. While the summer of 1976 is well known for an exceptional heatwave in Northwest Europe, mean September and October temperatures were remarkably low over Eastern Europe, and 3.8 °C below the 1961–1990 mean at our sites. Our findings contribute to a better eco-physiological interpretation of BRs, and further demonstrate their ability to reveal ephemeral cooling not captured by dendrochronological ring width and latewood density measurements.
SMT solving for the validation of B and Event-B models
Authors: Schmidt Joshua , Leuschel Michael 
Published: November 2022

AbstractProBprovides a constraint solver for the B-method written in Prolog and can make use of different backends based on SAT and SMT solving. One such backend translates B and Event-B operators to SMT-LIB using the Z3 solver. This translation uses quantifiers to axiomatize some operators, which are not well-handled by Z3. Several relational constraints such as the transitive closure are not supported by this translation. In this article, we substantially improve the translation to SMT-LIB by employing a more constructive rather than axiomatized style using Z3’s lambda function. Thereby, we are able both to translate more B and Event-B operators to SMT-LIB and improve the overall performance. We further extendProB’s interface to Z3 to run different solver configurations in parallel. In addition, we present a direct implementation of SMT solving in Prolog usingProB’s constraint solver as a theory solver. We hereby aim to combine the strengths of conflict-driven clause learning for identifying contradictions withProB’s constraint solver for finding solutions. We deem this implementation to be worthwhile sinceProB’s constraint solver is tailored toward solving B and Event-B constraints, and we herewith avoid the dependency on an external SMT solver. Empirical results show that the new integration of Z3 has improved performance of constraint solving and enables to solve several constraints which cannot be solved byProB’s constraint solver. Furthermore, the direct implementation of SMT solving inProBshows benefits compared toProB’s constraint solver and the integration of Z3.
Spectrum and mortality of opportunistic infections among HIV/AIDS patients in southwestern China
Authors: Meng Sirun , Tang Qiao , Xie Zhiman , Wu Nianning , Qin Yingmei , Chen Rongfeng , Chen Xiaoyu , Chen Xiu , Li Yueqi , Shi Minjuan , Ye Li , Liang Hao , Jiang Junjun , Zhou Bo , Lin Jianyan 
Published: November 2022

AbstractWe describe the opportunistic infections (OIs) of HIV/AIDS to understand the spectrum, mortality, and frequency of multiple coinfected OIs among HIV/AIDS patients in southern China, where OIs are severe. We carried out a retrospective cohort study of hospitalized HIV-infected individuals at the Fourth People’s Hospital of Nanning, Guangxi, China, from Jan. 2011 to May. 2019. The chi-square test was used to analyze cross-infection; the Kaplan‒Meier analysis was used to compare mortality. A total of 12,612 HIV-infected patients were admitted to this cohort study. Among them, 8982 (71.2%) developed one or more OIs. The overall in-hospital mortality rate was 9.0%. Among the patients, 35.6% coinfected one OI, and 64.4% coinfected more than two OIs simultaneously. Almost half of the patients (60.6%) had CD4 + T-cell counts < 200 cells/μL. Pneumonia (39.8%), tuberculosis (35.3%), and candidiasis (28.8%) were the most common OIs. Coinfected cryptococcal meningitis and dermatitis are the most common combined OIs. The rate of anaemia (17.0%) was highest among those common HIV-associated complications. Multiple OIs are commonly found in hospitalized HIV/AIDS patients in southwestern China, which highlights the need for improved diagnosis and treatment.
Significance of cardiovascular comorbidity in patients with chronic myelomonocytic leukemia
Authors: Lackner David , Geissler Klaus 
Published: November 2022

SummaryIn a retrospective study, we analyzed the prevalence of common cardiovascular comorbidities in 310 patients with chronic myelomonocytic leukemia (CMML), their potential prognostic impact, and potential correlations with laboratory and molecular features. 115 (36%) patients had a documented cardiovascular comorbidity. In these patients, coronary heart disease 41/115 (36%), atrial fibrillation 34/115 (29%), and hypertension 75/115 (64%) were documented. None of these conditions had a significant impact on survival. Unexpectedly, patients with cardiovascular comorbidity had a lower number of circulating blasts and a lower prevalence of EZH2 mutations. Moreover, time to transformation was significantly longer in these patients. Cardiovascular comorbidity does not seem to have a major impact on prognosis in CMML patients. The unexpected lower transformation rate in these patients needs to be further investigated.
An extended modelling technique with generalized strains for flexible multibody systems
Authors: Meijaard J. P. 
Published: November 2022

AbstractA new method, which is an extension of a finite-element formulation, introduces generalized strains related to nodal coordinates by implicit equations, which can be treated as constraints. This formulation allows a larger freedom in developing elements, so it eases the building of elements with a higher accuracy. In many cases, this enables modelling flexible multibody systems with fewer elements and fewer degrees of freedom for a given accuracy or using more accurate models. Because the systems are modelled with coordinates and constraints, all familiar analysis techniques can be applied, such as simulation, calculation of static solutions, linearization and an input–output description. The method is tested for planar and spatial beam elements based on assumed strains. Some examples of large static deflection and dynamics are presented, which show the advantage over some existing element formulations.
Special Issue Conclusion
Authors: Bucher Hannah , Stroppe Anne-Kathrin , Burger Axel M. , Faas Thorsten , Schoen Harald , Debus Marc , Roßteutscher Sigrid , Cohen Denis , Huber Robert A. , Jankowski Michael , John Melvin , Menzner Jan , Schimpf Christian H. , Schnaudt Christian , Steiner Nils D. , Traunmüller Richard , Unkelbach Fabienne , Vogel Vera , Wegscheider Carsten , Welz Robert , Wuttke Alexander 
Published: November 2022

