bluuebunny/crossref_metadata_2025_split huggingface dataset:
The variable magnetic field of V889 Her and the challenge of detecting exoplanets around young Suns using Gaussian process regression
Authors: Brown E L , Marsden S C , Jeffers S V , Heitzmann A , Barnes J R , Folsom C P 
Published: January 2024

ABSTRACT
Discovering exoplanets orbiting young Suns can provide insight into the formation and early evolution of our own solar system, but the extreme magnetic activity of young stars obfuscates exoplanet detection. Here we monitor the long-term magnetic field and chromospheric activity variability of the young solar analogue V889 Her, model the activity-induced radial velocity variations, and evaluate the impacts of extreme magnetism on exoplanet detection thresholds. We map the magnetic field and surface brightness for 14 epochs between 2004 and 2019. Our results show potential 3–4 yr variations of the magnetic field that evolves from weak and simple during chromospheric activity minima to strong and complex during activity maxima but without any polarity reversals. A persistent, temporally varying polar spot coexists with weaker, short-lived lower-latitude spots. Due to their different decay time-scales, significant differential rotation, and the limited temporal coverage of our legacy data, we were unable to reliably model the activity-induced radial velocity using Gaussian Process regression. Doppler Imaging can be a useful method for modelling the magnetic activity jitter of extremely active stars using data with large phase gaps. Given our data and using Doppler Imaging to filter activity jitter, we estimate that we could detect Jupiter-mass planets with orbital periods of $\sim$3 d. A longer baseline of continuous observations is the best observing strategy for the detection of exoplanets orbiting highly active stars.
The radio to GeV picture of PSR B1259-63 during the 2021 periastron passage
Authors: Chernyakova M , Malyshev D , van Soelen B , Mc Keague S , O’Sullivan S P , Buckley D 
Published: January 2024

ABSTRACT
PSR B1259-63 is a gamma-ray binary system with a radio pulsar orbiting an O9.5Ve star, LS 2883, with a period of ${\sim} 3.4$ yr. Close to the periastron the system is detected at all wavelengths, from radio to the TeV energies. The emission in this time period is believed to originate from the interaction of LS 2883 and pulsar’s outflows. The observations of four periastra passages taken in 2010–2021 show strong correlation of the radio and X-ray light curves with two peaks just before and after the periastron. The observations of the latest 2021 periastron passage reveal the presence of the 3rd X-ray peak and subsequent disappearance of radio/X-ray flux correlation. In this paper, we present the results of our optical, radio, and X-ray observational campaigns on PSR B1259-63 performed in 2021 accompanied with the analysis of the publicly available GeV Fermi/LAT data. We compare the properties of different periastron passages, discuss the obtained results and show that they can be explained in terms of the 2-zone emission model proposed by us previously.
Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism
Authors: Lee JunMo , Yang Ji Hyun , Weber Andreas P M , Bhattacharya Debashish , Kim Woe-Yeon , Yoon Hwan Su 
Published: January 2024

Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion
Authors: Harada Ryo , Hirakawa Yoshihisa , Yabuki Akinori , Kim Eunsoo , Yazaki Euki , Kamikawa Ryoma , Nakano Kentaro , Eliáš Marek , Inagaki Yuji 
Published: January 2024

Abstract
DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.
Measurement of chromosomal instability and level of DNA damage in peripheral blood mononuclear cells of endometrial cancer patients
Authors: Marković Aleksandra , Grujičić Darko , Živković Radojević Marija , Milošević-Djordjević Olivera 
Published: January 2024

