bluuebunny/crossref_metadata_2025 huggingface dataset:
Recruitment and Losses through the Life Cycle for Intertidal Clams in Willapa Bay, Washington
Authors: Grason Emily W. , Garcia Lidia , Ong Ella , Ruesink Jennifer L.
Published: August 2024

When bivalve aquaculture production relies on natural recruitment, yields may decline due to density‐independent constraints at multiple life stages. These life stage transitions include larval settlement, which is typically variable with rapid losses of newly settled individuals and the additional mortality from predation or abiotic factors (e.g., temperature, desiccation, and physical disturbance) as the bivalves grow. Recruitment monitoring and outplants were used to evaluate the potential limiting factors affecting different life stages in two nonnative clam species, Manila clams, Ruditapes philippinarum, and softshell clams, Mya arenaria in Willapa Bay, Washington, USA. Recruits (250–500 µm) did not differ in cumulative abundance in 2023 relative to prior years of monitoring (five recruitment seasons between 2011 and 2017). Recruits surviving to the end of the summer represented 12% or less of those that had arrived, but still showed spatial patterns consistent with rates of arrival. Manila clams outplanted across an elevation gradient suffered high mortality below mean lower low water regardless of size class (small: 8 mm and large: 20 mm), where native rock crabs (Cancer productus) were abundant. Clam growth declined at higher tidal elevations consistent with inundation time. European green crabs (Carcinus maenas) were relatively abundant at midtidal levels where commercial clam aquaculture typically occurs in the bay and where small clams were particularly reduced without predator protection from mesh. While these data support that green crabs may be reducing survival of 1‐year‐old clams at midintertidal elevations, they also identify earlier bottlenecks to repopulating commercial clam beds, which point out why seeding clams is used to maintain consistent production. Further exploration is needed before green crabs can be singled out as a new limit on clam yields relative to the roles of predation across the size classes of clams in Willapa Bay.
Neoadjuvant Endocrine Therapy Compared to Neoadjuvant Chemotherapy in Node‐Positive HR+, HER2− Breast Cancer (Nodal pCR and the Rate of ALND): A Systematic Review and Meta‐Analysis
Authors: Vasigh Mahtab , Karoobi Mohammadreza , Williams Austin D. , Abreha Fasika Molla , Bleicher Richard J. , Yazd Seyed Mostafa Meshkati , Shamsi Tahereh , Omranipour Ramesh , Elahi Ahmad , Farhat David , Habibi Mehran
Published: August 2024

Introduction. Patients with hormone receptor‐positive (HR+), HER2‐negative (HER2−) breast cancers have the lowest response to neoadjuvant therapy of all subtypes. The role of neoadjuvant endocrine therapy (NET) in clinically node‐positive (cN+), HR+, HER2− patients is evaluated in this meta‐analysis. Methods. This study was performed between January 2010 and August 2022. We evaluated the node pathologic complete response (pCR) and axillary lymph node dissection (ALND) rates after neoadjuvant endocrine therapy (NET). Results. 18,037 HR+, HER2−, cN+ stage II and stage III breast cancer patients within eleven studies received neoadjuvant treatments. 3,707 (20.6%) patients received NET and 14,330 (79.4%) received NAC. The average age of the NET patients was higher than that of the neoadjuvant chemotherapy (NAC) patients (64.1 versus 47.6 years old, p < 0.001). 45.0% and 26.9% of the NET and the NAC groups underwent a lumpectomy. The pooled estimates of node pCR in NET and NAC groups were 8.9% and 14.9%, and the pooled proportion of ALND was 39.1% and 58.5%, respectively. Conclusion. The rate of node pCR was lower among cN+ patients who received NET compared to the NAC group. The rate of ALND among cN+ NET patients was lower than the NAC group, revealing more patients with residual nodal disease do not get ALND in the NET group. Further prospective studies are required to compare survival outcomes as a more reliable surrogate.
Antimicrobial Activity of TP4 Recombinant Peptide Alone and in Combination With ZnO NPs on Foodborne Bacteria: Potential as a Milk Preservative
Authors: Salari Parisa , Ghazvini Kiarash , Bahreini Masoumeh , Salarpour Najmeh , Sharifmoghadam Mohammad Reza
Published: August 2024

Bacterial resistance, including resistant foodborne pathogenic bacteria, is developing daily, thus becoming a growing public health concern worldwide. Antimicrobial peptides (AMPs) such as tilapia piscidin 4 (TP4) are a class of small peptides widely present in nature that are promising antimicrobial agents that could potentially be considered food preservatives. This study is aimed at investigating the effect of TP4 alone and in combination with zinc oxide nanoparticles (ZnO NPs) on foodborne bacteria in milk. First, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of TP4 and its combination with ZnO NPs (synergistic effect) were measured against four standard foodborne bacteria using the microdilution and checkerboard methods, respectively. According to the results, TP4 showed a high antibacterial effect against four tested strains. Also, TP4 combination with ZnO NPs showed a relative synergistic effect against three tested strains. Then, a time‐kill assay was performed to evaluate the antibacterial effect of TP4 over time on selected bacteria. The results showed that within 24 h, a TP4 concentration of ≥1 × MIC prevented the growth of Gram‐negative and Gram‐positive bacteria. The microbial load of pasteurized and raw milk was also associated with population reduction against the 2 × MIC concentration of TP4. To evaluate the cytotoxicity of TP4, the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MTT) analysis was performed on the human embryonic kidney‐293 (HEK‐293) cell line and the half‐maximal inhibitory concentration (IC50) was evaluated as 71.61 μg/mL, indicating the nontoxicity of this peptide. Finally, the results showed that TP4 peptide reduces the microbial load of milk, and due to its safety, it can be used as a food preservative.
Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander C. , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E. , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F.
Published: August 2024

Purpose:

Early detection of neurofibromatosis type 1 (NF1)–associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, enabling early definitive treatment and potentially averting deadly outcomes. In this study, we describe a cell-free DNA (cfDNA) fragmentomic approach that distinguishes nonmalignant, premalignant, and malignant forms of PNST in the cancer predisposition syndrome, NF1.