AbstractThe GLES Open Science Challenge 2021 was a pilot project aimed at demonstrating that registered reports are an appropriate and beneficial publication format in quantitative political science that helps to increase transparency and replicability in the research process and thus yields substantial and relevant contributions to our discipline. The project resulted in the publication of this special issue, which includes seven registered reports based on data from the German Longitudinal Election Study (GLES) collected in the context of the 2021 German federal election. This concluding article of the special issue brings together the perspectives of the participating authors, reviewers, organizers, and editors in order to take stock of the different experiences gained and lessons learned in the course of the project. We are confident that future projects of a similar nature in political science, as well as authors, reviewers, and editors of registered reports, will benefit from these reflections.
Biodegradable methylcellulose biopolymer-derived activated porous carbon for dual energy application
Authors: Nath Gaurav , Singh Pramod K. , Dhapola Pawan Singh , Sharma Tejas , Patil Girish P. , Jadhav Chandradip D. , Singh Abhimanyu , Konwar Subhrajit , Savilov Serguei V. , Singh Diksha , Yahya M. Z. A. 
Published: November 2022

AbstractActivated porous carbon was synthesized from methylcellulose biopolymer through a two-step mechanism involving H3PO4 as an activating agent and then thermally carbonized in a tubular furnace under an inert atmosphere at 850 °C. The product was next rinsed with strong HCl, neutralized with deionized water, and dried in an oven at 80 °C. Then, to fully understand the behavior of the activated porous carbon, it was characterized using techniques such as X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS), RAMAN spectroscopy, Brunauer–Emmett–Teller (BET), and thermal gravimetric analysis (TGA). Additionally, we have created dye-sensitive solar cells and an electric double-layer capacitor (EDLC) using this porous carbon produced from methylcellulose (DSSC). We used the above-mentioned prepared porous carbon for the electrode portion of the Electric Double-Layer Capacitor (EDLC) fabrication, and the maximized polymer electrolyte film made from the methyl cellulose (MC) biopolymer combined with 60 wt.% of 1-ethyl-3-methylimidazolium tricyanomethanide ionic liquid (IL), with a maximum conductivity of 1.93 × 10−2 S/cm, for the electrolyte. The fabricated EDLC device shows a specific capacitance of 60.8 F/gm at 5 mV/s scan rate which was confirmed by cyclovoltammetry and a low-frequency impedance plot in the CH electrochemical workstation. The DSSC device was fabricated using the same porous carbon as a material for the counter-electrode and the same composition polymer electrolyte that had been used in the EDLC as the electrolyte for the DSSC which yields an efficiency of 0.86%. The fill factor and other parameters were also calculated from the JV characteristics that had been characterized and obtained in the solar simulator.
Effect of lysergic acid diethylamide (LSD) on reinforcement learning in humans
Authors: Kanen Jonathan W. , Luo Qiang , Rostami Kandroodi Mojtaba , Cardinal Rudolf N. , Robbins Trevor W. , Nutt David J. , Carhart-Harris Robin L. , den Ouden Hanneke E. M. 
Published: November 2022

AbstractBackgroundThe non-selective serotonin 2A (5-HT2A) receptor agonist lysergic acid diethylamide (LSD) holds promise as a treatment for some psychiatric disorders. Psychedelic drugs such as LSD have been suggested to have therapeutic actions through their effects on learning. The behavioural effects of LSD in humans, however, remain incompletely understood. Here we examined how LSD affects probabilistic reversal learning (PRL) in healthy humans.MethodsHealthy volunteers received intravenous LSD (75μg in 10 mL saline) or placebo (10 mL saline) in a within-subjects design and completed a PRL task. Participants had to learn through trial and error which of three stimuli was rewarded most of the time, and these contingencies switched in a reversal phase. Computational models of reinforcement learning (RL) were fitted to the behavioural data to assess how LSD affected the updating (‘learning rates’) and deployment of value representations (‘reinforcement sensitivity’) during choice, as well as ‘stimulus stickiness’ (choice repetition irrespective of reinforcement history).ResultsRaw data measures assessing sensitivity to immediate feedback (‘win-stay’ and ‘lose-shift’ probabilities) were unaffected, whereas LSD increased the impact of the strength of initial learning on perseveration. Computational modelling revealed that the most pronounced effect of LSD was the enhancement of the reward learning rate. The punishment learning rate was also elevated. Stimulus stickiness was decreased by LSD, reflecting heightened exploration. Reinforcement sensitivity differed by phase.ConclusionsIncreased RL rates suggest LSD induced a state of heightened plasticity. These results indicate a potential mechanism through which revision of maladaptive associations could occur in the clinical application of LSD.