bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery
Authors: Landa Boris , Kluger Yuval 
Published: December 2024

Abstract
Detecting and recovering a low-rank signal in a noisy data matrix is a fundamental task in data analysis. Typically, this task is addressed by inspecting and manipulating the spectrum of the observed data, e.g. thresholding the singular values of the data matrix at a certain critical level. This approach is well established in the case of homoskedastic noise, where the noise variance is identical across the entries. However, in numerous applications, the noise can be heteroskedastic, where the noise characteristics may vary considerably across the rows and columns of the data. In this scenario, the spectral behaviour of the noise can differ significantly from the homoskedastic case, posing various challenges for signal detection and recovery. To address these challenges, we develop an adaptive normalization procedure that equalizes the average noise variance across the rows and columns of a given data matrix. Our proposed procedure is data-driven and fully automatic, supporting a broad range of noise distributions, variance patterns and signal structures. Our approach relies on random matrix theory results that describe the resolvent of the noise via the so-called Dyson equation. By leveraging this relation, we can accurately infer the noise level in each row and each column directly from the resolvent of the data. We establish that in many cases, our normalization enforces the standard spectral behaviour of homoskedastic noise—the Marchenko–Pastur (MP) law, allowing for simple and reliable detection of signal components. Furthermore, we demonstrate that our approach can substantially improve signal recovery in heteroskedastic settings by manipulating the spectrum after normalization. Lastly, we apply our method to single-cell RNA sequencing and spatial transcriptomics data, showcasing accurate fits to the MP law after normalization.
Convergence study of IB methods for Stokes equations with prescribed velocity boundary conditions
Authors: Li Zhilin , Pan Kejia , Ruiz-Álvarez Juan 
Published: December 2024

Abstract
Peskin’s Immersed Boundary (IB) model and method are among the most important modeling tools and numerical methods. The IB method has been known to be first order accurate in the velocity for incompressible Stokes and Navier–Stokes equations. The convergence of the IB method for Stokes equations with periodic boundary conditions is discussed in Liu & Mori (2014, $L^p$ convergence of the immersed boundary method for stationary Stokes problems. SIAM J. Numer. Anal., 52, 496–514) and Mori (2008, Convergence proof of the velocity field for a Stokes flow immersed boundary method. Comm. Pure Appl. Math., 61, 1213–1263). However, almost no rigorous theoretical proof can be found in the literature for Stokes equations with a prescribed velocity boundary condition. In this paper, it has been shown that the pressure of the Stokes equation has a convergence order $O(\sqrt{h})$ in the $L^{2}$ norm, while the velocity has an $O(h |\!\log h| )$ convergence order in the infinity norm in two-space dimensions. The proofs are based on splitting the singular source terms, discrete Green functions on finite lattices with homogeneous Dirichlet and Neumann boundary conditions, properties of discrete delta functions and the convergence proof of the IB method for elliptic interface problems (Li (2015) On convergence of the immersed boundary method for elliptic interface problems. Math. Comp., 84, 1169–1188). The conclusion in this paper can apply to problems with different boundary conditions as long as the problems are well-posed. The proof process also provides an efficient way to decouple the Stokes equations into three Helmholtz/Poisson equations without affecting the order of convergence. Nontrivial numerical examples are also provided to confirm the theoretical analysis.
Plasmodium falciparum African PfCRT Mutant Isoforms Conducive to Piperaquine Resistance Are Infrequent and Impart a Major Fitness Cost
Authors: Hagenah Laura M , Yeo Tomas , Schindler Kyra A , Jeon Jin H , Bloxham Talia S , Small-Saunders Jennifer L , Mok Sachel , Fidock David A 
Published: December 2024

Abstract

Background
Piperaquine, used in combination with dihydroartemisinin, has been identified as a promising partner drug for uncomplicated treatment and chemoprevention of Plasmodium falciparum malaria in Africa. In light of the earlier spread of piperaquine resistance in Southeast Asia, mediated primarily by mutations in the drug efflux transporter PfCRT, we have explored whether PfCRT mutations would represent a probable path to piperaquine resistance becoming established in Africa.

