bluuebunny/crossref_metadata_2025 huggingface dataset:
The Hierarchical Coevolutionary Units of Ecological Networks
Authors: Maia Kate Pereira , Guimarães Paulo Roberto
Published: October 2024

In ecological networks, cohesive groups of species may shape the evolution of interactions, serving as coevolutionary units. Ranging across network scales, from motifs to isolated components, elucidating which cohesive groups are more determinant for coevolution remains a challenge in ecology. We address this challenge by integrating 376 empirical mutualistic and antagonistic networks and coevolutionary models. We identified cohesive groups at four network scales containing a significant proportion of potential direct coevolutionary effects. Cohesive groups displayed hierarchical organisation, and potential coevolutionary effects overflowing lower‐scale groups were contained by higher‐scale groups, underscoring the hierarchy's impact. However, indirect coevolutionary effects blurred group boundaries and hierarchy, particularly under strong selection from ecological interactions. Thus, under strong selection, indirect effects render networks themselves, and not cohesive groups, as the likely coevolutionary units of ecological systems. We hypothesise hierarchical cohesive groups to also shape how other forms of direct and indirect effects propagate in ecological systems.
Coexistence of Competing Plants Under Plant–Soil Feedback
Authors: Senthilnathan Athmanathan , D'Andrea Rafael
Published: October 2024

Plant–soil feedback (PSF), the reciprocal interaction between plants and their soil environment, is a fundamental ecological process that can influence coexistence and functional structure in plant communities. Current theory establishes that PSF may enhance diversity or lead to exclusion depending on whether soil conditioning disproportionately benefits heterospecific or conspecific individuals. However, a more complete picture of the impact of PSF requires understanding how PSF interacts with competition. To that end, here we propose an integrated mathematical model combining trait‐based competition and soil‐explicit PSF. Contrary to the current paradigm, we find that soil conditioning that disproportionately favours conspecific individuals can promote coexistence. Additionally, we show that priority effects are common when soil‐conditioning species differ in their edaphic preferences. These effects can allow species with large differences in competitive ability to coexist under certain soil conditions. Our results provide testable predictions tying community‐level functional patterns in plant communities to PSF and competition.
Microbial Dormancy Supports Multi‐Species Coexistence Under Resource Fluctuations
Authors: Letten Andrew D. , Yamamichi Masato , Richardson James A. , Ke Po‐Ju
Published: October 2024

The ability for microbes to enter dormant states is adaptive under resource fluctuations and has been linked to the maintenance of diversity. Nevertheless, the mechanism by which microbial dormancy gives rise to the density‐dependent feedbacks required for stable coexistence under resource fluctuations is not well understood. Via analysis of consumer‐resource models, we show that the stable coexistence of dormancy and non‐dormancy strategists is a consequence of the former benefiting more from resource fluctuations while simultaneously reducing overall resource variability, which sets up the requisite negative frequency dependence. Moreover, we find that dormants can coexist alongside gleaner and opportunist strategies in a competitive‐exclusion‐defying case of three species coexistence on a single resource. This multi‐species coexistence is typically characterised by non‐simple assembly rules that cannot be predicted from pairwise competition outcomes. The diversity maintained via this three‐way trade‐off represents a novel phenomenon that is ripe for further theoretical and empirical inquiry.
Mycorrhizal Symbiosis Increases Plant Phylogenetic Diversity and Regulates Community Assembly in Grasslands
Authors: Zhang Entao , Wang Yang , Chen Shiping , Zhou Daowei , Shangguan Zhouping , Huang Jianhui , He Jin‐Sheng , Wang Yanfen , Sheng Jiandong , Tang Lisong , Li Xinrong , Dong Ming , Wu Yan , Hu Shuijin , Bai Yongfei
Published: October 2024

The intricate mechanisms controlling plant diversity and community composition are cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1315 grassland sites in China to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and community assembly. We show that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche‐based community assembly. Conversely, non‐mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the mechanisms shaping ecological communities and the way for more informed conservation that acknowledges the complex interplay between symbiosis and community dynamics.
The impact of unions on compensation consultants and CEO pay
Authors: Nanda Vikram , Nishikawa Takeshi , Prevost Andrew
Published: September 2024

Research on executive compensation finds unions to be associated with lower executive compensation, particularly incentive pay, while other work documents the role of compensation consultants in facilitating stronger CEO incentives and pay. We propose and test the implications of a simple theoretical framework that integrates these empirical findings. We find empirical support for our model's prediction that in environments less favorable to union organization (e.g., right‐to‐work states), firms with higher unionization rates strategically engage consultants to counter union influence, place greater value on their advice as gauged by consultant fees, and offer managers greater equity incentives opposed by unions. On the other hand, in strongly prolabor environments, unions are more successful at curtailing consultant use and have greater influence on the level of pay and incentives.
“I Am Forever Changed”: A Phenomenological Study of the Existential Experiences of Parents of Children and Young People With Complex Care Needs
Authors: Nygård Carina , Clancy Anne , Kitzmüller Gabriele
Published: October 2024

Aim

To explore the existential lived experiences of parents of children and young people with complex care needs.

Design

An explorative qualitative design.

Methods

We conducted 16 in‐depth interviews with parents of children and young people with complex care needs across Norway from February to May 2022. Data collection and analysis were guided by the theoretical framework of van Manen's phenomenology of practice approach.

