bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants
Authors: Yajima Hisano , Nomai Tomo , Okumura Kaho , Maenaka Katsumi ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito Jumpei , Hashiguchi Takao , Sato Kei , Matsuno Keita , Nao Naganori , Sawa Hirofumi , Mizuma Keita , Li Jingshu , Kida Izumi , Mimura Yume , Ohari Yuma , Tanaka Shinya , Tsuda Masumi , Wang Lei , Oda Yoshikata , Ferdous Zannatul , Shishido Kenji , Mohri Hiromi , Iida Miki , Fukuhara Takasuke , Tamura Tomokazu , Suzuki Rigel , Suzuki Saori , Tsujino Shuhei , Ito Hayato , Kaku Yu , Misawa Naoko , Plianchaisuk Arnon , Guo Ziyi , Hinay Alfredo A. , Usui Kaoru , Saikruang Wilaiporn , Lytras Spyridon , Uriu Keiya , Yoshimura Ryo , Kawakubo Shusuke , Nishumura Luca , Kosugi Yusuke , Fujita Shigeru , M.Tolentino Jarel Elgin , Chen Luo , Pan Lin , Li Wenye , Yo Maximilian Stanley , Horinaka Kio , Suganami Mai , Chiba Mika , Yasuda Kyoko , Iida Keiko , Strange Adam Patrick , Ohsumi Naomi , Tanaka Shiho , Ogawa Eiko , Fukuda Tsuki , Osujo Rina , Yoshimura Kazuhisa , Sadamas Kenji , Nagashima Mami , Asakura Hiroyuki , Yoshida Isao , Nakagawa So , Takayama Kazuo , Hashimoto Rina , Deguchi Sayaka , Watanabe Yukio , Nakata Yoshitaka , Futatsusako Hiroki , Sakamoto Ayaka , Yasuhara Naoko , Suzuki Tateki , Kimura Kanako , Sasaki Jiei , Nakajima Yukari , Irie Takashi , Kawabata Ryoko , Sasaki-Tabata Kaori , Ikeda Terumasa , Nasser Hesham , Shimizu Ryo , Begum Mst Monira , Jonathan Michael , Mugita Yuka , Leong Sharee , Takahashi Otowa , Ueno Takamasa , Motozono Chihiro , Toyoda Mako , Saito Akatsuki , Kosaka Anon , Kawano Miki , Matsubara Natsumi , Nishiuchi Tomoko , Zahradnik Jiri , Andrikopoulos Prokopios , Padilla-Blanco Miguel , Konar Aditi
Published: September 2024

Due to the incessant emergence of various SARS-CoV-2 variants with enhanced fitness in the human population, controlling the COVID-19 pandemic has been challenging. Understanding how the virus enhances its fitness during a pandemic could offer valuable insights for more effective control of viral epidemics. In this manuscript, we review the evolution of SARS-CoV-2 from early 2022 to the end of 2023—from Omicron BA.2 to XBB descendants. Focusing on viral evolution during this period, we provide concrete examples that SARS-CoV-2 has increased its fitness by enhancing several functions of the spike (S) protein, including its binding affinity to the ACE2 receptor and its ability to evade humoral immunity. Furthermore, we explore how specific mutations modify these functions of the S protein through structural alterations. This review provides evolutionary, molecular, and structural insights into how SARS-CoV-2 has increased its fitness and repeatedly caused epidemic surges during the pandemic.
Complete genome sequence of antibiotic-producing
Streptomyces
sp. HBERC⁃20821, isolated from Wawushan Hill, Sichuan Province, China
Authors: Zhang Yifan , Wan Zhongyi , Chen Ling , Zhu Lei , Qiu Yimin , Chen Wei , Liu Xiaoyan , Min Yong
Published: September 2024

The complete genome of a
Streptomyces
capable of producing multiple antibiotics was sequenced. Strain HBERC-20821 was isolated from a soil sample collected at Wawushan Hill, Sichuan Province, China. Genomic information will facilitate our systematic genetic manipulation of the strain at the gene level, enhancing its antibiotic production.
Draft genome sequence of
Bacillus velezensis
endophytically isolated from roots of
Polygala paniculata
Authors: de Paula Nogueira Cruz Felipe , Marques de Andrade Paulo Henrique , Paiva de Sousa Cristina , Teixeira Lacava Paulo
Published: September 2024

Polygala paniculata
is a medicinal plant that harbors a remaining unknown microbiome. Those plants are known for their analgesic and anti-inflammatory properties and are widely found in the Brazilian Atlantic Forest. Herein, we report the isolation of the endophyte
Bacillus velezensis
GPP30 with a draft genome estimated at 4.0 Mpb.
Complete genome sequence of
Sphingobacterium multivorum
strain FW102 with β-galactosidase activity in drinking fountain water
Authors: Kim Sung Guk , Wang Sharon X.
Published: September 2024

Sphingobacterium multivorum
is a ubiquitous environmental microbe in nature, particularly abundant in soil and water sources. Recently,
S. multivorum
has been considered to be a potential opportunistic pathogen in humans. We report the 5,9540,064-bp genome sequence of
S. multivorum
strain FW102
,
isolated from drinking fountain water and predicted to have multiple copies of β-galactosidase genes.
Nonepisodic angioedema with eosinophilia subsequent to acute parvovirus B19 infection
Authors: Minamii Takahiro , Nishioka Hiroaki
Published: September 2024