Methods
We edited PfCRT mutations known to mediate piperaquine resistance in Southeast Asia into P falciparum asexual blood-stage parasites expressing 3 prevalent African mutant PfCRT haplotypes. Gene-edited clones were profiled in antimalarial concentration-response and competitive fitness assays.

Results
pfcrt-edited parasites expressing the contemporary Southeast Asian T93S or I218F mutations added to the GB4 and Cam783 haplotypes common in Africa did not mediate piperaquine resistance, with partial survival only at low drug concentrations. In contrast, parasites expressing these mutations on the rare PfCRT FCB haplotype, observed mostly in Northeast Africa, acquired a moderate level of piperaquine resistance. Dd2GB4, Dd2Cam783, and Dd2FCB lines edited to express the T93S or I218F mutations showed increased susceptibility to chloroquine. Piperaquine-resistant African PfCRT isoforms conferred a substantial fitness cost, manifesting as reduced asexual blood-stage parasite growth rates.

Conclusions
These findings suggest that piperaquine-resistant PfCRT mutations that emerged in Southeast Asia mediate resistance only in a limited subset of African PfCRT haplotypes, with fitness costs that we suspect would likely preclude dissemination in high-transmission malaria-endemic African regions.
Key bacteria decomposing animal and plant detritus in deep sea revealed via long-term in situ incubation in different oceanic areas
Authors: Li Jianyang , Dong Chunming , Xiang Shizheng , Wei Huiyang , Lai Qiliang , Wei Guangshan , Gong Linfeng , Huang Zhaobin , Zhou Donghui , Wang Guangyi , Shao Zongze 
Published: December 2024

Abstract
Transport of organic matter (OM) occurs widely in the form of animal and plant detritus in global oceans, playing a crucial role in global carbon cycling. While wood- and whale-falls have been extensively studied, the in situ process of OM remineralization by microorganisms remains poorly understood particularly in pelagic regions on a global scale. Here, enrichment experiments with animal tissue or plant detritus were carried out in three deep seas for 4–12 months using the deep-sea in situ incubators. We then performed community composition analyses as well as metagenomic and metatranscriptomic analyses. The results revealed strikingly similar microbial assemblages responsible for decomposing animal and plant detritus. Genes encoding peptidases and glucoside hydrolases were highly abundant and actively transcribed in OM enrichments, which confirmed the roles of these enriched microbial assemblages in organic decomposition. Marinifilaceae, Desulfocapsaceae, Spirochaetaceae, and o-Peptostreptococcales were found to potentially contribute to nitrogen fixation. These core bacteria, acting as cosmopolitan anaerobes in decomposing fast-sinking particulate OM, may have been underestimated in terms of their role in deep-sea microbial-mediated biogeochemical cycles during conventional sampling and diversity survey.
High quality Bathyarchaeia MAGs from lignocellulose-impacted environments elucidate metabolism and evolutionary mechanisms
Authors: Nesbø Camilla Lothe , Kublanov Ilya , Yang Minqing , Sharan Anupama Achal , Meyer Torsten , Edwards Elizabeth A 
Published: December 2024

Abstract
The archaeal class Bathyarchaeia is widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analyzed 35 Bathyarchaeia metagenome-assembled genomes (MAGs), including the first complete circularized MAG (cMAG) of the Bathy-6 subgroup, from the metagenomes of three full-scale pulp and paper mill anaerobic digesters and three laboratory methanogenic enrichment cultures maintained on pre-treated poplar. Thirty-three MAGs belong to the Bathy-6, lineage while two are from the Bathy-8 lineage. In our previous analysis of the microbial community in the pulp mill digesters, Bathyarchaeia were abundant and positively correlated to hydrogenotrophic and methylotrophic methanogenesis. Several factors likely contribute to the success of the Bathy-6 lineage compared to Bathy-8 in the reactors. The Bathy-6 genomes are larger than those of Bathy-8 and have more genes involved in lignocellulose degradation, including carbohydrate-active enzymes not present in the Bathy-8. Bathy-6 also shares the Bathyarchaeal O-demethylase system recently identified in Bathy-8. All the Bathy-6 MAGs had numerous membrane-associated pyrroloquinoline quinone-domain proteins that we suggest are involved in lignin modification or degradation, together with Radical-S-adenosylmethionine (SAM) and Rieske domain proteins, and AA2, AA3, and AA6-family oxidoreductases. We also identified a complete B12 synthesis pathway and a complete nitrogenase gene locus. Finally, comparative genomic analyses revealed that Bathyarchaeia genomes are dynamic and have interacted with other organisms in their environments through gene transfer to expand their gene repertoire.
Income Inequality and Growth: Calibration and Simulation for the Kenyan Economy
Authors: Mbara Gilbert 
Published: December 2024

