bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of Depression in People With Human Immunodeficiency Virus: A Nationwide Population-based Matched Cohort Study
Authors: Vollmond Cecilie V , Tetens Malte M , Paulsen Fie W , Gerstoft Jan , Kronborg Gitte , Johansen Isik S , Larsen Carsten S , Wiese Lothar , Dalager-Pedersen Michael , Leth Steffen , Mortensen Preben B , Lebech Anne-Mette , Obel Niels , Omland Lars H
Published: July 2023

Background

Human immunodeficiency virus (HIV) infection is associated with depression. However, previous studies have not addressed familial factors.

Methods

Nationwide, population-based, matched cohort study of people with HIV (PWH) in Denmark between 1995 and 2021 who were matched on sex and date of birth with a comparison cohort randomly selected from the Danish population. Family-related factors were examined by inclusion of siblings of those in the cohorts. We calculated hazard ratios (HRs) for depression, receipt of antidepressants, electroconvulsive therapy (ECT), and suicide, as well as the yearly proportions of study cohorts with psychiatric hospital contact due to depression and receipt of antidepressants from 10 years before to 10 years after study inclusion.

Results

We included 5943 PWH and 59 430 comparison cohort members. Median age was 38 years, and 25% were women. We observed an increased risk of depression, receipt of antidepressants, ECT, and suicide among PWH in the 2 first years of observation (HR, 3.3; 95% confidence interval [CI]: 2.5–4.4), HR, 3.0 (95% CI: 2.7–3.4), HR, 2.8 (95% CI: .9–8.6), and HR, 10.7 (95% CI: 5.2–22.2), thereafter the risk subsided but remained increased. The proportions of PWH with psychiatric hospital contact due to depression and receipt of antidepressants were increased prior to and especially after HIV diagnosis. Risk of all outcomes was substantially lower among siblings of PWH than among PWH (HR for receipt of antidepressants, 1.1; 95% CI: 1.0–1.2).

Conclusions

PWH have an increased risk of depression. Family-related factors are unlikely to explain this risk.
Electrocardiographic characteristics of right-bundle-branch-block premature ventricular complexes predicting absence of left ventricular scar in athletes with apparently structural normal heart
Authors: Calò Leonardo , Panattoni Germana , Tatangelo Mario , Brunetti Giulia , Graziano Francesca , Monzo Luca , Danza Maria Ludovica , Fedele Elisa , Grieco Domenico , Crescenzi Cinzia , Rebecchi Marco , Stazi Alessandra , Bressi Edoardo , De Ruvo Ermenegildo , Golia Paolo , Gaita Fiorenzo , Corrado Domenico , Zorzi Alessandro
Published: July 2023

Aims

Left ventricular scar is an arrhythmic substrate that may be missed by echocardiography and diagnosed only by cardiac magnetic resonance (CMR), which is a time-consuming and expensive imaging modality. Premature ventricular complexes (PVCs) with a right-bundle-branch-block (RBBB) pattern are independent predictors of late gadolinium enhancement (LGE) but their positive predictive value is low. We studied which electrocardiographic features of PVCs with an RBBB pattern are associated with a higher probability of the absence of an underlying LGE.

Methods

The study included 121 athletes (36 ± 16 years; 48.8% men) with monomorphic PVCs with an RBBB configuration and normal standard clinical investigations who underwent CMR. LGE was identified in 35 patients (29%), predominantly in those with PVCs with a superior/intermediate axis (SA-IntA) compared to inferior axis (IA) (38% vs. 10%, P = 0.002). Among patients with SA-IntA morphology, the contemporary presence of qR pattern in lead aVR and V1 was exclusively found in patients without LGE at CMR (51.0% vs. 0%, P < 0.0001). Among patients with IA, the absence of LGE correlated to a narrow ectopic QRS (145 ± 16 vs. 184 ± 27 msec, P < 0.001).

Conclusions

Among athletes with apparently idiopathic PVCs with a RBBB configuration, the presence of a concealed LGE at CMR was documented in 29% of cases, mostly in those with a SA-IntA. In our experience, the contemporary presence of qR pattern in lead aVR and V1 in PVCs with RBBB/SA-IntA morphology or, on the other hand, a relatively narrow QRS in PVCs with an IA, predicted absence of LGE.
Decreased TAX1BP1 participates in systemic lupus erythematosus by regulating monocyte/macrophage function
Authors: Qian Tian , Huo Bengang , Deng Xiaorong , Song Xiaoli , Jiang Yiwei , Yang Jurong , Hao Fei
Published: July 2023