Nonepisodic angioedema with eosinophilia (NEAE) is characterised by a single episode of angioedema localised to the extremities and peripheral eosinophilia. While NEAE can develop in response to infection or vaccination, NEAE associated with acute parvovirus B19 (B19V) infection is rare. We describe the case of a young woman with NEAE that developed during acute B19V infection. She presented with 1-week history of pruritus and polyarthralgia in the extremities, followed by the development of peripheral oedema, and was positive for anti-B19V IgM antibody. Her arthralgia improved within 2 weeks without any specific intervention; however, the oedema and pruritic erythema persisted and the peripheral eosinophil count increased. A short course of prednisolone therapy for suspected NEAE alleviated the symptoms, which have not recurred for more than 2 years. Thus, we believe that the patient was affected by NEAE and that NEAE can develop following acute B19 infection.
Cavernous haemangioma of the masseter muscle: transoral approach
Authors: Peixoto Pedro Polastri Lima , Ashidani Paulo Otávio Alves , Ness Marcos Mello , Conti de Freitas Luiz Carlos
Published: September 2024

Intramuscular haemangiomas (IH) are rare lesions, accounting for less than 1% of all haemangiomas. This article presents the case of a woman in her 40s with a swelling in her left cheek. CT revealed an intramuscular lesion within the masseter, suggestive of a venous malformation. Surgical treatment was carried out with intraoral access to the lesion, allowing for complete removal, resulting in temporary swelling and trismus. There was no facial paralysis. We discuss information on IH in the head and neck and their surgical approaches.
Necrotising enterocolitis suspicion in newborns with duct-dependent congenital heart disease: prognosis and risk factor
Authors: El Louali Fedoua , Prom Camille , Myriem Belghiti Alaoui , Gran Celia , Fouilloux Virginie , Lenoir Marien , Ligi Isabelle , Ovaert Caroline , Michel Fabrice
Published: September 2024

Introduction

The main risk factors of necrotising enterocolitis (NEC) are prematurity and low birth weight. The aim of our study was to identify risk factors for NEC in patients with duct-dependent congenital heart disease (CHD).

Study design

Newborns with duct-dependent CHD and NEC were matched 1:1 to those without NEC. Matched criteria were gestational age, birth weight, antenatal versus postnatal diagnosis and type of CHD.

Results

Twenty-three infants were included in each group. In the NEC group, mortality, length of intensive care unit stay and length of hospital stay were significantly higher (p=0.035; p<0.0001; p<0.0001). Lower diastolic blood pressure (DBP), negative flow balance, peritoneal dialysis and epinephrine-infusion were significantly associated with NEC (respectively, p=0.008, p=0.002, p=0.007, p=0.017). In multivariate analysis, DBP≤30 mm Hg remained the only independent risk factor of NEC (OR=8.70; 95% CI (1.46 to 53.50), p=0.019).

Conclusion

A DBP lower than 30 mm Hg was in our matched population of newborns with duct-dependent CHD, independently associated with NEC.
Metabolic reprogramming by mutant GNAS creates an actionable dependency in intraductal papillary mucinous neoplasms of the pancreas
Authors: Makino Yuki , Rajapakshe Kimal I , Chellakkan Selvanesan Benson , Okumura Takashi , Date Kenjiro , Dutta Prasanta , Abou-Elkacem Lotfi , Sagara Akiko , Min Jimin , Sans Marta , Yee Nathaniel , Siemann Megan J , Enriquez Jose , Smith Paytience , Bhattacharya Pratip , Kim Michael , Dede Merve , Hart Traver , Maitra Anirban , Thege Fredrik Ivar
Published: September 2024

Background

Oncogenic ‘hotspot’ mutations ofKRASandGNASare two major driver alterations in intraductal papillary mucinous neoplasms (IPMNs), which arebona fideprecursors to pancreatic ductal adenocarcinoma. We previously reported that pancreas-specificKrasG12DandGnasR201Cco-expression in p48Cre; KrasLSL-G12D; Rosa26LSL-rtTA; Tg (TetO-GnasR201C) mice (‘Kras;Gnas’ mice) caused development of cystic lesions recapitulating IPMNs.

Objective

We aim to unveil the consequences of mutantGnasR201Cexpression on phenotype, transcriptomic profile and genomic dependencies.

Design

We performed multimodal transcriptional profiling (bulk RNA sequencing, single-cell RNA sequencing and spatial transcriptomics) in the‘Kras;Gnas’ autochthonous model and tumour-derived cell lines (Kras;Gnascells), whereGnasR201Cexpression is inducible. A genome-wide CRISPR/Cas9 screen was conducted to identify potential vulnerabilities inKrasG12D;GnasR201Cco-expressing cells.

Results

Induction ofGnasR201C—and resulting G(s)alpha signalling—leads to the emergence of a gene signature of gastric (pyloric type) metaplasia in pancreatic neoplastic epithelial cells. CRISPR screening identified the synthetic essentiality of glycolysis-related genesGpi1andSlc2a1inKrasG12D;GnasR201Cco-expressing cells. Real-time metabolic analyses inKras;Gnascells and autochthonousKras;Gnasmodel confirmed enhanced glycolysis onGnasR201Cinduction. Induction ofGnasR201CmadeKrasG12Dexpressing cells more dependent on glycolysis for their survival. Protein kinase A-dependent phosphorylation of the glycolytic intermediate enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) was a driver of increased glycolysis onGnasR201Cinduction.