Results

Four distinct but interwoven themes reflecting the comprehensive and holistic nature of parents' existential lived experiences emerged: lived body: “I am forever changed”; lived space: Seeking sanctuary; lived time: “Time doesn't seem to exist”; and lived self‐other: Parents' changing relationships.

Conclusions

Parents' ongoing efforts to manage fluctuations in their daily lives profoundly affect the existential aspects of their well‐being, suggesting that respectful and attentive nurse–parent relationships can nurture existential growth.

Implications for the Profession and Patient Care

There is a crucial need for a genuine nursing presence characterised by an attitude of open sensitivity and attentive listening to parents' existential experiences. Nurses should embrace the opportunity to engage in respectful and attentive dialogues with parents. Acknowledging that the insights emerging from these conversations can improve integrated and personalised nursing services worldwide.

Impact

Parents of children and young people with complex care needs often experience suboptimal healthcare. Additionally, access to quality healthcare services, particularly in rural areas, is limited, creating inefficiencies and coordination challenges. This study provides nurses, other health care professionals, researchers, and decision‐makers with valuable perspectives on supporting parents' existential needs which may significantly impact their overall well‐being and coping abilities, contributing to a more compassionate approach to family care.

Reporting Method

Consolidated Criteria for Reporting Qualitative Research (COREQ).

Patient or Public Contribution

Parents of children and young people with complex care needs provided valuable feedback on the findings and implications of this work.
Error monitoring under working memory load: An electrocortical investigation
Authors: Watanabe Brandon K. , Bauer Elizabeth A. , MacNamara Annmarie
Published: September 2024

Error monitoring is essential for detecting errors and may facilitate behavioral adjustments that can reduce or prevent future errors. At times, error monitoring must occur while individuals are engaged in other, cognitively demanding tasks that might consume processing resources necessary for error monitoring. Here, we set out to determine whether concurrent working memory (WM) load interferes with error monitoring, as measured using event‐related potentials, the error‐related negativity (Ne/ERN), and error positivity (Pe). Fifty‐four participants (n = 33 female) completed an arrowhead flanker task, with trials presented under low (2 letter) or high (6 letter) WM load. Participants were required to hold letter strings in memory and to recall these letters at the end of a set of flanker trials. Results showed that WM load reduced the Pe but did not affect the Ne/ERN. Therefore, WM load appeared to attenuate later, more elaborated stages of error processing, though initial error detection was unaffected. Additionally, high WM load slowed reaction times overall, but did not lead to a significant increase in errors. As such, slower responses may have helped participants maintain comparable accuracy for low‐load versus high‐load trials. Overall, results indicate that WM load interferes with the evaluation of error significance, which could interfere with behavioral adaptations over time.
Asociación entre las dimensiones antropométricas de la mano y la fuerza de agarre en un grupo de trabajadores administrativos de la ciudad de Bogotá, Colombia
Authors: Monroy Siva Magda Viviana , Zea Forero Christian Ricardo , Rodríguez Silva Luisa Alejandra , Vargas Sánchez Karen Daniela
Published: October 2024

El ser humano en su proceso evolutivo ha convertido a las manos en un instrumento fundamental para su supervivencia y relación con el entorno. La fuerza de agarre de la mano es un indicador de capacidad física y de bienestar del ser humano, por lo cual es relevante caracterizarla. El objetivo de este artículo fue determinar la asociación existente entre la fuerza de agarre y las medidas antropométricas de la mano en un grupo de trabajadores administrativos de la ciudad de Bogotá.  Participaron 315 personas entre 18 y 63 años, a quienes se les midió ocho dimensiones de la mano y la fuerza de agarre en las dos manos.  Mediante una regresión lineal se estableció que las medidas antropométricas que tienen relación significativa con la fuerza de agarre son AMM, EM, DA y CMM para la mano dominante, y AMM, EM, DA para la mano no dominante. Se determinó que las medidas antropométricas tienen un 52% de incidencia en la fuerza de la mano dominante, y un 50.6% para la fuerza de la mano no dominante. Asimismo, se concluyó que los hombres reportan mayor fuerza que las mujeres, y en general se presenta mayor fuerza en la mano dominante.
Identification of an ionic mechanism for ERα-mediated rapid excitation in neurons
Authors: Yu Meng , Yin Na , Feng Bing , Gao Peiyu , Yu Kaifan , Liu Hesong , Liu Hailan , Li Yongxiang , Ginnard Olivia Z. , Conde Kristine M. , Wang Mengjie , Fang Xing , Tu Longlong , Bean Jonathan C. , Liu Qingzhuo , Deng Yue , Yang Yuxue , Han Junying , Jossy Sanika V. , Burt Megan L. , Wong Huey Zhong , Yang Yongjie , Arenkiel Benjamin R. , He Yang , Guo Shaodong , Gourdy Pierre , Arnal Jean-Francois , Lenfant Francoise , Wang Zhao , Wang Chunmei , He Yanlin , Xu Yong
Published: October 2024

