bluuebunny/crossref_metadata_2025 huggingface dataset:
Fighting against biofilm: The antifouling and antimicrobial material
Authors: Li Chao , Gao Dongdong , Li Chunmei , Cheng Gang , Zhang Lijun
Published: July 2024

Biofilms are groups of microorganisms protected by self-secreted extracellular substances. Biofilm formation on the surface of biomaterial or engineering materials becomes a severe challenge. It has caused significant health, environmental, and societal concerns. It is believed that biofilms lead to life-threatening infection, medical implant failure, foodborne disease, and marine biofouling. To address these issues, tremendous effort has been made to inhibit biofilm formation on materials. Biofilms are extremely difficult to treat once formed, so designing material and coating bearing functional groups that are capable of resisting biofilm formation has attracted increasing attention for the last two decades. Many types of antibiofilm strategies have been designed to target different stages of biofilm formation. Development of the antibiofilm material can be classified into antifouling material, antimicrobial material, fouling release material, and integrated antifouling/antimicrobial material. This review summarizes relevant research utilizing these four approaches and comments on their antibiofilm properties. The feature of each method was compared to reveal the research trend. Antibiofilm strategies in fundamental research and industrial applications were summarized.
Synthesis and reactivity of an N-heterocyclic carbene–stabilized diazoborane
Authors: Zhang Chonghe , Cummins Christopher C. , Gilliard Robert J.
Published: July 2024

Diazo compounds and organic azides are widely used as reagents for accessing valuable molecules in multiple areas of fundamental and applied chemistry. Their capacity to undergo versatile chemical transformations arises from the reactive nature of an incipient dinitrogen molecule at the terminal position. In this work, we report the synthesis and characterization of an N-heterocyclic carbene (NHC)–stabilized diazoborane—a boron-centered analog of organic azides and diazoalkanes. The diazoborane displays a strong tendency to release dinitrogen, thus serving as a borylene source, in analogy to organic azides and diazoalkanes serving as nitrene and carbene sources, respectively. Also reminiscent of diazoalkane and organic azide reactivity, the diazoborane serves as a 1,3-dipole that undergoes uncatalyzed [3+2] cycloaddition with an unactivated terminal alkyne, affording a five-membered heterocycle after a two-step rearrangement.
Symbiosis of a lytic bacteriophage and
Yersinia pestis
and characteristics of plague in
Marmota himalayana
Authors: Lyu Dongyue , Duan Qun , Duan Ran , Qin Shuai , Zheng Xiaojin , Lu Xinmin , Bukai Asaiti , Zhang Peng , Han Haonan , He Zhaokai , Sha Hanyu , Wu Di , Xiao Meng , Jing Huaiqi , Wang Xin
Published: July 2024

Surveillance for animal plague was conducted in the
Marmota himalayana
plague focus of the Qinghai–Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of
Yersinia pestis
isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (
P
< 0.05). Twenty-one
Y. pestis-
specific phages were isolated, among which one
Y. pestis
lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with
Y. pestis
. Microscopy revealed the coexistence of lysed and non-lysed colonies of
Y. pestis
AKS2022HT87. Genome-wide analysis showed that certain strains of the
Y. pestis
AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and
Y. pestis
observed
in vitro
was highlighted in this study, laying the basis for further exploring the relationship between
Y. pestis
and its bacteriophages.

IMPORTANCE

Bacteriophages and host bacteria commonly coexist
in vivo
or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging
in vitro
due to limited medium nutrients. In this work, the natural symbiosis between
Yersinia pestis
and specific phages has been discovered in a
Marmota himalayana
specimen. Epidemiological analysis presented the characteristics of the
Y. pestis
and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the
Y. pestis
and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.
AcMNPV-miR-2 affects
Autographa californica
nucleopolyhedrovirus infection by regulating the expression of
ac28
and several other viral early genes
Authors: Yu Xinghua , Teng Tingkai , Duan Zhuowen , Wang Jinwen
Published: July 2024

Virus-encoded microRNAs (miRNAs) exert diverse regulatory roles in the biological processes of both viruses and hosts. This study delves into the functions of AcMNPV-miR-2, an early miRNA encoded by
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV). AcMNPV-miR-2 targets viral early genes
ac28
(
lef-6
),
ac37
(
lef-11
),
ac49
, and
ac63
. Overexpression of AcMNPV-miR-2 leads to reduced production of infectious budded virions (BVs) and diminished viral DNA replication. Delayed polyhedron formation was observed through light and transmission electron microscopy, and the larval lifespan extended in oral infection assays. Moreover, the mRNA expression levels of two Lepidoptera-specific immune-related proteins, Gloverin and Spod-11-tox, significantly decreased. These findings indicate that AcMNPV-miR-2 restrains viral load, reducing host immune sensitivity. This beneficial effect enables the virus to combat host defense mechanisms and reside within the host for an extended duration.

