bluuebunny/crossref_metadata_2025_split huggingface dataset:
Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant
Authors: Khachaturyan Marina , Reusch Thorsten B H , Dagan Tal 
Published: September 2023

Abstract
Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.
Biomarkers of Alzheimer’s Disease and Cerebrovascular Disease in Relation to Depressive Symptomatology in Individuals With Subjective Cognitive Decline
Authors: Zapater-Fajarí Mariola , Diaz-Galvan Patricia , Cedres Nira , Rydberg Sterner Therese , Rydén Lina , Sacuiu Simona , Waern Margda , Zettergren Anna , Zetterberg Henrik , Blennow Kaj , Kern Silke , Hidalgo Vanesa , Salvador Alicia , Westman Eric , Skoog Ingmar , Ferreira Daniel 
Published: September 2023

Abstract

Background
Subjective cognitive decline (SCD) has gained recent interest as a potential harbinger of neurodegenerative diseases such as Alzheimer’s disease (AD) and cerebrovascular disease (CVD). In addition, SCD can be related to depressive symptomatology. However, the association between AD and CVD biomarkers, depressive symptomatology, and SCD is still unclear. We investigated the association of AD and CVD biomarkers and depressive symptomatology with SCD in individuals with subjective memory complaints (SCD-memory group) and individuals with subjective concentration complaints (SCD-concentration group).

Methods
We recruited a population-based cohort of 217 individuals (all aged 70 years, 53% female participants, 119 SCD-memory individuals, 23 SCD-concentration individuals, and 89 controls). AD and CVD were assessed through cerebrospinal fluid levels of the Aβ42/40 ratio and phosphorylated tau, and white matter signal abnormalities on magnetic resonance imaging, respectively. Associations between biomarkers, depressive symptomatology, and SCD were tested via logistic regression and correlation analyses.

Results
We found a significant association between depressive symptomatology with SCD-memory and SCD-concentration. Depressive symptomatology was not associated with AD and CVD biomarkers. Both the phosphorylated tau biomarker and depressive symptomatology predicted SCD-memory, and the Aβ42/40 ratio and depressive symptomatology predicted SCD-concentration.

Conclusions
The role of depressive symptomatology in SCD may differ depending on the stage within the spectrum of preclinical AD (as determined by amyloid-beta and tau positivity), and does not seem to reflect AD pathology. Our findings contribute to the emerging field of subclinical depressive symptomatology in SCD and clarify the association of different types of subjective complaints with distinct syndromic and biomarker profiles.
Reduced Activity of Glutamatergic Neurons in the Prelimbic Medial Prefrontal Cortex Underlies the Inherent Aging-Related Physiological Reduction in Social Dominance
Authors: Shan Qiang , Lin Xiaoli , Yu Xiaoxuan , Guo Wenye , Tian Yao 
Published: September 2023

Abstract
Human society is aging, and the percentage of the population of older adults is increasing at an unprecedented rate. It is increasingly appreciated that social behaviors change with aging. One such example is the possible aging-related reduction in dominance status. This change has been thought to underlie older adults’ peculiar vulnerability to fraud, which has become a major challenge in the present aging society. However, whether this change is an inherent physiological process, and, if so, its underlying microscopic physiological mechanism, is not known. This study used groups of mice in a design that minimized effects that could confound any inherent process of dominance and verified that social dominance does inherently reduce with aging. This study further identified an aging-related microscopic functional alteration, that is, a reduction in the activity of glutamatergic pyramidal neurons in the prelimbic medial prefrontal cortex; and established that this reduction in neuronal activity serves as an intrinsic physiological mechanism underlying the macroscopic aging-related reduction in dominance. This study, by exploiting modern neurobiological techniques, sheds light on our understanding of human social behaviors during aging and may help develop strategies to counter related social challenges among the older adults population.
Sex, Science, and Society: Reckonings and Responsibilities for Biologists
Authors: Lewis A Kelsey , Sharpe Sam L 
Published: September 2023

