bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast
Authors: Mares-Mayagoitia Jorge Alberto , Lafarga-De la Cruz Fabiola , Micheli Fiorenza , Cruz-Hernández Pedro , de-Anda-Montañez Juan A , Hyde John , Hernández-Saavedra Norma Y , Mejía-Ruíz Paulina , De Jesús-Bonilla Vladimir S , Vargas-Peralta Carmen E , Valenzuela-Quiñonez Fausto 
Published: December 2023

Abstract
Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, United States to Baja California Sur, Mexico, exposed to a latitudinal environmental gradient in the California Current System. Management of the pink abalone contrasts between Mexico and the United States; Mexico has an active fishery organized in four administrative areas, while the United States has kept the fishery in permanent closure since 1996. However, the impact of environmental factors on genetic variation along the species distribution remains unknown, and understanding this relationship is crucial for effective spatial management strategies. This study aims to investigate the neutral and adaptive genomic structure of H. corrugata. A total of 203 samples from 13 locations were processed using ddRADseq, and covering the species’ distribution. Overall, 2,231 neutral, nine potentially adaptive and three genomic–environmental association loci were detected. The neutral structure identified two groups: 1) California, United States and 2) Baja California Peninsula, México. In addition, the adaptive structure analysis also detected two groups with genetic divergence observed at Punta Eugenia. Notably, the seawater temperature significantly correlated with the northern group (temperate) and the southern (warmer) group. This study is a valuable foundation for future research and conservation initiatives, emphasizing the importance of considering neutral and adaptive genetic factors when developing management strategies for marine species.
Constructive theories through a modal lens
Authors: Tesi Matteo 
Published: December 2023

Abstract
We present a uniform proof-theoretic proof of the Gödel–McKinsey–Tarski embedding for a class of first-order intuitionistic theories. This is achieved by adapting to the case of modal logic the methods of proof analysis in order to convert axioms into rules of inference of a suitable sequent calculus. The soundness and the faithfulness of the embedding are proved by induction on the height of the derivations in the augmented calculi. Finally, we define an extension of the modal system for which the result holds with respect to geometric intuitionistic.
Transcriptome profiling and in silico docking analysis of phosphine resistance in rice weevil, Sitophilus oryzae (Coleoptera: Curculionidae)
Authors: Selvapandian Upasna , Nallusamy Saranya , Singh Sonu Kumar , Mannu Jayakanthan , Shanmugam Varanavasiappan , Ravikumar Caroline , Subbarayalu Mohankumar 
Published: December 2023

Abstract
The rice weevil, Sitophilus oryzae (Linnaeus, Coleoptera: Curculionidae), is a serious cosmopolitan pest that affects grain in storage and has developed high levels of resistance toward phosphine. In this study, RNA-seq data was used to study the phosphine resistance mechanisms in S. oryzae. Resistant and susceptible populations of S. oryzae were identified based on phosphine bioassays conducted in 32 populations collected across Tamil Nadu, India. Differential expression of mitochondrial (COX1, COX2, COX3, ND2, ND3, ATP6, and ATP8) and detoxification genes (Cyps, Gsts, and Cbe) were observed in the resistant and susceptible populations of S. oryzae. The previously characterized phosphine resistant gene, dld (dihydrolipoamide dehydrogenase) linked to the rph2 locus, was found to be up-regulated in resistant S. oryzae population (ISO-TNAU-RT) treated with phosphine. Also, the genes involved in Tricarboxylic acid (TCA) cycle were significantly down-regulated. In addition, a significant up-regulation in the expression of the antioxidant enzymes superoxide dismutase (2.5×) and catalase (2.1×) in ISO-TNAU-RT populations was recorded. Furthermore, a distinct amino acid substitution, Lysine &gt; Glutamic acid (K141E) was identified in resistant phenotypes. In silico docking studies of both resistant and susceptible DLD protein with phosphine molecule revealed that the amino acid residues involved in the interaction were different. This suggested that the amino acid substitution might lead to structural modifications which reduces the affinity of the target (phosphine). This study provides insight on the various genes, pathways, and functional mechanisms having a significant role in phosphine resistance in S. oryzae.
Prevalence of germline BRCA1/2 pathogenic variants in Japanese patients treated with castration-resistant prostate cancer and efficacy of CRPC treatment in real-world clinical practice
Authors: Maekawa Shigekatsu , Takata Ryo , Sekiguchi Kie , Kagabu Masahiro , Toyoshima Moe , Tamada Shinji , Takahashi Kenta , Ikarashi Daiki , Matsuura Tomohiko , Kato Renpei , Kato Yoichiro , Kanehira Mitsugu , Sugimura Jun , Abe Takaya , Baba Tsukasa , Obara Wataru 
Published: December 2023