IMPORTANCE

Virus-encoded miRNAs have been extensively studied for their pivotal roles in finetuning viral infections. Baculoviruses, highly pathogenic in insects, remain underexplored concerning their encoded miRNAs. Previous reports outlined three AcMNPV-encoded miRNAs, AcMNPV-miR-1, -miR-3, and -miR-4. This study delves into the functions of another AcMNPV-encoded miRNA, AcMNPV-miR-2 (Ac-miR-2). Through a comprehensive analysis of target gene expression, the impact on larvae, and variations in host immune-related gene expression, we elucidate a functional pathway for Ac-miR-2. This miRNA suppresses viral load and infectivity and prolongs lifespans of infected larva by downregulating specific viral early genes and host immune-related genes. These mechanisms ultimately serve the virus's primary goal of enhanced propagation. Our study significantly contributes to understanding of the intricate regulatory mechanisms of virus-encoded miRNAs in baculovirus infections.
Supplemental Material: Balancing the oceanic Zn isotope budget: The key role of deep-sea pelagic sediments
Authors: Zhang Ganglan , Zhu Yaotao , Deng Yinan , al. et
Published: July 2024

Analytical methods, figures, and tables.  
Supplemental Material: Ultrahigh-temperature metamorphism revealed by felsic granulite xenoliths in southern Tibet
Authors: Sun Wen-Rui , al. et
Published: July 2024

Figures S1–S6 and Tables S1–S6. 
Comparison between patient characteristics, aetiology and outcomes in patients with and without cirrhosis with hepatocellular carcinoma diagnosed in a regional centre
Authors: Lamb Carly , Tham Jennifer , Goh Tee Lin , Barclay Stephen , Priest Matthew , Forrest Ewan H , Fraser Andrew , Kay David , Kasthuri Ram , Evans Jeff , Stanley Adrian J
Published: July 2024

Introduction

Hepatocellular carcinoma (HCC) is increasing in incidence across the UK. Most patients have underlying cirrhosis, but a significant minority do not. Progression and outcomes of HCC in patients without cirrhosis remains unclear.

This study aimed to establish the proportion and characteristics of patients with HCC occurring in those with and without cirrhosis in the West of Scotland.

Methods

Data were collected from our prospectively collected database on patient demographics, liver disease aetiology, stage at presentation and outcomes for patients with a diagnosis of HCC confirmed at the Regional West of Scotland multidisciplinary team from 2009 to 2015.

Results

638 patients were included. 138 (21.6%) did not have cirrhosis and were older at diagnosis than those with cirrhosis (72 years vs 68 years, p=0.001). A higher proportion of those without cirrhosis presented with more advanced HCC (Barcelona clinic liver cancer (BCLC) score B or above; p=0.003).

Patients with cirrhosis had median survival of 8 months, compared with those without cirrhosis (11.5 months) but survival was similar in both groups on Kaplan-Meier analysis (p=0.119). There was no difference in survival between these groups when adjusted for cancer stage.

Survival was influenced by BCLC score in both cirrhotic and non-cirrhotic groups, as was survival by Child-Pugh score in patients with cirrhosis. Among the patients who underwent transarterial chemoembolisation (TACE), those with cirrhosis had worse survival (p=0.044).

Conclusion

21.6% of patients with a new diagnosis of HCC in our region did not have underlying cirrhosis. Patients with non-cirrhotic HCC were diagnosed at an older age, with more advanced stage of HCC. There was no difference in overall survival between patients with HCC with and without cirrhosis, however, survival after TACE was higher in those without cirrhosis.
Ocular protection practice and associated factors among welders in small-scale industries in Hosanna town, Southern Ethiopia, 2023
Authors: Birhan Getenet Shumet , Wossoro Henock Erkeno , Admassu Nebiyat Feleke , Eticha Biruk Lelisa
Published: July 2024

Purpose

Good eye protection is the most important factor in preventing eye injuries. Most eye injuries are due to the improper use or lack of use of eye protection equipment. Therefore, this study aims to assess eye protection practice and associated factors among welders in small-scale industries in Hosanna town of Southern Ethiopia.

Methods

A cross-sectional study was conducted on 420 welders between 14 August and 14 September 2023. A structured questionnaire was used to collect the data entered into Epi-data V.4.6 and analysed using a statistical package for social science V.25.0. Descriptive statistics was used to describe the characteristics of study participants. Binary logistic regression analysis was carried out to identify factors associated with eye protection practice. Finally, the OR with a corresponding 95% CI was computed to show the strength of the association. A p value <0.05 was considered to declare statistical significance.

Results

A total of 420 study participants were included. Good eye protection practice was 43.6% (95% CI 43.41 to 43.79). Monthly income between 4000 and 8000 and above 8000 Ethiopian birr, knowledge (adjusted OR (AOR)=3.90, 95% CI 1.96 to 7.78), permanent work pattern (AOR=2.86, 95% CI 1.59 to 5.17), previous ocular trauma (AOR=3.09, 95% CI 1.53 to 6.22) were positively associated with good eye protection practice.

Conclusion

The results of this study revealed poor eye protection practice among welders. Factors such as monthly income, previous ocular injury, work pattern and knowledge of eye Personal Protective Equipment were significantly associated with eye protection practice.
Risk assessment for perfluorooctanoic acid (PFOA) in air, blood serum and water: mortality from liver and kidney disease
Authors: Park Robert M
Published: July 2024

Background

Cancer and non-cancer associations have been observed with PFAS (perfluoroalkyl and polyfluoroalkyl) substances in the general population, in populations from locally contaminated environments and in exposed workers.