Systemic lupus erythematosus (SLE) involves disorders of innate and adaptive immune pathways. Tax1-binding protein 1 (TAX1BP1) modulates the production of antibodies in B cells and the T-cell cycle by regulating the NF-κB signaling pathway. However, the potential association of TAX1BP1 with SLE and its role in monocytes/macrophages have not been fully elucidated. In this study, we utilized whole-exome sequencing (WES) in combination with Sanger sequencing and identified 16 gene mutations, including in TAX1BP1, in an SLE family. TAX1BP1 protein expression with western blotting detection was reduced in SLE patients and correlated with disease activity negatively. Furthermore, RNA sequencing and 4D Label-Free Phosphoproteomic analysis were employed to characterize the transcriptome and phosphoproteome profiles in THP-1 and THP-1-differentiated M1 macrophages with TAX1BP1 knockdown. Silencing of TAX1BP1 in THP-1 and THP-1-differentiated M1 macrophages led to an increase in cluster of differentiation 80 (CD80) expression and differential changes in CD14 and CD16 expression, as assessed by flow cytometry. Additionally, western blot analysis showed that knockdown of TAX1BP1 led to a reduction in TRAF6 and p-p65 in THP-1-differentiated macrophages, with or without lipopolysaccharide (LPS) or tumor necrosis factor (TNF)-α stimulation. Taken together, our findings suggest that TAX1BP1 participates in SLE activity by regulating antigen presentation in monocytes and inflammatory responses in M1 macrophages.
Light tolerance of extended spectrum β-lactamase producing Escherichia coli strains after repetitive exposure to far-UVC and blue LED light
Authors: Gardner Amanda , Soni Aswathi , Cookson Adrian , Brightwell Gale
Published: July 2023

Aims

The aim of this study was to investigate dual far-UVC (Ultraviolet-C) (222 nm) and blue LED (Light Emitting Diode) (405 nm) light on the inactivation of extended spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) and to determine if repetitive exposure to long pulses of light resulted in changes to light tolerance, and antibiotic susceptibility.

Methods and results

Antimicrobial efficiency of dual and individual light wavelengths and development of light tolerance in E. coli was evaluated through a spread plate method after exposure to light at 25 cm. Dual light exposure for 30 min resulted in a 5–6 log10 CFU mL−1 reduction in two ESBL-Ec and two antibiotic-sensitive control E. coli strains. The overall inhibition achieved by dual light treatment was always greater than the combined reductions (log10 CFU) observed from exposure to individual light wavelengths (combined 222–405 nm), indicating a synergistic relationship between blue LED and far-UVC light when used together. Repetitive long pulses of dual and individual far-UVC light exposure resulted in light tolerance in two ESBL-Ec strains but not the antibiotic-sensitive E. coli strains. Subsequent passages of repetitive light-treated ESBL-Ec strains continued to exhibit light tolerance. Antibiotic susceptibility was determined through a standard disk diffusion method. No changes were observed in the antibiotic susceptibility profiles for any of the four strains after exposure to either dual or individual wavelengths.

Conclusions

Dual light exposure was effective in the disinfection of ESBL-Ec in solution; however, antibiotic-resistant E. coli were able to develop light tolerance after repetitive exposure to light.
Profiteers of Misery
Authors: Pizzi Jeremy
Published: July 2023

Since its hailing as the ‘supreme international crime’ during the Nuremberg Trials, aggression has largely been neglected relative to other core international crimes. However, the escalation of the Russo-Ukrainian War starting in early 2022 is being held as an opportunity to breathe new life into this de facto dormant norm. This article seeks to address novel concerns as to the scope of liability permitted by the crime of aggression, which arise from Russia’s enthusiastic use of private military and security companies (PMSCs) in this conflict. It first overviews the relevant terminology applicable to the use of private armed personnel. It then asserts the value of pursuing accountability for both aggression and PMSCs. The article continues by evaluating the requirements of aggression’s ‘leadership element’, which seeks to restrict liability to high-level leaders. As an illustrative case study, it applies this to the Wagner Group’s military operations in Ukraine. This article confirms that senior corporate officers of PMSCs may, in principle, satisfy the leadership requirement of aggression, opening up the door for their liability and urging closer scrutiny of such matters.
A novel human papillomavirus and host DNA methylation score and detection of cervical adenocarcinoma
Authors: Gradissimo Ana , Clarke Megan A , Xue Xiaonan , Castle Philip E , Raine-Bennett Tina R , Schiffman Mark , Wentzensen Nicolas , Strickler Howard D , Burk Robert D
Published: July 2023

Background

The widespread introduction of Pap testing in the 1960s was followed by substantial reductions in the incidence of cervical squamous cell cancer (SCC). However, the incidence of cervical adenocarcinoma (ADC) did not decrease, likely because of low Pap test sensitivity for ADC and adenocarcinoma in situ (AIS). This study assessed a novel human papillomavirus (HPV) and host DNA Methylation Score for AIS and ADC screening.

Methods

We measured methylation levels at CpG sites in the L2/L1 open reading frames of HPV16, HPV18, and HPV45—as well as 2 human loci, DCC and HS3ST2. Specifically, we tested exfoliated cervicovaginal cells from women in the HPV Persistence and Progression (PaP) cohort who were positive for 1 of HPV16, 18, or 45, including: 1) 176 with AIS/ADC, 2) 353 with cervical intraepithelial neoplasia–3 (CIN3) or SCC, and 3) controls who either cleared (HPV-Clearers; n = 579) or had persistent HPV16, 18, or 45 infection (HPV-Persisters; n = 292). CpG site–specific methylation percentages were measured using our reported next-generation methods. The Methylation Score was the average methylation percentage across all 35 CpG sites tested.

Results

Each individual CpG site had higher methylation percentages in exfoliated cervicovaginal cells collected from patients with AIS/ADC, and as well as those with CIN3/SCC, relative to either control group (weakest P  = .004). The Methylation Score for AIS/ADC had a sensitivity of 74% and specificity of 89%. The multivariate odds ratio (OR) between the Methylation Score (4th vs 1st quartile) for AIS/ADC was ORq4-q1 = 49.01 (PBenjamini-Hochberg = 4.64E-12), using HPV-Clearers as controls. CIN3/SCC had similar, albeit weaker, associations with the Methylation Score.