Experimental Design:

cfDNA was isolated from plasma samples of a novel cohort of 101 patients with NF1 and 21 healthy controls and underwent whole-genome sequencing. We investigated diagnosis-specific signatures of copy-number alterations with in silico size selection as well as fragment profiles. Fragmentomics were analyzed using complementary feature types: bin-wise fragment size ratios, end motifs, and fragment non-negative matrix factorization signatures.

Results:

The novel cohort of patients with NF1 validated that our previous cfDNA copy-number alteration–based approach identifies malignant PNST (MPNST) but cannot distinguish between benign and premalignant states. Fragmentomic methods were able to differentiate premalignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management.

Conclusions:

Novel cfDNA fragmentomic signatures distinguish AN from benign plexiform neurofibromas and MPNST, enabling more precise clinical diagnosis and management. This study pioneers the early detection of malignant and premalignant PNST in NF1 and provides a blueprint for decentralizing noninvasive cancer surveillance in hereditary cancer predisposition syndromes.
Supplementary Table ST-1 from Neem Leaf Glycoprotein Disrupts Exhausted CD8+ T-Cell–Mediated Cancer Stem Cell Aggression
Authors: Chakravarti Mohona , Bera Saurav , Dhar Sukanya , Sarkar Anirban , Choudhury Pritha Roy , Ganguly Nilanjan , Das Juhina , Sultana Jasmine , Guha Aishwarya , Biswas Souradeep , Das Tapasi , Hajra Subhadip , Banerjee Saptak , Baral Rathindranath , Bose Anamika
Published: August 2024

The file contains Supplementary Table ST-1
Supplementary Fig. 2 from Long Noncoding RNA MSL3P1 Regulates CUL3 mRNA Cytoplasmic Transport and Stability and Promotes Lung Adenocarcinoma Metastasis
Authors: Shao Ming-Ming , Li Xin , Wei Rui-Qi , Chen Qing-Yu , Zhang Xin , Qiao Xin , Li Hui
Published: August 2024

Epigenomic regulation of MSL3P in LUAD
Supplementary Figure S6 from MYC Family Amplification Dictates Sensitivity to BET Bromodomain Protein Inhibitor Mivebresib (ABBV075) in Small-Cell Lung Cancer
Authors: Plotnik Joshua P. , Zha Zheng , Feng Weiguo , Lee Irene , Riehm Jacob , McClure Ryan A. , Sandoval Stephanie , Uziel Tamar , Murphy Erin , Lu Xin , Lam Lloyd T.
Published: August 2024

Supplementary Figure S6
Figure S1 from Pediatric Chordoma: A Tale of Two Genomes
Authors: O’Halloran Katrina , Hakimjavadi Hesamedin , Bootwalla Moiz , Ostrow Dejerianne , Kerawala Rhea , Cotter Jennifer A. , Yellapantula Venkata , Kaneva Kristiyana , Wadhwani Nitin R. , Treece Amy , Foreman Nicholas K. , Alexandrescu Sanda , Velazquez Vega Jose , Biegel Jaclyn A. , Gai Xiaowu
Published: August 2024

Supplementary Figure 1. Mitochondrial gene variant hotspot analysis in the pediatric chordoma cohort based on VEP variant classifications.
Supplementary Figure 2 from NSCLC Extracellular Vesicles Containing miR-374a-5p Promote Leptomeningeal Metastasis by Influencing Blood‒Brain Barrier Permeability
Authors: Jin Jie , Cui Yumeng , Niu Huicong , Lin Yanli , Wu Xiaojie , Qi Xuejiao , Bai Kaixuan , Zhang Yu , Wang Youliang , Bu Hui
Published: August 2024

Identification of EVs from CSF.
Supplementary table 1 from Kinesin Facilitates Phenotypic Targeting of Therapeutic Resistance in Advanced Prostate Cancer
Authors: Archer Maddison , Begemann Diane , Gonzalez-Kozlova Edgar , Nepali Prerna R. , Labanca Estefania , Shepherd Peter , Dogra Navneet , Navone Nora , Kyprianou Natasha
Published: August 2024

Table of antibodies used
Data from MYC Family Amplification Dictates Sensitivity to BET Bromodomain Protein Inhibitor Mivebresib (ABBV075) in Small-Cell Lung Cancer
Authors: Plotnik Joshua P. , Zha Zheng , Feng Weiguo , Lee Irene , Riehm Jacob , McClure Ryan A. , Sandoval Stephanie , Uziel Tamar , Murphy Erin , Lu Xin , Lam Lloyd T.
Published: August 2024

Abstract
Small-cell lung cancer (SCLC) accounts for nearly 15% of all lung cancers. Although patients respond to first-line therapy readily, rapid relapse is inevitable, with few treatment options in the second-line setting. Here, we describe SCLC cell lines harboring amplification of MYC and MYCN but not MYCL1 or non-amplified MYC cell lines exhibit superior sensitivity to treatment with the pan-BET bromodomain protein inhibitor mivebresib (ABBV075). Silencing MYC and MYCN partially rescued SCLC cell lines harboring these respective amplifications from the antiproliferative effects of mivebresib. Further characterization of genome-wide binding of MYC, MYCN, and MYCL1 uncovered unique enhancer and epigenetic preferences.