The major female ovarian hormone, 17β-estradiol (E
2
), can alter neuronal excitability within milliseconds to regulate a variety of physiological processes. Estrogen receptor-α (ERα), classically known as a nuclear receptor, exists as a membrane-bound receptor to mediate this rapid action of E
2
, but the ionic mechanisms remain unclear. Here, we show that a membrane channel protein, chloride intracellular channel protein-1 (Clic1), can physically interact with ERα with a preference to the membrane-bound ERα. Clic1-mediated currents can be enhanced by E
2
and reduced by its depletion. In addition, Clic1 currents are required to mediate the E
2
-induced rapid excitations in multiple brain ERα populations. Further, genetic disruption of Clic1 in hypothalamic ERα neurons blunts the regulations of E
2
on female body weight balance. In conclusion, we identified the Clic1 chloride channel as a key mediator for E
2
-induced rapid neuronal excitation, which may have a broad impact on multiple neurobiological processes regulated by E
2
.
In situ continuous hydrogen-bonded engineering for intrinsically stretchable and healable high-mobility polymer semiconductors
Authors: Yue Haoguo , Wang Ying , Luo Shaochuan , Guo Junfeng , Jin Jun , Li Gongxi , Meng Zhihao , Zhang Lei , Zhou Dongshan , Zhen Yonggang , Hu Wenping
Published: October 2024

As a key component for wearable electronics, intrinsically stretchable and healable semiconducting polymers are scarce because carrier mobility is often reduced with increasing stretchability and self-healability. Here, we combine stepwise polymerization and thermal conversion to introduce in situ continuous hydrogen bonding sites in a polymer backbone without breaking the conjugation or introducing bulky softer side chains, benefiting the intrachain and interchain charge transport. We demonstrate that a regular sequence structure facilitated the formation of big nanofibers with a high degree of aggregation, providing the loose and porous thin film with simultaneously improved charge transport, stretchability, and self-healability. The mobility of damaged devices can be recovered to 81% after a healing treatment. Fully stretchable transistor based on the designed polymer exhibited a greatly enhanced mobility up to 1.08 square centimeters per volt per second under 100% strain, which is an unprecedented value and constitutes a major step for the development of intrinsically stretchable and healable semiconducting polymers.
Oxidative stability of chelated Sn(II)
(aq)
at neutral pH: The critical role of NO
3
−
ions
Authors: Zhang Shaoyi , Govindaraju Gokul V. , Cheng Chi-Yuan , Daep Carlo Amorin , Chen Dandan , Castro Cristina , Corrigan Patrick S. , Masters James G. , Pan Long , Xu Guofeng , Brinzari Tatiana V. , Myers Carl P.
Published: October 2024

Tin(II) compounds are versatile materials with applications across fields such as catalysis, diagnostic imaging, and therapeutic drugs. However, oxidative stabilization of Sn(II) has remained an unresolved challenge as its reactivity with water and dioxygen results in loss of functionality, limiting technological advancement. Approaches to slow Sn(II) oxidation with chelating ligands or sacrificial electron donors have yielded only moderate improvements. We demonstrate here that the addition of nitrate to pyrophosphate-chelated Sn(II)
(aq)
suppresses Sn(II) oxidation in water across a broad pH range. Evidence of hydroxyl radical concentration reduction and detection of a radical nitrogen species that only forms in the presence of chelated Sn(II) point to a radical-based reaction mechanism. While this chemistry can be broadly applied, we present that this approach maintains Sn(II)’s antibacterial and anti-inflammatory efficacies as an example of sustained oral chemotherapeutic functionality.
Large expansion of plasma commensal viruses is associated with SIV pathogenesis in
Macaca leonina
Authors: Li Yanpeng , Song Tian-Zhang , Cao Le , Zhang Han-Dan , Ma Yingying , Tian Ren-Rong , Zheng Yong-Tang , Zhang Chiyu
Published: October 2024

Human immunodeficiency virus-1 (HIV-1) infection disrupts the homeostatic equilibrium between the host and commensal microbes. However, the dynamic changes of plasma commensal viruses and their role in HIV/simian immunodeficiency virus (SIV) pathogenesis are rarely reported. Here, we investigated the longitudinal changes of plasma virome, inflammation levels, and disease markers using an SIV-infected
Macaca leonina
model. Large expansions of plasma
Anelloviridae
,
Parvoviridae
,
Circoviridae
and other commensal viruses, and elevated levels of inflammation and D-dimer were observed since the chronic phase of SIV infection.
Anelloviridae
abundance appears to correlate positively with the CD4
+
T cell count but negatively with SIV load especially at the acute phase, whereas other commensal viruses’ abundances show opposite correlations with the two disease markers. Antiretroviral therapy slightly reduces but does not substantially reverse the expansion of commensal viruses. Furthermore, 1387 primate anellovirus open reading frame 1 sequences of more than 1500 nucleotides were annotated. The data reveal different roles of commensal viruses in SIV pathogenesis.
Expanding the tool box for native structural biology:
19
F dynamic nuclear polarization with fast magic angle spinning
Authors: Movellan Kumar Tekwani , Zhu Wenkai , Banks Daniel , Kempf James , Runge Brent , Gronenborn Angela M. , Polenova Tatyana
Published: October 2024

Obtaining atomic-level information on components in the cell is a major focus in structural biology. Elucidating specific structural and dynamic features of proteins and their interactions in the cellular context is crucial for understanding cellular processes. We introduce
19
F dynamic nuclear polarization (DNP) combined with fast magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy as a powerful technique to study proteins in mammalian cells. We demonstrate our approach on the severe acute respiratory syndrome coronavirus 2 5F-Trp-N
NTD
protein, electroporated into human cells. DNP signal enhancements of 30- to 40-fold were observed, translating into over 1000-fold experimental time savings. High signal-to-noise ratio spectra were acquired on nanomole quantities of a protein in cells in minutes. 2D
19
F-
19
F dipolar correlation spectra with remarkable sensitivity and resolution were obtained, exhibiting
19
F-
19
F cross peaks associated with fluorine atoms as far as ~10 angstroms apart. This work paves the way for
19
F DNP-enhanced MAS NMR applications in cells for probing protein structure, dynamics, and ligand interactions.
Identifying metabolic limitations in the tumor microenvironment
Authors: Cognet Guillaume , Muir Alexander
Published: October 2024

