bluuebunny/crossref_metadata_2025 huggingface dataset:
Harnessing diversity and antagonism within the pig skin microbiota to identify novel mediators of colonization resistance to methicillin-resistant
Staphylococcus aureus
Authors: Wei Monica , Flowers Laurice , Knight Simon A. B. , Zheng Qi , Murga-Garrido Sofia , Uberoi Aayushi , Pan Jamie Ting-Chun , Walsh Jasmine , Schroeder Erin , Chu Emily W. , Campbell Amy , Shin Daniel , Bradley Charles W. , Duran-Struuck Raimon , Grice Elizabeth A.
Published: July 2023

The microbiota mediate multiple aspects of skin barrier function, including colonization resistance to pathogens such as
Staphylococcus aureus
. The endogenous skin microbiota limits
S. aureus
colonization via competition and direct inhibition. Novel mechanisms of colonization resistance are promising therapeutic targets for drug-resistant infections, such as those caused by methicillin-resistant
S. aureus
(MRSA). Here, we developed and characterized a swine model of topical microbiome perturbation and MRSA colonization. As in other model systems, topical antimicrobial treatment had a little discernable effect on community diversity though the overall microbial load was sensitive to multiple types of intervention, including swabbing. In parallel, we established a porcine skin culture collection and screened 7,700 isolates for MRSA inhibition. Using genomic and phenotypic criteria, we curated three isolates to investigate whether prophylactic colonization would inhibit MRSA colonization
in vivo
. The three-member consortium together, but not individually, provided protection against MRSA colonization, suggesting cooperation and/or synergy among the strains. Inhibitory isolates were represented across all major phyla of the pig skin microbiota and did not have a strong preference for inhibiting closely related species, suggesting that relatedness is not a condition of antagonism. These findings reveal the porcine skin as an underexplored reservoir of skin commensal species with the potential to prevent MRSA colonization and infection.

IMPORTANCE

The skin microbiota is protective against pathogens or opportunists such as
S. aureus
, the most common cause of skin and soft tissue infections.
S. aureus
can colonize normal skin and nasal passages, and colonization is a risk factor for infection, especially on breach of the skin barrier. Here, we established a pig model to study the competitive mechanisms of the skin microbiota and their role in preventing colonization by MRSA. This drug-resistant strain is also a livestock pathogen, and swine herds can be reservoirs of MRSA carriage. From 7,700 cultured skin isolates, we identified 37 unique species across three phyla that inhibited MRSA. A synthetic community of three inhibitory isolates provided protection together, but not individually,
in vivo
in a murine model of MRSA colonization. These findings suggest that antagonism is widespread in the pig skin microbiota, and these competitive interactions may be exploited to prevent MRSA colonization.
Faunal provinciality in the Late Cretaceous Western Interior Seaway using network modeling
Authors: Purcell Ceara , Scuderi Louis , Myers Corinne
Published: July 2023

The Western Interior Seaway (WIS) was historically divided into latitudinal faunal provinces that were taxonomically distinct from the adjacent Gulf Coastal Plain (GCP) and that shifted in space due to sea-level changes. However, no rigorous quantitative analyses using recent taxonomic updates have reassessed these provinces and their associations. We used network modeling of macroinvertebrate WIS and GCP fauna to test whether biotic provinces existed and to examine their relationships with abiotic change. Results suggest a cohesive WIS unit existed across the Campanian, and distinct WIS and GCP provinces existed in the Maastrichtian. Sea-level changes coincided with changes in network metrics. These results indicate that, while the WIS did not contain subprovinces in the Late Cretaceous, environmental factors influenced faunal associations and their communication over time.
Close intervention sessions complement intensive insulin therapy in paediatric diabetes: a longitudinal study
Authors: Foran Jason , Egan Aisling , Somers Eric , O’Connell Susan M
Published: July 2023

Objective

To examine the impact of multidisciplinary team input and intensive insulin therapy on glycaemic control in children and adolescents with diabetes over a 13-year period.

Design

Two statistical approaches were used to interrogate the dataset. First a matched pair analysis to compare insulin treatment-type effect (pump vs multiple daily injections (MDIs)), followed by panel data regression to assess the impact of intensive re-education on glycated haemoglobin (HbA1c), in addition to treatment type.

Setting

A large tertiary paediatric diabetes centre using a prospectively maintained database of clinical encounters from 2007 to 2020.

Main outcome measures

Difference in HbA1c between treatment types (matching methodology) and expected change in HbA1c with treatment type and re-education (panel data).

Results

Compared with MDI, matched pump patients had a lower HbA1c 6 months after pump commencement (ΔHbA1c=-0.53%, CI -0.34% to -0.72%; n=106). This effect was robust in controlling for socioeconomic deprivation (ΔHbA1c=-0.74%, CI -0.40% to -1.08%; n=29). Panel data analysis demonstrated a -0.55% reduction in HbA1c with pump therapy compared with MDI therapy (CI -0.43% to -0.67%). Patients who had intensive re-education had recorded an HbA1c of 0.95% (CI 0.85% to 1.05%) greater than otherwise identical patients prior to re-education. Following these sessions, HbA1c dropped by a mean -0.81% (CI -0.68% to -0.95%) within 6 months. These were also robust in controlling for socioeconomic factors.