Implications: Our study suggests that chromatin landscapes can establish cell states with unique gene expression programs, conveying sensitivity to epigenetic inhibitors such as mivebresib.
Figure S6 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer
Authors: Matusiak Magdalena , Hickey John W. , van IJzendoorn David G.P. , Lu Guolan , Kidziński Lukasz , Zhu Shirley , Colburg Deana R.C. , Luca Bogdan , Phillips Darci J. , Brubaker Sky W. , Charville Gregory W. , Shen Jeanne , Loh Kyle M. , Okwan-Duodu Derick K. , Nolan Garry P. , Newman Aaron M. , West Robert B. , van de Rijn Matt
Published: August 2024

This Figure shows the spatial interaction of FOLR2+ macrophages with Plasma Cells in normal colon lamina propria, normal breast, normal lymph node, and breast cancer adjacent normal tissue. It also illustrates ligand-receptor interactions predicted to occur between FOLR2+ macrophages and Plasma Cells.
Figure S5 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer
Authors: Matusiak Magdalena , Hickey John W. , van IJzendoorn David G.P. , Lu Guolan , Kidziński Lukasz , Zhu Shirley , Colburg Deana R.C. , Luca Bogdan , Phillips Darci J. , Brubaker Sky W. , Charville Gregory W. , Shen Jeanne , Loh Kyle M. , Okwan-Duodu Derick K. , Nolan Garry P. , Newman Aaron M. , West Robert B. , van de Rijn Matt
Published: August 2024

Thus Figure illustrates how macrophage subsets detected using scRNAseq, 4-color IF, and CODEX correspond to each other and shows representative examples of protein marker expression across macrophage niches.
Figure S4 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer
Authors: Matusiak Magdalena , Hickey John W. , van IJzendoorn David G.P. , Lu Guolan , Kidziński Lukasz , Zhu Shirley , Colburg Deana R.C. , Luca Bogdan , Phillips Darci J. , Brubaker Sky W. , Charville Gregory W. , Shen Jeanne , Loh Kyle M. , Okwan-Duodu Derick K. , Nolan Garry P. , Newman Aaron M. , West Robert B. , van de Rijn Matt
Published: August 2024

This Figure shows protein marker expression across different cell types detected in CODEX experiment, macrophage distance to the closest tumor cell, macrophage distribution across different tissue niches, and tissue niche distribution across different anatomical locations.
Supplementary Table 25 from Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors
Authors: Pecci Federica , Nakazawa Seshiru , Ricciuti Biagio , Harada Guilherme , Lee Jessica K. , Alessi Joao V. , Barrichello Adriana , Vaz Victor R. , Lamberti Giuseppe , Di Federico Alessandro , Gandhi Malini M. , Gazgalis Dimitris , Feng William W. , Jiang Jie , Baldacci Simon , Locquet Marie-Anaïs , Gottlieb Felix H. , Chen Monica F. , Lee Elinton , Haradon Danielle , Smokovich Anna , Voligny Emma , Nguyen Tom , Goel Vikas K. , Zimmerman Zachary , Atwal Sumandeep , Wang Xinan , Bahcall Magda , Heist Rebecca S. , Iqbal Sumaiya , Gandhi Nishant , Elliott Andrew , Vanderwalde Ari M. , Ma Patrick C. , Halmos Balazs , Liu Stephen V. , Che Jianwei , Schrock Alexa B. , Drilon Alexander , Jänne Pasi A. , Awad Mark M.
Published: August 2024

TCGA PanCancer Atlas Studies included in cohort #1 downloaded from cBioPortal.
Supplementary Table 23 from Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors
Authors: Pecci Federica , Nakazawa Seshiru , Ricciuti Biagio , Harada Guilherme , Lee Jessica K. , Alessi Joao V. , Barrichello Adriana , Vaz Victor R. , Lamberti Giuseppe , Di Federico Alessandro , Gandhi Malini M. , Gazgalis Dimitris , Feng William W. , Jiang Jie , Baldacci Simon , Locquet Marie-Anaïs , Gottlieb Felix H. , Chen Monica F. , Lee Elinton , Haradon Danielle , Smokovich Anna , Voligny Emma , Nguyen Tom , Goel Vikas K. , Zimmerman Zachary , Atwal Sumandeep , Wang Xinan , Bahcall Magda , Heist Rebecca S. , Iqbal Sumaiya , Gandhi Nishant , Elliott Andrew , Vanderwalde Ari M. , Ma Patrick C. , Halmos Balazs , Liu Stephen V. , Che Jianwei , Schrock Alexa B. , Drilon Alexander , Jänne Pasi A. , Awad Mark M.
Published: August 2024

Oncogenic / likely oncogenic MET TKD mutations in RCC compared to those detected in NSCLC in cohort #2.
Table S5 from ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer
Authors: Xu Yaru , Yang Yuqiu , Wang Zhaoning , Sjöström Martin , Jiang Yuyin , Tang Yitao , Cheng Siyuan , Deng Su , Wang Choushi , Gonzalez Julisa , Johnson Nickolas A. , Li Xiang , Li Xiaoling , Metang Lauren A. , Mukherji Atreyi , Xu Quanhui , Tirado Carla R. , Wainwright Garrett , Yu Xinzhe , Barnes Spencer , Hofstad Mia , Chen Yu , Zhu Hong , Hanker Ariella B. , Raj Ganesh V. , Zhu Guanghui , He Housheng H. , Wang Zhao , Arteaga Carlos L. , Liang Han , Feng Felix Y. , Wang Yunguan , Wang Tao , Mu Ping
Published: August 2024