Conclusion

Multiple orthogonal approaches demonstrate thatKrasG12DandGnasR201Cco-expression results in a gene signature of gastric pyloric metaplasia and glycolytic dependency during IPMN pathogenesis. The observed metabolic reprogramming may provide a potential target for therapeutics and interception of IPMNs.
A history of community-based initiatives that led to crop improvement and protection in the Canadian prairies
Authors: McCallum Brent D. , Dickison Virginia , Geddes Charles M. , Hervet Vincent A.D. , Vankosky Meghan , Kaminski David , Entz Martin , Turkington T. Kelly
Published: September 2024

From the early days of agricultural production in the 1800s through to the present day, farmers, agronomists, and other motivated people have worked to improve crop production through pest management and surveillance, selection of crop genotypes and agronomic innovations such as reduced and zero-tillage. These essential contributions also helped raise awareness of the practical problems that farmers have faced, of the potential solutions to those problems, and the problems that remain to be solved. In many cases, farmers have organized their efforts to support research to address agricultural challenges through commodity organizations who actively fund research, raise awareness of science, and encourage participation in activities such as pest monitoring and on-farm research trials. This review highlights some of the important contributions of Canadian community scientists. The future of a biovigilance approach to crop production depends on the continued participation of agricultural community members.
Higher order fractal differential equations
Authors: Golmankhaneh Alireza Khalili , Depollier Claude , Pham Diana
Published: September 2024

This paper provides a summary of the fractal calculus framework. It presents higher-order homogeneous and nonhomogeneous linear fractal differential equations with [Formula: see text]-order. Solutions for these equations with constant coefficients are obtained through the method of variation of parameters and the method of undetermined coefficients. The solution space for higher [Formula: see text]-order linear fractal differential equations is defined, showcasing its non-integer dimensionality. The solutions to [Formula: see text]-order linear fractal differential equations are graphically depicted to illustrate their non-differentiability. Additionally, equations of motion governing the behavior of two masses in fractal time are proposed and solved.
The
ad
79 Vesuvius eruption revisited: the pyroclastic density currents
Authors: Scarpati Claudio , Santangelo Ileana , Chiominto Giulia , Perrotta Annamaria , Branney Michael J. , Fedele Lorenzo
Published: September 2024

Seventeen pyroclastic density currents (PDCs) were produced before, during and after the Plinian phase of the
ad
79 eruption of Vesuvius. Their deposits were correlated using the proportions of components, together with the recognition of distinctive intercalated regionally traceable fall marker layers, revealing sectoral and distance-dependent variations. During an extensive field analysis, 27 lithostratigraphic units were detected and mapped and the lateral and vertical variations of 15 lithofacies were documented, described and interpreted. The total volume of PDC units is 1.25 km
3
. We consider that the early PDCs were generated by partial collapses from the sustained Plinian eruption column, whereas the subsequent post-Plinian PDCs were generated by more sustained pyroclastic fountaining. New facies mapping revealed lateral migration and extended travel distances for some of the currents. Most of the lobed PDCs remained relatively uniform, whereas the radial PDCs exhibited fluctuating waxing and waning pulses and changed gradationally down-current. Re-evaluation of the timing of caldera collapse and the transition from a magmatic to a phreatomagmatic eruption style suggests that substrate fracturing during incremental caldera subsidence may have allowed the gradual ingress of groundwater into the erupting magma. These results provide a new chronology of the eruption, revealing that the post-Plinian collapse phase lasted
c.
12 h.
Vilyui and Priverkhoyansk Composite Tectono-Sedimentary Elements, Northeastern East Siberia
Authors: Prokopiev A. V. , Ershova V. B. , Drachev S. S. , Vasiliev D. A. , Shimanskiy S. V.
Published: September 2024

A vast region of the Northeastern Siberia west of the Verkhoyansk Range includes two large sedimentary basins, Vilyui and Priverkhoyansk. Combined, these basins constitute the Lena-Vilyui Petroleum Province, which contains the largest gas reserves in the northeastern Asia. Both basins have a long and complex geological history that resulted in the accumulation of over 14 km-thick succession of Upper Proterozoic, Paleozoic, Mesozoic and Cenozoic sedimentary rocks. According to the volume's terminology, we subdivide this sedimentary body into two composite tectono-sedimentary elements (CTSE), the Vilyui and Priverkhoyansk (VI CTSE and PV CTSE), which closely correspond to the same-named basins. The CTSEs consist of ten distinct tectono-sedimentary elements (TSEs), each representing a distinct tectonic setting. This region has been studied very irregularly. In total, more than 400 deep wells have been drilled, mostly within the VI CTSE and only a few tens - in the PV CTSE. Eleven gas and gas condensate accumulations have been discovered in the VI CTSE. The PV CTSE remains poorly explored with only two commercial discoveries made as of the present-day.
Building a Coding Assistant via the Retrieval-Augmented Language Model
Authors: Li Xinze , Wang Hanbin , Liu Zhenghao , Yu Shi , Wang Shuo , Yan Yukun , Fu Yukai , Gu Yu , Yu Ge
Published: September 2024