Conclusions

Compared with matched peers on MDI regimens, patients on pump therapy have lower expected HbA1c, an effect sustained for up to 8 years. Intensive re-education is associated with a significant drop in previously elevated HbA1c levels.
Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues
Authors: Jamrozik Euzebiusz , Munung Nchangwi Syntia , Abeler-Dorner Lucie , Parker Michael
Published: July 2023

Phylogenetic analyses of HIV are an increasingly accurate method of clarifying population-level patterns of transmission and linking individuals or groups with transmission events. Viral genetic data may be used by public health agencies to guide policy interventions focused on clusters of transmission or segments of the population in which transmission is concentrated. Analyses of HIV phylogenetics in high-income countries have often found that clusters of transmission play a significant role in HIV epidemics. In sub-Saharan Africa, HIV phylogenetic analyses to date suggest that clusters of transmission play a relatively minor role in local epidemics. Such analyses could nevertheless be used to guide priority setting and HIV public health programme design in Africa for sub-populations in which transmission events are more concentrated. Phylogenetic analysis raises ethical issues, in part due to the range of potential benefits and potential harms (ie, risks). Potential benefits include (1) improving knowledge of transmission patterns, (2) informing the design of focused public health interventions for subpopulations in which transmission is concentrated, (3) identifying and responding to clusters of transmission, (4) reducing stigma (in some cases) and (5) informing estimates of the (cost-)effectiveness of HIV treatment programmes. Potential harms include (1) privacy infringements, (2) increasing stigma (in some cases), (3) reducing trust in public health programmes, and (4) increased prosecution of legal cases where HIV transmission, homosexuality or sex work is criminalised. This paper provides analysis of relevant issues with a focus on sub-Saharan Africa in order to inform consultations regarding ethical best practice for HIV phylogenetics.
Exponential stabilization of conformable fractional bilinear systems with multiple inputs
Authors: Kasmi Souad , Mabrouk Fehmi , Omri Faouzi
Published: July 2023

In this paper, we consider a class of conformable fractional bilinear systems with multiple inputs. We study the exponential stabilization problem for these systems by using the quadratic Lyapunov functions and some additional hypothesis on the unit sphere. A numerical example is given to illustrate the efficiency of the obtained result.
On the anatomy and structural control of a dyke swarm that fed caldera-forming ignimbrite eruptions
Authors: Tomek Filip , Olšanská Irena , Trubač Jakub , Černý Jan , Rejšek Jan , Ackerman Lukáš
Published: July 2023

The evolution of eruptive vents related to calderas is not fully understood. We focus on a structural, rock-magnetic and geochemical investigation of a 314 Ma rhyolite dyke swarm associated with the late-orogenic Altenberg–Teplice Caldera, Bohemian Massif, eastern Variscan belt. The whole-rock major element, trace element and Nd–Pb isotope geochemistry along with the published U–Pb zircon geochronology link the extra-caldera dyke swarm with intra-caldera ignimbrites. The magnetic fabrics determined using the anisotropy of magnetic susceptibility are interpreted to record a continuum from magma ascent to emplacement and eruption during sinistral shearing. The latter evidences an interplay with regional tectonics associated with the activity of crustal-scale shear zones. The sinistral kinematics and strike of the dyke swarm, the elongation of caldera intrusive units, and the kinematics of major caldera faults are consistent with the dextral Riedel shear system, where the dykes correspond to antithetic R’ or X shears. Such a kinematic configuration implies that the maximum and minimum principal stresses were oriented roughly north–south and east–west, respectively. The relation between the stress field and the caldera elongation and orientation is not typical. We suggest that a pre-existing mutually perpendicular set of cross-cutting structural lineaments largely controlled the magma chamber and caldera formation.

Supplementary material
: The whole-rock major, trace element and isotope geochemical tables, magnetic fabrics source data and details of methods are available at
https://doi.org/10.6084/m9.figshare.c.6715893
Rock joint detection from 3D point clouds based on colour space
Authors: Ge Yunfeng , Cao Bei , Chen Qian , Wang Yu
Published: July 2023

To facilitate the automation accuracy of rock joint mapping, a new method based on colour space was proposed for the semi-automatic identification and orientation calculation of rock joints. The developed method in this study comprises four-step: (1) the point colour space and point curvature were calculated based on the point normal and the
X
-
, Y
- and
Z
-coordinates, respectively; (2) the rock joint sets were identified from point clouds based on the difference in point colour space and point curvature; (3) each single rock joint was extracted from the aforementioned joint sets using a density-based spatial clustering of applications with noise (DBSCAN); and (4) the orientation was determined according to the point normals of the fitting planes of the points on each detected rock joint. A dodecahedron was used to demonstrate the procedures of the rock joint detection and orientation calculation, and two outcrop cases were selected to further verify the effectiveness of the proposed method. The results of all cases indicate that the orientation difference between manual measurement and the proposed method was less than 2°. The codes that support the findings of this study have been shared publicly on GitHub (
https://github.com/DisDet/DisDetCIELAB
).
Study of the strength properties and micromechanisms of nano-Al
2
O
3
-modified predisintegrated carbonaceous mudstone based on orthogonal design
Authors: Fu Hong-yuan , Yu Xiao-wei , Liu Jie , Zeng Ling , Chen Xiao-wei
Published: July 2023

