bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASAS-NANP symposium: mathematical modeling in animal nutrition—Making sense of big data and machine learning: how open-source code can advance training of animal scientists
Authors: Brennan Jameson R , Menendez Hector M , Ehlert Krista , Tedeschi Luis O 
Published: November 2023

Abstract
Advancements in precision livestock technology have resulted in an unprecedented amount of data being collected on individual animals. Throughout the data analysis chain, many bottlenecks occur, including processing raw sensor data, integrating multiple streams of information, incorporating data into animal growth and nutrition models, developing decision support tools for producers, and training animal science students as data scientists. To realize the promise of precision livestock management technologies, open-source tools and tutorials must be developed to reduce these bottlenecks, which are a direct result of the tremendous time and effort required to create data pipelines from scratch. Open-source programming languages (e.g., R or Python) can provide users with tools to automate many data processing steps for cleaning, aggregating, and integrating data. However, the steps from data collection to training artificial intelligence models and integrating predictions into mathematical models can be tedious for those new to statistical programming, with few examples pertaining to animal science. To address this issue, we outline how open-source code can help overcome many of the bottlenecks that occur in the era of big data and precision livestock technology, with an emphasis on how routine use and publication of open-source code can help facilitate training the next generation of animal scientists. In addition, two case studies are presented with publicly available data and code to demonstrate how open-source tutorials can be utilized to streamline data processing, train machine learning models, integrate with animal nutrition models, and facilitate learning. The National Animal Nutrition Program focuses on providing research-based data on animal performance and feeding strategies. Open-source data and code repositories with examples specific to animal science can help create a reinforcing mechanism aimed at advancing animal science research.
ASAS-NANP symposium: mathematical modeling in animal nutrition: agent-based modeling for livestock systems: the mechanics of development and application
Authors: Kaniyamattam Karun , Tedeschi Luis O 
Published: November 2023

Abstract
Over the last three decades, agent-based modeling/model (ABM) has been one of the most powerful and valuable simulation-based decision modeling techniques used to study the complex dynamic interactions between animals and their environment. ABM is a relatively new modeling technique in the animal research arena, with immense potential for routine decision-making in livestock systems. We describe ABM’s fundamental characteristics for developing intelligent modeling systems, exemplify its use for livestock production, and describe commonly used software for designing and developing ABM. After that, we discuss several aspects of the developmental mechanics of an ABM, including (1) how livestock researchers can conceptualize and design a model, (2) the main components of an ABM, (3) different statistical methods of analyzing the outputs, and (4) verification, validation, and replication of an ABM. Then, we perform an overall analysis of the utilities of ABM in different subsystems of the livestock systems ranging from epidemiological prediction to nutritional management to livestock market dynamics. Finally, we discuss the concept of hybrid intelligent models (i.e., merging real-time data streams with intelligent ABM), which have applications in artificial intelligence-based decision-making for precision livestock farming. ABM captures individual agents’ characteristics, interactions, and the emergent properties that arise from these interactions; thus, animal scientists can benefit from ABM in multiple ways, including understanding system-level outcomes, analyzing agent behaviors, exploring different scenarios, and evaluating policy interventions. Several platforms for building ABM exist (e.g., NetLogo, Repast J, and AnyLogic), but they have unique features making one more suitable for solving specific problems. The strengths of ABM can be combined with other modeling approaches, including artificial intelligence, allowing researchers to advance our understanding further and contribute to sustainable livestock management practices. There are many ways to develop and apply mathematical models in livestock production that might assist with sustainable development. However, users must be experienced when choosing the appropriate modeling technique and computer platform (i.e., modeling development tool) that will facilitate the adoption of mathematical models by certifying that the model is field-ready and versatile enough for untrained users.
Diffuse large B-cell lymphoma associated with papillary thyroid carcinoma: a case report and systematic review on management and outcomes
Authors: Lincango Eddy P , Serrano Luis F , Vallejo Sebastian , Solis-Pazmino Paola , Garcia-Bautista Andrea , Acosta William , Ponce Oscar J , Salazar-Vega Jorge , Garcia Cristhian 
Published: November 2023