Abstract
Endometrial cancer is one of the most common invasive gynecologic malignancies in developed countries. The aim of this study was to evaluate chromosomal instability and level of DNA damage in peripheral blood mononuclear cells (PBMCs) of newly diagnosed endometrial cancer patients in relation to health status (diagnosis), age, histological grade of cancer, residence, smoking, number of pregnancies, miscarriages, and abortions. The analyzed sample consisted of 60 individuals, 30 endometrial cancer patients with an average age of 64.37 ± 7.08, and 30 healthy control women with an average age of 60.23 ± 11.55. Chromosomal instability was evaluated by the cytokinesis-block micronucleus (CBMN) assay, and the level of DNA damage by the single-cell gel electrophoresis (comet) assay in PBMCs. The average frequencies of micronuclei (MNi), nucleoplasmic bridges (NPBs) as well as nuclear buds (NBUDs) were significantly higher in cancer patients compared to controls (P &lt; .0005). There was no difference in the nuclear division index (NDI) among the analyzed samples. The comet assay showed that the patients had a significantly increased genetic damage index (GDI) compared with controls (P &lt; .0005). Using linear regression analysis, we found that health status (diagnosis) had the strongest influence on the MN frequency as well as GDI (P &lt; .0005). Our results indicated that there is a high level of genetic damage in both the level of DNA and the level of chromosomes in the PBMCs of newly diagnosed patients with endometrial cancer, where the frequency and level of damage were significantly affected by health status, grade of cancer, residence, number of pregnancies, miscarriages, and abortions.
Geno2pheno: recombination detection for HIV-1 and HEV subtypes
Authors: Pirkl Martin , Büch Joachim , Friedrich Georg , Böhm Michael , Turner Dan , Degen Olaf , Kaiser Rolf , Lengauer Thomas 
Published: January 2024

Abstract
Even after three decades of antiretroviral therapy for HIV-1 (human immunodeficiency virus 1), therapy failure is a continual challenge. This is especially so if the viral variant is a recombinant of subtypes. Thus, improved diagnosis of recombined subtypes can help with the selection of therapy. We are using a new implementation of the previously published computational method recco to detect de novo recombination of known subtypes, independent of and in addition to known circulating recombinant forms (CRFs). We detect an optimal path in a multiple alignment of viral reference sequences based on mutation calls and probable breakpoints for recombination. A tuning parameter is used to favor either mutation calls or breakpoints. Besides novel recombinants, our tool g2p-recco integrated in the geno2pheno web service (https://geno2pheno.org) can successfully detect known recombinant events given only the full consensus references (without CRFs) of the involved subtypes with breakpoints. In addition, the tool can be applied to other viruses, i.e. hepatitis E virus (HEV). In this fashion, we could also detect several previously unknown recombinations in HEV.
Invasive growth of brain metastases is linked to CHI3L1 release from pSTAT3-positive astrocytes
Authors: Dankner Matthew , Maritan Sarah M , Priego Neibla , Kruck Georgia , Nkili-Meyong Andriniaina , Nadaf Javad , Zhuang Rebecca , Annis Matthew G , Zuo Dongmei , Nowakowski Alexander , Biondini Marco , Kiepas Alexander , Mourcos Caitlyn , Le Phuong , Charron François , Inglebert Yanis , Savage Paul , Théret Louis , Guiot Marie-Christine , McKinney R Anne , Muller William J , Park Morag , Valiente Manuel , Petrecca Kevin , Siegel Peter M 
Published: January 2024

Abstract

Background
Compared to minimally invasive brain metastases (MI BrM), highly invasive (HI) lesions form abundant contacts with cells in the peritumoral brain parenchyma and are associated with poor prognosis. Reactive astrocytes (RAs) labeled by phosphorylated STAT3 (pSTAT3) have recently emerged as a promising therapeutic target for BrM. Here, we explore whether the BrM invasion pattern is influenced by pSTAT3+ RAs and may serve as a predictive biomarker for STAT3 inhibition.

Methods
We used immunohistochemistry to identify pSTAT3+ RAs in HI and MI human and patient-derived xenograft (PDX) BrM. Using PDX, syngeneic, and transgenic mouse models of HI and MI BrM, we assessed how pharmacological STAT3 inhibition or RA-specific STAT3 genetic ablation affected BrM growth in vivo. Cancer cell invasion was modeled in vitro using a brain slice-tumor co-culture assay. We performed single-cell RNA sequencing of human BrM and adjacent brain tissue.

Results
RAs expressing pSTAT3 are situated at the brain–tumor interface and drive BrM invasive growth. HI BrM invasion pattern was associated with delayed growth in the context of STAT3 inhibition or genetic ablation. We demonstrate that pSTAT3+ RAs secrete Chitinase 3-like-1 (CHI3L1), which is a known STAT3 transcriptional target. Furthermore, single-cell RNA sequencing identified CHI3L1-expressing RAs in human HI BrM. STAT3 activation, or recombinant CHI3L1 alone, induced cancer cell invasion into the brain parenchyma using a brain slice-tumor plug co-culture assay.