Pretrained language models have shown strong effectiveness in code-related tasks, such as code retrieval, code generation, code summarization, and code completion tasks. In this article, we propose COde assistaNt viA retrieval-augmeNted language model (CONAN), which aims to build a code assistant by mimicking the knowledge-seeking behaviors of humans during coding. Specifically, it consists of a code structure-aware retriever (CONAN-R) and a dual-view code representation-based retrieval-augmented generation model (CONAN-G). CONAN-R pretrains CodeT5 using Code-Documentation Alignment and Masked Entity Prediction tasks to make language models code structure-aware and learn effective representations for code snippets and documentation. Then CONAN-G designs a dual-view code representation mechanism for implementing a retrieval-augmented code generation model. CONAN-G regards the code documentation descriptions as prompts, which help language models better understand the code semantics. Our experiments show that CONAN achieves convincing performance on different code generation tasks and significantly outperforms previous retrieval augmented code generation models. Our further analyses show that CONAN learns tailored representations for both code snippets and documentation by aligning code-documentation data pairs and capturing structural semantics by masking and predicting entities in the code data. Additionally, the retrieved code snippets and documentation provide necessary information from both program language and natural language to assist the code generation process. CONAN can also be used as an assistant for Large Language Models (LLMs), providing LLMs with external knowledge in shorter code document lengths to improve their effectiveness on various code tasks. It shows the ability of CONAN to extract necessary information and help filter out the noise from retrieved code documents.
Access Characteristic-Guided Remote Swapping Across Mobile Devices
Authors: Li Wentong , Lv Yina , Luo Longfei , Song Yunpeng , Shi Liang
Published: September 2024

Memory swapping ensures smooth application switching for mobile systems by caching applications in the background. To further play the role of memory swapping, remote swapping across mobile devices has been widely studied, which caches applications to nearby remote devices by remote paging. However, due to the massive remote I/Os and unguaranteed swap throughput, the current remote swapping is limited with an unsatisfactory user experience, especially under variable network conditions. This paper first studies the access characteristics of applications and clarifies the impact of various network traffic on remote swapping. Motivated by these, an efficient access characteristic-guided remote swapping framework (ACR-Swap
+
) is proposed to optimize remote swapping across mobile devices with resilient remote paging. ACR-Swap
+
 first performs selective remote paging based on the swap-in frequency of different processes and then prefetches data across devices based on the process running states. Finally, it conducts hierarchical remote paging to avoid the impact of network traffic on remote swapping. Evaluations on Google Pixel 6 show that ACR-Swap
+
 reduces the application switching latency by 21.6% and achieves a negligible performance fluctuation under various network traffic compared to the state of the art.
Industry Transformations for High Service Provisioning with Lower Energy and Material Demand: A Review of Models and Scenarios
Authors: Wiedenhofer Dominik , Streeck Jan , Wiese Frauke , Verdolini Elena , Mastrucci Alessio , Ju Yiyi , Boza-Kiss Benigna , Min Jihoon , Norman Jonathan , Wieland Hanspeter , Bento Nuno , León María Fernanda Godoy , Magalar Leticia , Mayer Andreas , Gingrich Simone , Hayashi Ayami , Jupesta Joni , Ünlü Gamze , Niamir Leila , Cao Tao , Zanon-Zotin Marianne , Plank Barbara , Vélez-Henao Johan , Masanet Eric , Krey Volker , Akimoto Keigo , Grubler Arnulf , van Ruijven Bas , Pauliuk Stefan
Published: September 2024

Developing transformative pathways for industry's compliance with international climate targets requires model-based insights into how supply- and demand-side measures affect industry, material cycles, global supply chains, socioeconomic activities, and service provisioning that support societal well-being. We review the recent literature modeling the industrial system in low energy and material demand futures, which mitigates environmental impacts without relying on risky future negative emissions and technological fixes. We identify 77 innovative studies drawing on nine distinct industry modeling traditions. We critically assess system definitions and scopes, biophysical and thermodynamic consistency, granularity and heterogeneity, and operationalization of demand and service provisioning. We find that combined supply- and demand-side measures could reduce current economy-wide material use by 56%, energy use by 40% to 60%, and greenhouse gas emissions by 70% to net zero. We call for strengthened interdisciplinary collaborations between industry modeling traditions and demand-side research to produce more insightful scenarios, and we discuss challenges and recommendations for this emerging field.
Fluoroscopic‐Guided Removal of Jejunal Sharp Foreign Body: An Alternative Approach to Surgery
Authors: Qatomah Abdulrahman , McQueen Simon , Qatomah Wafa , Qatomah Aishah , Bessissow Ali
Published: September 2024

Introduction. Foreign body (FB) ingestion represents a frequently encountered scenario in clinical practice. Most ingested FBs typically pass spontaneously, requiring no intervention. Endoscopic removal stands out as the least invasive method, with only a minimal 1% needing surgical intervention. Case Presentation. We present a case of a 30‐year‐old male who ingested multiple FBs located in the stomach and small bowel. While successful removal of the stomach FB was achieved through endoscopy, the second FB in the small bowel proved challenging due to perforation concerns and limited expertise. Given a history of prior surgical intervention resulting in a large incisional hernia, surgical removal was discouraged. Consequently, a collaborative decision involving surgeon and interventional radiologist (IR) led to the adoption of a fluoroscopic‐guided removal approach facilitated by IR techniques. Conclusion. This case highlights the potential for a less invasive alternative in situations where both endoscopic and surgical interventions are deemed not feasible.
Supplementary Figure S12 from Arginine Methylation of DDX3 by PRMT1 Mediates Mitochondrial Homeostasis to Promote Breast Cancer Metastasis
Authors: Hsu Wen-Jing , Chiang Ming-Chen , Chao Yi-Chun , Chang Yu-Chu , Hsu Ming-Chien , Chung Chu-Hung , Tsai I-Lin , Chu Cheng-Ying , Wu Han-Chung , Yang Ching-Chieh , Lee Chi-Ching , Lin Cheng-Wei
Published: September 2024

PRMT1/DDX3 axis contributes to breast cancer metastasis.
Figure S8 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Figure S8R
Figure S5 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Figure S5
Figure S4 from Targeting the immunoglobulin IGSF9 enhances anti-tumor T cell activity and sensitivity to anti-PD-1 immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: September 2024