Methods

A quantitative risk assessment on the PFAS substance perfluorooctanoic acid (PFOA) was conducted for six outcomes using two occupational mortality studies that reported sufficient data to estimate exposure-relationships in relation to serum PFOA levels. Excess lifetime mortality risks were calculated using a life table procedure that applies an exposure response to time-dependent PFOA serum levels for a surviving hypothetical population from ages 20 to 85. Both occupational and general population exposures were described as serum levels, and as air and drinking water concentrations.

Results

The estimated occupational inhalation concentrations conferring the benchmark one-per-thousand lifetime risk were 0.21 µg/m3for chronic kidney disease, 1.0 µg/m3for kidney cancer and (from the two studies) 0.67 and 1.97 µg/m3for chronic liver disease. Specific excess lifetime risks estimated in the general population at current PFOA serum levels (~ 1 ng/mL) range 1.5–32 per 100 000 which corresponds to drinking water concentrations of less than 10 ppt.

Conclusion

Over eight outcome risk estimates, the serum PFOA concentrations conferring 1/1000 occupational lifetime risk ranged 44 to 416 ng/mL corresponding to air concentrations ranging 0.21 to 1.99 µg/m3. The analyses provide a preliminary PFOA quantitative risk assessment for liver and kidney disease mortality which, together with reported assessments for several other end-points, would inform policy on PFAS.
Social determinants of food insecurity experienced by Ecuadorian women during the COVID-19 pandemic of Summer 2020: an online survey at the individual level
Authors: Carpio Arias Tannia Valeria , Guijarro-Garvi Marta , Morejón-Terán Yadira Alejandra , Ruíz-Cantero María Teresa
Published: July 2024

The COVID-19 pandemic has amplified concerns about food insecurity, prompting its investigation. An online pilot survey anonymously gathered responses from a non-probabilistic sample of 2058 Ecuadorian women. The Food and Agriculture Organization's Food Insecurity Experience Scale was used to measure moderate or severe food insecurity (MSFI). Data quality was assessed using the Rasch item response theory model; this is a single-parameter logistic model that considers food insecurity severity as a latent trait. The analysis produced MSFI prevalence rates with 90% confidence level margins of error (90%MoE). The highest MSFI was found in women: lacking resources for personal expenses (29.53%, 90%MoE = 3.21) compared to those who had them (12.47, 90%MoE = 1.40); who live in the Amazon region (21.37, 90%MoE = 4.24) versus those living in Highlands (17.66%, 90%MoE = 1.77) or in Coast (13.44%, 90%MoE = 2.40); with three or more children (20.97%, 90%MoE = 4.71) against those without children (12.63%, 90%MoE = 3.57); who experienced income reduction during confinement (18.31%, 90%MoE = 2) compared to those who did not (15.71%, 90%MoE = 1.85); and who are rural (18.13%, 90%MoE = 2.83) versus urban residents (16.63%, 90%MoE = 1.55). This study highlights that the most vulnerable Ecuadorian women experienced the highest food insecurity levels during lockdown, emphasizing the need to consider the intersection between income and sociodemographic factors and their impact on women's food insecurity in future research and policymaking.
Exceptional sequences in semidistributive lattices and the poset topology of wide subcategories
Authors: Barnard Emily , Hanson Eric J.
Published: July 2024

Let [Formula: see text] be a finite-dimensional algebra over a field. We describe how Buan and Marsh’s [Formula: see text]-exceptional sequences can be used to give a “brick labeling” of a certain poset of wide subcategories of finitely generated [Formula: see text]-modules. When [Formula: see text] is representation-directed, we prove that there exists a total order on the set of bricks which makes this into an EL-labeling. Motivated by the connection between classical exceptional sequences and noncrossing partitions, we then turn toward the study of (well-separated) completely semidistributive lattices. Such lattices come equipped with a bijection between their completely join-irreducible and completely meet-irreducible elements, known as rowmotion or the “[Formula: see text]-map.” Generalizing known results for finite semidistributive lattices, we show that the [Formula: see text]-map determines exactly when a set of completely join-irreducible elements forms a “canonical join representation.” A consequence is that the corresponding “canonical join complex” is a flag simplicial complex, as has been shown for finite semidistributive lattices and lattices of torsion classes. Finally, we demonstrate how Jasso’s [Formula: see text]-tilting reduction of finite-dimensional algebras can be encoded using the [Formula: see text]-map. We use this to define [Formula: see text]-exceptional sequences for finite semidistributive lattices. These are distinguished sequences of completely join-irreducible elements which we prove specialize to [Formula: see text]-exceptional sequences in the algebra setting.
AN INTERPRETABLE GLAUCOMA DETECTION USING DUAL SCALE CROSS-ATTENTION VISION TRANSFORMER-BASED LONG SHORT TERM MEMORY WITH OPTICAL CUP AND DISK SEGMENTATION
Authors: KRISHNAMOORTHY V. , LOGESWARI S.
Published: July 2024