Abstract
Primary thyroid lymphoma is a rare thyroid cancer, comprising ˂5% of thyroid neoplasms. Most cases are diffuse large B-cell lymphoma (DLBCL). Coexistence with papillary thyroid cancer (PTC) is extremely rare. This study presents a case of a 55-year-old woman with DLBCL and micropapillary thyroid cancer who underwent lobectomy, chemotherapy, and radiotherapy. Additionally, we performed a systematic review of 10 cases, including the reported case. The risk of bias in case reports varied. DLBCL diagnoses were mainly made after surgery, with total thyroidectomy being the most common surgical procedure. Chemotherapy was administered in most cases, and radiotherapy was used in some cases. Long-term outcomes indicated a low recurrence rate. While some debate the role of surgery in thyroid lymphoma, this study suggests that surgery should be considered in selected cases. Further research is needed to determine optimal treatment strategies for DLBCL with PTC.
Generation of renal tubular organoids from adult SOX9+ kidney progenitor cells
Authors: Zhou Dewei , Li Dandan , Nie Hao , Duan Jun , Liu Sarah , Wang Yujia , Zuo Wei 
Published: November 2023

Abstract
The pathogenesis of several kidney diseases results in the eventual destruction of the renal tubular system, which can progress to end-stage renal disease. Previous studies have demonstrated the involvement of a population of SOX9-positive cells in kidney regeneration and repair process following kidney injury. However, the ability of these cells to autonomously generate kidney organoids has never been investigated. Here, we isolated SOX9+ kidney progenitor cells (KPCs) from both mice and humans and tested their differentiation potential in vitro. The data showed that the human SOX9+ KPC could self-assemble into organoids with kidney-like morphology. We also used single-cell RNA sequencing to characterize the organoid cell populations and identified four distinct types of renal tubular cells. Compared to the induced pluripotent stem cell-derived kidney organoids, KPC demonstrated more tubular differentiation potential but failed to differentiate into glomerular cells. KPC-derived organoid formation involved the expression of genes related to metanephric development and followed a similar mechanism to renal injury repair in acute kidney injury patients. Altogether, our study provided a potentially useful approach to generating kidney tubular organoids for future application.
The metallicity dependence of the stellar initial mass function
Authors: Tanvir Tabassum S , Krumholz Mark R 
Published: November 2023

ABSTRACT
During star formation, dust plays the crucial role of coupling gas to stellar radiation fields, allowing radiation feedback to influence gas fragmentation and thus the stellar initial mass function (IMF). Variations in dust abundance therefore provide a potential avenue by which variation in galaxy metallicity might affect the IMF. In this paper, we present a series of radiation-magnetohydrodynamic simulations in which we vary the metallicity and thus the dust abundance from 1 per cent of solar to 3× solar, spanning the range from the lowest metallicity dwarfs to the most metal-rich early-type galaxies (ETGs) found in the local Universe. We design the simulations to keep all dimensionless parameters constant so that the interaction between feedback and star-forming environments of varying surface density and metallicity is the only factor capable of breaking the symmetry between the simulations and modifying the IMF, allowing us to isolate and understand the effects of each environmental parameter cleanly. We find that shifts in the IMF with varying metallicity at a fixed surface density are smaller than the shifts in varying surface density at a fixed surface metallicity. We also find that metallicity-induced IMF variations are too small to explain the mass-to-light ratio shifts seen in the ETGs. We therefore conclude that metallicity variations are much less important than variations in surface density in driving changes in the IMF and that the latter rather than the former are most likely responsible for the IMF variations found in ETGs.
Pulse profile modelling of thermonuclear burst oscillations – II. Handling variability
Authors: Kini Yves , Salmi Tuomo , Vinciguerra Serena , Watts Anna L , Choudhury Devarshi , Bogdanov Slavko , Buchner Johannes , Meisel Zach , Suleimanov Valery 
Published: November 2023