This study aimed to improve the mechanical properties of predisintegrated carbonaceous mudstone (PCM) used as an embankment fill. The four factors used in the orthogonal design test were nano-Al
2
O
3
content, cement content, water content and compaction. After the tests were completed the strength characteristics and micromechanisms of PCM modified by nano-Al
2
O
3
and cement were studied using triaxial compression tests, X-ray diffraction analysis and SEM observations. The results show that the failure mode of PCM changes from bulging failure to shear failure when the nano-Al
2
O
3
and cement contents are increased. The order in which the factors affected the cohesion of PCM is cement content, nano-Al
2
O
3
content, water content and compaction. At a given cement content, the cohesion of PCM with an optimal compaction of 96% and a water content of 8% increases and then decreases with increasing nano-Al
2
O
3
content. The increase in the internal friction angle is proportional to the nano-Al
2
O
3
content when the cement content is between 0 and 4%. Controlling the nano-Al
2
O
3
and cement contents to 0.3 and 8%, respectively, results in a synergistic effect of both materials on the shear strength. Nano-Al
2
O
3
improves the cohesion and friction strength of PCM by accelerating the hydration of cement and optimizing the structure of the hydration products.
ACM WSDM 2023 Report
Authors: Lauw Hady W. , Chua Tat-Seng , Si Luo , Terzi Evimaria , Tsaparas Panayiotis , Tomkins Andrew
Published: July 2023

The 16th ACM International Conference on Web Search and Data Mining (WSDM 2023) was successfully held on 2/27 - 3/3/2023 at Carlton Hotel, Singapore. It was held as in-person conference that also featured rich virtual elements. The five-day event began with tutorials and Industry Day. The middle three days were dedicated to keynote speeches, single-session presentations, poster reception, and demo sessions. The final day was event-filled with workshops, WSDM Cup Day, Doctoral Consortium, and Smart City Day. This brief report provides an overview of WSDM 2023 with organization and program details and statistics from Conference Chairs and Program Committee Chairs, as well as a message from the WSDM Steering Committee Chair. Further details can be found at https://www.wsdm-conference.org/2023/. At the conclusion of this report, we express our deep gratitude to authors, volunteers, special interest groups (SIGs), steering committee, sponsors and supporters.
How Flexible is CXL's Memory Protection?
Authors: Stark Samuel W. , Markettos A. Theodore , Moore Simon W.
Published: July 2023

CXL, a new interconnect standard for cache-coherent memory sharing, is becoming a reality - but its security leaves something to be desired. Decentralized capabilities are flexible and resilient against malicious actors, and should be considered while CXL is under active development.
Attribution and Obfuscation of Neural Text Authorship: A Data Mining Perspective
Authors: Uchendu Adaku , Le Thai , Lee Dongwon
Published: July 2023

Two interlocking research questions of growing interest and importance in privacy research are Authorship Attribution (AA) and Authorship Obfuscation (AO). Given an artifact, especially a text t in question, an AA solution aims to accurately attribute t to its true author out of many candidate authors while an AO solution aims to modify t to hide its true authorship. Traditionally, the notion of authorship and its accompanying privacy concern is only toward human authors. However, in recent years, due to the explosive advancements in Neural Text Generation (NTG) techniques in NLP, capable of synthesizing human-quality openended texts (so-called "neural texts"), one has to now consider authorships by humans, machines, or their combination. Due to the implications and potential threats of neural texts when used maliciously, it has become critical to understand the limitations of traditional AA/AO solutions and develop novel AA/AO solutions in dealing with neural texts. In this survey, therefore, we make a comprehensive review of recent literature on the attribution and obfuscation of neural text authorship from a Data Mining perspective, and share our view on their limitations and promising research directions.
SIGCSE Board DEIA Update
Authors: Clear Alison , Becker Brett A. , Denner Jill , Garcia Dan , Duran Rodrigo , Rankin Yolanda A. , Sheard Judy , Decker Adrienne
Published: July 2023

The SIGCSE board is committed to creating a welcoming, safe, and inclusive environment for all members of the SIGCSE community. As stated in our email on October 7th 2022: "The SIGCSE Board is taking these matters very seriously and is working on specific next steps and a timeline for addressing them. We are committed to developing ways forward to ensure the safety and respect of all members of the SIGCSE community."
Characteristics Comparison of Nanochannel GaN-on-Si and GaN-on-SiC HEMTs
Authors: Lai Yu-Jun , Liu Yu-Chen , Hsu Yung-Feng , Wu Meng-Chyi
Published: July 2023

