bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modified surgical fusion: VATS and BABA approach for ectopic intrathoracic and cervical thyroidectomy
Authors: Thalasta Puneeth , Dhar Anita , Parshad Rajinder , Agarwal Shipra 
Published: June 2024

Ectopic goitre, presenting as an isolated thoracic mass without connection to the main thyroid gland enlargement, is a rare occurrence. We describe a case where a patient reported persistent dry cough and back pain for 1 year, along with throat discomfort unresponsive to medication. A 2×1 cm swelling was noted over the right anterior aspect of the neck. Extensive evaluation, including chest X-rays and contrast-enhanced CT of the thorax, revealed a mediastinal mass suggestive of an ectopic thyroid.This case presents a distinctive scenario involving the simultaneous presence of ectopic mediastinal and cervical thyroid lesions. Both were effectively managed using a minimally invasive approach, combining video-assisted thoracic surgery for the excision of the mediastinal mass and a bilateral axillo-breast approach for the cervical lesion in a single procedure. This approach yielded minimal morbidity, aesthetically pleasing outcomes and rapid recovery. Remarkably, such a case has not been previously documented in the available literature.
Selection for feed efficiency improves production traits and digestibility and its relationship to the fecal microbiota in both Large White dam and sire lines
Authors: Beens Laura , Rajendiran Ethendhar , Derakhshani Hooman , Mejicanos Gustavo , Yang Chengbo , Nyachoti Martin , Lei Huaigang , Verschuren Lisanne , Bergsma Rob , Rodas-Gonzalez Argenis 
Published: June 2024

This study evaluated production traits, apparent total tract digestibility (ATTD), and fecal microbiota composition in finishing boars ( n = 207) selected for feed efficiency (FE; low = LFE; high = HFE) based on estimated breeding value for feed conversion ratio (FCR) within a Large White dam and sire genetic lines. Also, the association between gut microbiota with production and digestibility traits was investigated. Regardless of the genetic line, HFE pigs presented low FCR ( P < 0.05), had thinner back fat ( P < 0.05) and had greater loin depth ( P < 0.05) than LFE pigs. Also, HFE pigs had a significantly higher ATTD for Ca and a tendency for a higher crude protein ( P = 0.06) and phosphorous ( P = 0.10) ATTD than LFE pigs. No significant differences in alpha- and beta-diversity measurements for fecal microbiota were seen between FE groups in each genetic line. The genera Lactobacillus and Prevotella were associated ( P < 0.01) with some growth performance (e.g., feed intake), carcass traits (e.g., backfat thickness), and nutrient digestibility (e.g., Ca). In conclusion, HFE pigs had favourable production traits and higher digestibility of key nutrients than LFE pigs; however, the bacterial genera were associated with phenotypic traits but not by genetic merit.
Ab initio description of monopole resonances in light- and medium-mass nuclei
Authors: Porro A. , Duguet T. , Ebran J. -P. , Frosini M. , Roth R. , Somà V. 
Published: June 2024

AbstractGiant resonances (GRs) are a striking manifestation of collective motions in mesoscopic systems such as atomic nuclei. Until recently, theoretical investigations have essentially relied on the (quasiparticle) random phase approximation ((Q)RPA), and extensions of it, based on phenomenological energy density functionals (EDFs). As part of a current effort to describe GRs within an ab initio theoretical scheme, the present work promotes the use of the projected generator coordinate method (PGCM). This method, which can handle anharmonic effects while satisfying symmetries of the nuclear Hamiltonian, displays a favorable (i.e. mean-field-like) scaling with system’s size. Presently focusing on the isoscalar giant monopole resonance (GMR) of light- and medium-mass nuclei, PGCM’s potential to deliver wide-range ab initio studies of GRs in closed- and open-shell nuclei encompassing pairing, deformation, and shape coexistence effects is demonstrated. The comparison with consistent QRPA calculations highlights PGCM’s unique attributes and sheds light on the intricate interplay of nuclear collective excitations. The present paper is the first in a series of four and focuses on technical aspects and uncertainty quantification of ab initio PGCM calculations of GMR using the doubly open-shell$$^{46}$$46Ti as an illustrative example. The second paper displays results for a set of nuclei of physical interest and proceeds to the comparison with consistent (deformed) ab initio QRPA calculations. While the third paper analyzes useful moments of the monopolar strength function and different ways to access them within PGCM calculations, the fourth paper focuses on the effect of the symmetry restoration on the monopole strength function.
AKT Inhibition Sensitizes to Polo-Like Kinase 1 Inhibitor Onvansertib in Prostate Cancer
Authors: Nouri Mannan , Varkaris Andreas , Ridinger Maya , Dalrymple Susan L. , Dennehy Christopher M. , Isaacs John T. , Einstein David J. , Brennen W.N. , Balk Steven P. 
Published: June 2024