ABSTRACT
Pulse profile modelling is a relativistic ray-tracing technique that can be used to infer masses, radii, and geometric parameters of neutron stars. In a previous study, we looked at the performance of this technique when applied to thermonuclear burst oscillations from accreting neutron stars. That study showed that ignoring the variability associated with burst oscillation sources resulted in significant biases in the inferred mass and radius, particularly for the high count rates that are nominally required to obtain meaningful constraints. In this follow-on study, we show that the bias can be mitigated by slicing the bursts into shorter segments where variability can be neglected, and jointly fitting the segments. Using this approach, the systematic uncertainties on the mass and radius are brought within the range of the statistical uncertainty. With about 106 source counts, this yields uncertainties of approximately 10 per cent for both the mass and radius. However, this modelling strategy requires substantial computational resources. We also confirm that the posterior distributions of the mass and radius obtained from multiple bursts of the same source can be merged to produce outcomes comparable to that of a single burst with an equivalent total number of counts.
Characterization of high-velocity stars in the S-PLUS internal fourth data release
Authors: Quispe-Huaynasi F , Roig F , Placco V M , Beraldo e Silva L , Daflon S , Pereira C B , Kanaan A , Mendes de Oliveira C , Ribeiro T , Schoenell W 
Published: November 2023

ABSTRACT
In general, the atypical high velocity of some stars in the Galaxy can only be explained by invoking acceleration mechanisms related to extreme astrophysical events in the Milky Way. Using astrometric data from Gaia and the photometric information in 12 filters of the S-PLUS, we performed a kinematic, dynamical, and chemical analysis of 64 stars with Galactocentric velocities higher than 400 $\mathrm{km\, s}^{-1}$. All the stars are gravitationally bound to the Galaxy and exhibit halo kinematics. Some of the stars could be remnants of structures such as the Sequoia and the Gaia-Sausage/Enceladus. Supported by orbital and chemical analysis, we identified Gaia DR3 5401875170994688896 as a star likely to be originated at the centre of the Galaxy. Application of a machine learning technique to the S-PLUS photometric data allows us to obtain very good estimates of magnesium abundances for this sample of high-velocity stars.
X-ray scaling relations of early-type galaxies in IllustrisTNG and a new way of identifying backsplash objects
Authors: Wang Yunchong , Vogelsberger Mark , Kim Dong-Woo , Borrow Josh , Smith Aaron , Hernquist Lars , Lin Wenjie 
Published: November 2023

ABSTRACT
We investigate how feedback and environment shapes the X-ray scaling relations of early-type galaxies (ETGs), especially at the low-mass end. We select central-ETGs from the TNG100 box of IllustrisTNG that have stellar masses $\log _{10}(M_{\ast }/\mathrm{M_{\odot }})\in [10.7, 11.9]$. We derive mock X-ray luminosity (LX, 500) and spectroscopic-like temperature (Tsl, 500) of hot gas within R500 of the ETG haloes using the MOCK-X pipeline. The scaling between LX, 500 and the total mass within 5 effective radii ($M_{5R_{\rm e}}$) agrees well with observed ETGs from Chandra. IllustrisTNG reproduces the observed increase in scatter of LX, 500 towards lower masses, and we find that ETGs with $\log _{10} (M_{5R_{\rm e}}/\mathrm{M_{\odot }}) \leqslant 11.5$ with above-average LX, 500 experienced systematically lower cumulative kinetic AGN feedback energy historically (vice versa for below-average ETGs). This leads to larger gas mass fractions and younger stellar populations with stronger stellar feedback heating, concertedly resulting in the above-average LX, 500. The LX, 500–Tsl, 500 relation shows a similar slope to the observed ETGs but the simulation systematically underestimates the gas temperature. Three outliers that lie far below the LX–Tsl relation all interacted with larger galaxy clusters recently and demonstrate clear features of environmental heating. We propose that the distinct location of these backsplash ETGs in the LX–Tsl plane could provide a new way of identifying backsplash galaxies in future X-ray surveys.
Interferometric apodization by homothety – II. Experimental validation
Authors: Chafi J , El Azhari Y , Azagrouze O , Jabiri A , Boskri A , Benkhaldoun Z , Habib A 
Published: November 2023