Conclusions

HPV16/18/45-infected women with Methylation Scores in the highest quartile had very high odds of AIS/ADC, suggesting they may warrant careful histologic evaluation of the cervical transition zone (eg, conization or loop electrosurgical excision procedure [LEEP]).
Development of a new Phobos spectral simulant: spectral properties from visible to the mid-infrared range
Authors: Wargnier Antonin , Poggiali G , Doressoundiram A , Gautier T , Beck P , Buch A , Ruscassier N , Fornasier S , Barucci M A
Published: July 2023

Phobos is the target of the Martian Moons eXploration (MMX), the next sample return mission of the Japanese space agency (JAXA). The mission will investigate the origin of Phobos and Deimos – the two martian moons, using a suite of dedicated instruments. Infrared analysis of the surface composition will be performed by the MIRS spectrometer onboard MMX. Within the scientific studies performed in preparation for the mission, we developed a new laboratory spectral simulant that well reproduces the red and featureless spectrum of Phobos. Our results show that a visible and near-infrared simulant can be developed using dark, opaque materials such as anthracite and coal to reduce the reflectance and absorption features. To investigate the reliability of our proposed simulant in terms of composition and mineralogy, we discussed the similarities and differences in the mid-infrared (MIR) range between our laboratory simulant and some past observations acquired on Phobos. Spectra with different observation geometries were also acquired for our simulant, which give information about grain size and textures of the surface. The simulant developed in our study presents a better match for the Phobos spectrum in the visible and near-infrared compared to the previously proposed simulants.
ketju – resolving small-scale supermassive black hole dynamics in gadget-4
Authors: Mannerkoski Matias , Rawlings Alexander , Johansson Peter H , Naab Thorsten , Rantala Antti , Springel Volker , Irodotou Dimitrios , Liao Shihong
Published: July 2023

We present the new public version of the ketju supermassive black hole (SMBH) dynamics module, as implemented into gadget-4. ketju adds a small region around each SMBH where the dynamics of the SMBHs and stellar particles are integrated using an algorithmically regularized integrator instead of the leapfrog integrator with gravitational softening used by gadget-4. This enables modelling SMBHs as point particles even during close interactions with stellar particles or other SMBHs, effectively removing the spatial resolution limitation caused by gravitational softening. ketju also includes post-Newtonian (PN) corrections, which allows following the dynamics of SMBH binaries to sub-parsec scales and down to tens of Schwarzschild radii. Systems with multiple SMBHs are also supported, with the code also including the leading non-linear cross terms that appear in the PN equations for such systems. We present tests of the code showing that it correctly captures, at sufficient mass resolution, the sinking driven by dynamical friction and binary hardening driven by stellar scattering. We also present an example application demonstrating how the code can be applied to study the dynamics of SMBHs in mergers of multiple galaxies and the effect they have on the properties of the surrounding galaxy. We expect that the presented ketju SMBH dynamics module can also be straightforwardly incorporated into other codes similar to gadget-4, which would allow coupling small-scale SMBH dynamics to the rich variety of galactic physics models that exist in the literature.
The impact of rare events on the chemical enrichment in dwarf galaxies
Authors: Fukagawa Nao , Prantzos Nikos
Published: July 2023

In the environments where the abundance of heavy elements is low, rare events are expected to impact the chemical enrichment. Dwarf galaxies have small masses, low average metallicities and in general low star formation rates, and thus investigating the chemical enrichment provides understanding on the impact of each source of elements on the chemical abundance. Using a chemical evolution model in which the rarity is introduced, we investigate the impact of rare events on the chemical enrichment for Local Group dwarf galaxies. In the model, the occurrence of individual sources of elements is estimated with the star formation history derived by the colour–magnitude diagram. The abundance ratios of trans-iron elements to iron predicted by the model show the oscillation at the lowest metallicities because of the r-process events. In the case of a galaxy of a lower mass, the oscillation caused by neutron star mergers is also seen at higher metallicities, which suggests that the rarity can be important in lower-mass systems. Regarding the source of the chemical enrichment, we observe that the r-process sites seem to contribute more to the production of trans-iron elements at low metallicities, but massive stars of different rotating velocities also contribute to create part of the dispersion of the abundance ratios through the s-process. Both observational and theoretical data, including nucleosynthesis calculations and the chemical abundance of metal-poor stars, are needed to obtain deeper insights into the sources of the chemical enrichment at low metallicities.
The impact of black hole scaling relation assumptions on the mass density of black holes
Authors: Matt Cayenne , Gültekin Kayhan , Simon Joseph
Published: July 2023

