bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions
Authors: Srinivasan Shanchana , Jnana Apoorva , Murali Thokur Sreepathy 
Published: April 2024

AbstractMicrobial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.
Epiberberine: a potential rumen microbial urease inhibitor to reduce ammonia release screened by targeting UreG
Authors: Zhang Xiaoyin , Xiong Zhanbo , He Yue , Zheng Nan , Zhao Shengguo , Wang Jiaqi 
Published: April 2024

Abstract
Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future.

Key points
• Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis.
• Urease accessory protein UreG is an effective target for design of urease inhibitor.
• Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants.
Phylogenetic network classes through the lens of expanding covers
Authors: Francis Andrew , Marchei Daniele , Steel Mike 
Published: April 2024

AbstractIt was recently shown that a large class of phylogenetic networks, the ‘labellable’ networks, is in bijection with the set of ‘expanding’ covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks can be characterised purely in terms of properties of their associated covers. These classes include the tree-based, tree-child, orchard, tree-sibling, and normal networks. In the opposite direction, we give an example of how a restriction on the set of expanding covers can define a new class of networks, which we call ‘spinal’ phylogenetic networks.
Gastrointestinale Stromatumoren
Authors: Wardelmann Eva , Kuntze Anna , Voloshin Artem , Elges Sandra , Trautmann Marcel , Hartmann Wolfgang 
Published: April 2024

ZusammenfassungGastrointestinale Stromatumoren (GIST) stellen seit über 20 Jahren ein Paradigma für die zielgerichtete Therapie mit Tyrosinkinaseinhibitoren dar. Eine elementare Voraussetzung für eine mögliche neoadjuvante oder adjuvante Behandlung bei lokalisierten GIST bzw. eine additive Therapie bei metastasierten GIST ist die molekulare Typisierung der Tumoren, idealerweise bereits bei Erstdiagnose. Zudem ist auf die Möglichkeit einer hereditären oder syndromalen Prädisposition zu achten, da sich hieraus auch therapeutische Konsequenzen und eine andere Nachsorgestrategie ergeben.
Investigating the effects of Mn content on the morphology and dielectric properties of CdS nanoparticles
Authors: Azab A. A. , Ibrahim R. S. , Seoudi R. 
Published: April 2024

AbstractCdS nanoparticles doped with Mn were synthesized by chemical precipitation using varying concentrations of Mn at Cd1-xMnxS, where (x) = 0.00, 0.03, 0.05, and 0.07. The samples were examined using scanning electron microscopy (SEM), energy dispersive X-ray techniques (EDX), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, dielectric properties, and AC conductivity measurements. SEM micrograph shows that pure CdS nanomaterial has agglomerates primarily composed of nanoparticles, whereas the sample with a concentration of 0.03 contains smaller particles. In response to the phonon confinement effect, The Raman spectra of CdS nanoparticles exhibited peaks at 303 cm−1and 603 cm−1. In contrast, the Raman spectra of Mn:CdS nanocomposites displayed a prominent fundamental mode at 301 cm−1and a less pronounced overtone mode at 601 cm−1. The dielectric properties and the AC conductivity of CdS have been investigated over a wide frequency range of 0.1 Hz to 10 MHz and at a variety of temperatures ranging from 298 to 423K. The real and imaginary parts of the complex dielectric constant (εʹ, εʹʹ), the electric modulus, and AC conductivity of CdS were found to depend on Mn content at different temperatures.
Multinomial Restricted Unfolding
Authors: Rooij Mark de , Busing Frank 
Published: April 2024

AbstractFor supervised classification we propose to use restricted multidimensional unfolding in a multinomial logistic framework. Where previous research proposed similar models based on squared distances, we propose to use usual (i.e., not squared) Euclidean distances. This change in functional form results in several interpretational advantages of the resulting biplot, a graphical representation of the classification model. First, the conditional probability of any class peaks at the location of the class in the Euclidean space. Second, the interpretation of the biplot is in terms of distances towards the class points, whereas in the squared distance model the interpretation is in terms of the distance towards the decision boundary. Third, the distance between two class points represents an upper bound for the estimated log-odds of choosing one of these classes over the other. For our multinomial restricted unfolding, we develop and test a Majorization Minimization algorithm that monotonically decreases the negative log-likelihood. With two empirical applications we point out the advantages of the distance model and show how to apply multinomial restricted unfolding in practice, including model selection.
On the Existence of Small Strictly Neumaier Graphs
Authors: Abiad Aida , De Boeck Maarten , Zeijlemaker Sjanne 
Published: April 2024