A comparative investigation on device characteristics of GaN-on-Si and GaN-on-SiC high electron mobility transistors (HEMTs) fabricated with the gate lengths of 175, 150, and 125 nm is conducted. The device performance of the HEMTs is evaluated through DC current-voltage, small-signal, and large-signal measurements. The HEMTs with 125 nm gate length exhibit better characteristics than the HEMTs with other gate lengths. Besides, obvious increases of maximum transconductance (Gm), drain current density (JD), on/off current ratio, cutoff frequency (fT), maximum oscillation frequency (fmax), power gain, and power-added efficiency (PAE) are observed for GaN-on-SiC HEMTs as compared with those for the GaN-on-Si HEMTs. The GaN-on-SiC HEMT with a gate length of 125 nm delivers a maximum Gm of 299 mS mm−1, a JD larger than 1.1 A mm−1, an on/off current ratio of 3.8 × 104, a fT of 59.4 GHz, a fmax of 62.3 GHz, a power gain of 17.6 dB, and PAE of 63.8%, which make it promising for RF power amplifier application.
Integrating Physical Activity Strategies to Lower Hyperglycaemia in Structured Education Programmes for Children and Young People with Type 1 Diabetes Improves Glycaemic Control without Augmenting the Risk of Hypoglycaemia
Authors: Pemberton John Stuart , Gupta Ankita , Lau Gar Mun , Dickinson India , Iyer Pranav Viswanath , Uday Suma
Published: July 2023

Objectives. Investigate the effect of using short bursts of moderate-intensity activity between meals to lower hyperglycaemia on glucose metrics. Design and Methods. Children and young people with type 1 diabetes (CYPD) attending continuous glucose monitoring education were taught to use moderate-intensity activity to lower high glucose levels (to <10.0 mmol/L using 10–15 minlowers ∼2.0 mmol/L) between meals. Retrospective cross-sectional data analysis of CYPD at a single tertiary centre between 2019 and 2022. Data were collected on demographics and glucose metrics (HbA1c, time in range (TIR, 3.9–10.0 mmol/L), time above range (TAR, >10.0 mmol/L), time below range (TBR, <3.9 mmol/L)). Minutes of activity usually performed to lower a glucose level of 14.0 mmol/L trending steady at 6 months grouped the CYPD into low (<5 min), mild (5–10 min), or moderate (11–20 min) activity groups. Results. 125 (n = 53, 40% male) CYPD with a mean (standard deviations) age of 12.3 (±3.7) years and diabetes duration of 7.0 ± 3.7 years were included. HbA1c improved from 58.5 (±8.6) mmol/mol at baseline to 54.9 (±7.2) mmol/mol at 6 months (

p
<
0.001

). Low, mild, and moderate activity was reported by 30% (n = 37), 34% (n = 43), and 36% (n = 45), respectively. At 6 months, HbA1c (52.0 vs. 54.3 vs. 59.4 mmol/mol,

p
<
0.001

), TIR (68.0% vs. 59.71 vs. 51.1%,

p
<
0.001

) and TAR (29.9% vs. 38.3% vs. 45.3%,

p
<
0.001

) were significantly different across the moderate, mild, and low activity groups, respectively. No association was found for TBR (2.16% vs. 2.32% vs. 2.58%,

p
=
0.408

) across groups. Conclusion. Increasing the use of moderate-intensity activity to lower hyperglycaemia between meals is associated with improved glucose control without increasing hypoglycaemia for CYPD.
Association between Polyunsaturated Fatty Acid Profile and Bronchial Inflammation in Bronchiolitis Obliterans
Authors: Jerkic Silvija P. , Bächle Laura , Duecker Ruth Pia , Gronau Lucia , Chiocchetti Andreas G. , Zielen Stefan , Schubert Ralf
Published: July 2023

Introduction. Bronchiolitis obliterans (BO) is a chronic lung disease, which occurs after an insult to the lower airways, in particular after airway infections or after stem cell transplantation, and which results in persistent inflammation. N–3 and n–6 polyunsaturated fatty acids (PUFA) have been shown to influence the inflammatory processes in chronic inflammatory conditions. Since BO is maintained by persistent pulmonary inflammation, a disbalanced n–6/n–3 fatty acid profile could support the inflammatory process in patients with BO and therefore, could become an approach to new therapeutic options. Methods. Twenty-five patients with BO (age: 13; 7–39) and 26 healthy controls (age: 19; 7–31) participated in the study. Lung function (forced viral capacity (FVC), forced expiratory volume 1 (FEV1), residual volume (RV)), and lung clearance index (LCI) were measured. Induced sputum was analyzed for cytology and cytokine levels (IL-1ß, IL-6, IL-8, TNF-α) using cytometric bead array (CBA). The PUFA profile was determined in the serum and induced sputum by gas chromatography. Results. Patients presented with significantly lower FVC and FEV1 as well as higher RV and LCI measurements compared to the control group. Apart from a massive airway inflammation indicated by elevated numbers of total cells and neutrophils, the CBA analysis showed significantly increased levels of IL-1β, IL-6, and IL-8. The analysis of PUFA in sputum and serum revealed a significant difference in the ratio between the n–6 PUFA arachidonic acid (AA) and the n–3 PUFA docosahexaenoic acid (DHA) (AA : DHA). Furthermore, the AA : DHA ratio significantly correlated with the inflammatory cytokines in induced sputum. Conclusion. Lung function in BO is significantly impaired and associated with uncontrolled neutrophil-dominated airway inflammation. Furthermore, the imbalance in the AA/DHA ratio in favor of n–6 PUFA demonstrates a pro-inflammatory microenvironment in the cell membrane, which correlates with the inflammatory cytokines in induced sputum and might be an option for an anti-inflammatory therapy in BO.
Assessing 3D Seismic Plastic Damages of Arch Dams Considering Optimum Mesh Spaces Based on FOS Analyses and 2023 Kahramanmaraş, Hatay, Malatya, and Gaziantep Earthquakes in Turkey
Authors: Cavuslu Murat , Dagli Emrah
Published: July 2023