Abstract
Polo-like kinase 1 (PLK1) inhibitors have had limited antitumor efficacy as single agents, and focus of current efforts is on combination therapies. We initially confirmed that the PLK1-specific inhibitor onvansertib (ONV) could enhance responses to a PARP inhibitor (olaparib) in prostate cancer xenografts. To identify more effective combinations, we screened a library of bioactive compounds for efficacy in combination with ONV in LNCaP prostate cancer cells, which identified a series of compounds including multiple AKT inhibitors. We confirmed in vitro synergy between ONV and the AKT inhibitor ipatasertib (IPA) and found that the combination increased apoptosis. Mechanistic studies showed that ONV increased expression of the antiapoptotic protein SURVIVIN and that this was mitigated by IPA. Studies in three PTEN-deficient prostate cancer xenograft models showed that cotreatment with IPA and ONV led to significant tumor growth inhibition compared with monotherapies. Together, these in vitro and in vivo studies demonstrate that the efficacy of PLK1 antagonists can be enhanced by PARP or AKT inhibition and support further development of these combination therapies.
Abstract PO-012: Gain-of-function small molecules to reprogram oncogenic transcription in lymphoma
Authors: Gourisankar Sai , Sarott Roman , Karim Basel , Nettles Sabin , Yang Haopeng , Dwyer Brendan , Simanauskaite Juste , Tse Jason , Abuzaid Hind , Hinshaw Stephen M , Green Michael R , Crabtree Gerald R , Gray Nathanael S 
Published: June 2024

Abstract
Conventional pharmacotherapy in oncology centers on target-centric silencing of aberrant protein function through small molecule inhibitors, degraders, or CRISPR/RNAi. In contrast, here we leverage induced proximity to develop pharmacology that activates dominant signaling pathways for a therapeutic effect. To develop this concept, we describe a new class of bivalent small molecules that reprogram cancer-driving gene expression to activate cell death signaling in diffuse large B cell lymphomas (DLBCL). These molecules, called Transcriptional Chemical Inducers of Proximity (TCIPs), operate at fractional occupancy of their protein targets, without genomic modifications to the cell or organism. The first TCIPs transiently re-localized elongation factors such as BRD4 (TCIP1, PMID 37495688) to loci regulated by the transcription factor BCL6, inducing the expression of pro-apoptotic genes regulated by BCL6. In new, unpublished work, CDK-TCIPs have been made to re-direct the activity of transcriptional elongation kinases such as CDK9, CDK12, or CDK13 to induce the expression of pro-apoptotic BCL6-target genes. Profiling in ∼900 barcoded cancer cell lines show that the molecules exhibit potent cell killing potency in a highly DLBCL lineage-restricted manner. Cytotoxicity to healthy lymphocytes is 100- to 10,000-fold lower, although germinal center B cells are ablated in a dose-dependent manner consistent with the role of BCL6 in the germinal center. Biochemical, cell biological, proteomic, and genomic studies demonstrate that CDK-TCIPs operate via a gain-of-function mechanism reliant on the ternary complex formed by the bivalent molecule. Instead of global enzyme inhibition or degradation, CDK-TCIPs borrow and re-localize a fraction of total CDK activity to BCL6-bound chromatin, producing pharmacology from the induction of pro-apoptotic gene transcription. The findings suggest a path to rational design of new gain-of-function chemotherapeutic strategies to rewire cell signaling using induced proximity.
Citation Format: Sai Gourisankar, Roman Sarott, Basel Karim, Sabin Nettles, Haopeng Yang, Brendan Dwyer, Juste Simanauskaite, Jason Tse, Hind Abuzaid, Stephen M Hinshaw, Michael R Green, Gerald R Crabtree, Nathanael S Gray. Gain-of-function small molecules to reprogram oncogenic transcription in lymphoma [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-012.
Abstract PO-019: Ubiquitin E3 ligase OSTM1 regulates the cAMP/PKA/CREB pathway and suppresses B-cell malignancies
Authors: Tariq Muhammad Usama , Shen Julia , Jung Jaeyong , Sheshadri Namratha , Yan Junrong , Li Rongrong , Lu Kevin , Liu Tong , Li Hong , Wang Yue Lynn , Xie Ping , Zong Wei-Xing 
Published: June 2024