Abstract

Objective
The companion diagnosis for olaparib, a poly (ADP-ribose) polymerase inhibitor for prostate cancer, aims to detect BRCA1/2 gene variants. In clinical practice, the frequency of germline BRCA1/2 variants in patients receiving castration-resistant prostate cancer treatment is unknown. We aimed to evaluate the prevalence of germline BRCA1/2 variants and their relationship to prognosis and treatment efficacy in castration-resistant prostate cancer.

Methods
Between June 2021 and 2023, 92 patients receiving castration-resistant prostate cancer treatment were examined for germline BRCA1/2 variants using BRACAnalysis CDx®. Furthermore, the associations between BRCA1/2 pathogenic variants and clinical outcomes were assessed.

Results
Of the 92 patients referred for genetic testing, 6 (6.5%) carried germline pathogenic variants in BRCA1/2. The BRCA2 variant was the most frequent (n = 5), followed by BRCA1 variant (n = 1). Among the five variants in BRCA2, the p.Asp427Thrfs*3 variant was identified for the first time in prostate cancer. Overall survival from castration-resistant prostate cancer for patients with BRCA1/2 variants was significantly shorter than for patients without BRCA1/2 variants (P = 0.043). Progression-free survival of androgen receptor signaling inhibitors for patients with BRCA1/2 variants was significantly shorter than for those without (P = 0.003). Progression-free survival of taxane chemotherapy was significantly shorter in patients with BRCA1/2 variants than in those without (P = 0.0149).

Conclusions
In clinical practice, 6.5% of patients treated with castration-resistant prostate cancer carried germline BRCA1/2 pathogenic variants. Japanese castration-resistant prostate cancer patients with germline BRCA1/2 mutants have a poor prognosis and may be less responsive to treatment with androgen receptor signaling inhibitors and taxane-based chemotherapy for castration-resistant prostate cancer.
A comparison of the population ecology of 4 Cryptomys hottentotus subspecies
Authors: Süess Tobias , Finn Kyle T , Janse van Vuuren Andries K , Hart Daniel W , Bennett Nigel C 
Published: December 2023

Abstract
Selection pressures underpinning the evolution of mammalian sociality and body mass variation have spurred great interest for several decades. Because they inhabit a wide range of geographic localities and habitats, African mole-rat subspecies of Cryptomys hottentotus present a unique opportunity to further our understanding of intra- and interspecific variation of sociality and body mass in mammalian species. We compared the demographics and body masses among 4 C. hottentotus subspecies: the Mahali mole-rat, C. h. mahali; highveld mole-rat, C. h. pretoriae; Natal mole-rat, C. h. natalensis; and common mole-rat, C. h. hottentotus within the context of their respective microclimates and evolutionary history. We propose that all ancestral C. hottentotus subspecies were arid-adapted and thus formed large colonies (as found today in the Mahali mole-rat). However, as the subspecies dispersed to occupy habitats of varying aridity and temperature across South Africa, selection for a particular colony size range in each subspecies arose to provide an adaptive fitness benefit to survive in its habitat. Consequently, the Mahali mole-rat—which remained in a warm and arid environment—retained the largest mean colony size, followed by the Natal mole-rat, which—even though inhabiting a hyper-mesic environment—selected for increased colony sizes to offset the energy requirement of thermoregulation (through huddling) in the cooler montane environments they prefer. The common mole-rat and the highveld mole-rat possessed the smallest mean colony sizes, likely the result of inhabiting a mesic and warm environment. At the same time, body mass variation in the C. hottentotus complex is likely linked to colony size variation, with subspecies having the largest colonies possessing the lowest individual body mass.
The mosquitoes (Diptera: Culicidae) of the Mexican Yucatan Peninsula: a comprehensive review on the use of taxonomic names
Authors: Talaga Stanislas , le Goff Gilbert , Arana-Guardia Roger , Baak-Baak Carlos Marcial , García-Rejón Julián Everardo , García-Suárez Omar , Rodríguez-Valencia Víctor Manuel , Tolsá-García María José , Suzán Gerardo , Roiz David 
Published: December 2023