Conclusions
Together, these data reveal that pSTAT3+ RA-derived CHI3L1 is associated with BrM invasion, implicating STAT3 and CHI3L1 as clinically relevant therapeutic targets for the treatment of HI BrM.
Single-nucleus expression characterization of non-enhancing region of recurrent high-grade glioma
Authors: Patel Kunal S , Tessema Kaleab K , Kawaguchi Riki , Dudley Lindsey , Alvarado Alvaro G , Muthukrishnan Sree Deepthi , Perryman Travis , Hagiwara Akifumi , Swarup Vivek , Liau Linda M , Wang Anthony C , Yong William , Geschwind Daniel H , Nakano Ichiro , Goldman Steven A , Everson Richard G , Ellingson Benjamin M , Kornblum Harley I 
Published: January 2024

Abstract

Background
Non-enhancing (NE) infiltrating tumor cells beyond the contrast-enhancing (CE) bulk of tumor are potential propagators of recurrence after gross total resection of high-grade glioma.

Methods
We leveraged single-nucleus RNA sequencing on 15 specimens from recurrent high-grade gliomas (n = 5) to compare prospectively identified biopsy specimens acquired from CE and NE regions. Additionally, 24 CE and 22 NE biopsies had immunohistochemical staining to validate RNA findings.

Results
Tumor cells in NE regions are enriched in neural progenitor cell-like cellular states, while CE regions are enriched in mesenchymal-like states. NE glioma cells have similar proportions of proliferative and putative glioma stem cells relative to CE regions, without significant differences in % Ki-67 staining. Tumor cells in NE regions exhibit upregulation of genes previously associated with lower grade gliomas. Our findings in recurrent GBM paralleled some of the findings in a re-analysis of a dataset from primary GBM. Cell-, gene-, and pathway-level analyses of the tumor microenvironment in the NE region reveal relative downregulation of tumor-mediated neovascularization and cell-mediated immune response, but increased glioma-to-nonpathological cell interactions.

Conclusions
This comprehensive analysis illustrates differing tumor and nontumor landscapes of CE and NE regions in high-grade gliomas, highlighting the NE region as an area harboring likely initiators of recurrence in a pro-tumor microenvironment and identifying possible targets for future design of NE-specific adjuvant therapy. These findings also support the aggressive approach to resection of tumor-bearing NE regions.
The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma
Authors: Krynina Olha , de Ståhl Teresita Díaz , Jylhä Cecilia , Arthur Cecilia , Giraud Geraldine , Nyman Per , Fritzberg Anders , Sandgren Johanna , Tham Emma , Sandvik Ulrika 
Published: January 2024

Abstract

Background
Low-grade gliomas (LGGs) represent children’s most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples.

Methods
We examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants.

Results
Our findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (&lt;1.9 ng).

Conclusions
While CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.
Potential roles for efferocytosis in glioblastoma immune evasion
Authors: Lorimer Ian A J 
Published: January 2024

Abstract
Glioblastoma is an aggressive and incurable brain cancer. This cancer establishes both local and systemic immunosuppression that creates a major obstacle to effective immunotherapies. Many studies point to tumor-resident myeloid cells (primarily microglia and macrophages) as key mediators of this immunosuppression. Myeloid cells exhibit a high level of plasticity with respect to their phenotype and are capable of both stimulating and repressing immune responses. How glioblastomas recruit myeloid cells and exploit them to avoid the immune system is an active area of research. Macrophages can acquire an immunosuppressive phenotype as a consequence of exposure to cytokines such as TGFB1 or IL4; in addition, macrophages can acquire an immunosuppressive phenotype as a consequence of the engulfment of apoptotic cells, a process referred to as efferocytosis. There is substantial evidence that glioblastoma cells are able to secrete cytokines and other factors that induce an immunosuppressive phenotype in macrophages and microglia. However, less is known about the contribution of efferocytosis to immunosuppression in glioblastoma. Here I review the literature in this area and discuss the potential of efferocytosis inhibition to improve glioblastoma response to immunotherapy.
The anomalous effect of electric field on friction for microscale structural superlubric graphite/Au contact
Authors: Wang Yelingyi , Wang Jin , Wu Tielin , Chen Weipeng , Peng Deli , Wu Zhanghui , Ma Ming , Zheng Quanshui 
Published: January 2024