We examine the effect of supermassive black hole (SMBH) mass scaling relation choice on the inferred SMBH mass population since redshift z ∼ 3. To make robust predictions for the gravitational wave background (GWB), we must have a solid understanding of the underlying SMBH demographics. Using the SDSS and 3D-HST + CANDELS surveys for 0 < z < 3, we evaluate the inferred SMBH masses from two SMBH–galaxy scaling relations: MBH–Mbulge and MBH–σ. Our SMBH mass functions come directly from stellar mass measurements for MBH–Mbulge, and indirectly from stellar mass and galaxy radius measurements along with the galaxy mass fundamental plane for MBH–σ. We find that there is a substantial difference in predictions especially for z > 1, and this difference increases out to z = 3. In particular, we find that using velocity dispersion predicts a greater number of SMBHs with masses greater than 109 M⊙. The GWB that pulsar timing arrays find evidence for is higher in amplitude than expected from GWB predictions which rely on high-redshift extrapolations of local SMBH mass–galaxy scaling relations. The difference in SMBH demographics resulting from different scaling relations may be the origin for the mismatch between the signal amplitude and predictions. Generally, our results suggest that a deeper understanding of the potential redshift evolution of these relations is needed if we are to draw significant insight from their predictions at z > 1.
The effect of restrictive fluid management on outcomes among geriatric hip fractures: a retrospective cohort study at five level I trauma centers
Authors: Willis Jordan , Jarvis Stephanie , Berg Gina M. , Corrigan Chad , Madayag Robert , Reynolds Cassandra , Tanner Allen , Marshall Gary , Palacio Lascano Carlos , Bar-Or David
Published: July 2023

Objective:

Restrictive fluid management (RFM) for hemodynamically unstable trauma patients has reduced mortality rates. The objective was to determine whether RFM benefits geriatric hip fracture patients, who are usually hemodynamically stable.

Design:

Retrospective propensity-matched study.

Setting:

Five Level I trauma centers (January 1, 2018–December 12, 2018).

Patients:

Geriatric patients (65 years or older) with hip fractures were included in this study. Patients with multiple injuries, nonoperative management, and preoperative blood products were excluded.

Intervention:

Patients were grouped by fluid volume (normal saline, lactated Ringer, dextrose, electrolytes, and medications) received preoperatively or ≤24 hours of arrival; patients with standard fluid management (SFM) received ≥150 mL and RFM <150 mL of fluids.

Main Outcome Measurements:

The primary outcomes were length of stay (LOS), delayed ambulation (>2 days postoperatively), and mortality. Paired Student t-tests, Wilcoxon paired rank sum tests, and McNemar tests were used; an α value of < 0.05 was considered statistically significant.

Results:

There were 523 patients (40% RFM, 60% SFM); after matching, there were 95 patients per arm. The matched patients were well-balanced, including no difference in time from arrival to surgery. RFM and SFM patients received a median of 80 mL and 1250 mL of preoperative fluids, respectively (P< 0.001). Postoperative fluid volumes were 1550 versus 2000 mL, respectively, (P= 0.73), and LOSs were similar between the two groups (5 versus 5 days,P= 0.83). Mortality and complications, including acute kidney injuries, were similar. Delayed ambulation rates were similar overall. When stratified by preinjury ambulation status, SFM was associated with delayed ambulation for patients not walking independently before injury (P= 0.01), but RFM was not (P= 0.09).

Conclusions:

RFM seems to be safe in terms of laboratory results, complications, and disposition. SFM may lead to delayed ambulation for patients who are not walking independently before injury.
Instrument validation of the consumers’ religio-spiritual insights in context of advertising during religious festivals
Authors: Ansari Junaid , Hyder Syed Irfan
Published: July 2023

Purpose

This paper aims to understand the religio-spiritual insights of the consumers and investigate their relationship with the consumers’ attitude towards advertising and its antecedents. Religious festivals, such as Ramadan, are celebrated with high religio-spiritual contemplations, which are often targeted by intensive marketing campaigns. During these religious festivals, consumers’ attitude toward advertising is influenced when television commercials contain “unnecessary” entertainment, “inappropriate casting” of celebrities with less credibility, “cluttered” information, “phony claims” related to good for economy and “annoying content” increasing consumers’ irritation.

Design/methodology/approach

This study developed a higher-order construct of religio-spiritual insights and used “Theory of Reasoned Action” for measuring the effect of religio-spiritual insights on consumers’ attitude toward advertising. Exploratory sequential mixed methods research design was used to develop and validate the instrument. A total of 30 semi-structured interviews were conducted during i-depth analysis phase to generate themes and questionnaire. During instrument validation phase, 839 Muslim consumers were surveyed by using the questionnaire, and instrument was validated by using the co-variance-based structural equation modeling approach.

Findings

This study develops and validates the instrument of religio-spiritual insights and identifies its significant direct and mediating effects between the consumer’s attitude toward advertising and its determinants.

Originality/value

The newly developed instrument of religio-spiritual insights is based on six dimensions, namely, “beliefs and practices,” “association with higher power,” “interconnectedness,” “self-actualization,” “heart and mind involvement,” “knowledge and meanings.” This instrument of religio-spiritual insights was validated and then tested by using a conceptual framework based on the several variables, such as attitude toward advertising, irritation, good for economy, entertainment, credibility and information.
Gender‐affirming care in the assessment and treatment of psychosis risk: Considering minority stress in current practice and future research
Authors: Ceccolini Christopher J. , Green James B. , Friedman‐Yakoobian Michelle S.
Published: July 2023

Introduction

Although research has documented the marked disparities in rates of psychosis‐spectrum diagnoses in various socially marginalized populations, there is limited research addressing the needs of gender expansive individuals in the context of psychosis‐spectrum illnesses using a minority stress lens. As clinical high‐risk for psychosis (CHR‐p) assessment and treatment becomes accessible to increasingly diverse populations, there is a need for clinicians to demonstrate greater clinical competency working with individuals across diverse social backgrounds and identities.