Abstract
The Yucatan Peninsula is a biogeographic province of the Neotropical region which is mostly encompassed by the 3 Mexican states of Campeche, Quintana Roo, and Yucatán. During the development of the International Joint Laboratory ELDORADO (Ecosystem, bioLogical Diversity, habitat mOdifications and Risk of emerging PAthogens and Diseases in MexicO), a French–Mexican collaboration between the IRD (Institut de Recherche pour le Développement) and UNAM (Universidad Nacional Autónoma de México) in Mérida, it became evident that many putative mosquito species names recorded in the Mexican Yucatan Peninsula were misidentifications/misinterpretations or from the uncritical repetition of incorrect literature records. To provide a stronger foundation for future studies, the mosquito fauna of the Mexican Yucatan Peninsula is here comprehensively reviewed using current knowledge of taxonomy, ecology, and distribution of species through extensive bibliographic research, and examination of newly collected specimens. As a result, 90 mosquito species classified among 16 genera and 24 subgenera are recognized to occur in the Mexican Yucatan Peninsula, including 1 new peninsula record and 3 new state records.
NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine
Authors: Foresti Chiara , Orduña Luis , Matus José Tomás , Vandelle Elodie , Danzi Davide , Bellon Oscar , Tornielli Giovanni Battista , Amato Alessandra , Zenoni Sara 
Published: December 2023

AbstractDuring late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes involved in berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves resulted in low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61 and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14, the osmotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene WRKY52, and NAC61 itself was validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulatory network that governs stilbenoid metabolism and osmotic, oxidative, and biotic stress responses that are the hallmark of late- and post-ripening grape stages.
WISDOM Project - XVI. The link between circumnuclear molecular gas reservoirs and active galactic nucleus fuelling
Authors: Elford Jacob S , Davis Timothy A , Ruffa Ilaria , Bureau Martin , Cappellari Michele , Gensior Jindra , Iguchi Satoru , Liang Fu-Heng , Liu Lijie , Lu Anan , Williams Thomas G 
Published: December 2023

ABSTRACT
We use high-resolution data from the millimetre-Wave Interferometric Survey of Dark Object Masses (WISDOM) project to investigate the connection between circumnuclear gas reservoirs and nuclear activity in a sample of nearby galaxies. Our sample spans a wide range of nuclear activity types including radio galaxies, Seyfert galaxies, low-luminosity active galactic nuclei (AGN) and inactive galaxies. We use measurements of nuclear millimetre continuum emission along with other archival tracers of AGN accretion/activity to investigate previous claims that at, circumnuclear scales (&lt;100 pc), these should correlate with the mass of the cold molecular gas. We find that the molecular gas mass does not correlate with any tracer of nuclear activity. This suggests the level of nuclear activity cannot solely be regulated by the amount of cold gas around the supermassive black hole (SMBH). This indicates that AGN fuelling, that drives gas from the large-scale galaxy to the nuclear regions, is not a ubiquitous process and may vary between AGN type, with time-scale variations likely to be very important. By studying the structure of the central molecular gas reservoirs, we find our galaxies have a range of nuclear molecular gas concentrations. This could indicate that some of our galaxies may have had their circumnuclear regions impacted by AGN feedback, even though they currently have low nuclear activity. Alternatively, the nuclear molecular gas concentrations in our galaxies could instead be set by secular processes.
Hypoxia-induced galectin-8 maintains stemness in glioma stem cells via autophagy regulation
Authors: Liu Dan , Zhu Hongtao , Cheng Lidong , Li Ran , Ma Xiaoyu , Wang Jing , Wang Junwen , Zhang Suojun , Li Yingjie , Shu Kai , Yu Xingjiang , Li Chuanzhou 
Published: December 2023