Abstract
We investigate the notable decline in wealth and income inequality in the Kenya over the 10 year period between 2005 to 2015. Using a calibrated continuous time heterogeneous agent model, we attribute up to 80% of the variation in top wealth and income inequality to a persistent but slow increase in the return to capital, a low risk free rate, and rising ‘effective’ income tax rates. Our study suggests that a macroeconomic environment characterised by low risk-free interest rates anchored by low debt-to-fiscal revenue ratios are key to reducing both wealth and income inequality.
Involvement of CorA of Mycobacterium smegmatis in exerting intrinsic resistance towards structurally unrelated antibiotics
Authors: Chatterjee Debasmita , Daya Manasi A R , Rastogi Sumit Kumar , Panda Aditya Prasad , Biju Bayomi , Bhattacharyya Debleena , Ghosh Anindya Sundar 
Published: December 2024

Abstract

Aim
Ubiquitous magnesium transporter, CorA of Mycobacterium smegmatis is well known for its role in maintaining magnesium homeostasis. However, little is known about its involvement in exerting antimicrobial resistance. Here, by using molecular genetics, in vivo and in silico studies, we tried to envisage the role of CorA of M. smegmatis in antimicrobial resistance of M. smegmatis and Escherichia coli.

Methods and results
Expression of corA in M. smegmatis and E. coli decreased the susceptibility of the host cells towards various antibiotics and anti-tubercular drugs, which was elucidated by determining minimum inhibitory concentrations using the micro-broth dilution method. The intracellular antibiotic accumulation assay indicated that the host cells expressing corA accumulated less EtBr, norfloxacin, and ofloxacin than the control cells. Moreover, the presence of a sub-inhibitory concentration of Mg2+ further decreased the susceptibility towards the drugs tested. Furthermore, CorA enhanced the biofilm-forming ability of cells expressing it.

Conclusion
CorA (MSMEG_5056), a magnesium transporter of M. smegmatis influences the extrusion of multiple structurally unrelated classes of drugs and enhances the biofilm formation of E. coli and M. smegmatis.
Modernizing USP Melatonin Liquid Chromatographic Analyses for Increased Throughput and Reduced Environmental Impact
Authors: Yang Jinchuan , Rainville Paul D , Harden Stephanie N 
Published: December 2024

Abstract

Background
Melatonin supplements are often used to alleviate jetlag and other sleep-depletion-related disorders. Recent studies found large inconsistencies between labeled values and actual contents of melatonin within products, which has led to concerns over the quality of melatonin supplements. In order to facilitate the QC testing of melatonin supplements, an improved and more modern approach to the liquid chromatographic analysis of melatonin is required. In addition, growing public concern over the environmental footprint of analytical laboratories exacerbates the need to modernize legacy analytical procedures with more eco-friendly or greener approaches.

Objective
This study aims to optimize the routine liquid chromatographic analyses that are prescribed in the US Pharmacopeia (USP) melatonin monograph on an HPLC system without fundamentally modifying the methods.

Methods
The melatonin assay and test for melatonin-related compounds (impurities) were optimized on a C18 column packed with 2.5 µm particles. The column length and the gradient elution parameters were adjusted following the guidelines in “Adjustment of Chromatographic Conditions” in USP General Chapter &lt;621&gt;. The mobile phase compositions were optimized to meet the system suitability requirements that were specified in the USP melatonin monograph. The flow rate was optimized for better separation efficiency.