AbstractA Neumaier graph is a non-complete edge-regular graph containing a regular clique. In this work, we prove several results on the existence of small strictly Neumaier graphs. In particular, we present a theoretical proof of the uniqueness of the smallest strictly Neumaier graph with parameters (16, 9, 4; 2, 4), we establish the existence of a strictly Neumaier graph with parameters (25, 12, 5; 2, 5), and we disprove the existence of strictly Neumaier graphs with parameters (25, 16, 9; 3, 5), (28, 18, 11; 4, 7), (33, 24, 17; 6, 9), (35, 2212; 3, 5), (40, 30, 22; 7, 10) and (55, 34, 18; 3, 5). Our proofs use combinatorial techniques and a novel application of integer programming methods.
En-bloc spondylectomy in the lumbar spine: indications, results and complications in a series of 47 patients affected by primary malignant bone tumors
Authors: Luzzati Alessandro , Conti Stefano , Sperduti Isabella , Scotto Di Uccio Alessandra , Mazzoli Simone , Cannavò Luca , Scotto Gennaro , Zoccali Carmine 
Published: April 2024

Abstract
Introduction
Wide Surgery is the reference treatment for malignant and aggressive benign primary bone tumors in the spine. When located in the lumbar spine, En-Bloc Spondylectomy (EBS) remains a complex challenge. Moreover, surgery is complicated by the presence of the diaphragm in the thoracolumbar junction and the hinderance of the iliac wings at the lumbosacral levels. Therefore, EBS in the lumbar spine frequently requires combined approaches.
The purpose of this study is to describe clinical presentation, tumor characteristics and results of a series of 47 consecutive patients affected by malignant primary bone tumors of the lumbar spine who underwent EBS.

Materials and methods
47 patients were reviewed. Complications were distinguished in early and late whether they occurred before or after 30 days from surgery.
Overall survival (OS), disease-free survival (DFS) and local recurrence-free survival (LRFS) were calculated by the Kaplan–Meier product-limit method from surgery until relapse or death.

Results
27 patients presented to observation after a first intralesional approach in a non-specialized center. Chordoma was the most represented histotype. Vertebrectomies were: 23 one-level, 10 two-level, 12 three-level and 2 four-level. Reconstructions were always carried out with screws and rods. The main postoperative complication was blood loss, while hardware failure was the main long-term complication.
The 5-year LRFS was 75.5%, the 5-year DFS was 54.3%, and 5-year OS was 63.6%.

Conclusions
The surgical margin obtained during the index surgery was statistically associated with Local Recurrence, DFS and OS, underlining the importance of treating patients in reference centers.
Postradiation trismus in head and neck cancer survivors: a qualitative study of effects on life, rehabilitation, used coping strategies and support from the healthcare system
Authors: Aghajanzadeh Susan , Karlsson Therese , Tuomi Lisa , Engström My , Finizia Caterina 
Published: April 2024

Abstract
Purpose
This study aimed to explore the experiences of head and neck cancer (HNC) survivors with postradiation trismus, specifically how oncological treatment affected their lives, rehabilitation, use of coping strategies, and healthcare experiences. Methods: A qualitative descriptive approach was used and semi-structured interviews of 10 HNC survivors with postradiation trismus were conducted 6–30 months after completing oncological treatment. The interviews were transcribed verbatim and analyzed by qualitative content analysis.

Results
The analysis of interviews yielded four main categories: Bodily symptoms, Effects on life, Support from the healthcare system, and Strategies to handle life and symptoms. Participants reported ongoing problems with xerostomia, dysgeusia, eating, and limited physical fitness. Pain related to trismus was not a major issue in this cohort. Participants expressed limitations in their social lives due to their eating difficulties, yet a sense of thankfulness for life and overall satisfaction with the healthcare they received. Psychological and practical coping strategies developed by the participants were also revealed.

Conclusion
The results highlight areas of unmet need among HNC survivors that healthcare providers can target by establishing multi-professional teams dedicated to individualizing post-cancer rehabilitation care.
The extent of androgen receptor and HER2 expression allows for targeted therapy in most cases of salivary duct carcinoma: analysis of clinical and histopathological data in a tertiary care center
Authors: Mayer Marcel , Wolber Philipp , Prinz Johanna , Jansen Louis , Esser Julia , Shabli Sami , Quaas Alexander , Klußmann Jens Peter , Sharma Shachi Jenny , Nachtsheim Lisa , Arolt Christoph 
Published: April 2024

Abstract
Purpose
The incidence of salivary duct carcinoma (SDC) seems to be underestimated due to inaccurate classification. Further, the frequency of SDC patients with targeted therapy options according to current guidelines is unclear. Therefore, this study aimed at (a) describing the proportion of SDC among salivary gland carcinoma (SGC) before and after reclassification of cases initially classified as adenocarcinoma, not otherwise specified (ANOS); and (b) quantifying the frequency of SDC patients with targeted therapy options.