Methods

We examined rates of gender expansive (GE) patients seeking evaluation at an urban‐based CHR‐p clinic and compared the diagnostic profile of GE individuals to cisgender patients. Post‐hoc analyses were conducted on clinical variables with significant differences between the cisgender and GE groups.

Results

The proportion of GE patients seeking evaluation increased from 2017 (9.3%) to 2021 (16.7%). Compared to cisgender youth, GE patients had significantly higher depressive, social anxiety, borderline personality disorder symptoms, higher levels of suicidality and non‐suicidal self‐injurious behaviour, and lower role functioning. Gender identity was predictive of suicidality controlling for social anxiety, borderline symptoms, and role functioning.

Conclusions

We review implications for CHR‐p treatment and discuss ways to integrate minority stress theory and gender‐affirming practices into coordinated specialty care for CHR‐p patients.
Hungry Lotka–Volterra lattice under nonzero boundaries, block‐Hankel determinant solution, and biorthogonal polynomials
Authors: Chen Xiao‐Min , Yan An‐Hui
Published: July 2023

In this paper, we first extend the hungry Lotka–Volterra lattice to a case of nonzero boundary conditions and present its corresponding exact solution expressed in terms of a block‐Hankel determinant. Then, we establish a connection between this hungry Lotka–Volterra lattice under nonzero boundary conditions and a set of biorthogonal polynomials. It turns out that the hungry Lotka–Volterra lattice under nonzero boundary conditions possesses a Lax pair expressed in terms of the biorthogonal polynomials. Moreover, we consider two special cases of the hungry Lotka–Volterra lattice. For the case , it reduces to the Lotka–Volterra lattice under nonzero boundary condition, which has been discussed in literature. We also present the result for in detail, which extends a known result to a case of nonzero boundary functions. All these results are obtained by virtue of Hirota's bilinear method and determinant techniques.
Uniqueness and some related estimates for Dirichlet problem with fractional Laplacian
Authors: Li Congming , Liu Chenkai
Published: July 2023

The non‐uniqueness of solutions of basic Dirichlet‐type problems is a surprising feature of the fractional Laplace equation. This paper establishes a somewhat sharp uniqueness condition for the fractional Laplace equation. We derive the ‐estimate for fractional Laplacian operators to better understand this phenomenon. We introduce several naturally weighted fractional Sobolev spaces and establish embedding relationships among them. These existence‐uniqueness conditions and the spaces we introduce here are intrinsically related to the fractional Laplacian and provide basic information for studying related problems.
MSME Promotion, Inequality and Decentralized Wealth Creation: A Strategic Policy Perspective
Authors: Royal Saransh , Singh Kamaljit , Chander Ramesh
Published: July 2023

The study aims to ascertain the impact of micro, small and medium enterprises (MSMEs) growth on wealth creation and its distribution in India concerning macroeconomic variables such as GDP (Gross Domestic Product) per capita, unemployment, Foreign direct investment (FDI), human development index (HDI) and the urban population (URP). The research has examined the underlying short-term association using ECM, FMOLS, DOLS and CCR to estimate the long-run association between the identified variables. It documents a positive relationship between the share of the B50 populace and the FDI. On the other hand, per capita GDP, in the long run, had a negative association with MSME share, URP and HDI. Similarly, for the top 10 percentile (T10) share, there was a positive relationship between MSME share and URP. Therefore, the results document a decentralized wealth creation for an MSME-focused development strategy in the short run to address skewed wealth creation in emerging societies.
Supplemental Table 3 from Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Authors: Edwards Kathryn C. , Khan Asia , Sharma Eva , Wang Lanqing , Feng June , Blount Benjamin C. , Sosnoff Connie S. , Smith Danielle M. , Goniewicz Maciej L. , Pearson Jennifer , Villanti Andrea C. , Delnevo Cristine D. , Bover-Manderski Michelle T. , Hatsukami Dorothy K. , Niaura Raymond , Everard Colm , Kimmel Heather L. , Duffy Kara , Rostron Brian L. , Del Valle-Pinero Arseima Y. , van Bemmel Dana M. , Stanton Cassandra A. , Hyland Andrew
Published: July 2023

Supplemental Table 3 provides prevalence rates of any tobacco use using cotinine cut-points.
Supplementary Table 2 from Sex-specific Associations between Body Mass Index and Thyroid Cancer Incidence among Korean Adults
Authors: Kim Kyoung-Nam , Kim Kyungsik , Lee Sangjun , Park Sue K.
Published: July 2023

Supplementary Table 2 shows the associations between body mass index (BMI) and thyroid cancer incidence in the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS) using the Western BMI cutoff
Table S7 from Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci
Authors: Lai John , Wong Chi Kuen , Schmidt Daniel F. , Kapuscinski Miroslaw K. , Alpen Karen , MacInnis Robert J. , Buchanan Daniel D. , Win Aung K. , Figueiredo Jane C. , Chan Andrew T. , Harrison Tabitha A. , Hoffmeister Michael , White Emily , Le Marchand Loic , Pai Rish K. , Peters Ulrike , Hopper John L. , Jenkins Mark A. , Makalic Enes
Published: July 2023