Results
The optimized HPLC methods not only met the USP system suitability requirements in relative retention time (RRT), resolution, and RSD but also demonstrated excellent linearity, sensitivity, accuracy, and precision (repeatability), and would have a lower environmental impact.

Conclusion
The optimized HPLC methods for assay of melatonin and test of its related compounds achieved significantly increased throughput and a reduced environmental impact, without fundamentally modifying the methods.

Highlights
The optimized HPLC methods are significantly faster and more eco-friendly. These methods can be implemented on HPLC systems without a full re-validation.
Cannabidiol can affect morphology, morphometry, enzymatic and microbial activity of rabbit digestive system
Authors: Musco Nadia , Pascon Giulia , Addeo Nicola Francesco , Zarantoniello Matteo , Lanzieri Mariarosaria , Olivotto Ike , Tulli Francesca , Iervolino Valeria , Amato Ruggero , Lombardi Pietro , Bovera Fulvia 
Published: December 2024

Abstract
The present research aimed to evaluate the effects of the continuative dietary administration of a hemp oil extract containing cannabinoids (cannabidiol, CBD) on the macroscopic morphology, morphometry, and enzymatic activity of different intestinal tracts as well as on the production of short-chain fatty acids (SCFAs) in the cecum of growing rabbits. The research was performed on 16 rabbits randomly selected from 2 experimental groups (8 per group). In detail, 42 sixty-day-old New Zealand White × California rabbits (sex ratio 1:1, average weight 1621.3 ± 46.2 g) were homogeneously divided into 2 groups (21 animals/group), namely control and CBD. Both groups were fed the same commercial diet, but the CBD one was supplemented with 0.1 mL of hemp extract in coconut-based oil corresponding to 10 mg of CBD/animal/d. Up to 92 d of age (for 27 d), individual live weight and feed intake were measured weekly. At 92 d of age, 8 rabbits/group (sex ratio 1:1) were moved to a specialized slaughterhouse, and the gastrointestinal tract was separated from the carcass. Samples from 8 rabbits per dietary treatment were used for the histomorphological analysis of small and large intestines. In addition, duodenum, jejunum, ileum, and cecum were processed for enzymatic analysis. The caecal contents were used for the SCFAs determination. The administration of CBD did not affect feed intake and the final rabbits’ whole body weight (P &gt; 0.05), but some changes were detected in the gastrointestinal tract of the animals. CBD seemed to interfere with protein digestion, with a significantly lower activity of the enzymes related to peptides in the small intestine and a consequent increase of the fermentative activity of caecal microbiota. This effect, in combination with a general decrease of fermentative activity in the caecal content of rabbits submitted to CBD treatment, was responsible for a change in the SCFA proportion mainly regarding the reduction of butyrate production (P &lt; 0.01) that resulted significant higher in CTR group compared to CBD. This last result is very important for intestinal health. Such fermentation activity modification was coupled with changes in the relative abundance of goblet cells in the colon. Overall, our findings suggest that a relatively long-term administration of CBD may affect digestion in rabbits, in particular at enzymatic and fermentative levels.
How many species of shrimps (Decapoda: Caridea, Dendrobranchiata, Stenopodidea) in Brazil? Diversity, geographic distribution, and history of taxonomic studies based on the Catálogo Taxonômico da Fauna do Brasil (Taxonomic Catalog of the Brazilian Fauna)
Authors: Terossi Mariana , Cardoso Irene 
Published: December 2024