Mouse IGSF9 was detected before and after MC38 implantation.
Supplementary Figures from Targeting BCL6 in gastrointestinal stromal tumor promotes p53-mediated apoptosis to enhance the antitumor activity of imatinib
Authors: Zeng Xiangyu , Zhao Fei , Jia Jie , Ma Xianxiong , Jiang Qi , Zhang Ruizhi , Li Chengguo , Wang Tao , Liu Weizhen , Hao Yalan , Tao Kaixiong , Lou Zhenkun , Zhang Peng
Published: September 2024

Supplementary Figures
Supp. Figure 5 from Parkin deficiency suppresses antigen presentation to promote tumor immune evasion and immunotherapy resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: September 2024

Figure S5
Supp. Figure 3 from Parkin deficiency suppresses antigen presentation to promote tumor immune evasion and immunotherapy resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: September 2024

Figure S3
Supplementary Data from Syk Inhibition Reprograms Tumor-Associated Macrophages and Overcomes Gemcitabine-Induced Immunosuppression in Pancreatic Ductal Adenocarcinoma
Authors: Rohila Deepak , Park In Hwan , Pham Timothy V. , Weitz Jonathan , Hurtado de Mendoza Tatiana , Madheswaran Suresh , Ishfaq Mehreen , Beaman Cooper , Tapia Elisabette , Sun Siming , Patel Jay , Tamayo Pablo , Lowy Andrew M. , Joshi Shweta
Published: September 2024

Supplementary table
Nutrient Levels and Nutrient Sources in Pancreatic Tumors
Authors: Groessl Sven , Palm Wilhelm
Published: September 2024

It has been known that poor tumor perfusion and dysregulated cancer cell metabolism give rise to tumor microenvironments with unphysiologic nutrient levels, but the precise alterations in metabolite abundance are not well defined. In a 2015 study in Cancer Research, Kamphorst and colleagues published a detailed comparison of the metabolome from human pancreatic tumors and benign tissues. Tumors were depleted in glucose and various nonessential amino acids but, surprisingly, enriched in essential amino acids. The authors attributed these nutrient imbalances to macropinocytosis of extracellular proteins, a RAS-driven amino acid acquisition pathway that was found to be increased in human tumors and supports pancreatic cancer cell growth during amino acid starvation. These findings substantially contributed to the understanding of altered nutrient levels in tumors and extracellular proteins as noncanonical nutrients. Intratumoral nutrient levels in different cancer contexts and signaling pathways that regulate nutrient acquisition by cancer cells remain a focus of current research.

See related article by Kamphorst and colleagues, Cancer Res 2015;75:544–53
Cancer-Associated Fibroblasts: From Spectators to Protagonists in Pancreatic Cancer Progression
Authors: Mucciolo Gianluca , Li Wenlong , Biffi Giulia
Published: September 2024

Our knowledge of the origins, heterogeneity, and functions of cancer-associated fibroblasts (CAF) in pancreatic ductal adenocarcinoma (PDAC) has exponentially increased over the last two decades. This has been facilitated by the implementation of new models and single-cell technologies. However, a few key studies preceded the current exciting times in CAF research and were fundamental in initiating the investigation of CAFs and of their roles in PDAC. With their study published in Cancer Research in 2008, Hwang and colleagues have been first to successfully isolate and immortalize human pancreatic stellate cells (HPSC) from PDAC tissues. This new tool allowed them to probe the roles of CAFs in PDAC as never done before. By performing complementary in vitro and in vivo analyses, the authors demonstrated the involvement of HPSCs in PDAC malignant cell proliferation, invasion, and therapy resistance. Here, we leverage that seminal study as a framework to discuss the advances made over the last 16 years in understanding the complexity and central roles of CAFs in PDAC progression.

See related article by Hwang and colleagues, Cancer Res 2008;68:918–26
The Pivotal Role of Germline BRCA2 Pathogenic Variants in “Apparently Sporadic” Pancreatic Cancer
Authors: Brody Jonathan R. , Klein Alison P.
Published: September 2024

In 1996, Goggins and colleagues demonstrated the importance of germline BRCA2 pathogenic variants in the development of apparently sporadic pancreatic ductal adenocarcinoma (PDAC). Previously, the group identified homozygous deletion of the 13q region in PDACs, enabling the identification of the BRCA2 gene. This 1996 article first revealed loss of BRCA2, both germline and somatic, as a key driver of PDAC at a time when there was still doubt if PDAC even had an inherited component. Contrary to the prevailing wisdom, not all individuals with inherited pathogenic BRCA2 variants had a family history of cancer. The innovative bedside-to-bench nature of this work revealed that individuals with these variants would be missed if genetic testing was limited only to those meeting the family history criteria. Therefore, Goggins and colleagues advocated that universal genetic testing may be indicated for pancreatic cancer at a time when genetic testing was in its infancy. Twenty-three years later, in 2019, universal testing for pancreatic cancer became standard of care in the United States. Additionally, this work and future-related publications by the Kern Laboratory set the stage for targeting BRCA2 and related DNA repair mutations in pancreatic cancer via a synthetic lethal therapeutic approach. The provocative discussion initiated by this team in this publication is still inspiring the field today. In this seminal publication, Goggins and colleagues profoundly impacted the direction of pancreatic cancer research, leading to a more sophisticated approach to designing earlier detection and precision treatment strategies for pancreatic cancer.