In this paper, the three-dimensional (3D) seismic plastic damage performance of the Ermenek Arch Dam (220 m), which was built in Karaman, Turkey, in 2009, is investigated by including different gallery spaces. 3D modeling of the dam is performed using the finite-difference method, and four various gallery spaces are added to the dam model considering their original oval geometries. WIPP-Drucker (WD) material model is utilized for the dam’s concrete material in creep and seismic damage analyses. Moreover, the Mohr–Coulomb material model is utilized for the foundation. Quiet nonreflecting and free-field boundary conditions are taken into account in the earthquake analyses, and reflecting (fix) boundary condition is used in the factor of safety (FOS) analyses in order to minimize the reflection of earthquake waves at the boundaries. First, the FOS analyses of the Ermenek Dam are performed considering the WD material model, and the optimum mesh space is determined according to FOS analyses. Then, 3D earthquake analyses are performed for 10 important strong ground motions that occurred in Kahramanmaraş, Hatay, Malatya, and Gaziantep in 2023. As a result of the FOS analyses, it is suggested that the mesh length of arch dams should not be chosen randomly while performing the earthquake analyses, and the FOS analyses of arch dams should be carried out using the WD material model before choosing the mesh space. Besides, it is concluded that selected ground motions for seismic analyses have created significant plastic damage around the galleries of the Ermenek Arch Dam, and gallery spaces are of great importance for the seismic plastic damage behavior of arch dams.
Electrohydraulic Servo Shaker Control Based on the Single Layer Flexible Structure Load
Authors: Wang Tao , Song Jinchun
Published: July 2023

As a kind of equipment commonly applied in laboratory vibration test simulation, the shaker has been widely used in many important fields of scientific research on experimental engineering vibration. It is employed for the numerical simulation of seismic activities of large buildings to quickly and quantitatively detect and calculate building components related to different building forces, analyze and study various changes of on-site structural forms and the influence mechanism of common earthquake damages or deformations with the actual existence of large-scale seismic activities, as well as to test the antiseismic strengthening structure of buildings to reduce the impact of destructive earthquakes on buildings losses. In general, the load of the shaker is regarded as a rigid structure. But in terms of the load of an electrohydraulic servo shaker with a flexible structure, the system control tends to be nonlinear accompanied by the output signals distorted. In order to achieve the goal of improving the waveform accuracy of shaking tables, it is necessary to combine the corresponding control algorithm strategy. Hence, in compliance with the working principles and functions of shaking table systems, the reasons for the coupling between flexible structure loads and shaking tables are carefully analyzed in this paper. Meanwhile, a control strategy based on the Luenberger observer control method is proposed to effectively realize the coupling suppression within the system and make the output signals of the shaking table reach the required accuracy. Finally, by comparing the frequency characteristic curves of the system before and after the introduction of the Luenberger observer, as well as the output and input analog signals, it can be seen that the Luenberger observer can effectively suppress the impact of oscillations within the system and reproduce the accuracy of the input signals.
Supplementary Table 4_Marker genes all and some per cluster_GO and curated pathways per cluster from A Rare Subset of Primary Tumor Cells with Concomitant Hyperactivation of Extracellular Matrix Remodeling and dsRNA-IFN1 Signaling Metastasizes in Breast Cancer
Authors: Roda Niccolò , Cossa Andrea , Hillje Roman , Tirelli Andrea , Ruscitto Federica , Cheloni Stefano , Priami Chiara , Dalmasso Alberto , Gambino Valentina , Blandano Giada , Polazzi Andrea , Falvo Paolo , Gatti Elena , Mazzarella Luca , Luzi Lucilla , Migliaccio Enrica , Pelicci Pier Giuseppe
Published: July 2023

Supplementary Table including Marker genes (ALL and SOME settings) per cluster and GO and curated pathways per cluster
Supplementary Table 3_Clonal distribution analysis from A Rare Subset of Primary Tumor Cells with Concomitant Hyperactivation of Extracellular Matrix Remodeling and dsRNA-IFN1 Signaling Metastasizes in Breast Cancer
Authors: Roda Niccolò , Cossa Andrea , Hillje Roman , Tirelli Andrea , Ruscitto Federica , Cheloni Stefano , Priami Chiara , Dalmasso Alberto , Gambino Valentina , Blandano Giada , Polazzi Andrea , Falvo Paolo , Gatti Elena , Mazzarella Luca , Luzi Lucilla , Migliaccio Enrica , Pelicci Pier Giuseppe
Published: July 2023