Methods
All patients with SDC or ANOS treated in a tertiary care center between 1996 and 2023 were identified. Histopathological diagnosis was verified for patients primarily diagnosed with SDC and reviewed for patients initially diagnosed with ANOS. Clinical data for SDC patients were retrieved from clinical charts. Immunohistochemical (IHC) androgen receptor (AR) and HER2 staining was performed.

Results
Among 46 SDC, 34 were primarily diagnosed as SDC and 12 had initially been classified as ANOS. The proportion of SDC among SGC was 12.1% and was rising when comparing the time periods 2000–2015 (7.1–11.5%) versus 2016–2023 (15.4–18.1%). Nuclear AR staining in > 70% of tumor cells was found in 56.8% and HER2 positivity (IHC 3 +) in 36.4% of cases. 70.5% of patients showed AR staining in > 70% of tumor cells and/or HER2 positivity and therefore at least one molecular target. 5-year overall and disease-free survival (DFS) were 62.8% and 41.0%. Multivariate Cox regression revealed positive resection margins (HR = 4.0, p = 0.03) as independent negative predictor for DFS.

Conclusions
The results suggest a rising SDC incidence and show that the extent of the AR and HER2 expression allows for targeted therapy in most SDC cases.
Metasomatic ijolite, glimmerite, silicocarbonatite, and antiskarn formation: carbonatite and silicate phase equilibria in the system Na2O–CaO–K2O–FeO–MgO–Al2O3–SiO2–H2O–O2–CO2
Authors: Anenburg Michael , Walters Jesse B. 
Published: April 2024

AbstractSilicocarbonatites are carbonatite rocks containing > 20% silicate minerals. Their formation is not well understood due to low silica solubility in carbonatite melts and negligible amounts of silicate minerals on carbonatite melt cotectics at upper crustal conditions. We explore whether silicocarbonatites can be thought of as antiskarns: rocks formed by leaching of SiO2from siliceous wall rocks by carbonatite melts, and its deposition as solid silicate minerals by reaction with chemical components already present in the carbonatite melt. Solid state thermodynamic modelling at 1–5 kbar and 500–800 °C predicts that calcite–dolomite–magnetite assemblages will transform to dolomite-free silicocarbonatites with an increase in silica contents. In sodic systems, the formation of aegirine and alkali amphiboles suppresses silica activity despite elevated silica contents. Therefore, dolomite remains stable, but Fe3+is consumed, firstly from magnetite breakdown, and secondly by coupled Fe oxidation and reduction of CO2to CO, CH4, and graphite, particularly at higher pressures. Despite a net increase in Fe3+/Fe2+, the system evolves to increasingly lower oxygen fugacity. In aluminous systems, nepheline indicates high temperatures whereas alkali feldspars form at lower temperatures. Modelling of potassic systems demonstrates stability of mostly phlogopite-rich biotites, leading to Fe2+increase in all other carbonate and silicate phases. We find that perthites are expected in high pressures whereas two feldspars are more likely in lower pressures.Aspects of the clinopyroxene natural compositional trend (diopside to hedenbergite to aegirine) of carbonatite systems can be explained by silica contamination. Ferrous clinopyroxenes typically require low alumina and are predicted in potassic or low temperature sodic systems, primarily at mid to high pressures. Silica contamination permits the formation of silicocarbonatite-like assemblages in a way that is not limited by SiO2solubility in carbonatite melts. Glimmerites and clinopyroxene-rich rocks (such as the ijolite series) that often occur around carbonatite rocks at the contact with silica-oversaturated wall rocks can be explained as the extreme end of silica contamination of carbonatite melts. Therefore, these clinopyroxenites and glimmerites can form solely via metasomatic processes without the presence of a silicate melt.
Prediction model for anabolic androgenic steroid positivity in forensic autopsy cases – a new tool to the autopsy room
Authors: Vauhkonen Paula , Oura Petteri , Kriikku Pirkko , Lindroos Katarina , Mäyränpää Mikko Ilari 
Published: April 2024