Supplementary Table S7 shows the number of risk regions that are common to both CCFR and GECCO datasets in stage 1 DEPTH analysis, as well as whether they are detected by logistic regression analysis or were in previous CRC GWAS studies.
Supplementary Table 1 from Sex-specific Associations between Body Mass Index and Thyroid Cancer Incidence among Korean Adults
Authors: Kim Kyoung-Nam , Kim Kyungsik , Lee Sangjun , Park Sue K.
Published: July 2023

Supplementary Table 1 shows the characteristics of the cohort participants and incident thyroid cancer cases in the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS) and the Korean Multi-center Cancer Cohort (KMCC)
Table S6 from Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci
Authors: Lai John , Wong Chi Kuen , Schmidt Daniel F. , Kapuscinski Miroslaw K. , Alpen Karen , MacInnis Robert J. , Buchanan Daniel D. , Win Aung K. , Figueiredo Jane C. , Chan Andrew T. , Harrison Tabitha A. , Hoffmeister Michael , White Emily , Le Marchand Loic , Pai Rish K. , Peters Ulrike , Hopper John L. , Jenkins Mark A. , Makalic Enes
Published: July 2023

Supplementary Table S6 shows the number of risk regions identified by first stage DEPTH analysis.
Table S1 from Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci
Authors: Lai John , Wong Chi Kuen , Schmidt Daniel F. , Kapuscinski Miroslaw K. , Alpen Karen , MacInnis Robert J. , Buchanan Daniel D. , Win Aung K. , Figueiredo Jane C. , Chan Andrew T. , Harrison Tabitha A. , Hoffmeister Michael , White Emily , Le Marchand Loic , Pai Rish K. , Peters Ulrike , Hopper John L. , Jenkins Mark A. , Makalic Enes
Published: July 2023

Supplementary Table S1 shows the original number of cases and controls in both the CCFR and GECCO datasets.
Figure S2 from Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci
Authors: Lai John , Wong Chi Kuen , Schmidt Daniel F. , Kapuscinski Miroslaw K. , Alpen Karen , MacInnis Robert J. , Buchanan Daniel D. , Win Aung K. , Figueiredo Jane C. , Chan Andrew T. , Harrison Tabitha A. , Hoffmeister Michael , White Emily , Le Marchand Loic , Pai Rish K. , Peters Ulrike , Hopper John L. , Jenkins Mark A. , Makalic Enes
Published: July 2023

Supplementary Figure S2 of a principle components analysis showing the CCFR and GECCO datasets cluster with European Caucasians.
Data from Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Authors: Edwards Kathryn C. , Khan Asia , Sharma Eva , Wang Lanqing , Feng June , Blount Benjamin C. , Sosnoff Connie S. , Smith Danielle M. , Goniewicz Maciej L. , Pearson Jennifer , Villanti Andrea C. , Delnevo Cristine D. , Bover-Manderski Michelle T. , Hatsukami Dorothy K. , Niaura Raymond , Everard Colm , Kimmel Heather L. , Duffy Kara , Rostron Brian L. , Del Valle-Pinero Arseima Y. , van Bemmel Dana M. , Stanton Cassandra A. , Hyland Andrew
Published: July 2023

AbstractBackground:
Sex and racial/ethnic identity-specific cut-points for validating tobacco use using Wave 1 (W1) of the Population Assessment of Tobacco and Health (PATH) Study were published in 2020. The current study establishes predictive validity of the W1 (2014) urinary cotinine and total nicotine equivalents-2 (TNE-2) cut-points on estimating Wave 4 (W4; 2017) tobacco use.
Methods:
For exclusive and polytobacco cigarette use, weighted prevalence estimates based on W4 self-report alone and with exceeding the W1 cut-point were calculated to identify the percentage missed without biochemical verification. Sensitivity and specificity of W1 cut-points on W4 self-reported tobacco use status were examined. ROC curves were used to determine the optimal W4 cut-points to distinguish past 30-day users from non-users, and evaluate whether the cut-points significantly differed from W1.
Results:
Agreement between W4 self-reported use and exceeding the W1 cut-points was high overall and when stratified by demographic subgroups (0.7%–4.4% of use was missed if relying on self-report alone). The predictive validity of using the W1 cut-points to classify exclusive cigarette and polytobacco cigarette use at W4 was high (>90% sensitivity and specificity, except among polytobacco Hispanic smokers). Cut-points derived using W4 data did not significantly differ from the W1-derived cut-points [e.g., W1 exclusive = 40.5 ng/mL cotinine (95% confidence interval, CI: 26.1–62.8), W4 exclusive = 29.9 ng/mL cotinine (95% CI: 13.5–66.4)], among most demographic subgroups.
Conclusions:
The W1 cut-points remain valid for biochemical verification of self-reported tobacco use in W4.
Impact:
Findings from can be used in clinical and epidemiologic studies to reduce misclassification of cigarette smoking status.
Data from Cigarette and Alternative Tobacco Product Use among Adult Cancer Survivors Enrolled in 9 ECOG-ACRIN Clinical Trials
Authors: Streck Joanna M. , Lee Ju-Whei , Walter Angela Wangari , Rosen Rachel L. , Gareen Ilana F. , Kircher Sheetal Mehta , Herman Benjamin A. , Carlos Ruth C. , Kumar Shaji , Mayer Ingrid A. , Saba Nabil F. , Fenske Timothy S. , Neal Joel W. , Atkins Michael B. , Hodi F. Stephen , Kyriakopoulos Christos E. , Tempany Clare , Shanafelt Tait D. , Wagner Lynne I. , Land Stephanie R. , Park Elyse R. , Ostroff Jamie S.
Published: July 2023