Glaucoma is a kind of eye disease that tends to generate harm to the optic nerve. It is a neurodegenerative illness, which develops intraocular hypertension because of its maximized aqueous humor and blockage between the cornea and iris. It causes destruction to the optic nerve head, which transfers visual stimulus to the brain from the eyes. This results in loss of visual field and blindness. For vision, glaucoma is known to be a sneak thief due to its complexity in detecting it in the early stage. It requires continuous screening to determine the neurological disorder. Effective identification of glaucoma requires more cost and time, but it also causes human error in the detection phase based on resource availability. The problems based on the robustness of the algorithm are not solved in the earlier method especially relative to that human expert counterpart. Therefore, effective glaucoma detection with the help of deep learning is developed to recognize eye disease in the early stage. At first, the input eye images are taken from the available sites. Subsequently, the procedure for segmentation is done using the Optimized Dilated Mobile-Unet[Formula: see text] (ODMUnet[Formula: see text]) to segment the optic disc and optic cup in the input images. Here, the parameters in the developed ODMUnet[Formula: see text] are optimized using an Improved Drawer Algorithm (IDrA). The segmented “optic disc and optic cup” images are given to the developed Dual Scale Cross-Attention Vision Transformer-based Long Short-Term Memory (DSCAViT-LSTM) for glaucoma detection. The experimental outcomes of the recommended model are evaluated with other deep learning techniques to ensure its efficacy.
MALEXNET-EUNET: MULTI-CLASS LIVER CANCER CLASSIFICATION AND SEGMENTATION USING A HYBRID DEEP LEARNING SYSTEM
Authors: MOPARTHI NAGESWARA RAO , UNHELKAR BHUVAN , CHAKRABARTI PRASUN
Published: July 2024

Background and objective: One of the most prevalent and significant causes of cancer-related mortality worldwide is considered to be liver cancer. Techniques for automatically segmenting and classifying liver tumors are crucial for supporting medical professionals during the tumor diagnostic process. Classifying liver tumors is challenging due to noise, nonhomogeneity, and the significant appearance diversity observed in tumor tissue. Also, in recent years, most of the research has performed binary classification, but there is still a lack of research on multi-class liver cancer classification. Therefore, we perform a multi-class liver cancer classification and segmentation in this research. Methods: We propose a hybrid deep learning-based multi-class liver cancer classification and segmentation system in this research. The collected CT images are pre-processed in four stages: contrast enhancement, noise filtering, smoothing and sharpening, and liver region segmentation. Next, the binary, texture, histogram, and rotational, scalability, and translational (RST) features are extracted from the pre-processed images. Then, the average correlation (AC) and probability of error (POE) approaches are applied to selecting relevant features and excluding less significant features. After feature selection, a modified AlexNet (MAlexNet) model is used to classify the multi-class classification of liver tumors. Finally, the identified liver tumor regions are segmented using the enhanced U-Net (EUNet) model. Results: Identified liver tumors are accurately classified into three different categories using the proposed classification model: hemangioma (HEM), hepatocellular carcinoma (HCC), and metastatic carcinoma (MET), with an average accuracy of 99.19%. We have collected the multi-class liver cancer CT images from real time patients. The results of the experiments show that proposed hybrid system provides adequate overall accuracy, is less noise-sensitive, and outperforms other state-of-the-art techniques such as SVM, Faster RCNN, Mask RCNN, and SAR-U-Net on a wide range of CT images. Conclusion: Radiologists and doctors can identify liver tumors more accurately using the suggested innovative framework.
An Interview with Martin Robillard - 2024 SIGSOFT Awardee
Authors: Forti Stefano
Published: July 2024

Martin Robillard received the 2024 SIGSOFT Influential Educator Award for his significant contributions to hands-on software design education, including a textbook (Introduction to Software Design with Java) and a learner-focused software modeling tool (JetUML). He is currently a Professor in the School of Computer Science at McGill University, Montréal, Canada, he is a Distinguished Member of the ACM and a Fellow of the Alexander von Humboldt Foundation. He received his Ph.D. in Computer Science from the University of British Columbia. His research interests fall within the area of software engineering, focussing on human-centred software development. He was awarded six ACM SIGSOFT Distinguished Paper Awards for his work on recommendation systems, software traceability, and software documentation. Recently, he has been working on software documentation generation, test suite quality, and information privacy.
Establishing Metrics to Encourage Broader Use of Atomic Requirements - A Call for Exchange and Experimentation
Authors: Honig William L.
Published: July 2024

There are seemingly many advantages to being able to identify, document, test, and trace single or "atomic" requirements during system development and maintenance. Ongoing work with Agile development has focused on "user stories" that can capture individual features for implementation. However, it is still difficult to evaluate the quality of such requirements and teaching their creation is difficult.

Based on a working definition of atomic requirement, this paper proposes a set of metrics for their evaluation. Ten metrics designed to measure atomic requirements are presented here: five used on individual requirements statements and five applied to a requirements document or set of requirement statements.

Example metrics for individual requirements include Requirement Atomic Completeness and Requirement Atomic Verifiability. Requirement Traceability is a proposed metric for a set of atomic requirements (such as a traditional requirements specification document.)

Further work is needed to make the suggested metrics more consistent and precise, including exploring the use of tools that may automate some of the measures. However, a first step is to refine the metrics themselves and ensure they adequately measure atomic requirement quality.

Hence this note shares the proposed metrics to encourage discussion and to recommend experimentation. The author is applying the metrics in software engineering courses doing team software development.