ABSTRACT
This work presents the results of experimental laboratory tests on the apodization of circular and rectangular apertures using the Interferometric Apodization by Homothety (IAH) technique. The IAH approach involves splitting the amplitude of the instrumental PSF into two equal parts. One of the two produced PSFs undergoes homothety to change its transverse dimensions while its amplitude is properly controlled. The two PSFs are then combined to produce an apodized image. The diffraction wings of the resulting PSF are subsequently reduced by some variable reduction factor, depending on an amplitude parameter γ and a spread parameter η. This apodization approach was implemented in the laboratory using an interferometric set-up based on the Mach–Zehnder Interferometer (MZI). The experimental results exhibit a strong agreement between theory and experiment. For instance, the average experimental contrast obtained at a low angular separation of 2.4λ/D does not exceed 5 × 10−4. This work also allowed us to study the influence on the apodizer’s performance of some parameters, such as the wavelength and the density of the neutral filters.
Characterization of genes involved in micronutrients and toxic metals detoxification in Brassica napus by genome-wide cDNA library screening
Authors: Peng Jia-Shi , Zhang Xue-Jie , Xiong Jia-Ni , Zhou Ying , Wang Wei-Li , Chen Si-Ying , Zhang Da-Wei , Gu Tian-Yu 
Published: November 2023

Abstract
Stresses caused by deficiency/excess of mineral nutrients or of pollution of toxic metals have already become a primary factor in limiting crop production worldwide. Genes involved in minerals and toxic metals accumulation/tolerance could be potential candidates for improving crop plants with enhanced nutritional efficiency and environmental adaptability. In this study, we first generated a high-quality yeast expression cDNA library of Brassica napus (Westar), and 46 genes mediating excess micronutrients and toxic metals detoxification were screened using the yeast genetic complementation system, including 11, 5, 6, 14, 6, and 5 genes involved in cadmium (Cd), zinc (Zn), iron (Fe), manganese (Mn), boron (B), and copper (Cu) tolerance, respectively. Characterization of genes mediating excess ions stress resistance in this study is beneficial for us to further understand ions homeostasis in B. napus.
The Development of Non-affective Psychotic Syndromes in the 19th Century: LeGrand du Saulle and His 1871 Monograph “Le Délire De Persécutions” (Persecutory Delusions)
Authors: Kendler Kenneth S , Justis Virginia 
Published: November 2023

Abstract
While the origins of two of Kraepelin’s three subtypes of dementia praecox (DP), catatonic and hebephrenic, are well understood, no similar clear narrative exists for his concepts of paranoia and paranoid DP, which require a consideration of both German and French sources. An important milestone in the French literature is the massive 524 page monograph entitled “Le Délire Des Persécutions” published in 1871 by Henri Legrand du Saulle which contained extensive, clinically detailed descriptions of a wide range of cases with prominent, organized persecutory delusions. Many of his cases reported auditory hallucinations (AH), and some bizarre, Schneiderian delusions. The delusional content could evolve to include prominent somatic and/or grandiose themes. Using a symptomatic diagnostic framework, Legrand du Saulle proposed that this syndrome represented an independent “species” of mental illness. He sought to give a voice to the affected individuals, including a chapter devoted entirely to their writings. He described several clinically fascinating features of such patients including how often they moved residence to unsuccessfully flee their persecutors and how delusional beliefs could be communicated to spouses and relatives. Unlike Kraepelin, he was little interested in their course of illness or rates of deterioration, except to note that recoveries occurred in 20% of cases. The clinical richness of this work substantially exceeded that in the contemporaneous German literature. Most of the cases described by du Saulle would fit easily into the two major non-affective delusional syndromes articulated 28 years later in Kraepelin’s famous 6th edition of his textbook: paranoia and paranoid DP.
Spontaneous activity in peripheral sensory nerves: a systematic review
Authors: Choi Dongchan , Goodwin George , Stevens Edward B. , Soliman Nadia , Namer Barbara , Denk Franziska 
Published: November 2023