Solid tumors are characterized by dysfunctional vasculature that limits perfusion and delivery of nutrients to the tumor microenvironment. Limited perfusion coupled with the high metabolic demand of growing tumors has led to the hypothesis that many tumors experience metabolic stress driven by limited availability of nutrients such as glucose, oxygen, and amino acids in the tumor. Such metabolic stress has important implications for the biology of cells in the microenvironment, affecting both disease progression and response to therapies. Recently, techniques have been developed to identify limiting nutrients and resulting metabolic stresses in solid tumors. These techniques have greatly expanded our understanding of the metabolic limitations in tumors. This review will discuss these experimental tools and the emerging picture of metabolic limitations in tumors arising from recent studies using these approaches.
LRRK2 regulates production of reactive oxygen species in cell and animal models of Parkinson’s disease
Authors: Keeney Matthew T. , Rocha Emily M. , Hoffman Eric K. , Farmer Kyle , Di Maio Roberto , Weir Julie , Wagner Weston G. , Hu Xiaoping , Clark Courtney L. , Castro Sandra L. , Scheirer Abigail , Fazzari Marco , De Miranda Briana R. , Pintchovski Sean A. , Shrader William D. , Pagano Patrick J. , Hastings Teresa G. , Greenamyre J. Timothy
Published: October 2024

Oxidative stress has long been implicated in Parkinson’s disease (PD) pathogenesis, although the sources and regulation of reactive oxygen species (ROS) production are poorly defined. Pathogenic mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are associated with increased kinase activity and a greater risk of PD. The substrates and downstream consequences of elevated LRRK2 kinase activity are still being elucidated, but overexpression of mutant LRRK2 has been associated with oxidative stress, and antioxidants reportedly mitigate LRRK2 toxicity. Here, using CRISPR-Cas9 gene-edited HEK293 cells, RAW264.7 macrophages, rat primary ventral midbrain cultures, and PD patient–derived lymphoblastoid cells, we found that elevated LRRK2 kinase activity was associated with increased ROS production and lipid peroxidation and that this was blocked by inhibitors of either LRRK2 kinase or NADPH oxidase 2 (NOX2). Oxidative stress induced by the pesticide rotenone was ameliorated by LRRK2 kinase inhibition and was absent in cells devoid of LRRK2. In a rat model of PD induced by rotenone, a LRRK2 kinase inhibitor prevented the lipid peroxidation and NOX2 activation normally seen in nigral dopaminergic neurons in this model. Mechanistically, LRRK2 kinase activity was shown to regulate phosphorylation of serine-345 in the p47
phox
subunit of NOX2. This, in turn, led to translocation of p47
phox
from the cytosol to the membrane-associated gp91
phox
(NOX2) subunit, activation of the NOX2 enzyme complex, and production of ROS. Thus, LRRK2 kinase activity may drive cellular ROS production in PD through the regulation of NOX2 activity.
Dynamic structural remodeling of LINC01956 enhances temozolomide resistance in
MGMT
-methylated glioblastoma
Authors: Liao Xinyi , Zhang Shuxia , Li Xincheng , Qian Wanying , Li Man , Chen Suwen , Wu Xingui , Yu Xuexin , Li Ziwen , Tang Miaoling , Xu Yingru , Yu Ruyuan , Zhang Qiliang , Wu Geyan , Zhang Nu , Song Libing , Li Jun
Published: October 2024

The mechanisms underlying stimuli-induced dynamic structural remodeling of RNAs for the maintenance of cellular physiological function and survival remain unclear. Here, we showed that in
MGMT
promoter–methylated glioblastoma (GBM), the RNA helicase DEAD-box helicase 46 (DDX46) is phosphorylated by temozolomide (TMZ)–activated checkpoint kinase 1 (CHK1), resulting in a dense-to-loose conformational change and an increase in DDX46 helicase activity. DDX46-mediated tertiary structural remodeling of LINC01956 exposes the binding motifs of LINC01956 to the 3′ untranslated region of O
6
-methylguanine DNA methyltransferase (
MGMT
). This accelerates recruitment of
MGMT
mRNA to the RNA export machinery and transportation of
MGMT
mRNA from the nucleus to the cytoplasm, leading to increased MGMT abundance and TMZ resistance. Using patient-derived xenograft (PDX) and tumor organoid models, we found that treatment with the CHK1 inhibitor SRA737abolishes TMZ-induced structural remodeling of LINC01956 and subsequent MGMT up-regulation, resensitizing TMZ-resistant
MGMT
promoter–methylated GBM to TMZ. In conclusion, these findings highlight a mechanism underlying temozolomide-induced RNA structural remodeling and may represent a potential therapeutic strategy for patients with TMZ-resistant
MGMT
promoter–methylated GBM.
Syndromic scoliosis in a patient with arthrochalasia Ehlers-Danlos syndrome corrected with a Wood-Rigo-Cheneau derotational brace
Authors: Brown Michael , Krasney Leighann , Lavallee Mark
Published: September 2024