Table S5. Lineage-Specific and AR Target Gene Signatures
Supplementary Figure 3 from Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors
Authors: Pecci Federica , Nakazawa Seshiru , Ricciuti Biagio , Harada Guilherme , Lee Jessica K. , Alessi Joao V. , Barrichello Adriana , Vaz Victor R. , Lamberti Giuseppe , Di Federico Alessandro , Gandhi Malini M. , Gazgalis Dimitris , Feng William W. , Jiang Jie , Baldacci Simon , Locquet Marie-Anaïs , Gottlieb Felix H. , Chen Monica F. , Lee Elinton , Haradon Danielle , Smokovich Anna , Voligny Emma , Nguyen Tom , Goel Vikas K. , Zimmerman Zachary , Atwal Sumandeep , Wang Xinan , Bahcall Magda , Heist Rebecca S. , Iqbal Sumaiya , Gandhi Nishant , Elliott Andrew , Vanderwalde Ari M. , Ma Patrick C. , Halmos Balazs , Liu Stephen V. , Che Jianwei , Schrock Alexa B. , Drilon Alexander , Jänne Pasi A. , Awad Mark M.
Published: August 2024

Comparison of missense MET TKD defined as “probably pathogenic” and “probably benign” according to three in silico tools. Comparison of (A) secondary structure features, (B) relative solvent accessible surface area (RSA), and (C) mutant amino acid properties of missense MET TKD mutations of unknown biological function according to OncoKB. Mutations were defined as “probably pathogenic” for likely pathogenicity across all three tools and as “probably benign” for likely benign across all three scores. OR: odds ratio; 95% CI: 95% confidence interval.
Supplementary Figure 17 from Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors
Authors: Pecci Federica , Nakazawa Seshiru , Ricciuti Biagio , Harada Guilherme , Lee Jessica K. , Alessi Joao V. , Barrichello Adriana , Vaz Victor R. , Lamberti Giuseppe , Di Federico Alessandro , Gandhi Malini M. , Gazgalis Dimitris , Feng William W. , Jiang Jie , Baldacci Simon , Locquet Marie-Anaïs , Gottlieb Felix H. , Chen Monica F. , Lee Elinton , Haradon Danielle , Smokovich Anna , Voligny Emma , Nguyen Tom , Goel Vikas K. , Zimmerman Zachary , Atwal Sumandeep , Wang Xinan , Bahcall Magda , Heist Rebecca S. , Iqbal Sumaiya , Gandhi Nishant , Elliott Andrew , Vanderwalde Ari M. , Ma Patrick C. , Halmos Balazs , Liu Stephen V. , Che Jianwei , Schrock Alexa B. , Drilon Alexander , Jänne Pasi A. , Awad Mark M.
Published: August 2024

Equilibration of interactions that drives ATP affinity in the presence MET H1094Y mutant. (A) Representative structure of the ATP bound cMET H1094Y with the regions of interest highlighted [subsection of the 5 pleated beta sheet bundle containing H1094Y and direct interactions (red), hinge binding region (green)]. (B) H1094Y forms novel π- π stacking interactions (T stacking with an upper cut-off of 5.0 angstroms) with Y1158. (C) π- π stacking from Y1158 stabilizes the ATP hydrogen bonding network.
Supplementary Figure S8 from St. Jude Survivorship Portal: Sharing and Analyzing Large Clinical and Genomic Datasets from Pediatric Cancer Survivors
Authors: Matt Gavriel Y. , Sioson Edgar , Shelton Kyla , Wang Jian , Lu Congyu , Zaldivar Peraza Airen , Gangwani Karishma , Paul Robin , Reilly Colleen , Acić Aleksandar , Liu Qi , Sandor Stephanie R. , McLeod Clay , Patel Jaimin , Wang Fan , Im Cindy , Wang Zhaoming , Sapkota Yadav , Wilson Carmen L. , Bhakta Nickhill , Ness Kirsten K. , Armstrong Gregory T. , Hudson Melissa M. , Robison Leslie L. , Zhang Jinghui , Yasui Yutaka , Zhou Xin
Published: August 2024

Exporting data for haplotype analysis
Data from Phosphocreatine Promotes Epigenetic Reprogramming to Facilitate Glioblastoma Growth Through Stabilizing BRD2
Authors: Chen Lishu , Qi Qinghui , Jiang Xiaoqing , Wu Jin , Li Yuanyuan , Liu Zhaodan , Cai Yan , Ran Haowen , Zhang Songyang , Zhang Cheng , Wu Huiran , Cao Shuailiang , Mi Lanjuan , Xiao Dake , Huang Haohao , Jiang Shuai , Wu Jiaqi , Li Bohan , Xie Jiong , Qi Ji , Li Fangye , Liang Panpan , Han Qiuying , Wu Min , Zhou Wenchao , Wang Chenhui , Zhang Weina , Jiang Xin , Zhang Kun , Li Huiyan , Zhang Xuemin , Li Ailing , Zhou Tao , Man Jianghong
Published: August 2024

Abstract
Glioblastoma (GBM) exhibits profound metabolic plasticity for survival and therapeutic resistance, while the underlying mechanisms remain unclear. Here, we show that GBM stem cells reprogram the epigenetic landscape by producing substantial amounts of phosphocreatine (PCr). This production is attributed to the elevated transcription of brain-type creatine kinase, mediated by Zinc finger E-box binding homeobox 1. PCr inhibits the poly-ubiquitination of the chromatin regulator bromodomain containing protein 2 (BRD2) by outcompeting the E3 ubiquitin ligase SPOP for BRD2 binding. Pharmacological disruption of PCr biosynthesis by cyclocreatine (cCr) leads to BRD2 degradation and a decrease in its targets’ transcription, which inhibits chromosome segregation and cell proliferation. Notably, cyclocreatine treatment significantly impedes tumor growth and sensitizes tumors to a BRD2 inhibitor in mouse GBM models without detectable side effects. These findings highlight that high production of PCr is a druggable metabolic feature of GBM and a promising therapeutic target for GBM treatment.