AbstractBackgroundGlioma stem cells (GSCs) are the root cause of relapse and treatment resistance in glioblastoma (GBM). In GSCs, hypoxia in the microenvironment is known to facilitate the maintenance of stem cells, and evolutionally conserved autophagy regulates cell homeostasis to control cell population. The precise involvement of autophagy regulation in hypoxic conditions in maintaining the stemness of GSCs remains unclear.MethodsThe association of autophagy regulation and hypoxia was first assessed by in silico analysis and validation in vitro. Glioma databases and clinical specimens were used to determine galectin-8 (Gal-8) expression in GSCs and human GBMs, and the regulation and function of Gal-8 in stemness maintenance were evaluated by genetic manipulation in vitro and in vivo. How autophagy was stimulated by Gal-8 under hypoxia was systematically investigated.ResultsHypoxia enhances autophagy in GSCs to facilitate self-renewal, and Gal-8 in the galectin family is specifically involved and expressed in GSCs within the hypoxic niche. Gal-8 is highly expressed in GBM and predicts poor survival in patients. Suppression of Gal-8 prevents tumor growth and prolongs survival in mouse models of GBM. Gal-8 binds to the Ragulator-Rag complex at the lysosome membrane and inactivates mTORC1, leading to the nuclear translocation of downstream TFEB and initiation of autophagic lysosomal biogenesis. Consequently, the survival and proliferative activity of GSCs are maintained.ConclusionsOur findings reveal a novel Gal-8-mTOR-TFEB axis induced by hypoxia in the maintenance of GSC stemness via autophagy reinforcement, highlighting Gal-8 as a candidate for GSCs-targeted GBM therapy.
Scientific objectives and payload configuration of the Chang'E-7 mission
Authors: Wang Chi , Jia Yingzhuo , Xue Changbin , Lin Yangting , Liu Jianzhong , Fu Xiaohui , Xu Lin , Huang Yun , Zhao Yufen , Xu Yigang , Gao Rui , Wei Yong , Tang Yuhua , Yu Dengyun , Zou Yongliao 
Published: December 2023

ABSTRACT
As the cornerstone mission of the fourth phase of the Chinese Lunar Exploration Program, Chang'E-7 (CE-7) was officially approved, and implementation started in 2022, including a main probe and a communication relay satellite. The main probe, consisting of an orbiter, a lander, a rover and a mini-flying probe, is scheduled to be launched in 2026. The lander will land on Shackleton crater's illuminated rim near the lunar south pole, along with the rover and mini-flying probe. The relay satellite (named Queqiao-2) will be launched in February 2024 as an independent mission to support relay communication during scientific exploration undertaken by Chang’E-4, the upcoming Chang’E-6 in 2024 and subsequent lunar missions. The CE-7 mission is mainly aimed at scientific and resource exploration of the lunar south pole. We present CE-7’s scientific objectives, the scientific payloads configuration and the main functions for each scientific payload with its key technical specifications.
A Systematic Review of the Therapeutic Outcome of Mucormycosis
Authors: Sigera L Shamithra M , Denning David W 
Published: December 2023

Abstract

Background
Mucormycosis is a potentially lethal mycosis. We reviewed peer-reviewed publications on mucormycosis to assess therapeutic outcomes.

Methods
A systematic literature search using the Ovid MEDLINE and EMBASE databases identified manuscripts describing human mucormycosis diagnosed according to European Organization for Research and Treatment of Cancer and the Mycoses Study Group criteria with therapeutic outcomes published from 2000 to 2022.

Results
In 126 articles, 10 335 patients were described, most from Asia (n = 6632, 66%). Diabetes was the most frequent underlying disease (n = 6188, 60%); 222 (2.1%) patients had no underlying diseases. The dominant clinical form was rhino-orbitocerebral (n = 7159, 69.3%), followed by pulmonary (n = 1062, 10.3%). Of 5364 patients with outcome data, amphotericin B monotherapy (n = 3749, mortality 31.5%) was most frequent, followed by amphotericin B + azole (n = 843, mortality 6.6%; P &lt; .0001), amphotericin B followed by azole (n = 357, mortality 13.7%; P &lt; .0001), posaconazole only (n = 250, mortality 17.2%; P &lt; .0001), and isavuconazole only (n = 65, mortality 24.6%; P = .24). Duration and dose of antifungals varied widely. Documented outcomes from surgical resections in 149 patients found that 47 of 125 died (37.6%), compared with 16 of 24 (66.7%) patients who did not undergo surgery (P = .008).