AbstractBackground:
While cigarette smoking has declined among the U.S. general population, sale and use of non-cigarette alternative tobacco products (ATP; e.g., e-cigarettes, cigars) and dual use of cigarettes/ATPs are rising. Little is known about ATP use patterns in cancer survivors enrolled in clinical trials. We investigated prevalence of tobacco product use, and factors associated with past 30-day use, among patients with cancer in national trials.
Methods:
Cancer survivors (N = 756) enrolled in 9 ECOG-ACRIN clinical trials (2017–2021) completed a modified Cancer Patient Tobacco Use Questionnaire (C-TUQ) which assessed baseline cigarette and ATP use since cancer diagnosis and in the past 30 days.
Results:
Patients were on average 59 years old, 70% male, and the mean time since cancer diagnosis was 26 months. Since diagnosis, cigarettes (21%) were the most common tobacco product used, followed by smokeless tobacco use (5%), cigars (4%), and e-cigarettes (2%). In the past 30 days, 12% of patients reported smoking cigarettes, 4% cigars, 4% using smokeless tobacco, and 2% e-cigarettes. Since cancer diagnosis, 5.5% of the sample reported multiple tobacco product use, and 3.0% reported multiple product use in the past 30 days. Males (vs. females; OR 4.33; P = 0 < 0.01) and individuals not living with another person who smokes (vs. living with; OR, 8.07; P = 0 < 0.01) were more likely to use ATPs only versus cigarettes only in the past 30 days.
Conclusions:
Among patients with cancer, cigarettes were the most prevalent tobacco product reported.
Impact:
Regardless, ATPs and multiple tobacco product use should be routinely assessed in cancer care settings.
Data from Sex-specific Associations between Body Mass Index and Thyroid Cancer Incidence among Korean Adults
Authors: Kim Kyoung-Nam , Kim Kyungsik , Lee Sangjun , Park Sue K.
Published: July 2023

AbstractBackground:
The potential differences by sex in the association between body mass index (BMI) and thyroid cancer risk remain unconfirmed.
Methods:
Data from the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS; 2002–2015; population size = 510,619) and the Korean Multi-center Cancer Cohort (KMCC) data (1993–2015; population size = 19,026) were used. We constructed Cox regression models, adjusted for potential confounders, to evaluate the association between BMI and thyroid cancer incidence in each cohort, and assessed the consistency of the results.
Results:
In the NHIS-HEALS, 1,351 and 4,609 incident thyroid cancer cases occurred during the follow-up among men and women, respectively. Compared with BMI of 18.5–22.9 kg/m2, BMI of 23.0–24.9 [no. of cases = 410; HR, 1.25; 95% confidence interval (CI), 1.08–1.44], 25.0–29.9 (no. of cases = 522; HR, 1.32; 95% CI, 1.15–1.51), and ≥30.0 kg/m2 (no. of cases = 48; HR, 1.93; 95% CI, 1.42–2.61) were associated with an increased risk of incident thyroid cancer among males. Among females, BMI of 23.0–24.9 (no. of cases = 1,300; HR, 1.17; 95% CI, 1.09–1.26) and 25.0–29.9 (no. of cases = 1,406; HR, 1.20; 95% CI, 1.11–1.29) were associated with incident thyroid cancer. The analyses using the KMCC demonstrated results consistent with wider CIs.
Conclusions:
Sex differences in the associations between BMI and thyroid cancer incidence were observed in Korean cohorts.
Impact:
BMI <23 kg/m2 may help prevent incident thyroid cancer, especially among men.
Supplemental Table 5 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

Enrichment values for ER associating proteins in endometrial and breast cancer cell lines
Supplemental Figure 4 from Mitochondrial Uncoupling Inhibits Reductive Carboxylation in Cancer Cells
Authors: Jiang Haowen , He Clifford Jiajun , Li Albert M. , He Bo , Li Yang , Zhou Meng-Ning , Ye Jiangbin
Published: July 2023

S4. Mitochondrial uncoupler NEN inhibits reductive carboxylation under hypoxia.
Supplemental Table 1 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

Differentially expressed genes from in vitro RNA-seq experiments
Supplemental Figure 7 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

In vivo exploration of novel therapeutic targets in ER active and mutant endometrial cancer
Supplemental Figure 6 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