Significance: Glioblastoma (GBM) exhibits an adaptable metabolism crucial for survival and therapy resistance. We demonstrate that GBM stem cells modify their epigenetics by producing phosphocreatine (PCr), which prevents bromodomain containing protein 2 (BRD2) degradation and promotes accurate chromosome segregation. Disrupting PCr biosynthesis impedes tumor growth and improves the efficacy of BRD2 inhibitors in mouse GBM models.
An Engineered Self-biomineralized Oncolytic Adenovirus Induces Effective Antitumor Immunity and Synergizes With Immune Checkpoint Blockade
Authors: Wang Shibing , Yang Xue , Ma Ying-Yu , Wu Junjie , Jin Ketao , Zhao Ruibo , Zou Hai , Mou Xiaozhou
Published: August 2024

Oncolytic adenoviruses (oADV) are promising cancer treatment agents. However, in vivo hepatic sequestration and the host immunologic response against the agents limit the therapeutic potential of oADVs. In this study, we present a combined method with a rational design for improving oADV infection efficiency, immunogenicity, and treatment efficacy by self-biomineralization. We integrated the biomimetic nucleopeptide W6p into the capsid of oADV using reverse genetics, allowing calcium phosphate mineralization to be biologically induced on the surface of oADV under physiologic conditions, resulting in a mineral exterior. This self-biomineralized, modified oADV (oADV-W6-CaP) enhanced infection efficiency and therapeutic efficacy in coxsackievirus and adenovirus receptor (CAR)–negative cancer cells wherein protecting them against neutralization by preexisting neutralizing antibodies. In subcutaneous mouse tumor models, systemic injection of oADV-W6-CaP demonstrated improved antitumor effectiveness, which was associated with increased T-cell infiltration and CD8+ T-cell activation. In addition, the anticancer immune response elicited by oADV-W6-CaP was dependent on CD8+ T cells, which mediated long-term immunologic memory and systemic antitumor immunity against the same tumor. Finally, the addition of PD1 or CD47 inhibition boosted the anticancer effects of oADV-W6-CaP and increased the rate of complete tumor clearance in tumor-bearing animals. The self-biomineralized oADV shifted the suppressive tumor microenvironment from a “cold” to “hot” state and synergized with immune checkpoint blockade to exert outstanding tumoricidal effects, demonstrating promising potential for cancer immunotherapy.
Management of T1 Colorectal Cancer
Authors: Tanaka Hidenori , Yamashita Ken , Urabe Yuji , Kuwai Toshio , Oka Shiro
Published: August 2024

Background: Approximately 10% of patients with submucosal invasive (T1) colorectal cancer (CRC) have lymph node metastasis (LNM). The risk of LNM can be stratified according to various histopathological factors, such as invasion depth, lymphovascular invasion, histological grade, and tumor budding. Summary: T1 CRC with a low risk of LNM can be cured by local excision via endoscopic resection (ER), whereas surgical resection (SR) with lymph node dissection is required for high-risk T1 CRC. Current guidelines raise concern that many patients receive unnecessary SR, even though most patients achieve a radical cure. Novel diagnostic techniques for LNM, such as nomograms, artificial intelligence systems, and genomic analysis, have been recently developed to identify more low-risk T1 CRC cases. Assessing the curability and the necessity of additional treatment, including SR with lymph node dissection and chemoradiotherapy, according to histopathological findings of the specimens resected using ER, is becoming an acceptable strategy for T1 CRC, particularly for rectal cancer. Therefore, complete resection with negative vertical and horizontal margins is necessary for this strategy. Advanced ER methods for resecting the muscle layer or full thickness, which may guarantee complete resection with negative vertical margins, have been developed. Key Message: Although a necessary SR should not be delayed for T1 CRC given its unfavorable prognosis when SR with lymph node dissection is performed, the optimal treatment method should be chosen based on the risk of LNM and the patient’s life expectancy, physical condition, social characteristics, and wishes.
Associations between Plant-Based Dietary Patterns and Sensory Impairments among Chinese Older Adults: Based on the Chinese Longitudinal Healthy Longevity Survey
Authors: Song Xingxu , Tian Zhong , Jiang Kexin , He Kai , Huang Yuhan , Hu Chengxiang , He Xue , Jin Lina , Tao Yuchun
Published: August 2024

Introduction: The aim of this study was to investigate the relationship between the plant-based dietary index and vision impairment (VI), hearing impairment (HI), and dual sensory impairment (DSI) among Chinese aged 65 and older. Methods: Based on the 2018 data from the Chinese Longitudinal Healthy Longevity Survey (CLHLS), a cross-sectional study was conducted on 14,859 samples. The assessment of dietary quality utilized the plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Logistic regression analysis was used to examine the associations between PDIs and sensory impairments. Additionally, restricted cubic spline analysis was utilized to investigate the nonlinear association between PDIs and sensory impairments. Results: Participants in the highest quintile of PDI exhibited reduced prevalence of VI (OR 0.78, 95% CI: 0.67–0.90, ptrend <0.001), HI (OR 0.83, 95% CI: 0.70–0.99, ptrend <0.001), and DSI (OR 0.62, 95% CI: 0.51–0.77, ptrend <0.001) relative to those in the lowest quintile. Moreover, individuals who ranked in the highest quintile for hPDI exhibited a 25% reduced risk of VI disease. Conversely, those in the highest quintile of uPDI were associated with increased prevalence of VI (OR 1.37, 95% CI: 1.17–1.61, ptrend <0.001), HI (OR 1.36, 95% CI: 1.12–1.65, ptrend <0.001), and DSI (OR 1.56, 95% CI: 1.25–1.95, ptrend <0.001). The relationship between PDIs increasing by every 10 units and sensory impairments showed similar patterns. Notably, hPDI demonstrated a nonlinear relationship with HI (pfor nonlinearity = 0.001), while the others exhibited linear associations. Conclusion: The increase in PDI and hPDI correlates with a reduced prevalence of one or more sensory impairments. Conversely, an increase in uPDI is associated with an elevated prevalence of multiple sensory impairments. Our study findings emphasize the significance of plant-based food quality, advocating for adherence to a plant-based dietary pattern while reducing the intake of less healthy plant foods and animal-based products.
Repensando o repensamento do “Princípio da Supremacia do Interesse Público sobre o Particular”: uma reabertura do debate, no plano da pré-compreensão jurídica
Authors: Peixoto Fábio Carvalho de Alvarenga
Published: August 2024