The goal is the eventual acceptance of a set of requirements metrics specifically designed to evaluate atomic requirements. Better metric definitions may lead to wider utilization of atomic requirements and improved requirements engineering in general.
Report on the 12th ACM/IEEE International Workshop on Software Engineering for Systems-of-Systems and Software Ecosystems - SESoS@ICSE 2024
Authors: Antonino Pablo , Bae Doo-Hwan , Bertolino Antonia , Lonetti Francesca
Published: July 2024

This article reports on the results of the 12th ACM/IEEE International Workshop on Software Engineering for Systems-of-Systems and Software Ecosystems (SESoS 2024) in which researchers and practitioners discussed ideas and experiences on the research and practice for the development and evolution of complex softwareintensive systems, more specifically systems-of-systems (SoS) and software ecosystems (SECO). SESoS 2024 was co-located with the 46th IEEE/ACM International Conference on Software Engineering (ICSE 2024). After a decade running this workshop, the SESoS community is advancing on how to cope with the different dimensions that should be considered in the engineering of those classes of systems (i.e. technological, organizational, and social), and also is taking awareness of newer challenges for inclusiveness and sustainability. In addition, benchmarks for conducting research on the areas as well as approaches for investigating emerging domains (smart ecosystems) and non-functional requirements on those systems were also pointed out as relevant challenges.
Renin-angiotensin system-mediated nitric oxide signaling in podocytes
Authors: Semenikhina Marharyta , Bohovyk Ruslan , Fedoriuk Mykhailo , Stefanenko Mariia , Klemens Christine A. , Oates Jim C. , Staruschenko Alexander , Palygin Oleg
Published: July 2024

The renin-angiotensin system plays a crucial role in the production of intracellular nitric oxide within podocytes. This mechanism operates through the activation of the angiotensin II type 2 receptor, leading to dynamic modifications in intracellular calcium levels and the actin filament network. This intricate process is vital for linking the activity of angiotensin receptors to podocyte function.
New Concepts on Module Arens Regularity for Module Banach Algebras
Authors: Pourbahri Rahpeyma Omid , Ebrahimi Bagha Davood , Soleimani Rad Ghasem
Published: July 2024

The main purpose of this paper is to introduce a new definition of ‐module Arens regularity, which extends former standard definition. Then a new module structure on the semigroup algebra as ‐module with nontrivial right and left module actions is constructed. Using this construction, it is also proved that is a ‐module Arens regular if and only if is finite.
Multilayer Network‐Based Evaluation of the Efficiency and Resilience of Network Flows
Authors: Rácz-Szabó András , Ruppert Tamás , Abonyi János
Published: July 2024

Supply chain optimization and resource allocation are challenging because of the complex dynamics of flows. We can classify these flows based on whether they perform value‐added or nonvalue‐added activities in our process. The aim of this article is to present a multilayered temporal network‐based model for the analysis of network flows in supply chain optimization and resource allocation. Implementation of a multilayered network distinguishes value‐added from nonvalue‐added resource flows, enabling a comprehensive view of the flow of resources in the system. Incorporating weighted edges representing the probabilities of time‐dependent flows identifies the resource needs and excesses at each supply site, addresses optimal transportation challenges for resource reallocation, and assesses the efficiency and robustness of the system by examining the overlaps in network layers. The proposed method offers a significant extension to the toolsets for network flow analysis, which has the potential to improve decision‐making processes for organizations dealing with complex resource management problems. The applicability of the proposed method is demonstrated by analyzing the temporal network extracted from taxi cab flows in New York City. With the application of the method, the results indicate that significant reductions in idle times are achievable.
Data from PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models
Authors: Meehan Terrence F. , Conte Nathalie , Goldstein Theodore , Inghirami Giorgio , Murakami Mark A. , Brabetz Sebastian , Gu Zhiping , Wiser Jeffrey A. , Dunn Patrick , Begley Dale A. , Krupke Debra M. , Bertotti Andrea , Bruna Alejandra , Brush Matthew H. , Byrne Annette T. , Caldas Carlos , Christie Amanda L. , Clark Dominic A. , Dowst Heidi , Dry Jonathan R. , Doroshow James H. , Duchamp Olivier , Evrard Yvonne A. , Ferretti Stephane , Frese Kristopher K. , Goodwin Neal C. , Greenawalt Danielle , Haendel Melissa A. , Hermans Els , Houghton Peter J. , Jonkers Jos , Kemper Kristel , Khor Tin O. , Lewis Michael T. , Lloyd K.C. Kent , Mason Jeremy , Medico Enzo , Neuhauser Steven B. , Olson James M. , Peeper Daniel S. , Rueda Oscar M. , Seong Je Kyung , Trusolino Livio , Vinolo Emilie , Wechsler-Reya Robert J. , Weinstock David M. , Welm Alana , Weroha S. John , Amant Frédéric , Pfister Stefan M. , Kool Marcel , Parkinson Helen , Butte Atul J. , Bult Carol J.
Published: July 2024

Abstract
Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62–66. ©2017 AACR.
NAT10 Phase Separation Regulates YTHDF1 Splicing to Promote Gastric Cancer Progression
Authors: Liu Songyi , Lin Chunlin , Lin Xiang , Lin Penghang , He Ruofan , Pan Xiaoyu , Lin Yan , Ye Jianxin , Zhu Guangwei
Published: July 2024