Synopsis
Individuals who may not fit European colonial ideas of dichotomous male or female bodies—those who are intersex—have been known across cultures and throughout human history. Unfortunately, acknowledgement of and engagement with this aspect of human biological diversity and the ongoing impact of binary misunderstandings of sex have been largely contained within the humanities and social sciences, while sex diversity beyond an assumed male/female binary has been either ignored or pathologized in the medical and biological sciences. The perceived social threat of intersex variation to the sex and gender binary has led to institutional and medical regulation of intersex people’s bodies, which has been the subject of increasing spotlight recently. Given the historical and ongoing role of the biological sciences in the pathologization of human sex variation and the deployment of medical technologies attempting to suppress this variation, we must actively acknowledge that our work does not exist and is not produced in a vacuum. Biological data demonstrate that sex is diverse and variable in animals, plants, and fungi. Despite this, the paradigm of binary sex has labeled diverse and variable sex as anomalous, especially in human populations. It is far past time to address this paradigm by actively examining the ways that our research, teaching, and communication engage with, articulate, and make legible particular narratives of sex diversity and variation.
Minireview: Glucocorticoid−Leptin Crosstalk: Role of Glucocorticoid–Leptin Counterregulation in Metabolic Homeostasis and Normal Development
Authors: Paul Bidisha , Buchholz Daniel R 
Published: September 2023

Synopsis
Glucocorticoids and leptin are two important hormones that regulate metabolic homeostasis by controlling appetite and energy expenditure in adult mammals. Also, glucocorticoids and leptin strongly counterregulate each other, such that chronic stress-induced glucocorticoids upregulate the production of leptin and leptin suppresses glucocorticoid production directly via action on endocrine organs and indirectly via action on food intake. Altered glucocorticoid or leptin levels during development can impair organ development and increase the risk of chronic diseases in adults, but there are limited studies depicting the significance of glucocorticoid-leptin interaction during development and its impact on developmental programming. In mammals, leptin-induced suppression of glucocorticoid production is critical during development, where leptin prevents stress-induced glucocorticoid production by inducing a period of short-hyporesponsiveness when the adrenal glands fail to respond to certain mild to moderate stressors. Conversely, reduced or absent leptin signaling increases glucocorticoid levels beyond what is appropriate for normal organogenesis. The counterregulatory interactions between leptin and glucocorticoids suggest the potential significant involvement of leptin in disorders that occur from stress during development.
“Death” and Its Discontents
Authors: Sparks Nicholas 
Published: September 2023

Abstract“Death” sits at the center of this issue of the Journal of Medicine and Philosophy. Each article, in its own fashion, touches on the problems of thinking about the nature of death in the light of contemporary scientific and medical advances. Three articles explicitly center on the ongoing debate over the Uniform Determination of Death Act, and three center on thematic issues surrounding death. Despite the topic, the discussion is lively and thoughtful. After introducing each article and sketching their contours, I offer some closing remarks on a central issue dredged up by these articles: the role of evaluative commitments and other interests in selecting criteria for the determination of death. These articles raise interesting questions about the relationship between the nature of “death” and ethical, epistemic, social-political, and economic values. This further opens up interesting lines of inquiry into medical epistemology. Finally, they broach deep questions about the nature of “function” and the relationship between organic and artificially sustained function.
ATMOSPHERIX: I- an open source high-resolution transmission spectroscopy pipeline for exoplanets atmospheres with SPIRou
Authors: Klein Baptiste , Debras Florian , Donati Jean-François , Hood Thea , Moutou Claire , Carmona Andres , Ould-elkhim Merwan , Bézard Bruno , Charnay Benjamin , Fouqué Pascal , Masson Adrien , Vinatier Sandrine , Baruteau Clément , Boisse Isabelle , Bonfils Xavier , Chiavassa Andrea , Delfosse Xavier , Dethier William , Hebrard Guillaume , Kiefer Flavien , Leconte Jérémy , Martioli Eder , Parmentier Vivien , Petit Pascal , Pluriel William , Selsis Franck , Teinturier Lucas , Tremblin Pascal , Turbet Martin , Venot Olivia , Wyttenbach Aurélien 
Published: September 2023