It is proposed to investigate the existence, in Brazilian Constitution, of a notion of primacy of public over private interests. At the current stage of dogmatics, two ideas of supremacy are confused: of public over private interests, and of collective over individual interests. Qualitative bibliographic research was carried out, which developed from the criticism directed by Humberto Ávila to the supremacy of public interest’s dogmatics. Method was compilatory and critical of the so-called “deconstructive” and reactionary positions. It was identified that the processes of semantization of public interest as collective interest, and of creation of an axiom of absolute supremacy — not originally sustained — serve to provide an easy solution to a problem that did not exist. It is also unveiled that the reasons for “deconstructing” the (supposed) axiom of the absolute supremacy of the public over private interests serve as a starting point for the discussion on the primacy of collective over individual interests. As a result, juridical pre-comprehensions, especially about state and constitution theories, have a decisive influence on the relationship of priority in the satisfaction of interests, even for the dogmatic current that maintains that the public interest can only be discovered by means of balancing.
O contrato temporário na jurisprudência do Supremo Tribunal Federal: da diferenciação entre nulidade e desvirtuamento e seus consectários legais
Authors: Moreno Junior Agamenon Alcântara , Campos Juliana Rose Ishikawa da Silva
Published: August 2024

This article aims to analyze the jurisprudence of the Federal Supreme Court regarding temporary contracts (art. 37, IX, CF/1988), especially with regard to the requirements for its validity and the concepts of “nullity” and “distortion”. The problem chosen for the research was the following: are the decisions given in themes 916 and 551 of the Federal Supreme Court conflicting or complementary? To what extent is it possible to differentiate the nullity of a temporary contract from its distortion and what are the consequences of this declaration? The article focused on the norms on the subject and the jurisprudence of the Federal Supreme Court, as well as other state courts regarding this, in addition to other bibliographic sources, such as, books and scientific articles. The starting point was the hypothesis that the national courts are misinterpreting the jurisprudence of the highest Court in the country, by treating the concepts of nullity and distortion as synonymous, imposing a burden on the public that is greater than what is due in many concrete cases, which is also mentioned in the text. In conclusion, the hypothesis raised is confirmed, in the sense that the themes analyzed are not conflicting, but rather complementary.
A tutela provisória e antecipada do direito de propriedade: a natureza jurídica do registro do mandado de imissão provisória na posse e dos títulos de sua cessão ou promessa de cessão
Authors: Mady Fernando Keutenedjian
Published: August 2024

O presente artigo trata da imissão provisória na posse, espécie de tutela provisória para antecipar possessórios para o expropriante. O objeto do artigo é examinar os pressupostos, requisitos e consequências de sua concessão e registro, bem como sua natureza jurídica. Na primeira seção, examina-se a evolução do registro da imissão provisória na posse, para que na segunda e terceira seja conceituada e definida a sua taxinomia. A terceira também tem por fim examinar posicionamentos sobre a natureza do instituto, quando efetivado pelo ente público, ou quem lhe faça às vezes. Na quarta seção explicita-se a teoria da afetação, que será a ferramenta para aferir os efeitos da medida antecipatória judicial e procurar responder as dúvidas sobre o momento da transmissão da propriedade para o expropriante e, depois, aos beneficiários por cessões ou promessas de cessão. Nas seções subsequentes são examinados os efeitos decorrentes da imissão provisória na posse. O exame usa o método de comparação de posições doutrinárias e jurisprudenciais, além de sistematizar seu procedimento para registro. A conclusão do tema é o norte alcançado após a interpretação das alterações legislativas e a definição de locus no direito registral.
The ability of isokinetic tests to predict vertical jumping performance in volleyball players
Authors: Ugrinowitsch Carlos , Barbanti Valdir José , Gonçalves Adilson , Peres Bergson Almeida
Published: August 2024

A predição da “performance” motora vem sendo uma questão básica para a ciência do esporte. Vários tipos de testes vêm sendo utilizados para tal, sendo os testes que avaliam a função muscular os mais utilizados. A especificidade do teste tem importância fundamental para que ele possua uma boa capacidade preditiva, contudo é muito difícil selecionar testes que simulem a “performance” motora mantendo valores elevados de validade e fidedignidade. Os objetivos do presente estudo foram: a) determinar a capacidade de predição da “performance” no salto vertical através de testes isocinéticos em diferentes faixas etárias; b) comparar os grupos para verificar se a “performance” no salto vertical e no teste isocinético evoluía na mesma razão, com o aumento da idade cronológica. A amostra foi composta por 30 jogadores de voleibol, divididos em três grupos por idade cronológica; jogadores com mais de 20 anos (G2o); jogadores entre 17 e 19 anos (G n) e jogadores entre 15 e 16 anos (Gi5). Os indivíduos foram submetidos a um teste de força para a musculatura extensora do joelho (dinamômetro Cybex 6000®), nas velocidades angulares de 180, 240 e 300°/s e a um teste de salto vertical (“Ergo Jump”), utilizando-se o “Squat Jump” (SJ). Somente o G2o obteve uma equação na qual o valor da variável obtida foi significante (p < 0,05). A comparação entre os grupos revelou que o G20 e o GJ7 significantemente mais fortes para todas as velocidades angulares do que o G i5, enquanto para o salto vertical somente o G20 foi superior ao G i5. Esse estudo indica que a variável de “força isocinética” não é um bom preditor da “performance” no salto vertical e que as variáveis não evoluíram na mesma razão com o aumento da idade cronológica
Test-retest reliability of EEG microstate metrics for evaluating noise reductions in simultaneous EEG-fMRI
Authors: Kuroda Toshikazu , Kobler Reinmar J. , Ogawa Takeshi , Tsutsumi Mizuki , Kishi Tomohiko , Kawanabe Motoaki
Published: August 2024