Abstract
B-cell malignancies (BCM) often arise from genomic alterations introduced during different stages of B-cell development. Here, we performed a whole genome targeting CRISPR/Cas9 screen in the immortalized yet non-transformed IL-3-dependent Ba/F3 murine pro-B cell line to identify genes whose loss confers IL-3 independence, reasoning that these genes may function as tumor suppressor genes (TSGs) in BCM. One of the candidate genes is osteoporosis-associated transmembrane protein 1 (OSTM1), an E3 ubiquitin ligase whose loss-of-function causes autosomal recessive osteoporosis. Informatics analysis of patient data showed that OSTM1 is frequently deleted across BCM, which co-occurs with the deletion of a well-characterized TSG Cdkn2a. Genetic silencing of OSTM1 in Ba/F3 cells conferred IL-3-independent survival and proliferation, as well as splenomegaly, lymphadenopathy, and abnormal peripheral blood cell count, indicative of transformation in vivo. Using mass spectrometry screens, we identified phosphodiesterase 3B (PDE3B) as an interacting partner of OSTM1. OSTM1 ubiquitylates PDE3B and promotes its proteasomal degradation. The OSTM1-PDE3B interaction and PDE3B degradation are negatively regulated by OSTM1 N-glycosylation. As PDE3B catalyzes the conversion of cAMP to AMP, it negatively regulates the cAMP-dependent PKA/CREB/CREBBP tumor suppressive pathway. Indeed, overexpression of PDE3B accelerated cell proliferation while PDE3B silencing in OSTM1 KO cells reversed the transformation phenotype in cell lines and in mouse allograft tumors. Importantly, a strong correlation between OSTM1 disruption, increased PDE3B stability, and decreased PKA/CREB/CEBBP signaling was observed in cell lines and in BCM patient datasets. Finally, CD19-Cre mediated B-cell specific ablation of OSTM1 cooperated with CDKN2A deletion to drive spontaneous immature B-cell lymphomagenesis in mice. Collectively, these results indicate that OSTM1 is a novel TSG which targets PDE3B for proteasomal degradation. Loss of OSTM1 enhances PDE3B stability and abrogates the tumor-suppressive role of cAMP/CREB/CREBBP pathway which promotes BCM.
Citation Format: Muhammad Usama Tariq, Julia Shen, Jaeyong Jung, Namratha Sheshadri, Junrong Yan, Rongrong Li, Kevin Lu, Tong Liu, Hong Li, Yue Lynn Wang, Ping Xie, Wei-Xing Zong. Ubiquitin E3 ligase OSTM1 regulates the cAMP/PKA/CREB pathway and suppresses B-cell malignancies [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-019.
A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development
Authors: Wang Qianghui , Han Ruobing , Xing Haihua , Li Heping 
Published: June 2024

Abstract
Background
Sika deer (Cervus nippon) holds significance among cervids, with three genomes recently published. However, these genomes still contain hundreds of gaps and display significant discrepancies in continuity and accuracy. This poses challenges to functional genomics research and the selection of an appropriate reference genome. Thus, obtaining a high-quality reference genome is imperative to delve into functional genomics effectively.