We present a boy in middle childhood with a medical history of arthrochalasiaEhlers-Danlos syndrome who was diagnosed with scoliosis as a toddler. His treatment began at a regional children’s hospital, where initial spine radiographs demonstrated a 43.6° dextroscoliosis curve with the apex at L3. He was initially treated with a Boston brace, and the family was informed that MAGEC (Magnetic Expansion Control) growing rods were likely the definitive treatment due to the high likelihood of progression given the patient’s large Cobb angle. However, the decision was made by the family and the Ehlers-Danlos syndrome specialist to proceed with the Wood-Rigo-Cheneau derotational brace.
Diversification of Antibodies: From V(D)J Recombination to Somatic Exon Shuffling
Authors: Lebedin Mikhail , de la Rosa Kathrin
Published: October 2024

Antibodies that gain specificity by a large insert encoding for an extra domain were described for the first time in 2016. In malaria-exposed individuals, an exon deriving from the leukocyte-associated immunoglobulin-like 1 (LAIR1) gene integrated via a copy-and-paste insertion into the immunoglobulin heavy chain encoding region. A few years later, a second example was identified, namely a dual exon integration from the leukocyte immunoglobulin-like receptor B1 (LILRB1) gene that is located in close proximity to LAIR1. A dedicated high-throughput characterization of chimeric immunoglobulin heavy chain transcripts unraveled, that insertions from distant genomic regions (including mitochondrial DNA) can contribute to human antibody diversity. This review describes the modalities of insert-containing antibodies. The role of known DNA mobility aspects, such as genomic translocation, gene conversion, and DNA fragility, is discussed in the context of insert-antibody generation. Finally, the review covers why insert antibodies were omitted from the past repertoire analyses and how insert antibodies can contribute to protective immunity or an autoreactive response.
Supplementary Table S2 from Radiodensities of Skeletal Muscle and Visceral Adipose Tissues Are Prognostic Factors in Clear-Cell Renal Cell Carcinoma
Authors: Bradshaw Patrick T. , Olsson Linnea T. , Sanchez Alejandro , Knezevic Andrea , Akin Oguz , Scott Jessica M. , Hakimi A. Ari , Russo Paul , Caan Bette J. , Mourtzakis Marina , Furberg Helena
Published: October 2024

Joint effects for relationship between body composition features and tumor characteristics for overall survival.
Supplementary Table S1 from Neighborhood Disadvantage and Prostate Tumor Aggressiveness among African American and European American Men
Authors: Boyle Joseph , Yau Jessica , Slade Jimmie L. , Butts Derrick A. , Wimbush Jessica , Park Jong Y. , Hussain Arif , Onukwugha Eberechukwu , Knott Cheryl L. , Wheeler David C. , Barry Kathryn Hughes
Published: October 2024

Supplementary Table S1: Summary of correlations between neighborhood disadvantage metrics.
Supplementary Figure S2 from Neighborhood Disadvantage and Prostate Tumor Aggressiveness among African American and European American Men
Authors: Boyle Joseph , Yau Jessica , Slade Jimmie L. , Butts Derrick A. , Wimbush Jessica , Park Jong Y. , Hussain Arif , Onukwugha Eberechukwu , Knott Cheryl L. , Wheeler David C. , Barry Kathryn Hughes
Published: October 2024

Supplementary Figure S2: Values of the Neighborhood Deprivation Index (NDI) for participants with residential addresses in Baltimore.
Supplementary Table 3 from Association between Long-term Energy Balance–Related Factors and Survival in Colorectal Cancer Overall and by Metabolic Warburg-Subtypes
Authors: Offermans Kelly , Jenniskens Josien C.A. , Simons Colinda C.J.M. , Samarska Iryna , Fazzi Gregorio E. , Smits Kim M. , Schouten Leo J. , Weijenberg Matty P. , Grabsch Heike I. , van den Brandt Piet A.
Published: October 2024

Supplementary Table 3 – Univariable hazard ratios for associations between long-term energy balance-related factors and overall survival of colorectal cancer patients within the Netherlands Cohort Study (NLCS, 1986-2006), according to Warburg-subtype.
Table S8 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S8 tabulates all the relevant citations of estimates and distributions of breast cancer risk factors used to conduct meta-analysis and compute attributable proportions, comparing Asian and European populations.
Table S6 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S6 compares effect sizes, distributions, and attributable proportions of breast cancer risk factors reported in prospective studies among pre-menopausal Asian and European women.
Table 1 from Sociodemographic Disparities in HER2+ Breast Cancer Trastuzumab Receipt: An English Population-Based Study
Authors: Norris Ruth P. , Dew Rosie , Greystoke Alastair , Cresti Nicola , Cain Henry , Todd Adam , Sharp Linda
Published: October 2024

Demographic and clinical characteristics of women with stage I–IV HER2+ breast cancer diagnosed between January 01, 2012 and December 31, 2017 (n = 36,985).
Supplementary Materials and Methods from Sociodemographic Disparities in HER2+ Breast Cancer Trastuzumab Receipt: An English Population-Based Study
Authors: Norris Ruth P. , Dew Rosie , Greystoke Alastair , Cresti Nicola , Cain Henry , Todd Adam , Sharp Linda
Published: October 2024

Supplementary Materials and Methods STROBE Checklist_Clean
Supplementary Figure S1 Early-stage Disease Analytical Cohort Flow Diagram from Sociodemographic Disparities in HER2+ Breast Cancer Trastuzumab Receipt: An English Population-Based Study
Authors: Norris Ruth P. , Dew Rosie , Greystoke Alastair , Cresti Nicola , Cain Henry , Todd Adam , Sharp Linda
Published: October 2024