Gastric cancer is an aggressive malignancy with poor patient outcomes. N-Acetyltransferase 10 (NAT10) is an acetyltransferase that has been reported to contribute to gastric cancer progression. In-depth investigation into the underlying molecular mechanisms driven by NAT10 could help identify therapeutic targets to improve gastric cancer treatment. In this study, we found that NAT10 forms condensates to regulate RNA dynamics and promote gastric cancer progression. In samples of patients with gastric cancer, elevated NAT10 expression correlated with an unfavorable prognosis, advanced disease stage, and metastasis. NAT10 enhanced the proliferation, migration, and invasion of gastric cancer cells; supported the growth of patient-derived organoids; and accelerated tumor development. A C-terminal intrinsically disordered region-mediated liquid–liquid phase separation of NAT10 and was essential for its tumor-promoting function in gastric cancer. Moreover, NAT10 interacted with the splicing factor serine/arginine-rich splicing factor 2 (SRSF2), leading to its acetylation and increased stability. Acetylated SRSF2 directly bound to the pre-mRNA of the m6A reader YTHDF1, resulting in enhanced YTHDF1 exon 4 skipping and upregulation of a short YTHDF1 transcript that could stimulate gastric cancer cell proliferation and migration. Furthermore, YTHDF1 exon 4 skipping correlated with NAT10 and SRSF2 expression and was associated with a more aggressive phenotype in samples of patients with gastric cancer. Together, this study uncovers the role of NAT10 liquid–liquid phase separation in modulating YTHDF1 splicing through SRSF2 acetylation to drive gastric cancer progression, providing insights into the oncogenic mechanism of NAT10.

Significance: Phase separation of NAT10 enables acetylation of SRSF2 that enhances YTHDF1 exon 4 skipping, which is a tumor-promoting axis in gastric cancer that represents potential therapeutic targets and prognostic biomarkers.
Table 2 from Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures
Authors: Mahmood Umair , Blake Andrew , Rathee Sanjay , Samuel Leslie , Murray Graeme , Sebag-Montefiore David , Gollins Simon , West Nicholas P. , Begum Rubina , Bach Simon P. , Richman Susan D. , Quirke Phil , Redmond Keara L. , Salto-Tellez Manuel , Koelzer Viktor H. , Leedham Simon J. , Tomlinson Ian , Dunne Philip D. , Buffa Francesca M. , Maughan Tim S. , Domingo Enric
Published: July 2024

RFS and OS outcomes in combined Grampian and GSE87211 cohorts (Cap+RT/5FU+RT subjects)
Table 1 from Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures
Authors: Mahmood Umair , Blake Andrew , Rathee Sanjay , Samuel Leslie , Murray Graeme , Sebag-Montefiore David , Gollins Simon , West Nicholas P. , Begum Rubina , Bach Simon P. , Richman Susan D. , Quirke Phil , Redmond Keara L. , Salto-Tellez Manuel , Koelzer Viktor H. , Leedham Simon J. , Tomlinson Ian , Dunne Philip D. , Buffa Francesca M. , Maughan Tim S. , Domingo Enric
Published: July 2024

Baseline characteristics of selected patients
Figure 3 from Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures
Authors: Mahmood Umair , Blake Andrew , Rathee Sanjay , Samuel Leslie , Murray Graeme , Sebag-Montefiore David , Gollins Simon , West Nicholas P. , Begum Rubina , Bach Simon P. , Richman Susan D. , Quirke Phil , Redmond Keara L. , Salto-Tellez Manuel , Koelzer Viktor H. , Leedham Simon J. , Tomlinson Ian , Dunne Philip D. , Buffa Francesca M. , Maughan Tim S. , Domingo Enric
Published: July 2024

Subtype-specific multivariate analysis of factors associated with Cap+RT or 5FU+RT subjects demonstrated strong associations of immune, radiosensitivity, and stromal signatures with complete responders in specific CMS subtypes (A). Interaction-specific univariate regression analysis of signatures associated with complete response (CR) in specific CMS subtypes demonstrated cytotoxic lymphocytes as an important predictor of CR in this treatment cohort (B and C).
Figure 1 from Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures
Authors: Mahmood Umair , Blake Andrew , Rathee Sanjay , Samuel Leslie , Murray Graeme , Sebag-Montefiore David , Gollins Simon , West Nicholas P. , Begum Rubina , Bach Simon P. , Richman Susan D. , Quirke Phil , Redmond Keara L. , Salto-Tellez Manuel , Koelzer Viktor H. , Leedham Simon J. , Tomlinson Ian , Dunne Philip D. , Buffa Francesca M. , Maughan Tim S. , Domingo Enric
Published: July 2024

Multivariate logistic regression analysis of all subjects in the combined dataset adjusted by cohort, T stage, and N stage. *OR is reported as “OR per SD” to account for diverse distributions. LateTA score, late transient-amplifying score; Ma-TBRS, macrophage TGFβ response signature.
Data from Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures
Authors: Mahmood Umair , Blake Andrew , Rathee Sanjay , Samuel Leslie , Murray Graeme , Sebag-Montefiore David , Gollins Simon , West Nicholas P. , Begum Rubina , Bach Simon P. , Richman Susan D. , Quirke Phil , Redmond Keara L. , Salto-Tellez Manuel , Koelzer Viktor H. , Leedham Simon J. , Tomlinson Ian , Dunne Philip D. , Buffa Francesca M. , Maughan Tim S. , Domingo Enric
Published: July 2024