AbstractNon-prescription use of anabolic androgenic steroids (AAS) is associated with an increased risk of premature death. However, these substances are seldom screened in connection with forensic cause-of-death investigation, unless the forensic pathologist specifically suspects use, often based on a positive AAS use history. Since AAS use is often concealed from others, this practice may lead to mistargeting of these analyses and significant underestimation of the true number of AAS positive cases undergoing forensic autopsy. Thus, more accurate diagnostic tools are needed to identify these cases. The main objective of this study was to determine, whether a multivariable model could predict AAS urine assay positivity in forensic autopsies. We analyzed retrospectively the autopsy reports of all cases that had been screened for AAS during forensic cause-of-death investigation between 2016–2019 at the Finnish Institute for Health and Welfare forensic units (n = 46). Binary logistic regression with penalized maximum likelihood estimation was used to generate a nine-variable model combining circumferential and macroscopic autopsy-derived variables. The multivariable model predicted AAS assay positivity significantly better than a “conventional” model with anamnestic information about AAS use only (area under the receiver operating characteristic curve [AUC] = 0.968 vs. 0.802, p = 0.005). Temporal validation was conducted in an independent sample of AAS screened cases between 2020–2022 (n = 31), where the superiority of the multivariable model was replicated (AUC = 0.856 vs. 0.644, p = 0.004). Based on the model, a calculator predicting AAS assay positivity is released as a decision-aiding tool for forensic pathologists working in the autopsy room.
Giardia telomeres and telomerase
Authors: Lagunas-Rangel Francisco Alejandro 
Published: April 2024

AbstractGiardia duodenalis, the protozoan responsible for giardiasis, is a significant contributor to millions of diarrheal diseases worldwide. Despite the availability of treatments for this parasitic infection, therapeutic failures are alarmingly frequent. Thus, there is a clear need to identify new therapeutic targets. Giardia telomeres were previously identified, but our understanding of these structures and the critical role played by Giardia telomerase in maintaining genomic stability and its influence on cellular processes remains limited. In this regard, it is known that all Giardia chromosomes are capped by small telomeres, organized and protected by specific proteins that regulate their functions. To counteract natural telomere shortening and maintain high proliferation, Giardia exhibits constant telomerase activity and employs additional mechanisms, such as the formation of G-quadruplex structures and the involvement of transposable elements linked to telomeric repeats. Thus, this study aims to address the existing knowledge gap by compiling the available information (until 2023) about Giardia telomeres and telomerase, focusing on highlighting the distinctive features within this parasite. Furthermore, the potential feasibility of targeting Giardia telomeres and/or telomerase as an innovative therapeutic strategy is discussed.
The structure of the local time of Markov processes indexed by Lévy trees
Authors: Riera Armand , Rosales-Ortiz Alejandro 
Published: April 2024

AbstractWe construct an additive functional playing the role of the local time—at a fixed point x—for Markov processes indexed by Lévy trees. We start by proving that Markov processes indexed by Lévy trees satisfy a special Markov property which can be thought as a spatial version of the classical Markov property. Then, we construct our additive functional by an approximation procedure and we characterize the support of its Lebesgue-Stieltjes measure. We also give an equivalent construction in terms of a special family of exit local times. Finally, combining these results, we show that the points at which the Markov process takes the value x encode a new Lévy tree and we construct explicitly its height process. In particular, we recover a recent result of Le Gall concerning the subordinate tree of the Brownian tree where the subordination function is given by the past maximum process of Brownian motion indexed by the Brownian tree.
A Ray–Knight theorem for $$\nabla \phi $$ interface models and scaling limits
Authors: Deuschel Jean-Dominique , Rodriguez Pierre-François 
Published: April 2024

AbstractWe introduce a natural measure on bi-infinite random walk trajectories evolving in a time-dependent environment driven by the Langevin dynamics associated to a gradient Gibbs measure with convex potential. We derive an identity relating the occupation times of the Poissonian cloud induced by this measure to the square of the corresponding gradient field, which—generically—isnotGaussian. In the quadratic case, we recover a well-known generalization of the second Ray–Knight theorem. We further determine the scaling limits of the various objects involved in dimension 3, which are seen to exhibit homogenization. In particular, we prove that the renormalized square of the gradient field converges under appropriate rescaling to the Wick-ordered square of a Gaussian free field on$$\mathbb R^3$$R3with suitable diffusion matrix, thus extending a celebrated result of Naddaf and Spencer regarding the scaling limit of the field itself.
Investigation and comparison of permanent magnet rotors produced by different additive manufacturing methods
Authors: Wu Tong , Schwarzer David , Neuwald Tobias , Wüst Paul , Maczionsek Daniel , Seibicke Frank , Rauch Hartmut , Schäfer Uwe 
Published: April 2024

AbstractThe advancements in technology have led to a growing interest in additive manufacturing owing to its numerous benefits such as increased degree of freedom, high flexibility, and material conservation. It has gained particular attention in the production of electrical machines and their active components such as windings, electrical insulation, magnetic core packs, and permanent magnets. This paper investigates the use of two methods, namely fused deposition modeling and cold spray, in the production of hard magnetic components for rotors with surface-mounted magnets. A comparative study was conducted through a combination of finite element simulations and experimental tests.