Simultaneous electroencephalography-functional magnetic resonance imaging (EEG-fMRI) has potential for elucidating brain activities but suffers from severe noise/artifacts in EEG. While several countermeasures have been developed, it remains difficult to evaluate noise reductions in the absence of ground truth in EEG. We introduce a new evaluation method which takes advantage of high test-retest reliability of EEG microstate metrics. We assumed, if the reliability is high for a pair of EEG recorded outside an MR scanner on two different days, then it should also be high for a pair of EEG recorded inside and outside the scanner on the same day if MR-induced noise is absent. Thus, noise should be removed in a way that the reliability increases. Accordingly, we obtained EEG both inside and outside the scanner on two different days. Using ICC as an index, we examined test-retest reliability for 1) a pair of EEG outside the scanner across the days, 2) a pair of EEG inside and outside the scanner on the same day, and 3) a pair of EEG inside the scanner across the days. MR-induced noise, BCG artifact in particular, was reduced with joint decorrelation with varying thresholds. We obtained moderately high reliability in all the three pairs (ICCs > 0.5), suggesting sufficient noise reductions. Taking these steps, the quality of EEG improved as assessed with its traces, power spectra density, and microstate templates in resting state as well as event-related potentials in a visual oddball task. We discuss advantages and limitations of this new evaluation method.
Startle together, shout in chorus: collective bursts of alarm calls in a social rodent, the Harting’s vole (Microtus hartingi)
Authors: Volodin Ilya A. , Rutovskaya Marina V. , Golenishchev Fedor N. , Volodina Elena V.
Published: August 2024

We investigate the acoustic structure of alarm calls in a highly social rodent, the Harting’s vole (Microtus hartingi) and describe the phenomenon of collective shouting of bursts of alarm calls which could be produced in synchronized series. The alarm calls of Harting’s voles were recorded using an automatic device from 10 different family groups, containing from 4 to 15 potential callers, released to outdoor enclosures. Natural predators and humans served as call-eliciting stimuli. We reveal acoustic differences between urgent alarm calls, evoked by close-vicinity predators and identified from recordings by their calls and by rustle noise from the caller’s escape to burrow, and other alarm calls. We also reveal acoustic parameters between alarm calls produced in bursts and other alarm calls (produced in individual series or by a few non-synchronized callers). We discuss why the alarm calls of Harting’s voles are unusually high-frequency (about 17 kHz on average in the maximum fundamental frequency) among other vole species producing high-frequency alarms. Adaptive significance of producing the collective synchronized bursts of alarm calls by Harting’s voles remains unclear without direct observations of vocal vigilance in this species under natural conditions.
Pragmatism as a Compatible Theoretical Lens for Mixed Methods Research in Prehospital Care
Authors: Emond Kate , Bish Melanie , Mnatzaganian George
Published: August 2024

This study extends on work investigating the increased application of mixed methods research in prehospital care. The complexity and diversity of the prehospital environment warrants flexibility and applicability to guide the research process, yet little attention has focused on the theoretical lens used in prehospital research when using mixed methods research. Pragmatism’s characteristics of human inquiry, problem solving, and action align with a clinical reasoning approach, supporting the prehospital researchers epistemological understanding of the world. Through further exploration of this alignment, this article proposes pragmatism as a compatible theoretical lens for mixed methods in prehospital research.
Language Islands Worldwide – Theoretical and Methodological Issues
Authors: Rosenberg Peter
Published: August 2024

What can we learn from language island research? Answers drawn from German language island research refer to linguistics, ethnology and language politics. German language islands in Russia and Brazil are on the way to language shift. The varieties of these communities display varying degrees of decomposition and simplification in terms of morphology. Regular and irregular morphology are developing differently. How could these differences be explained? What is the impact of language contact? To what extent does variation within language change depend on the distinctiveness of this linguistic community? The contribution is about comparative language island research, relating linguistic results to the ethnographic background and the conditions of language politics.
Sandawe
Authors: Eaton Helen
Published: August 2024

The Sandawe language community in Tanzania is surrounded by languages from different African language families, yet retains a special distinctiveness in this context by virtue of its unusual phonology and its status as a relic of the original inhabitants of the area. It is also noteworthy how long the Sandawe situation has endured and how this has been possible. This paper examines the reasons for the Sandawe community’s situation and its continued survival. The description of the Sandawe situation takes in its history and the question of its linguistic classification. The sociocultural features of the community and the typological features of the language are then considered, particularly in comparison with the surrounding communities and their languages, as well as possibly related languages in southern Africa. Finally, the status of Sandawe as a linguistic island is discussed, with reference to different definitions of the concept.
Miini – A Lonely Bantu Outpost in the Vast North
Authors: Nurse Derek , Vianello Alessandra
Published: August 2024