Abstract
Response to neoadjuvant radiotherapy (RT) in rectal cancer has been associated with immune and stromal features that are captured by transcriptional signatures. However, how such associations perform across different chemoradiotherapy regimens and within individual consensus molecular subtypes (CMS) and how they affect survival remain unclear. In this study, gene expression and clinical data of pretreatment biopsies from nine cohorts of primary rectal tumors were combined (N = 826). Exploratory analyses were done with transcriptomic signatures for the endpoint of pathologic complete response (pCR), considering treatment regimen or CMS subtype. Relevant findings were tested for overall survival and recurrence-free survival. Immune and stromal signatures were strongly associated with pCR and lack of pCR, respectively, in RT and capecitabine (Cap)/5-fluorouracil (5FU)–treated patients (N = 387), in which the radiosensitivity signature (RSS) showed the strongest association. Upon addition of oxaliplatin (Ox; N = 123), stromal signatures switched direction and showed higher chances to achieve pCR than without Ox (p for interaction 0.02). Among Cap/5FU patients, most signatures performed similarly across CMS subtypes, except cytotoxic lymphocytes that were associated with pCR in CMS1 and CMS4 cases compared with other CMS subtypes (p for interaction 0.04). The only variables associated with survival were pCR and RSS. Although the frequency of pCR across different chemoradiation regimens is relatively similar, our data suggest that response rates may differ depending on the biological landscape of rectal cancer. Response to neoadjuvant RT in stroma-rich tumors may potentially be improved by the addition of Ox. RSS in preoperative biopsies provides predictive information for response specifically to neoadjuvant RT with 5FU.
Significance:
Rectal cancers with stromal features may respond better to RT and 5FU/Cap with the addition of Ox. Within patients not treated with Ox, high levels of cytotoxic lymphocytes associate with response only in immune and stromal tumors. Our analyses provide biological insights about the outcome by different radiotherapy regimens in rectal cancer.
The Influence of Corporate Social Responsibility in Supporting the Achievement of Firm Performance in The National Oil and Gas Companies of Indonesia
Authors: Darmawan Adi Putra Wawang
Published: July 2024

The presence of companies often triggers socio-economic that can disrupt the operations of oil companies. Previous research using stakeholder theory and the social license to operate theory contextualizes that operating companies need to focus on social and environmental responsibility to reduce socio-economic conflicts in local communities. A holistic CSR perspective becomes part of the company's strategic planning and core operations so that the company will be managed in the interests of its broad stakeholders to achieve maximum economic and social value in the long term. This research was conducted to analyse of the relationship between corporate social responsibility can provide social protection and it will generate profits for the company (business reasons). Researchers analyzed the relationship between corporate social responsibility and Firm Performance in The National Oil and Gas Companies of Indonesia, Pertamina in the period 2020 - 2022. The empirical analysis was conducted using Pertamina's sustainability performance highlights database with the measure of Economic, Environment, Social and Governance (ESDG aspect). This paper supports previous research which states that corporate social responsibility may not have a positive influence on Company Performance due to the complexity of the relationship. The results of this study indicate that the complexity of the relationship caused by the implementation of Pertamina Group's social and environmental responsibility activities is part of the implementation of the strategic role as a "locomotive of social development" as a state-owned enterprise (not always for business reasons), but it also aims to improve the company's reputation and credibility.
Transgender and Nonbinary Individuals’ Perceptions Regarding Gender-Affirming Hormone Therapy and Cardiovascular Health: A Qualitative Study
Authors: Rytz Chantal L. , Pattar Badal S.B. , Mizen Sara J. , Lieb Parker , Parsons Leigh Jeanna , Saad Nathalie , Dumanski Sandra M. , Beach Lauren B. , Marshall Zack , Newbert Amelia M. , Peace Lindsay , Ahmed Sofia B.
Published: July 2024

BACKGROUND:

Transgender and nonbinary individuals face substantial cardiovascular health uncertainties. The use of gender-affirming hormone therapy can be used to achieve one’s gender-affirming goals. As self-rated health is an important predictor of health outcomes, an understanding of how this association is perceived by transgender and nonbinary individuals using gender-affirming hormone therapy is required. The objective of this research was to explore transgender and nonbinary individuals’ perceptions of cardiovascular health in the context of using gender-affirming hormone therapy.

METHODS:

In this qualitative study, English-speaking transgender and nonbinary adults using gender-affirming hormone therapy for 3 months or more were recruited from across Canada using purposive and snowball sampling methods. Semistructured interviews were conducted through videoconference to explore transgender and nonbinary individuals’ perceptions of the association between gender-affirming hormone therapy and cardiovascular health between May and August 2023. Data were transcribed verbatim, and transcripts were analyzed independently by 3 reviewers using thematic analysis.

RESULTS:

Twenty-one participants were interviewed (8 transgender women, 9 transgender men, and 3 nonbinary individuals; median [range] age, 27 [20–69] years; 80% White participants). Three main themes were identified: cardiovascular health was not a primary concern in the decision-making process with regard to gender-affirming hormone therapy, the improved well-being associated with gender-affirming hormone therapy was felt to contribute to improved cardiovascular health, and health care provider knowledge and attitude facilitate the transition process.