ABSTRACT
Atmospheric characterization of exoplanets from the ground is an actively growing field of research. In this context, we have created the ATMOSPHERIX consortium: a research project aimed at characterizing exoplanets atmospheres using ground-based high-resolution spectroscopy. This paper presents the publicly available data analysis pipeline and demonstrates the robustness of the recovered planetary parameters from synthetic data. Simulating planetary transits using synthetic transmission spectra of a hot Jupiter that were injected into real SPIRou observations of the non-transiting system Gl 15 A, we show that our pipeline is successful at recovering the planetary signal and input atmospheric parameters. We also introduce a deep learning algorithm to optimize data reduction which proves to be a reliable, alternative tool to the commonly used principal component analysis. We estimate the level of uncertainties and possible biases when retrieving parameters such as temperature and composition and hence the level of confidence in the case of retrieval from real data. Finally, we apply our pipeline onto two real transits of HD 189733 b observed with SPIRou and obtain similar results than in the literature. In summary, we have developed a publicly available and robust pipeline for the forthcoming studies of the targets to be observed in the framework of the ATMOSPHERIX consortium, which can easily be adapted to other high resolution instruments than SPIRou (e.g. VLT-CRIRES, MAROON-X, ELT-ANDES).
Unravelling the nuclear dust morphology of NGC 1365: a two-phase polar–RAT model for the ultraviolet to infrared spectral energy distribution
Authors: Swain Subhashree , Shalima P , Latha K V P 
Published: September 2023

ABSTRACT
We present a 3D radiative transfer model for the spectral energy distribution (SED) of NGC 1365, which is a ‘changing look’ Seyfert 1.8 type active galactic nucleus (AGN). The SED from the ultraviolet (UV) to the infrared (IR) is constructed using archival data from the Ultra-Violet Imaging Telescope (UVIT) onboard AstroSat, along with IR data from the literature. The skirt radiative transfer code is used to model the SED and derive the geometry and composition of dust in this AGN. Similar to our earlier SED model of NGC 4151, the nuclear region of NGC 1365 is assumed to contain a ring or disc-like structure concentric to the accretion disc, composed of large (0.1–1 $\mu$m) graphite grains in addition to the two-phase dusty torus made up of interstellar-medium-type grains (Ring And Torus or RAT model). We also include, for the first time, an additional component of dusty wind in the form of a bipolar cone. We carry out a detailed analysis and derive the best-fitting parameters from a χ2 test to be Rin, r = 0.03 pc, σ = 26°, and τtotal = 20 for the assumed ring–torus–polar wind geometry. Our results suggest the presence of hot dust at a temperature T ∼ 1216 K at the location of the ring that absorbs and scatters the incident UV radiation and emits in the near-IR. In the mid-IR, the major contributors are the polar cone and warm dust with T ∼ 914 K at Rin, t = 0.1 pc. Not only are our model radii in agreement with IR interferometric observations, but also our study reiterates the role of high-resolution UV observations in constraining the dust grain size distribution in the nuclear regions of AGN.
Supermassive black holes in a mass-limited galaxy sample
Authors: Byrne Zachary , Drinkwater Michael J , Baumgardt Holger , Blyth David , Côté Patrick , Lüetzgendorf Nora , Spengler Chelsea , Ferrarese Laura , Mahajan Smriti , Pfeffer Joel , Sweet Sarah 
Published: September 2023