See related article by Goggins and colleagues, Cancer Res 1996;56:5360–4
Supplementary Table 6 from Associations between MICA and MICB genetic variants, protein levels, and colorectal cancer: Atherosclerosis Risk in Communities (ARIC)
Authors: Wang Shuo , Onyeaghala Guillaume C. , Pankratz Nathan , Nelson Heather H. , Thyagarajan Bharat , Tang Weihong , Norby Faye L. , Ugoji Chinenye , Joshu Corinne E. , Gomez Christian R. , Couper David J. , Coresh Josef , Platz Elizabeth A. , Prizment Anna E.
Published: September 2024

Supplemental Table 6 shows the associations of sMICA and sMICB levels (continuous variables) and pre-selected SNPsb with risk of CRC and subtypes of CRC.
Supplementary Table 5 from Associations between MICA and MICB genetic variants, protein levels, and colorectal cancer: Atherosclerosis Risk in Communities (ARIC)
Authors: Wang Shuo , Onyeaghala Guillaume C. , Pankratz Nathan , Nelson Heather H. , Thyagarajan Bharat , Tang Weihong , Norby Faye L. , Ugoji Chinenye , Joshu Corinne E. , Gomez Christian R. , Couper David J. , Coresh Josef , Platz Elizabeth A. , Prizment Anna E.
Published: September 2024

Supplemental table 5 shows the associations between pre-selected SNPs and risk of CRC with and without adjustment for sMICA and sMICB levels.
Supplementary Table 3 from Associations between MICA and MICB genetic variants, protein levels, and colorectal cancer: Atherosclerosis Risk in Communities (ARIC)
Authors: Wang Shuo , Onyeaghala Guillaume C. , Pankratz Nathan , Nelson Heather H. , Thyagarajan Bharat , Tang Weihong , Norby Faye L. , Ugoji Chinenye , Joshu Corinne E. , Gomez Christian R. , Couper David J. , Coresh Josef , Platz Elizabeth A. , Prizment Anna E.
Published: September 2024

Supplemental Table 3 shows the associations between pre-selected SNPs and CRC risk stratified by sex, race, or diabetes status.
Supplementary Table 2 from Associations between MICA and MICB genetic variants, protein levels, and colorectal cancer: Atherosclerosis Risk in Communities (ARIC)
Authors: Wang Shuo , Onyeaghala Guillaume C. , Pankratz Nathan , Nelson Heather H. , Thyagarajan Bharat , Tang Weihong , Norby Faye L. , Ugoji Chinenye , Joshu Corinne E. , Gomez Christian R. , Couper David J. , Coresh Josef , Platz Elizabeth A. , Prizment Anna E.
Published: September 2024

Supplemental Table 2 shows the associations between pre-selected SNPs and Visit 2 sMICA and sMICB levels (continuous variables) stratified by sex, race, or diabetes status.
Supplementary Table 7 from Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors
Authors: Sun Maxine , Cyr Marie-Christyne , Sandoval Johanna , Lemieux Perreault Louis-Philippe , Busque Lambert , Tardif Jean-Claude , Dubé Marie-Pierre
Published: September 2024

Supplementary Table 7: The effect of autosomal mosaic chromosomal alterations on death of cardiovascular disease causes, coronary artery disease causes, from cancer and any cause of death
Supplementary Table 13 from Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors
Authors: Sun Maxine , Cyr Marie-Christyne , Sandoval Johanna , Lemieux Perreault Louis-Philippe , Busque Lambert , Tardif Jean-Claude , Dubé Marie-Pierre
Published: September 2024

Supplementary Table 13: Cox regression analyses for the effect of mosaic chromosomal alterations on the risk of death of coronary artery disease causes by cancer type
Supplementary Table 12 from Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors
Authors: Sun Maxine , Cyr Marie-Christyne , Sandoval Johanna , Lemieux Perreault Louis-Philippe , Busque Lambert , Tardif Jean-Claude , Dubé Marie-Pierre
Published: September 2024

Supplementary Table 12: Cox regression analyses of the effect of mosaic chromosomal alterations on the risk of death of cardiovascular disease causes per cancer type
Supplementary Table 10 from Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors
Authors: Sun Maxine , Cyr Marie-Christyne , Sandoval Johanna , Lemieux Perreault Louis-Philippe , Busque Lambert , Tardif Jean-Claude , Dubé Marie-Pierre
Published: September 2024

Supplementary Table 10: The effect of expanded mosaic chromosomal alterations on death of cardiovascular disease causes, coronary artery disease causes, from cancer, and any cause of death
Supplementary Figure 2 from Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors
Authors: Sun Maxine , Cyr Marie-Christyne , Sandoval Johanna , Lemieux Perreault Louis-Philippe , Busque Lambert , Tardif Jean-Claude , Dubé Marie-Pierre
Published: September 2024

Supplementary Figure 2: Visual mapping of mosaic chromosomal alterations
Supplemental Table 7 from Nitrated polycyclic aromatic hydrocarbon (nitro-PAH) signatures and somatic mutations in diesel exhaust-exposed bladder tumors
Authors: Gonzalez Nicole , Rao Nina , Dean Michael , Lee Donghyuk , Hurson Amber N. , Baris Dalsu , Schwenn Molly , Johnson Alison , Prokunina-Olsson Ludmila , Friesen Melissa C. , Zhu Bin , Rothman Nathaniel , Silverman Debra T. , Koutros Stella
Published: September 2024