CONCLUSIONS:

Gender-affirming hormone therapy in transgender and nonbinary individuals is perceived to improve cardiovascular health. Given the positive associations between care aligned with patient priorities, self-rated health, and health outcomes, these findings should be considered as part of shared decision-making and person-centered care.
Digital extended personality: development and testing of а digital daily life self-management scale
Authors: Soldatova Galina U. , Ilyukhina Svetlana N.
Published: July 2024

Background. The explosion of digital technologies and gadgets acting as sociocultural tools, forming a new technologically rich ecosystem, raises more and more questions in the scientific community about considering technologies not only as tools, but as external extensions or additions of a person. Objectives. The aim of the work is to develop and validate the Self-Management of Digital Daily Life (SMDDL) scale for digital extended personality. Study Participants. The study sample consisted of 1,797 adolescents and youth aged 14–35 years. Methods. The study utilized the SMDDL scale developed by the authors. The scale includes 3 subscales. To assess convergent and discriminant validity we used the self-assessment of user activity and online social capital, the Digital Competence Index, the Internet Addiction Scale, technique for assessing changes in psychological boundaries when using technical means MIG-TS-2, and the Attitude Towards Technology questionnaire. Results. The structure of the scale was refined based on the results of exploratory and confirmatory factor analysis (subscales Digital Device Management, Digital Sociality, Experiencing Digital Daily Life, α = 0.80–0.88). Compared to youth, adolescents scored lower; males scored higher than females on the three subscales of the SMDDL. All of the SMDDL subscales are positively related to the user activity, technophilia, and a number of MIG-TS-2 scales. Of the three subscales, only Digital Device Management did not show a positive relationship with Internet addiction, but was positively related to digital competence and technorationalism. Conclusions. Based on the data obtained, a conclusion was made about the reliability, consistency, and validity of the developed SMDDL scale. User activity and technophilia are the conditions for the formation of an extended digital personality, while digital competence and technorationalism become the tools of self-management of the diversity of digital extensions. Internet addiction as one of the risks for a technologically extended personality can be offset by the ability to self-manage one's digital extensions.
How do Children Choose Toys and are These Choices Associated with Developmental Outcomes?
Authors: Gavrilova Мargarita N. , Sukhikh Vera L.
Published: July 2024

Background. Despite the depth of theoretical analysis of play activity there is a lack of empirical data on the choice of toys by modern children. A toy is a means of constructing play and, therefore, can largely influence its key characteristics. Objectives. The study is a continuation of an earlier series of works aimed at experimentally clarifying children's toy preferences and the relationship of these preferences to individual developmental performance. Study Participants. 202 children aged 4-5 years were participants in the study. Previously published data obtained on a sample of 3–4-year-old children were used to analyze the age dynamics in toy preference. Methods. The study used an experimental design with a multiple-choice forced-choice method. Diagnostics of children's mental development included assessment of the main components of regulatory functions and the ability to understand emotions and was performed using instruments standardised on a Russian sample. Results. It was shown that children prefer highly realistic and detailed toys. In particular, such factors as the toy being detailed, the possibility of its use in playing through familiar plots, the adequacy of role-playing actions with it and the possibility to endow it with human features proved to be fundamentally important for children. Conclusions. From the distribution of choices in experimental trials and children's verbal explanations, it can be confidently concluded that play activity is based on the laws described in the works of Vygotsky, Elkonin, and Smirnova. It is also shown that children who choose the most realistic toys have better verbal working memory, but have a weaker ability in cognitive flexibility. According to the obtained data, as children grow older, they tend to choose less anthropomorphic toys.
Tillandsia ramon-lopezii: a new species from Venezuela, similar to T. brachycaulos (Bromeliaceae)
Authors: RAMÍREZ-MORILLO IVÓN , FERNÁNDEZ-CONCHA GERMÁN CARNEVALI , PINZÓN JUAN P. , TAMAYO CEN IVÁN
Published: July 2024

A species of Tillandsia, Tillandsia ramon-lopezii, from northern Venezuela, is proposed as new. The new taxon belongs in a group of species that are morphologically similar to T. brachycaulos but whose relationships require clarification. A full description, relevant iconography, including scanning electron microscope (SEM) images of peltate foliar and floral bract scales, and a discussion of affinities are provided. The conservation status of the new species was assessed using the IUCN Red List Criteria as LC.
Morphological description and DNA barcoding of Diamesa achipseensis sp. nov. (Diptera: Chironomidae: Diamesinae) from Southwestern Caucasus
Authors: MAKARCHENKO EUGENYI A. , SEMENCHENKO ALEXANDER A. , PALATOV DMITRY M.
Published: July 2024

Illustrated description of adult male, as well as DNA barcoding, of Diamesa achipseensis sp. nov. in comparison with close related species D. caucasica Kownacki et Kownacka from Southwestern Caucasus are provided. Interspecific distances between D. achipseensis sp. nov. and D. caucasica are extremely low (0.64% in average) despite the identified morphological differences. High similarity of these species is new example of genetically indistinguishable of some species of the genus Diamesa Meigen.