ABSTRACT
The observed scaling relations between supermassive black hole masses and their host galaxy properties indicate that supermassive black holes influence the evolution of galaxies. However, the scaling relations may be affected by selection biases. We propose to measure black hole masses in a mass-limited galaxy sample including all non-detections to inprove constraints on galaxy mass – black hole mass scaling relations and test for selection bias. We use high-spatial resolution spectroscopy from the Keck and Gemini telescopes, and the Jeans Anisotropic Modelling method to measure black hole masses in early-type galaxies from the Virgo Cluster. We present four new black hole masses and one upper limit in our mass-selected sample of galaxies of galaxy mass (1.0–3.2) $\times 10^{10} \, \mathrm{M}_\odot$. This brings the total measured to 11 galaxies out of a full sample of 18 galaxies, allowing us to constrain scaling relations. We calculate a lower limit for the average black hole mass in our sample of $3.7 \times 10^{7} \, \mathrm{M}_\odot$. This is at an average galaxy stellar mass of $(1.81 \pm 0.14)\times 10^{10} \, \mathrm{M}_\odot$ and an average bulge mass of $(1.31 \pm 0.15) \times 10^{10} \, \mathrm{M}_\odot$. This lower limit shows that black hole masses in early-type galaxies are not strongly affected by selection biases.
Molecular and ionized gas in tidal dwarf galaxies: the spatially resolved star formation relation
Authors: Kovakkuni N , Lelli F , Duc P-A , Boquien M , Braine J , Brinks E , Charmandaris V , Combes F , Fensch J , Lisenfeld U , McGaugh S S , Mihos J C , Pawlowski M S , Revaz Y , Weilbacher P M 
Published: September 2023

ABSTRACT
Tidal dwarf galaxies (TDGs) are low-mass objects that form within tidal and/or collisional debris ejected from more massive interacting galaxies. We use CO(1–0) observations from Atacama Large Millimeter/submillimeter Array and integral-field spectroscopy from Multi-Unit Spectroscopic Explorer to study molecular and ionized gas in three TDGs: two around the collisional galaxy NGC 5291 and one in the late-stage merger NGC 7252. The CO and H α emission is more compact than the H i emission and displaced from the H i dynamical centre, so these gas phases cannot be used to study the internal dynamics of TDGs. We use CO, H i, and H α data to measure the surface densities of molecular gas (Σmol), atomic gas (Σatom), and star formation rate (ΣSFR), respectively. We confirm that TDGs follow the same spatially integrated ΣSFR–Σgas relation of regular galaxies, where Σgas = Σmol + Σatom, even though they are H i dominated. We find a more complex behaviour in terms of the spatially resolved ΣSFR–Σmol relation on subkpc scales. The majority ($\sim 60~{{\ \rm per\ cent}}$) of star-forming regions in TDGs lie on the same ΣSFR–Σmol relation of normal spiral galaxies but show a higher dispersion around the mean. The remaining fraction of star-forming regions ($\sim 40~{{\ \rm per\ cent}}$) lie in the starburst region and are associated with the formation of massive super star clusters, as shown by Hubble Space Telescope images. We conclude that the local star formation activity in TDGs proceeds in a hybrid fashion, with some regions comparable to normal spiral galaxies and others to extreme starbursts.
Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus
Authors: Wang Tianpeng , van Dijk Aalt D J , Bucher Johan , Liang Jianli , Wu Jian , Bonnema Guusje , Wang Xiaowu 
Published: September 2023

Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
NLGN4X TCR transgenic T cells to treat gliomas
Authors: Krämer Christoper , Kilian Michael , Chih Yu-Chan , Kourtesakis Alexandros , Hoffmann Dirk C , Boschert Tamara , Koopmann Philipp , Sanghvi Khwab , De Roia Alice , Jung Stefanie , Jähne Kristine , Day Bryan , Shultz Lenny D , Ratliff Miriam , Harbottle Richard , Green Edward W , Will Rainer , Wick Wolfgang , Platten Michael , Bunse Lukas 
Published: September 2023

Abstract

Background
Neuroligin 4 X-linked (NLGN4X) harbors a human leukocyte antigen (HLA)-A*02-restricted tumor-associated antigen, overexpressed in human gliomas, that was found to induce specific cytotoxic T cell responses following multi-peptide vaccination in patients with newly diagnosed glioblastoma.