Findings
Here we report a high-quality consensus genome of male sika deer. All 34 chromosomes are assembled into single-contig pseudomolecules without any gaps, which is the most complete assembly. The genome size is 2.7G with 23,284 protein-coding genes. Comparative genomics analysis found that the genomes of sika deer and red deer are highly conserved, an approximately 2.4G collinear regions with up to 99% sequence similarity. Meanwhile, we observed the fusion of red deer's Chr23 and Chr4 during evolution, forming sika deer's Chr1. Additionally, we identified 607 transcription factors (TFs) that are involved in the regulation of antler development, including RUNX2, SOX6, SOX8, SOX9, PAX8, SIX2, SIX4, SIX6, SPI1, NFAC1, KLHL8, ZN710, JDP2, and TWST2, based on this consensus reference genome.

Conclusions
Our results indicated that we acquired a high-quality consensus reference genome. That provided valuable resources for understanding functional genomics. In addition, discovered the genetic basis of sika-red hybrid fertility and identified 607 significant TFs that impact antler development.
Autism spectrum disorders detection based on multi-task transformer neural network
Authors: Gao Le , Wang Zhimin , Long Yun , Zhang Xin , Su Hexing , Yu Yong , Hong Jin 
Published: June 2024

AbstractAutism Spectrum Disorders (ASD) are neurodevelopmental disorders that cause people difficulties in social interaction and communication. Identifying ASD patients based on resting-state functional magnetic resonance imaging (rs-fMRI) data is a promising diagnostic tool, but challenging due to the complex and unclear etiology of autism. And it is difficult to effectively identify ASD patients with a single data source (single task). Therefore, to address this challenge, we propose a novel multi-task learning framework for ASD identification based on rs-fMRI data, which can leverage useful information from multiple related tasks to improve the generalization performance of the model. Meanwhile, we adopt an attention mechanism to extract ASD-related features from each rs-fMRI dataset, which can enhance the feature representation and interpretability of the model. The results show that our method outperforms state-of-the-art methods in terms of accuracy, sensitivity and specificity. This work provides a new perspective and solution for ASD identification based on rs-fMRI data using multi-task learning. It also demonstrates the potential and value of machine learning for advancing neuroscience research and clinical practice.
COVID-19 in patients with thymic epithelial tumors with or without Good’s syndrome: a single-center retrospective study
Authors: Pietroluongo Erica , Peddio Annarita , De Placido Pietro , Tortora Marianna , Ottaviano Margaret , Gelzo Monica , Cernera Gustavo , Foggia Maria , Buonomo Antonio Riccardo , Pinchera Biagio , Zappulo Emanuela , Mercinelli Simona , Cattaneo Letizia , Sardanelli Alessia , Viceconte Giulio , Scotto Riccardo , Schiano Moriello Nicola , Servetto Alberto , De Angelis Carmine , Arpino Grazia , Palmieri Giovannella , De Placido Sabino , Bianco Roberto , Castaldo Giuseppe , Gentile Ivan , Giuliano Mario 
Published: June 2024

Abstract
Introduction
Thymic epithelial tumors (TETs) are rare neoplasms often associated with immune-related disorders. Patients with Good’s syndrome (GS), an adult-acquired TET-related immunodeficiency, are at a high risk of mortality due to infectious diseases. This study aims to examine COVID-19 occurrence and severity in TET patients, with or without GS.

Methods
Clinical records of TET patients referred to the Regional Coordinating Center for Rare Tumors of Campania Region were retrospectively collected. During the observation period, elapsing from March 2020 to April 2023, the following data were collected: occurrence of SARS-CoV-2 infection; COVID-19 severity, according to the National Institute of Health (NIH) illness categories; COVID-19 treatment. COVID-19 occurrence and severity were assessed in the overall population and correlated with the presence of GS and/or other immune-related dysregulations.