Supplementary Table including the information about Clonal distribution analysis
Supplementary Figures and legends from A Rare Subset of Primary Tumor Cells with Concomitant Hyperactivation of Extracellular Matrix Remodeling and dsRNA-IFN1 Signaling Metastasizes in Breast Cancer
Authors: Roda Niccolò , Cossa Andrea , Hillje Roman , Tirelli Andrea , Ruscitto Federica , Cheloni Stefano , Priami Chiara , Dalmasso Alberto , Gambino Valentina , Blandano Giada , Polazzi Andrea , Falvo Paolo , Gatti Elena , Mazzarella Luca , Luzi Lucilla , Migliaccio Enrica , Pelicci Pier Giuseppe
Published: July 2023

Supplementary Figures 1 to 6 and corresponding legends
Table S5 from Caffeine Supplementation and FOXM1 Inhibition Enhance the Antitumor Effect of Statins in Neuroblastoma
Authors: Tran Gia-Buu , Ding Jane , Ye Bingwei , Liu Mengling , Yu Yajie , Zha Yunhong , Dong Zheng , Liu Kebin , Sudarshan Sunil , Ding Han-Fei
Published: July 2023

Go analysis of genes up-regulated by simvastatin
Supplementary Table S2 from Caffeine Supplementation and FOXM1 Inhibition Enhance the Antitumor Effect of Statins in Neuroblastoma
Authors: Tran Gia-Buu , Ding Jane , Ye Bingwei , Liu Mengling , Yu Yajie , Zha Yunhong , Dong Zheng , Liu Kebin , Sudarshan Sunil , Ding Han-Fei
Published: July 2023

Simvastatin responsive genes
Supplementary Data from Caffeine Supplementation and FOXM1 Inhibition Enhance the Antitumor Effect of Statins in Neuroblastoma
Authors: Tran Gia-Buu , Ding Jane , Ye Bingwei , Liu Mengling , Yu Yajie , Zha Yunhong , Dong Zheng , Liu Kebin , Sudarshan Sunil , Ding Han-Fei
Published: July 2023

Supplementary Figures S1-S7
Table S1 from TGFβ Antagonizes IFNγ-Mediated Adaptive Immune Evasion via Activation of the AKT–Smad3–SHP1 Axis in Lung Adenocarcinoma
Authors: Ye Fan , Cai Zihao , Wang Boyu , Zeng Chenxi , Xi Yu , Hu Shaojie , Qu Rirong , Yuan Zhiwei , Yue Jiaqi , Tian Yitao , Wang Xue , Fu Xiangning , Li Lequn
Published: July 2023

Table S1
Supplementary Data from TGFβ Antagonizes IFNγ-Mediated Adaptive Immune Evasion via Activation of the AKT–Smad3–SHP1 Axis in Lung Adenocarcinoma
Authors: Ye Fan , Cai Zihao , Wang Boyu , Zeng Chenxi , Xi Yu , Hu Shaojie , Qu Rirong , Yuan Zhiwei , Yue Jiaqi , Tian Yitao , Wang Xue , Fu Xiangning , Li Lequn
Published: July 2023

Table S2
Table S2 from MEN1 Degradation Induced by Neddylation and the CUL4B–DCAF7 Axis Promotes Pancreatic Neuroendocrine Tumor Progression
Authors: Xu Junfeng , Ye Zeng , Zhuo Qifeng , Gao Heli , Qin Yi , Lou Xin , Zhang Wuhu , Wang Fei , Wang Yan , Jing Desheng , Fan Guixiong , Zhang Yue , Chen Xuemin , Chen Jie , Xu Xiaowu , Yu Xianjun , Ji Shunrong
Published: July 2023

Clinicopathologic parameters of 50 PanNET patients
Data from A Rare Subset of Primary Tumor Cells with Concomitant Hyperactivation of Extracellular Matrix Remodeling and dsRNA-IFN1 Signaling Metastasizes in Breast Cancer
Authors: Roda Niccolò , Cossa Andrea , Hillje Roman , Tirelli Andrea , Ruscitto Federica , Cheloni Stefano , Priami Chiara , Dalmasso Alberto , Gambino Valentina , Blandano Giada , Polazzi Andrea , Falvo Paolo , Gatti Elena , Mazzarella Luca , Luzi Lucilla , Migliaccio Enrica , Pelicci Pier Giuseppe
Published: July 2023

Abstract
Metastatic breast cancer has a poor prognosis and is largely considered incurable. A better understanding of the molecular determinants of breast cancer metastasis could facilitate development of improved prevention and treatment strategies. We used lentiviral barcoding coupled to single-cell RNA sequencing to trace clonal and transcriptional evolution during breast cancer metastasis and showed that metastases derive from rare prometastatic clones that are underrepresented in primary tumors. Both low clonal fitness and high metastatic potential were independent of clonal origin. Differential expression and classification analyses revealed that the prometastatic phenotype was acquired by rare cells characterized by the concomitant hyperactivation of extracellular matrix remodeling and dsRNA-IFN signaling pathways. Notably, genetic silencing of key genes in these pathways (KCNQ1OT1 or IFI6, respectively) significantly impaired migration in vitro and metastasis in vivo, with marginal effects on cell proliferation and tumor growth. Gene expression signatures derived from the identified prometastatic genes predict metastatic progression in patients with breast cancer, independently of known prognostic factors. This study elucidates previously unknown mechanisms of breast cancer metastasis and provides prognostic predictors and therapeutic targets for metastasis prevention.
Significance:
Transcriptional lineage tracing coupled with single-cell transcriptomics defined the transcriptional programs underlying metastatic progression in breast cancer, identifying prognostic signatures and prevention strategies.
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: July 2023