Conclusions
Mucormycosis is more frequently reported in Asia than in Europe and is often linked to diabetes. Antifungal therapy, usually with surgery, is frequently effective for mucormycosis.
A Novel Germline Mutation of BRCA1 and Integrated Analysis With Somatic Mutation in a Chinese Multi-Cancer Family
Authors: Yang Xiling , Shang Li , Yang Liren , Sun Landi , Tuo Xiaoqian , Ma Sijia , Zhao Le , Li Xu , Yang Wenfang 
Published: December 2023

Abstract
The presence of mutations in the BRCA1 gene (MIM: 113705) is widely recognized as a significant genetic predisposition for ovarian cancer. This study investigated the genomic mutations in a Chinese family with a history of ovarian, breast, and rectal adenocarcinoma. A novel germline mutation (Phe1695Val) in BRCA1 was identified through whole-exome sequencing. Subsequently, we performed whole-genome sequencing to identify somatic mutations and analyze mutational signatures in individuals carrying the novel germline mutation. Our findings revealed a correlation between somatic mutational signatures and the BRCA1 germline mutation in the proband with ovarian cancer, while no such association was observed in the tumor tissue from the patient with breast cancer. Furthermore, distinct somatic driver mutations were identified, a truncated mutation in the TP53 gene in the ovarian tumor tissue, and a hotspot mutation in the PIK3CA gene in the breast cancer. According to our findings, the BRCA1 F1695V mutation is linked to ovarian cancer susceptibility in the family and causes specific somatic mutational profiles.
Development of a Novel Comprehensive Hepatocellular Carcinoma Outcome Prognostic Scoring System With Integration of Imaging Features
Authors: Tran Cao Hop S , Witt Russell G , Elsayes Khaled M , Baiomy Ali A , Xiao Lianchun , Palmquist Sarah , Lee Sunyoung S , Mohamed Yehia I , Mahvash Armeen , Tzeng Ching-Wei D , Chun Yun Shin , Koay Eugene Jon , Rashid Asif , Hassan Manal M , Yao James C , Vauthey Jean-Nicolas , Kaseb Ahmed O 
Published: December 2023

Abstract

Background
Accurate prognostic stratification of hepatocellular carcinoma (HCC) is vital for clinical trial enrollment and treatment allocation. Multiple scoring systems have been created to predict patient survival, but no standardized scoring systems account for radiologic tumor features. We sought to create a generalizable scoring system for HCC which incorporates standardized radiologic tumor features and more accurately predicts overall survival (OS) than established systems.

Methods
Clinicopathologic parameters were collected from a prospectively collected cohort of patients with HCC treated at a single institution. Imaging studies were evaluated for tumor characteristics. Patients were randomly divided into a training set for identification of covariates that impacted OS and a validation set. Cox models were used to determine the association of various factors with OS and a scoring system was created.

Results
We identified 383 patients with HCC with imaging and survival outcomes, n = 255 in the training set and 128 in the validation cohort. Factors associated with OS on multivariate analysis included: tumor margin appearance on CT or MRI (hazard ratio [HR] 1.37, 95% CI, 1.01-1.88) with infiltrative margins portending worse outcomes than encapsulated margins, massive tumor morphology (HR 1.64, 95% CI, 1.06-2.54); &gt;2 lesions (HR 2.06, 95% CI, 1.46-2.88), Child-Turcotte-Pugh class C (HR 3.7, 95% CI, 2.23-6.16), and portal vein thrombus (HR 2.41, 95% CI, 1.71-3.39). A new scoring system was developed and more predictive of OS than other well-established systems.

Conclusions
Incorporation of standardized imaging characteristics to established clinical and lab predictors of outcome resulted in an improved predictive scoring system for patients with HCC.