Results
Overall, 47 TET patients were included in the study; 27 of these (57.4%) had GS. All participants had received a full cycle of mRNA vaccine for SARS-CoV2., Thirty-one patients (66.0%) experienced COVID-19, of whom 18 (58.0%) had previously received a diagnosis of GS. No significant association of GS and/or other immune-related dysregulations with SARS-CoV-2 infection occurrence was detected (Fisher’s exact test p = 1 and p = 0.3587, respectively). Among patients with GS, 8 (45.0%) reported a COVID-19 severity score of ≥ 3; whereas, only 1 of the 13 patients without GS (7.7%) had a severity score of ≥ 3. The correlation between presence of GS and COVID-19 severity (score 1 or 2 vs. ≥ 3) was statistically significant (p = 0.0448). No statistically significant association between COVID-19 severity and other immune-related syndromes were found (p = 1). Of note, all the hospitalized patients for NIH 4 and 5 COVID-19 had GS.

Conclusions
Our data suggest that TET patients, especially those with GS, require a careful multidisciplinary monitoring for SARS-CoV-2 infection, in order to establish tailored treatments and prophylactic protocols.
Paraproteinaemic keratopathy simulating a crystalline keratopathy
Authors: Aramburu-González Andrea , López-Plandolit Antolin Silvia , Márquez-Navarro Jose Antonio 
Published: June 2024

Abstract
Background
Paraproteinemic keratopathy is a rare disorder characterized by the bilateral accumulation of polychromatic deposits diffusely in all corneal layers together or not with diffuse or patchy pseudo lipid deposits. We present an atypical case of paraproteinemic keratopathy which lead to an initial misdiagnosis of infectious crystalline keratopathy.

Case presentation
a 69-year-old woman with an asymptomatic keratopathy detected during a cataract intervention. Slit-lamp examination revealed several hyper refringent subepithelial foci with fern-shaped branches, resembling crystalline keratopathy, in her left eye. Anterior segment optical coherence tomography revealed exclusively subepithelial hyperreflective lesions limited to the anterior stroma. The progressive bilateralization and progression of the condition prompted us to include other entities with crystalline corneal deposits in our differential diagnosis. Hematological analysis showed a high number of free Kappa light chains. Despite the typical clinical appearance of crystalline keratopathy, the atypical evolution and test results led us to consider that monoclonal gammopathy could be the cause of this entity.

Conclusions
Paraproteinemic keratopathy may present in its early stages as a unilateral subepithelial crystalline keratopathy. Thus, it must always be taken into account in the differential diagnosis of any crystalline keratopathy, particularly when there are no predisposing factors for an infectious crystalline keratopathy. Early recognition of this rare entity is important to address the associated potentially serious systemic disease.
Associations between eating alone, its transition and depressive symptoms among Chinese middle-aged and older adults: evidence from two national cohorts
Authors: Qiu Baohua , Zhu Rongyu , Huang Xinlu , Qi Zhijuan , Zhang Lijuan 
Published: June 2024

Abstract
Background
Few studies have explored the longitudinal association between eating alone and depressive symptoms, and have focused on the effect of eating alone transition. This study aims to explore the longitudinal association between eating alone, its transition and depressive symptoms among two national surveys using a cohort study design.

Methods
The participants aged ≥ 45 years were recruited for the 2016 to 2018 waves China Family Panel Data (CFPS) and 2015 to 2018 waves China Health and Retirement Longitudinal Study (CHARLS). Eating alone was assessed by self-reported. Depressive symptoms were evaluated by Center for Epidemiologic Studies Depression Scale. Cox hazard regression was used to explore the associations between eating alone, its transition and depressive symptoms after adjusting for covariates.

Results
A total of 21,476 participants were included in this study. The Cox model showed that compared with commensality, eating alone was associated with a higher risk of depressive symptoms, both in the CFPS, CHARLS and pooled analysis. In addition, compared with commensality consistently, the transition from commensality to alone and eating alone consistently were associated with a higher risk of depressive symptoms. The sensitivity analyses showed that the association remained robust.

Conclusions
Eating alone and a change from commensality to eating alone were associated with higher risks of depressive symptoms among Chinese middle-aged and older adults in two cohorts. This study suggested that providing eating partners may be an effective intervention method to prevent depressive symptoms in middle-aged and older adults.