Identification of novel therapeutic targets in ER active and mutant endometrial cancer
Supplementary Table 2 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Primers used in this study
Data from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of lethal kidney cancer. Reprogramming of fatty acid and glucose metabolism resulting in the accumulation of lipids and glycogen in the cytoplasm is a hallmark of ccRCC. Here, we identified a micropeptide ACLY-BP encoded by the GATA3-suppressed LINC00887, which regulated lipid metabolism and promoted cell proliferation and tumor growth in ccRCC. Mechanistically, the ACLY-BP stabilizes the ATP citrate lyase (ACLY) by maintaining ACLY acetylation and preventing ACLY from ubiquitylation and degradation, thereby leading to lipid deposition in ccRCC and promoting cell proliferation. Our results may offer a new clue for the therapeutic approaches and the diagnostic assessment for ccRCC.
Implications:
This study identifies ACLY-BP encoded by LINC00887 as a lipid-related micropeptide that stabilizes ACLY to generate acetyl-CoA, driving lipid deposition and promoting cell proliferation in ccRCC.
Supplementary Figures S1-S6 and Tables S1-S5 from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration
Authors: Akagi Keiko , Symer David E. , Mahmoud Medhat , Jiang Bo , Goodwin Sara , Wangsa Darawalee , Li Zhengke , Xiao Weihong , Dunn Joe Dan , Ried Thomas , Coombes Kevin R. , Sedlazeck Fritz J. , Gillison Maura L.
Published: July 2023

Figure S1.1. Circos plots of human genomes.
Figure S1.2. Circos plots of HPV genomes.
Figure S1.3. PacBio HiFi read length distributions.
Figure S1.4. Oxford Nanopore (ONT) read length distributions.
Figure S2.1. Detection of circularized mitochondrial DNA by LR-seq reads.
Figure S2.2. Detection of HPV concatemers by LR-seq reads.
Figure S2.3. ONT reads show structural rearrangements in HPV concatemers.
Figure S3.1. Absence of sequence variants at breakpoints.
Figure S3.2. AmpliconArchitect predicts inaccurate HPV ecDNA structures.
Figure S4.1. Evolution of structural variants at Chr. 22 of Tumor 2.
Figure S4.2. Evidence of heterocateny in Tumor 5 and Tumor 3.
Figure S5.1. HPV integration into icDNA in GUMC-395, HeLa, and HTEC.
Figure S5.2. HPV integrants at Chr. 17 and Chr. X of VU147.
Figure S5.3. Metaphase FISH identifies HPV-containing ecDNAs in cell lines.
Figure S5.4. Circle-seq analysis of HeLa, GUMC-395, VU147, and HTEC cells.
Figure S6. Transcription levels of HPV genes.
Table S1.1. Depths of autosomal and mitochondrial genome sequencing coverage from WGS and LR-seq.
Table S1.2. Depths of autosomal and HPV genome sequencing coverage from WGS and LR-seq.
Table S2.1. Breakpoints and normal segment junctions in Tumor 4.
Table S2.2. Definition of genomic segments flanking HPV integrants in Tumor 4.
Table S3.1. Breakpoints and normal segment junctions in Tumor 2.
Table S3.2. Definition of genomic segments flanking HPV integrants in Tumor 2.
Table S3.3. Breakpoints and normal segment junctions in Tumor 5.
Table S3.4. Definition of genomic segments flanking HPV integrants in Tumor 5.
Table S3.5. Breakpoints and normal segment junctions in Tumor 3.
Table S3.6. Definition of genomic segments flanking HPV integrants in Tumor 3.
Table S4.1. Breakpoints and normal segment junctions in GUMC-395 cells.
Table S4.2. Definition of genomic segments flanking HPV integrants in GUMC-395 cells.
Table S5.1. Breakpoints and normal segment junctions in HeLa cells.
Table S5.2. Definition of genomic segments flanking HPV integrants in HeLa cells.
Table S5.3. Breakpoints and normal segment junctions in VU147 cells.
Table S5.4. Definition of genomic segments flanking HPV integrants in VU147 cells.
Table S5.5. Breakpoints and normal segment junctions in HTEC cells.
Table S5.6. Definition of genomic segments flanking HPV integrants in HTEC cells.
Supplementary Table S5 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

Fold change in potency against FGFR2 acquired resistance mutations
Data from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

Abstract
Oncogenic activation of fibroblast growth factor receptor 2 (FGFR2) drives multiple cancers and represents a broad therapeutic opportunity, yet selective targeting of FGFR2 has not been achieved. Although the clinical efficacy of pan-FGFR inhibitors (pan-FGFRi) validates FGFR2 driver status in FGFR2 fusion–positive intrahepatic cholangiocarcinoma, their benefit is limited by incomplete target coverage due to FGFR1- and FGFR4-mediated toxicities (hyperphosphatemia and diarrhea, respectively) and the emergence of FGFR2 resistance mutations. RLY-4008 is a highly selective, irreversible FGFR2 inhibitor designed to overcome these limitations. In vitro, RLY-4008 demonstrates >250- and >5,000-fold selectivity over FGFR1 and FGFR4, respectively, and targets primary alterations and resistance mutations. In vivo, RLY-4008 induces regression in multiple xenograft models—including models with FGFR2 resistance mutations that drive clinical progression on current pan-FGFRi—while sparing FGFR1 and FGFR4. In early clinical testing, RLY-4008 induced responses without clinically significant off-isoform FGFR toxicities, confirming the broad therapeutic potential of selective FGFR2 targeting.
Significance:
Patients with FGFR2-driven cancers derive limited benefit from pan-FGFRi due to multiple FGFR1–4-mediated toxicities and acquired FGFR2 resistance mutations. RLY-4008 is a highly selective FGFR2 inhibitor that targets primary alterations and resistance mutations and induces tumor regression while sparing other FGFRs, suggesting it may have broad therapeutic potential.