The article deals with Miini, spoken in the town of Brava. Some regard it as a northern Swahili dialect, others view it as a closely related language. The town and its speech form have existed for probably a millennium. During most of that period it flourished, surrounded by a community or communities speaking southern Somali dialects. When the Somali central government collapsed in 1991 it was invaded and occupied by the Habr Gidir clan, part of the larger Hawiye group. Most inhabitants who could left. It is currently severely endangered, having been largely replaced by Somali. It is treated under these headings: geography and population; history; political, socio-cultural, and economic context; linguistics; regularity/complexity/stability; contact phenomena; sociolinguistics; language variation; language use and attitudes, language and education; networks.
Temi – A Survivor in Difficult Sea
Authors: Nurse Derek , Derungs Christine
Published: August 2024

This article treats the Bantu language Temi, sometimes called Gitemi or Sonjo. The Temi language island is 125 kilometres from the nearest Bantu community and completely surrounded by historically hostile Maasai communities. As far as we know, Maasai were preceded by other non-Bantu communities for most of the last millennium. Community and language are both in good shape: in 1928 the population was 2,500, at Tanzanian independence in the 1960s it was 5,000, and now it is over 30,000. It is treated under these headings: geography and population; history; political, sociocultural, and economic context; linguistics; regularity/complexity/stability; contact phenomena; sociolinguistics; language use and attitudes; networks.
Le berbère zénaga de Mauritanie
Authors: Taine-Cheikh Catherine
Published: August 2024

Il existe, dans le sud-ouest de la Mauritanie, un îlot de locuteurs parlant une variété de berbère appelée le zénaga. Dans cet îlot, devenu entièrement bilingue, la pratique de l’arabe ḥassāniyya est devenue beaucoup plus courante que celle du berbère et ne cesse de se renforcer. L’article comporte trois parties après l’introduction. La première, consacrée à la situation actuelle des zénagophones, précise leur territoire, leur nombre, les valeurs qu’ils attribuent aux langues qu’ils parlent et ce qu’elles représentent par rapport à leur identité culturelle. La seconde porte sur l’histoire de la région et plus particulièrement celle des populations berbérophones, présentes au Sahara ouest-africain depuis le néolithique, qui connurent leur heure de gloire au XIe siècle avec l’épisode almoravide et un enclavement très progressif après l’arrivée des Bäni Ḥassān. La dernière partie propose une étude linguistique qui permet de situer le zénaga par rapport aux autres parlers berbères, de le comparer avec le parler tetserret qui lui est le plus proche et d’évaluer les effets du contact avec les langues voisines.
The Anii Language
Authors: Morton Deborah
Published: August 2024

The Anii language of Togo and Benin is surrounded by essentially unrelated languages because the ancestors of the current speakers migrated into their modern territory within the last few centuries. This paper presents what is known about the cultural history and current social context of the Anii people and argues that Anii is a progressive language island despite a social situation that is different from that of many traditional language islands. The analysis of Anii linguistic structures (including comparisons with related languages and the presentation of relevant dialect differences) provides further support for the analysis of Anii as a language island. Much of the data, particularly the comparative analyses, presented here have never been previously available to scholars. This paper thus sheds new light on a little-known language with a complicated history that is not yet well understood, as well as potentially expanding the definition of the term ‘language island’.
A Language Island in a Sea of Sand
Authors: Schiattarella Valentina
Published: August 2024

The Siwi language is spoken in the Siwa oasis in the Egyptian Western Desert. It is the easternmost place where a Berber variety (Afro-Asiatic) is spoken. Siwi is not the only language spoken in the oasis, as the entire population speaks at least one variety (Bedouin and/or Egyptian) of Arabic. Siwi speakers can be firmly differentiated from Egyptians or Bedouins settled in the oasis not only because of their language, but also because of an entire set of customs and traditions that contribute to creating their identity. Though recent factors brought by modernity are levelling the gap between Siwa and the other communities, and Arabic influence on the language is increasing, this article discusses some distinctive historical, socio-cultural and linguistic features of Siwa.
Korandje as a Songhay Language Island
Authors: Souag Lameen
Published: August 2024

Among the many language islands produced by the expansion of Songhay out of the middle Niger valley, Korandje stands out for its geographical isolation and linguistic divergence. Confined since perhaps 1200 CE to a single Algerian oasis well over a thousand kilometres from any other Songhay-speaking community, its speakers have extensively reshaped their language and identity under the influence of North African norms, while nevertheless keeping the former clearly distinct. Yet, following the socioeconomic and political changes of the 20th century, the survival of Korandje is now in doubt, as speakers increasingly adopt speech norms and linguistic ideologies negotiated outside the oasis.
Jesuit-Chinese Interaction and Collaboration in Chinese Sources
Authors: Han Qijin
Published: August 2024

Over recent decades, studies on the Jesuits’ activities in China and elsewhere have been considerably facilitated by collated and published correspondence written in Western languages. In order to broaden this scholarly discussion by including more sources from the Chinese side, this article makes a modest contribution by translating and analyzing two letters from Zhu Shi 祝石 (1602–after 1689), a remnant of the Ming dynasty and a Chinese Catholic, to Lodovico Buglio (1606–1682) and Ferdinand Verbiest (1623–1688), two Jesuit missionaries at the Manchu court. Transcriptions of the two letters are found in the collected works of Zhu, Zhi hao hao xue lu 知好好學錄 (Records of knowing how to appreciate good learning; n.d.). Noteworthy subjects reflected in the letters include, among others, Zhu’s involvement in the translation and revision of Buglio’s Chaoxingxue yao 超性學要 (Essentials of transcendental nature studies; 1654–1677), a contemporary explanation of the obstacles facing evangelism in China, and Verbiest’s cannon-casting activities during the Revolt of the Three Feudatories (or the San-Fan War; 1673–ca. 1681). A close examination of these two letters not only broadens the understanding of the social networks of the two missionaries and provides supplementary historical details, but also calls attention to the value of correspondence between Chinese literati and the missionaries.