Cosine similarities for all signatures
Supplemental Table 4 from Nitrated polycyclic aromatic hydrocarbon (nitro-PAH) signatures and somatic mutations in diesel exhaust-exposed bladder tumors
Authors: Gonzalez Nicole , Rao Nina , Dean Michael , Lee Donghyuk , Hurson Amber N. , Baris Dalsu , Schwenn Molly , Johnson Alison , Prokunina-Olsson Ludmila , Friesen Melissa C. , Zhu Bin , Rothman Nathaniel , Silverman Debra T. , Koutros Stella
Published: September 2024

specific TP53 mutations and ever diesel
Table S8 from Exploring the complex relationship between gut microbiota and risk of colorectal neoplasia using bidirectional Mendelian Randomization analysis
Authors: Li Wanxin , Zhou Xuan , Yuan Shuai , Wang Lijuan , Yu Lili , Sun Jing , Chen Jie , Xiao Qian , Wan Zhongxiao , Zheng Ju-Sheng , Zhang Cai-Xia , Larsson Susanna C. , Farrington Susan M. , Law Philip , Houlston Richard S. , Tomlinson Ian , Ding Ke-Feng , Dunlop Malcolm G. , Theodoratou Evropi , Li Xue
Published: September 2024

Table S8 shows the forward MR analyses of the six gut microbial metabolites with the risk of colorectal cancer.
Table S2 from Exploring the complex relationship between gut microbiota and risk of colorectal neoplasia using bidirectional Mendelian Randomization analysis
Authors: Li Wanxin , Zhou Xuan , Yuan Shuai , Wang Lijuan , Yu Lili , Sun Jing , Chen Jie , Xiao Qian , Wan Zhongxiao , Zheng Ju-Sheng , Zhang Cai-Xia , Larsson Susanna C. , Farrington Susan M. , Law Philip , Houlston Richard S. , Tomlinson Ian , Ding Ke-Feng , Dunlop Malcolm G. , Theodoratou Evropi , Li Xue
Published: September 2024

Table S2 shows the SNPs that associated with nine microbiota taxa (P<1×10-5).
Supplementary Table S2 from The Association of Neighborhood Characteristics and Frailty in Childhood Cancer Survivors: A Report from the St. Jude Lifetime Cohort Study
Authors: Schwartz Lindsay F. , Dhaduk Rikeenkumar , Howell Carrie R. , Brinkman Tara M. , Ehrhardt Matthew J. , Delaney Angela , Srivastava Deo Kumar , Lanctot Jennifer Q. , Armstrong Gregory T. , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Henderson Tara O.
Published: September 2024

Supplementary Table S2 shows the results of bivariate analyses between individual-level participant variables and frailty status
Supplementary Figure S1 from The Association of Neighborhood Characteristics and Frailty in Childhood Cancer Survivors: A Report from the St. Jude Lifetime Cohort Study
Authors: Schwartz Lindsay F. , Dhaduk Rikeenkumar , Howell Carrie R. , Brinkman Tara M. , Ehrhardt Matthew J. , Delaney Angela , Srivastava Deo Kumar , Lanctot Jennifer Q. , Armstrong Gregory T. , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Henderson Tara O.
Published: September 2024

Supplementary Figure S1: Geographic location of study participants (N=3806). In this map, each red dot indicates the address of each participant recorded at intake and geocoded for this study.
Supplementary Table S9 from Associations of post-diagnosis lifestyle with prognosis in women with invasive breast cancer
Authors: Troeschel Alyssa N. , Hartman Terryl J. , McCullough Lauren E. , Ergas Isaac J. , Collin Lindsay J. , Kwan Marilyn L. , Ambrosone Christine B. , Flanders W Dana , Bradshaw Patrick T. , Cespedes Feliciano Elizabeth M. , Roh Janise M. , Wang Ying , Valice Emily , Kushi Lawrence H.
Published: September 2024

Descriptive characteristics among 4,403a women diagnosed with invasive breast cancer in the Pathways Cohort, 2006–2018
Supplementary Table S4 from Associations of post-diagnosis lifestyle with prognosis in women with invasive breast cancer
Authors: Troeschel Alyssa N. , Hartman Terryl J. , McCullough Lauren E. , Ergas Isaac J. , Collin Lindsay J. , Kwan Marilyn L. , Ambrosone Christine B. , Flanders W Dana , Bradshaw Patrick T. , Cespedes Feliciano Elizabeth M. , Roh Janise M. , Wang Ying , Valice Emily , Kushi Lawrence H.
Published: September 2024

Interactions Between the 2-Year Post-Diagnosis Lifestyle score and Selected Characteristics with All-Cause Mortality, Breast Cancer-Specific Mortality, and Breast Cancer Recurrence in the Pathways Study.
Supplementary Table S1 from Associations of post-diagnosis lifestyle with prognosis in women with invasive breast cancer
Authors: Troeschel Alyssa N. , Hartman Terryl J. , McCullough Lauren E. , Ergas Isaac J. , Collin Lindsay J. , Kwan Marilyn L. , Ambrosone Christine B. , Flanders W Dana , Bradshaw Patrick T. , Cespedes Feliciano Elizabeth M. , Roh Janise M. , Wang Ying , Valice Emily , Kushi Lawrence H.
Published: September 2024

Categorization of the modified baseline and 2-year post-diagnosis lifestyle scores.
Supplementary Materials and Methods from Associations of post-diagnosis lifestyle with prognosis in women with invasive breast cancer
Authors: Troeschel Alyssa N. , Hartman Terryl J. , McCullough Lauren E. , Ergas Isaac J. , Collin Lindsay J. , Kwan Marilyn L. , Ambrosone Christine B. , Flanders W Dana , Bradshaw Patrick T. , Cespedes Feliciano Elizabeth M. , Roh Janise M. , Wang Ying , Valice Emily , Kushi Lawrence H.
Published: September 2024