Supplementary Figure S1 Early-stage Disease Analytical Cohort Flow Diagram_Clean
Supplementary Table S3 from Blood Magnesium Level and Risk of Hepatocellular Carcinoma in a Prospective Liver Cirrhosis Cohort
Authors: Zhang Xinyuan , Zhao Longgang , Dai Qi , Hou Tao , Danford Christopher J. , Lai Michelle , Zhang Xuehong
Published: October 2024

Association between magnesium prescription and risk of hepatocellular carcinoma in the Harvard Mass General Brigham Biobank Liver Cirrhosis Cohort.
Supplementary Figure S1 from Blood Magnesium Level and Risk of Hepatocellular Carcinoma in a Prospective Liver Cirrhosis Cohort
Authors: Zhang Xinyuan , Zhao Longgang , Dai Qi , Hou Tao , Danford Christopher J. , Lai Michelle , Zhang Xuehong
Published: October 2024

Probability of incident hepatocellular carcinoma over time by baseline magnesium quartile categories.
Supplementary Table S4 from Prospective Analysis of Circulating Biomarkers and Ovarian Cancer Risk in the UK Biobank
Authors: Sasamoto Naoko , Hathaway Cassandra A. , Townsend Mary K. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2024

Minerals, vitamins in blood and ovarian cancer risk in the UK Biobank by histologic subtype.
Supplementary Table S2 from Prospective Analysis of Circulating Biomarkers and Ovarian Cancer Risk in the UK Biobank
Authors: Sasamoto Naoko , Hathaway Cassandra A. , Townsend Mary K. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2024

Minerals, vitamins in blood and ovarian cancer risk in the UK Biobank.
Data from Blood Leukocyte DNA Methylation Markers of Periodontal Disease and Risk of Lung Cancer in a Case–Control Study Nested in the CLUE II Cohort
Authors: Mulvaney Rachel , Pan Yongyi , Zhao Naisi , Teles Flavia , Lu Jiayun , Platz Elizabeth A. , Kelsey Karl T. , Michaud Dominique S.
Published: October 2024

AbstractBackground:
Periodontal disease and DNA methylation markers have separately been associated with lung cancer risk. Examining methylation levels at genomic regions previously linked to periodontal disease may provide insights on the link between periodontal disease and lung cancer.
Methods:
In a nested case–control study drawn from the CLUE II cohort, we measured DNA methylation levels in 208 lung cancer cases and 208 controls. We examined the association between 37 DNA-methylated 5′—C—phosphate—G—3′ (CpG) sites at three genomic regions, homeobox 4 (HOXA4), zinc finger protein (ZFP57), and a long noncoding RNA gene located in Chr10 (ENSG00000231601), and lung cancer risk.
Results:
Statistically significant associations with lung cancer risk were observed for all 14 CpG sites from HOXA4 (OR ranging 1.41–1.62 for 1 SD increase in the DNA methylation level, especially within 15 years) and 1 CpG site on gene ENSG00000231601 (OR = 1.34 for 1 SD increase in the DNA methylation level). Although CpG sites on gene ZFP57 were not associated with lung cancer risk overall, statistically significant inverse associations were noted for six CpG sites when restricting follow-up to 15 years (OR = 0.73–0.77 for 1 SD increase in the DNA methylation level).
Conclusions:
Key methylation levels associated with periodontal disease are also associated with lung cancer risk. For both HOXA4 and ZFP57, the associations were stronger within 15 years of follow-up, which suggest that, if causal, the impact of methylation is acting late in the natural history of lung cancer.
Impact:
Identifying biological pathways that link periodontal disease and lung cancer could provide new opportunities for lung cancer detection and prevention.
Supplementary Figure S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Authors: Johanns Tanner M. , Garfinkle Elizabeth A.R. , Miller Katherine E. , Livingstone Alexandra J. , Roberts Kaleigh F. , Rao Venkata Lakshmi P. , Dowling Joshua L. , Chicoine Michael R. , Dacey Ralph G. , Zipfel Gregory J. , Kim Albert H. , Mardis Elaine R. , Dunn Gavin P.
Published: October 2024

CDR3beta sequences ranked by ratio
Data from miR-196b-5p Regulates Colorectal Cancer Cell Migration and Metastases through Interaction with HOXB7 and GALNT5
Authors: Stiegelbauer Verena , Vychytilova-Faltejskova Petra , Karbiener Michael , Pehserl Anna-Maria , Reicher Andreas , Resel Margit , Heitzer Ellen , Ivan Cristina , Bullock Marc , Ling Hui , Deutsch Alexander , Wulf-Goldenberg Annika , Adiprasito Jan Basri , Stoeger Herbert , Haybaeck Johannes , Svoboda Marek , Stotz Michael , Hoefler Gerald , Slaby Ondrej , Calin George Adrian , Gerger Armin , Pichler Martin
Published: October 2024

Abstract
Purpose: miR-196b-5p has been previously implicated in malignant transformation; however, its role in colorectal cancer has not been fully explored. In this study, we examine the clinical and biological relevance of miR-196b-5p, and the molecular pathways regulated by miR-196b-5p in colorectal cancer.