Methods
T cell receptor (TCR) discovery was performed using droplet-based single-cell TCR sequencing of NLGN4X-tetramer-sorted T cells postvaccination. The identified TCR was delivered to Jurkat T cells and primary human T cells (NLGN4X-TCR-T). Functional profiling of NLGN4X-TCR-T was performed by flow cytometry and cytotoxicity assays. Therapeutic efficacy of intracerebroventricular NLGN4X-TCR-T was assessed in NOD scid gamma (NSG) major histocompatibility complex (MHC) I/II knockout (KO) (NSG MHC I/II KO) mice bearing NLGN4X-expressing experimental gliomas.

Results
An HLA-A*02-restricted vaccine-induced T cell receptor specifically binding NLGN4X131–139 was applied for preclinical therapeutic use. Reactivity, cytotoxicity, and polyfunctionality of this NLGN4X-specific TCR are demonstrated in various cellular models. Intracerebroventricular administration of NLGN4X-TCR-T prolongs survival and leads to an objective response rate of 44.4% in experimental glioma-bearing NSG MHC I/II KO mice compared to 0.0% in control groups.

Conclusion
NLGN4X-TCR-T demonstrate efficacy in a preclinical glioblastoma model. On a global scale, we provide the first evidence for the therapeutic retrieval of vaccine-induced human TCRs for the off-the-shelf treatment of glioblastoma patients.Keywords cell therapy | glioblastoma | T cell receptor | tumor antigen
Improved early outcome prediction by MRI-based 3D tumor volume assessment in patients with CNS lymphomas
Authors: Lauer Eliza M , Riegler Ella , Mutter Jurik A , Alig Stefan K , Bleul Sabine , Kuehn Julia , Ranganathan Lavanya , Klingler Christian , Demerath Theo , Würtemberger Urs , Rau Alexander , Weiß Jakob , Eisenblaetter Michel , Bamberg Fabian , Prinz Marco , Finke Jürgen , Duyster Justus , Illerhaus Gerald , Diehn Maximilian , Alizadeh Ash A , Schorb Elisabeth , Reinacher Peter C , Scherer Florian 
Published: September 2023

Abstract

Background
Central nervous system lymphomas (CNSL) display remarkable clinical heterogeneity, yet accurate prediction of outcomes remains challenging. The IPCG criteria are widely used in routine practice for the assessment of treatment response. However, the value of the IPCG criteria for ultimate outcome prediction is largely unclear, mainly due to the uncertainty in delineating complete from partial responses during and after treatment.

Methods
We explored various MRI features including semi-automated 3D tumor volume measurements at different disease milestones and their association with survival in 93 CNSL patients undergoing curative-intent treatment.

Results
At diagnosis, patients with more than 3 lymphoma lesions, periventricular involvement, and high 3D tumor volumes showed significantly unfavorable PFS and OS. At first interim MRI during treatment, the IPCG criteria failed to discriminate outcomes in responding patients. Therefore, we randomized these patients into training and validation cohorts to investigate whether 3D tumor volumetry could improve outcome prediction. We identified a 3D tumor volume reduction of ≥97% as the optimal threshold for risk stratification (=3D early response, 3D_ER). Applied to the validation cohort, patients achieving 3D_ER had significantly superior outcomes. In multivariate analyses, 3D_ER was independently prognostic of PFS and OS. Finally, we leveraged prognostic information from 3D MRI features and circulating biomarkers to build a composite metric that further improved outcome prediction in CNSL.

Conclusions
We developed semi-automated 3D tumor volume measurements as strong and independent early predictors of clinical outcomes in CNSL patients. These radiologic features could help improve risk stratification and help guide future treatment approaches.