Abstract
The 4,461 shrimp species worldwide correspond to approximately 25% of the diversity of crustacean decapods. We surveyed the shrimp species known for Brazil based on the Catálogo Taxonômico da Fauna do Brasil (Taxonomic Catalog of the Brazilian Fauna). A total of 373 shrimp species are so far recorded from Brazil, of which 79% are Caridea, 19% Dendrobranchiata, and 2% Stenopodidea. Caridea is represented by 24 families and 294 species, Dendrobranchiata by seven families and 72 species, and Stenopodidea by three families and seven species. The Brazilian representatives of the three taxa respectively represent 8%, 14%, and 7% of the global species diversity and 21%, 49%, and 29% of the global generic biodiversity. Forty-three species of Caridea, three of Stenopodidea, and one of Dendrobranchiata are endemic to Brazil. Twelve non-native, alien species belonging to seven genera are reported for Caridea and Dendrobranchiata. The vast majority of all species are marine and brackish-water (328 species), 112 of which are from deep water (&gt; 500 m), and 45 from fresh water. Brazil is the confirmed type locality of 81 species, but this number may be higher. The authors of these species were only from Europe and the USA until 1950, but mostly Brazilian since. This compilation aims to provide information about Brazilian shrimps to assist future research in all areas and to help governmental or non-governmental (NGO) agencies in making decisions and recommendations about conservation issues.
Perspectives from federal and state public health departments on their participation in and the utility of Ixodes scapularis (Acari: Ixodidae) and Ixodes pacificus tick and tick-borne pathogen surveillance in the United States
Authors: Eisen Rebecca J , Foster Erik , Kjemtrup Anne , Saunders Megan E M , Brown Jennifer , Green Lee , Cervantes Kim , Prusinski Melissa A , White Jennifer , Barbarin Alexis M , Williams Carl , Kwit Natalie , Bernick Joshua , Gaines David , Dykstra Elizabeth , Oltean Hanna N , Dotseth Eric , Lee Xia , Osborn Rebecca 
Published: December 2024

Abstract
In response to notable increases in tick-associated illnesses in the United States, recent public health policies encouraged multi-sector collaborative approaches to preventing vector-borne diseases. Primary prevention strategies focus on educating the public about risks for tick-borne diseases and encouraging adoption of personal protection strategies. Accurate descriptions of when and where people are at risk for tick-borne diseases aid in the optimization of prevention messaging. Tick and tick-borne pathogen data can be used to fill gaps in epidemiological surveillance. However, the utility of acarological data is limited by their completeness. National maps showing the distribution of medically important tick species and the pathogens they carry are often incomplete or non-existent. Recent policies encourage accelerated efforts to monitor changes in the distribution and abundance of medically important ticks and the presence and prevalence of human pathogens that they carry, and to provide actionable, evidence-based information to the public, health care providers and public health policy makers. In 2018, the Centers for Disease Control and Prevention initiated a national tick surveillance program focused on Ixodes ticks. The national program coordinated and expanded upon existing efforts led by public health departments and academic institutions. Here, we describe experiences of state public health departments engaged in Ixodes tick surveillance, including information on why they initiated Ixodes surveillance programs, programmatic objectives, and strategies for maintaining tick surveillance programs. We share experiences and challenges in interpreting or communicating tick surveillance data to stakeholders and explore how the acarological data are used to complement epidemiological data.
The evolution of NCI’s Health Information National Trends Survey: methods, data, and future directions
Authors: Blake Kelly D , Moser Richard P , D’Angelo Heather , Gaysynsky Anna , Vanderpool Robin C 
Published: December 2024

Abstract
The National Cancer Institute’s (NCI’s) Health Information National Trends Survey® (HINTS®) was conceived in 1997 during a multidisciplinary conference focused on risk communication that included attendees representing the fields of psychology, health behavior, health education, public health, clinical medicine, and health journalism. The key recommendation from the conference was for NCI to develop a premiere communication-specific population survey to track health and cancer communication-related phenomena. This led to NCI developing and launching HINTS in 2003. HINTS is a cross-sectional, nationally representative survey of the US noninstitutionalized adult population (18 years and older) that collects data on the public’s need for, access to, and use of health- and cancer-related information and health- and cancer-related knowledge, attitudes, and behaviors. As of 2024, HINTS had been administered 17 times over a 21-year period. The resulting datasets can be used for secondary analysis to examine a range of social and behavioral research questions in cancer control and population sciences. The datasets can be examined individually or merged to test for trends over time or to create larger samples for analysis. The evolution of the program has included testing and changing instrument administration modes, oversampling specific populations, and assessing priority constructs, as well as conducting methodological experiments to keep pace with emerging trends in survey research. HINTS has also expanded beyond its cross-sectional format to include data linkages and a longitudinal panel, enabling researchers to address a wider range of research questions. HINTS methods, data products, and impact are discussed.