Abstract
In the peripheral nervous system, spontaneous activity in sensory neurons is considered to be one of the 2 main drivers of chronic pain states, alongside neuronal sensitization. Despite this, the precise nature and timing of this spontaneous activity in neuropathic pain is not well-established. Here, we have performed a systematic search and data extraction of existing electrophysiological literature to shed light on which fibre types have been shown to maintain spontaneous activity and over what time frame. We examined both in vivo recordings of preclinical models of neuropathic pain, as well as microneurography recordings in humans. Our analyses reveal that there is broad agreement on the presence of spontaneous activity in neuropathic pain conditions, even months after injury or years after onset of neuropathic symptoms in humans. However, because of the highly specialised nature of the electrophysiological methods used to measure spontaneous activity, there is also a high degree of variability and uncertainty around these results. Specifically, there are very few directly controlled experiments, with less directly comparable data between human and animals. Given that spontaneous peripheral neuron activity is considered to be a key mechanistic feature of chronic pain conditions, it may be beneficial to conduct further experiments in this space.
Reappraisal of Donor Age in Liver Transplantation: NASH as a Potential Target to Safely Utilize Old Liver Grafts
Authors: Kusakabe Jiro , Kozato Akio , Tajima Tetsuya , Bekki Yuki , Fujiki Masato , Tomiyama Koji , Nakamura Tsukasa , Matsushima Hajime , Hashimoto Koji , Sasaki Kazunari 
Published: November 2023

Background.
With the chronic shortage of donated organs, expanding the indications for liver transplantation (LT) from older donors is critical. Nonalcoholic steatohepatitis (NASH) stands out because of its unique systemic pathogenesis and high recurrence rate, both of which might make donor selection less decisive. The present study aims to investigate the usefulness of old donors in LT for NASH patients.

Methods.
The retrospective cohort study was conducted using the Scientific Registry Transplant Recipient database. The cohort was divided into 3 categories according to donor age: young (aged 16–35), middle-aged (36–59), and old donors (60–). Multivariable and Kaplan-Meier analyses were performed to compare the risk of donor age on graft survival (GS).

Results.
A total of 67 973 primary adult donation-after-brain-death LTs (2002–2016) were eligible for analysis. The multivariable analysis showed a reduced impact of donor age on GS for the NASH cohort (adjusted hazard ratio = 1.13, 95% confidence interval, 1.00-1.27), comparing old to middle-aged donors. If the cohort was limited to NASH recipients plus 1 of the following, recipient age ≥60, body mass index <30, or Model of End Stage Liver Disease score <30, adjusted hazard ratios were even smaller (0.99 [0.84–1.15], 0.92 [0.75–1.13], or 1.04 [0.91–1.19], respectively). Kaplan-Meier analysis revealed no significant differences in overall GS between old- and middle-aged donors in these subgroups (P = 0.86, 0.28, and 0.11, respectively).

Conclusions.
Donor age was less influential for overall GS in NASH cohort. Remarkably, old donors were equivalent to middle-aged donors in subgroups of recipient age ≥60, recipient body mass index <30, or Model of End Stage Liver Disease score <30.
Microbe Profile: Ehrlichia ruminantium – stealthy as it goes
Authors: Meyer Damien F. , Moumène Amal , Rodrigues Valérie 
Published: November 2023

Graphical abstract
Summary of

Ehrlichia ruminantium

infection.

E. ruminantium

bacterium is typically spread to ruminants by bite from infected ticks. Following adhesion of infectious elementary bodies to host cell,

E. ruminantium

establishes the depicted intracellular biphasic lifestyle by the means of secreted effector proteins that hijack host cellular pathways. Replicating bacteria (reticulate bodies) fill a large cytoplasmic vacuole named morula inside mammalian or tick cells. Formation of this vacuole is critical for bacterial development and subsequent lysis of the host cell leading to the establishment of heartwater disease. Genetic diversity is one remarkable and biologically significant feature of pathogens in the

Anaplasmataceae

family, including

E. ruminantium

. The maximum-likelihood phylogenetic tree of four representative species of

Ehrlichia

(

E. chaffeensis

str. Arkansas,

E. canis

str. Jake,

E. muris

AS145,

E. ruminantium

str. Gardel) with

Wolbachia

endosymbiont of D. melanogaster as an outgroup was reconstructed on the basis of concatenated nucleic acid alignment of proteins shared by all species (core genomes) with 100 bootstrap resamplings. Major hosts of these bacteria are indicated. Mb, megabase. ORFs, open reading frames. (All images created by S. Mateus, C. Noroy. O. Gros and D.F. Meyer.)