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 Figure S1 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: July 2023

Supplementary Figure S1. Chemical structures of five AAs. Analytes that were monitored for isomeric separation but not quantified are indicated with an asterisk.
Supplementary Table 7 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. , Funk Michele Jonsson , Olshan Andrew F. , Gupta Parul , Barritt A. Sidney , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: July 2023

Supplementary Table 7 includes baseline characteristics of individuals with cirrhosis eligible for HCC surveillance – Medicare only (N, %) (N=32,723).
Supplementary Table 6 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. , Funk Michele Jonsson , Olshan Andrew F. , Gupta Parul , Barritt A. Sidney , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: July 2023

Supplementary Table 6 includes baseline characteristics of individuals with cirrhosis eligible for HCC surveillance – Medicaid insurance only (N, %) (N=6,790).
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. , Funk Michele Jonsson , Olshan Andrew F. , Gupta Parul , Barritt A. Sidney , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: July 2023

Supplementary Table 3 includes hypothetical examples for calculating the Proportion of Time Covered measures.
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. , Funk Michele Jonsson , Olshan Andrew F. , Gupta Parul , Barritt A. Sidney , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: July 2023

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 15 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. , Funk Michele Jonsson , Olshan Andrew F. , Gupta Parul , Barritt A. Sidney , Sanoff Hanna K. , Wheeler Stephanie B. , Moon Andrew M. , Lund Jennifer L.
Published: July 2023

Supplementary Table 15 includes one-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 2 from Updated Review of Major Cancer Risk Factors and Screening Test use in the United States, with a Focus on Changes During the COVID-19 Pandemic
Authors: Star Jessica , Bandi Priti , Nargis Nigar , Islami Farhad , Yabroff K. Robin , Minihan Adair K. , Smith Robert A. , Jemal Ahmedin
Published: July 2023

Obesity and smoking prevalence by state from 2019 to 2021.
Table S3 from Incidence Trends and Survival in Early-Onset Esophagogastric Adenocarcinoma: A Swedish Population-Based Cohort Study
Authors: Radkiewicz Cecilia , Asplund Johannes , Lagergren Jesper
Published: July 2023

Early- (20-49) and later-onset (50-99) esophagogastric adenocarcinoma age-standardized incidence rate per 100,000 person-years by calendar period and age-adjusted annual percentage change over 1993-2019, with 95% confidence intervals (CI).
Supplemental Table 1 from Estimated Ovulatory Years Prior to Menopause and Postmenopausal Endogenous Hormone Levels
Authors: Cramer Daniel W. , Vitonis Allison F. , Huang Tianyi , Shafrir Amy L. , Eliassen A. Heather , Barbieri Robert L. , Hankinson Susan E.
Published: July 2023

Supplemental Table 1: Adjusted geometric mean hormone levels by lifetime ovulatory years quartile among postmenopausal women not using hormone therapy at the time of blood draw in the Nurses' Health Study; excluding hysterectomized women whose age at menopause was n=1683
Table S1 from Incidence Trends and Survival in Early-Onset Esophagogastric Adenocarcinoma: A Swedish Population-Based Cohort Study
Authors: Radkiewicz Cecilia , Asplund Johannes , Lagergren Jesper
Published: July 2023

Esophagogastric adenocarcinoma subtypes according to the International Classification of Diseases for Oncology 2nd revision (ICD-O-2).
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: July 2023

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: July 2023

Supplementary Table S2 shows adjusted or matched covariates and sex hormone measurement methods of studies included in the meta-analysis.
Supplementary Table S11 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: July 2023

Supplementary Table S11 shows statistically significant associations between prediagnostic circulating levels of sex hormone and the risk of gastrointestinal cancer NOT included in meta-analysis.
Supplementary Figure 2 from Recent Mortality Patterns and Time Trends for the Major Cancers in 47 Countries Worldwide
Authors: Sedeta Ephrem , Sung Hyuna , Laversanne Mathieu , Bray Freddie , Jemal Ahmedin
Published: July 2023

Supplementary Figure 2. Age-standardized mortality rates per 100,000 person-years and ten-year average annual percent change in cervical cancer in 47 countries.
Supplementary Figure S7 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: July 2023

Supplementary Figure S7 shows forest plots (1), sensitivity analysis (2) and funnel plots (3) of the associations between prediagnostic circulating sex hormone levels and rectal cancer risk.
Supplementary Figure S6 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: July 2023

Supplementary Figure S6 shows forest plots (1), sensitivity analysis (2) and funnel plots (3) of the associations between prediagnostic circulating sex hormone levels and colon cancer risk.
Supplemental Table S3 from Circadian Disruption and Colorectal Cancer Incidence in Black Women
Authors: Barber Lauren E. , VoPham Trang , White Laura F. , Roy Hemant K. , Palmer Julie R. , Bertrand Kimberly A.
Published: July 2023