ABSTRACT
The current-carrying friction characteristics are crucial for the performance of a sliding electrical contact, which plays critical roles in numerous electrical machines and devices. However, these characteristics are influenced by multiple factors such as material surface quality, chemical reactions, and atmospheric environment, leading to a challenge for researchers to comprehensively consider these impacts. Structural superlubricity (SSL), a state of nearly zero friction and no wear between contact solid surfaces, provides an ideal experimental system for these studies. Here, with microscale graphite flakes on atomic-flattened Au surface under applied voltages, we observed two opposite friction phenomena, depending only on whether the edge of graphite flake was in contact with the Au substrate. When in contact the friction force would increase with an increasing voltage, otherwise, the friction force would decrease. Notably, when the voltage was turned off, the friction force quickly recovered to its original level, indicating the absence of wear. Through atmosphere control and molecular dynamics simulations, we revealed the mechanism to be the different roles played by the water molecules confined at the interface or adsorbed near the edges. Our experimental results demonstrate the remarkable tunable and robust frictional properties of SSL under an electrical field, providing an ideal system for the fundamental research of not only sliding electrical contacts, but also novel devices which demand tunable frictions.
Exporting, investing and productivity dynamics in African manufacturing
Authors: Alka Kilishi A 
Published: January 2024

Abstract
Trade shocks generated by trade policy reform are important for firm productivity. In particular, export opportunities and access to imported intermediate inputs and capital goods can encourage firms to simultaneously export and invest. Using a panel dataset for manufacturing firms in Ghana, Kenya, Nigeria and Tanzania, I find strong and robust evidence for learning-by-exporting effect. I also find that firms that simultaneously export and invest have the highest returns to these activities compared with firms that export without investing, or firms that invest without exporting, or firms that do neither activity. The superior productivity performance of firms that engage in both activities is consistent with the idea that exporting and investing have complementary effects on a firm’s productivity: investing facilitates a firm’s ability to absorb export-related technology. Finally, I find that firm heterogeneity has important influence on the productivity gains associated with exporting and investing.
Growth signaling autonomy in circulating tumor cells aids metastatic seeding
Authors: Sinha Saptarshi , Farfel Alex , Luker Kathryn E , Parker Barbara A , Yeung Kay T , Luker Gary D , Ghosh Pradipta 
Published: January 2024

Abstract
Self-sufficiency (autonomy) in growth signaling, the earliest recognized hallmark of cancer, is fueled by the tumor cell's ability to “secrete-and-sense” growth factors (GFs); this translates into cell survival and proliferation that is self-sustained by autocrine/paracrine secretion. A Golgi-localized circuitry comprised of two GTPase switches has recently been implicated in the orchestration of growth signaling autonomy. Using breast cancer cells that are either endowed or impaired (by gene editing) in their ability to assemble the circuitry for growth signaling autonomy, here we define the transcriptome, proteome, and phenome of such an autonomous state, and unravel its role during cancer progression. We show that autonomy is associated with enhanced molecular programs for stemness, proliferation, and epithelial-mesenchymal plasticity. Autonomy is both necessary and sufficient for anchorage-independent GF-restricted proliferation and resistance to anticancer drugs and is required for metastatic progression. Transcriptomic and proteomic studies show that autonomy is associated, with a surprising degree of specificity, with self-sustained epidermal growth factor receptor (EGFR)/ErbB signaling. Derivation of a gene expression signature for autonomy revealed that growth signaling autonomy is uniquely induced in circulating tumor cells (CTCs), the harshest phase in the life of tumor cells when it is deprived of biologically available epidermal growth factor (EGF). We also show that autonomy in CTCs tracks therapeutic response and prognosticates outcome. These data support a role for growth signaling autonomy in multiple processes essential for the blood-borne dissemination of human breast cancer.