Experimental Design: miR-196b-5p expression was quantitated by qRT-PCR in 2 independent cohorts composed of 292 patients with colorectal cancer in total, to explore its biomarker potential. Transient and stable gain- and loss-of-function experiments were conducted in a panel of colorectal cancer cell lines and mice, to evaluate the impact of miR-196b-5p on proliferation, chemosensitivity, migration/invasion, and metastases formation in vitro and in vivo. The molecular pathways influenced by miR-196b-5p were characterized using whole transcriptome profiling, in silico target prediction tools, luciferase interaction assays, and phenocopy/rescue gene knockdown experiments.

Results: Low miR-196b-5p expression was significantly associated with metastases and poor outcomes in 2 independent colorectal cancer patient cohorts (P < 0.05, log-rank test). miR-196b-5p inhibition led to significantly increased colorectal cancer cell migration/invasion and metastases formation in mice, whereas ectopic overexpression showed the opposite phenotype. Molecular profiling and target confirmation identified an interaction between miR-196b-5p and HOXB7 and GALNT5, which in turn regulated colorectal cancer cell migration.

Conclusions: The association of low levels of miR-196b-5p and poor prognosis in patients with colorectal cancer can be explained by its influence on cancer cell migration and metastases formation. miR-196b-5p has an impact on colorectal cancer progression pathways through direct interaction with genes involved in cancer cell migration. Clin Cancer Res; 23(17); 5255–66. ©2017 AACR.
Supplementary Figure 1 from Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy
Authors: Seremak Juliette R. , Gupta Kunj Bihari , Bonigala Sunilkanth , Liu Elise , Marshall Brendan , Zhi Wenbo , Bokhtia Riham M. , Panda Siva S. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: October 2024

Supplementary Figure 1 with legend
Supplementary Figure S7 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Figure S7 shows the quantification of PDCD4 protein levels detected by Western blot in K562 and HL60 cells transfected with miR-181d mimics or inhibitor or their corresponding controls using the Image J program, with Actin for normalization.
Supplementary Figure S5 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Figure S5 shows Lin28B-mediated proliferation depends in part on miR-181d in K562 and HL60 cells
Supplementary Figure S4 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Figure S4 shows the protein level of Lin28A and Lin28B in HEK-293T cell line infected with lentiviruses expressing Lin28B (Lin28B).
Supplementary Figure 12 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Combination of FK866 and olaparib leads to sustained cell cycle arrest in G2.
Supplementary Figure 11 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Combination of PARPi and NAMPTi lead to unresolved double stranded breaks NAPRT silenced models.
Data from Lactate Induces Tumor Progression via LAR Motif-Dependent Yin-Yang 1 Degradation
Authors: Du Shujuan , Chen Xiaoting , Han Xiao , Wang Yuyan , Yu Dan , Li Ying , Zhu Caixia , Tong Yin , Gao Shujun , Wang Junwen , Wei Fang , Cai Qiliang
Published: October 2024

Abstract
The metabolic reprogramming of aerobic glycolysis contributes to tumorigenesis. High plasma lactate is a critical regulator in the development of many human malignancies; however, the underlying molecular mechanisms of cancer progression in response to lactate (LA) remain elusive. Here, we show that the reduction of Yin-Yang 1 (YY1) expression correlated with high LA commonly occurs in various cancer cell types, including B-lymphoma and cervical cancer. Mechanistically, LA induces YY1 nuclear export and degradation via HSP70-mediated autophagy adjacent to mitochondria in a histidine (His)-rich LA-responsive (LAR) motif-dependent manner. The mutation of the LAR motif blocks LA-mediated YY1 cytoplasmic accumulation and in turn enhances cell apoptosis. Furthermore, low expression of YY1 promotes colony formation, invasion, angiogenesis, and growth of cancer cells in response to LA in vitro and in vivo using a murine xenograft model. Taken together, our findings reveal a key LAR element and may serve as therapeutic target for intervening cancer progression.

Implications: We have shown that lactate can induce YY1 degradation via its His-rich LAR motif and low expression of YY1 promotes cancer cell progression in response to lactate, leading to better prediction of YY1 targeting therapy.
Finerenone Improves Outcomes in Patients with Heart Failure with Mildly Reduced or Preserved Ejection Fraction Irrespective of Age: A Prespecified Analysis of FINEARTS-HF
Authors: Chimura Misato , Petrie Mark C. , Schou Morten , Martinez Felipe A. , Henderson Alasdair D. , Claggett Brian L. , Desai Akshay S. , Kolkhof Peter , Viswanathan Prabhakar , Lage Andrea , Lam Carolyn S.P. , Senni Michele , Shah Sanjiv J. , Rohwedder Katja , Mueller Katharina , Voors Adriaan A. , Zannad Faiez , Pitt Bertram , Vaduganathan Muthiah , Jhund Pardeep S. , Solomon Scott , McMurray John J.V.
Published: September 2024

Background:
Finerenone improves outcomes in patients with HF and mildly reduced or preserved ejection fraction (HFmrHF/HFpEF). It is important to understand the efficacy and safety of finerenone in these patients according to age.

Methods:
The aim of this analysis was to evaluate the interaction between age and the efficacy and safety of finerenone in the FINEARTS-HF trial (Finerenone trial to investigate efficacy and safety compared to placebo in patients with heart failure). A total of 6,001 patients aged 40-97 years were stratified by quartile (Q 1-4) of baseline age: Q1 40-66 years (n=1,581), Q2 67-73 years (n=1,587), Q 3 74-79 years (n=1,421), and Q4 ≧ 80 years (n=1,412). FINEARTS-HF evaluated the impact of age on the efficacy of finerenone with respect to the primary composite outcome of cardiovascular death and total (first and recurrent) HF events, including HF hospitalization or urgent HF event, along with secondary efficacy and safety outcomes.