Supplementary text providing additional information regarding methods.
Supplementary Table S2 from Tobacco Smoke is a Major Source of Aromatic Amine Exposure in U.S. Adults: 2013-2014 National Health and Nutrition Examination Survey (NHANES)
Authors: Seyler Tiffany , Mazumder Shrila , Ahamed Rayaj , Zhu Wanzhe , Blount Benjamin C. , Apelberg Benjamin J. , Wang Lanqing
Published: September 2024

Supplementary Table S2: Sample-weighted multiple regression results with dietary categories for urinary 1AMN, 2AMN, 4ABP (n = 1,845) among participants who smoked cigarette exclusively and nonusers of tobacco products, 2013-2014 NHANES
Supplementary Table S3 from Circulating Sex Hormone Levels and Risk of Gastrointestinal Cancer: Systematic Review and Meta-Analysis of Prospective Studies
Authors: Liu Zhiqiang , Zhang Yingfan , Lagergren Jesper , Li Shanshan , Li Jingru , Zhou Zhixian , Hu Zhijian , Xie Shao-Hua
Published: September 2024

Supplementary Table S3 shows Newcastle-Ottawa Scale of included studies.
Supplementary Table S2 from Circulating Sex Hormone Levels and Risk of Gastrointestinal Cancer: Systematic Review and Meta-Analysis of Prospective Studies
Authors: Liu Zhiqiang , Zhang Yingfan , Lagergren Jesper , Li Shanshan , Li Jingru , Zhou Zhixian , Hu Zhijian , Xie Shao-Hua
Published: September 2024

Supplementary Table S2 shows adjusted or matched covariates and sex hormone measurement methods of studies included in the meta-analysis.
Supplementary Figure S4 from Circulating Sex Hormone Levels and Risk of Gastrointestinal Cancer: Systematic Review and Meta-Analysis of Prospective Studies
Authors: Liu Zhiqiang , Zhang Yingfan , Lagergren Jesper , Li Shanshan , Li Jingru , Zhou Zhixian , Hu Zhijian , Xie Shao-Hua
Published: September 2024

Supplementary Figure S4 shows forest plots, sensitivity analysis and funnel plot of the associations between prediagnostic circulating sex hormone levels and pancreatic cancer risk.
Supplementary Figure S1 from Circulating Sex Hormone Levels and Risk of Gastrointestinal Cancer: Systematic Review and Meta-Analysis of Prospective Studies
Authors: Liu Zhiqiang , Zhang Yingfan , Lagergren Jesper , Li Shanshan , Li Jingru , Zhou Zhixian , Hu Zhijian , Xie Shao-Hua
Published: September 2024

Supplementary Figure S1 shows forest plots (1), sensitivity analysis (2) and funnel plots (3) of the associations between prediagnostic circulating sex hormone levels and esophageal cancer risk.
Supplementary Table 2 from Medical Financial Hardship and Food Security among Cancer Survivors in the
United States
Authors: Hallgren Emily , Narcisse Marie-Rachelle , Andersen Jennifer A. , Willis Don E. , Thompson Tess , Bryant-Smith Gwendolyn , McElfish Pearl A.
Published: September 2024

Supplementary Table 2 shows the results of the analysis exploring the moderating effect of a cancer history on the relationship between medical financial hardship and food security among cancer survivors and individuals without a cancer history.
Supplementary Table 1 from Medical Financial Hardship and Food Security among Cancer Survivors in the
United States
Authors: Hallgren Emily , Narcisse Marie-Rachelle , Andersen Jennifer A. , Willis Don E. , Thompson Tess , Bryant-Smith Gwendolyn , McElfish Pearl A.
Published: September 2024

Supplementary Table 1 provides descriptive statistics of the characteristics of the sample of individuals without a cancer history.
Supplementary Table 8 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 8 includes one-year cumulative incidences for HCC surveillance overall and by insurance type, by calendar year of cirrhosis diagnosis (% and 95% confidence intervals).
Supplementary Table 5 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 5 includes baseline characteristics of individuals with cirrhosis eligible for HCC surveillance – private insurance only (N, %) (N=6,530).
Supplementary Table 3 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 3 includes hypothetical examples for calculating the Proportion of Time Covered measures.
Supplementary Table 2 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 2 includes the CPT/HCPCS codes for the HCC surveillance outcome definitions.
Supplementary Table 16 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 16 includes two-year cumulative incidences for HCC surveillance overall and by insurance type, by calendar year of cirrhosis diagnosis, without imputing deaths for individuals insured through private insurance (% and 95% confidence intervals).
Supplementary Table 14 from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

Supplementary Table 14 includes the two-year cumulative incidences by cirrhosis etiology and by insurance, excluding individuals with decompensated cirrhosis (% and 95% confidence intervals).
Supplementary Methods from Hepatocellular Carcinoma Surveillance Among Individuals with Cirrhosis: Trends by Payer, Etiology and Calendar Year, from a Statewide, Multi-Payer Dataset, 2010-2018
Authors: Hsu Christine D. , Henderson Louise M. , Jackson Bradford E. , Baggett Christopher D. , Jonsson Funk Michele , Olshan Andrew F. , Gupta Parul , Barritt A Sidney. , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: September 2024

The Supplementary Methods includes detailed descriptions for calculating the Proportion of Time Covered measures.