Characteristics of the chronotype analytic sample at the start of study follow-up according to categories of chronotype
Supplemental Figure S2 from Circadian Disruption and Colorectal Cancer Incidence in Black Women
Authors: Barber Lauren E. , VoPham Trang , White Laura F. , Roy Hemant K. , Palmer Julie R. , Bertrand Kimberly A.
Published: July 2023

Flow diagram and timeline of BWHS participants included in the chronotype analysis
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: July 2023

Descriptive characteristics among 4,403a women diagnosed with invasive breast cancer in the Pathways Cohort, 2006–2018
Supplementary Table S6 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: July 2023

Hazard Ratios and 95% Confidence Intervals for Associations of each of the 9 Components of the 2-Year Post-Diagnosis Lifestyle Score with All-Cause Mortality, Breast Cancer-Specific Mortality, and Breast Cancer Recurrence, Excluding Deaths and Recurrences Occurring within 4 Years of Diagnosis.
Supplementary Table 4 from Site-Specific Cancer Incidence by Race and Immigration Status in Canada 2006–2015: A Population-Based Data Linkage Study
Authors: Malagón Talía , Morais Samantha , Tope Parker , El-Zein Mariam , Franco Eduardo L.
Published: July 2023

Supplementary Table 4: Comparison of age-standardized incidence rates between CanCHECs and GLOBOCAN world regions of origin.
Supplementary Table S3 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: July 2023

Multivariable Cox Proportional Hazards Models for the Associations of Changes in Components of the Lifestyle Score on All-Cause Mortality and Breast Cancer Recurrence in the Pathways Study.
Supplementary Table S2 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: July 2023

Hazard ratios and 95% confidence intervals for associations of each of the 9 components of the 2-year post-diagnosis lifestyle score with all-cause mortality.
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: July 2023

Categorization of the modified baseline and 2-year post-diagnosis lifestyle scores.
Supplementary Table 1 from Site-Specific Cancer Incidence by Race and Immigration Status in Canada 2006–2015: A Population-Based Data Linkage Study
Authors: Malagón Talía , Morais Samantha , Tope Parker , El-Zein Mariam , Franco Eduardo L.
Published: July 2023

Supplementary Table 1: ICD-O-3 Topography and histology codes by cancer site
Supplementary Figure 1 from Site-Specific Cancer Incidence by Race and Immigration Status in Canada 2006–2015: A Population-Based Data Linkage Study
Authors: Malagón Talía , Morais Samantha , Tope Parker , El-Zein Mariam , Franco Eduardo L.
Published: July 2023

Supplementary Figure 1: Age-standardized incidence rates of cancer per 100,000 by racial group, comparing CanCHECs and different world regions from GLOBOCAN.
Data from Circadian Disruption and Colorectal Cancer Incidence in Black Women
Authors: Barber Lauren E. , VoPham Trang , White Laura F. , Roy Hemant K. , Palmer Julie R. , Bertrand Kimberly A.
Published: July 2023

AbstractBackground:
Animal and experimental studies suggest circadian disruption increases colorectal cancer risk, but evidence in humans is limited. We examined night shift work, chronotype, and residential position within a time zone, proxies for circadian disruption, in relation to colorectal cancer risk.
Methods:
Participants in the Black Women's Health Study, a prospective cohort of 59,000 Black American women established in 1995, reported history of night shift work and chronotype on follow-up questionnaires. Residential position within a time zone was estimated using participant addresses at each questionnaire cycle. Number of colorectal cancer cases and follow-up duration varied by analysis depending on timing of exposure assessment, ranging from 204 over the 2005 to 2018 night shift work study period to 452 over the 1995 to 2018 residential position study period. Cox proportional hazards regression was used to estimate multivariable-adjusted HRs and 95% confidence intervals (CI).
Results:
Compared with never having worked a night shift, working a night shift for ≥10 years was associated with increased colorectal cancer risk (HR = 1.64; 95% CI, 1.01–2.66). However, shorter duration was not. The HR for evening versus morning chronotype was 0.96 (95% CI, 0.73–1.27). Westward position of residence within a time zone was not associated with colorectal cancer risk (HR per 5-degree longitude increase: 0.92; 95% CI, 0.82–1.03).
Conclusions:
Our findings suggest a possible increased risk of colorectal cancer associated with long duration night shift work; however, results require confirmation in larger studies.
Impact:
Circadian disruption from long-term night shift work may contribute to colorectal cancer development in Black women.
Supplementary Table S4 from Loss of CDKN2A Cooperates with WWTR1(TAZ)–CAMTA1 Gene Fusion to Promote Tumor Progression in Epithelioid Hemangioendothelioma
Authors: Seavey Caleb N. , Hallett Andrea , Li Shuo , Che Kepeng , Pobbati Ajaybabu V. , Ma Shuang , Burtscher Ashley , Kanai Ryan , Lamar John M. , Rubin Brian P.
Published: July 2023

Supplemental Table 4. Bulk RNA sequencing of EHE cell linesDifferential gene expression between EHE cell lines and endothelial cells via DESEQ2. Overlap in transcripts that are overexpressed by EHE cells (LogFC2>2 and FDR<0.05) are listed. These overlaps were used to generate the Venn diagram in Figure 4G.