Results:
The incidence of primary outcome increased with age. Finerenone reduced the risk of the primary outcome consistently across all age categories: RR (95% CI) Q1 0.70 (0.53- 0.92), Q2 0.83 (0.64-1.07), Q3 0.98 (0.76-1.26), and Q4 0.85 (0.67-1.07); p for interaction =0.27. Similarly, a consistent effect was observed for the components of the primary outcome. The mean increase in Kansas City Cardiomyopathy Questionnaire-total symptom score from baseline to 12 months was greater with finerenone than placebo, with a consistent effect across all age categories: mean placebo-corrected change (95% CI) Q1 2.87 (1.09-4.66), Q2 1.24 (-0.59-3.07), Q3 0.94 (-0.98-2.86), and Q4 1.24 (-0.90-3.38); P-interaction=0.50. Adverse events were similar across all age categories. The odds of experiencing hypotension, elevated creatinine, or hyperkalemia (increased) or hypokalemia (decreased) related to finerenone did not differ by age.

Conclusions:
In the FINEARTS-HF trial, finerenone reduced the primary outcome and components of the primary outcome, and improved symptoms across a wide age spectrum. In addition, finerenone was safe and well-tolerated, irrespective of age.

Trial Registration:
URL: https://clinicaltrials.gov Unique Identifiers: NCT04435626 and EudraCT 2020-000306-29.
Retrieval-Pretrained Transformer: Long-range Language Modeling with Self-retrieval
Authors: Rubin Ohad , Berant Jonathan
Published: October 2024

Retrieval-augmented language models (LMs) have received much attention recently. However, typically the retriever is not trained jointly as a native component of the LM, but added post-hoc to an already-pretrained LM, which limits the ability of the LM and the retriever to adapt to one another. In this work, we propose the Retrieval-Pretrained Transformer (RPT), an architecture and training procedure for jointly training a retrieval-augmented LM from scratch and applying it to the task of modeling long texts. Given a recently generated text chunk in a long document, the LM computes query representations, which are then used to retrieve earlier chunks in the document, located potentially tens of thousands of tokens before. Information from retrieved chunks is fused into the LM representations to predict the next target chunk. We train the retriever component with a semantic objective, where the goal is to retrieve chunks that increase the probability of the next chunk, according to a reference LM. We evaluate RPT on four long-range language modeling tasks, spanning books, code, and mathematical writing, and demonstrate that RPT improves retrieval quality and subsequently perplexity across the board compared to strong baselines.
Impatiens fujianensis (Balsaminaceae), a new species from China: evidence from morphological and molecular analyses
Authors: MA LIANG , CHEN XIN–YAN , ZHOU CHENG-YUAN , CHEN SHI-PIN
Published: October 2024

We here describe and illustrate a new species, Impatiens fujianensis (Balsaminaceae), from Fujian Province in southern China. Morphological comparisons indicated that I. fujianensis is similar to I. noli-tangere and I. yilingiana but showed distinct differences in leaves, inflorescences, pedicels and flowers. The molecular phylogenetic analysis based on nuclear ribosomal internal transcribed spacer (ITS) and two plastid regions (atpB-rbcL and trnL-F) indicated that I. fujianensis is a distinct species, which forms an independent lineage. Both morphological and molecular evidence supported the status of I. fujianensis as a new species.
Aristolochia sanheensis (Aristolochiaceae), a new species from Yunnan, Southwest China
Authors: YANG JIAN-MEI , HUANG RUI-ZHOU , LIU JIA-ZHU , ZHANG CHAO-JIANG , YANG YU-RONG , YIN LUN
Published: October 2024

Aristolochia sanheensis, a new species from Yunnan, Southwest China, is described and illustrated for the first time. It is similar to A. luudamcui from northern Vietnam in the morphology of the calyx shape and the color of the inner calyx tube and limb, but is clearly distinguished by the limb triangular in lateral view, the prickly outgrowths of the inner limb, and the upper part of limb separated to ca. 1/2–2/3. It is evaluated as Critically Endangered (CR) according to the IUCN categories and criteria.
Critical Pedagogy in Addressing Social Inequality and Promoting Social Justice in Education
Authors: Lamsal Hiranya
Published: September 2024

How can critical pedagogy contribute in addressing social inequality and promoting social justice in education? In what ways McLaren, Giroux and Apple conceptualize the role of teacher and student, and the issue of power and domination in education? How do critical consciousness, critical thinking and critical action address in education along with implications for teaching and learning practices? These questions are the main concerns to be discussed through this paper. Critical pedagogy is the philosophy of education that develops the learners to critique regarding the structures of power and oppression and it also shows the social movement that combines education with critical theory. Similarly, it is a theory of education that focuses on the relationship between power, knowledge and social justice. This review paper attempts to explore the contribution of critical pedagogy in addressing social inequality and promoting social justice in education. It is qualitative in nature. It adopts the analysis of documents from books and journal articles related to the critical pedagogy. This review paper concludes that critical pedagogy as a revolutionary approach to education to combat various diverse types of oppression. Through critical analysis and questioning of social inequalities, the development of a sense of agency, and participation in transformational action for a more just and equitable society are all goals of critical pedagogy.