bluuebunny/crossref_metadata_2025 huggingface dataset:
The vector regulation hypothesis: dynamic competition between pathogen and vector behaviors constrains
Xylella fastidiosa
biofilm development in sharpshooter foreguts
Authors: Backus Elaine A. , Shugart Holly J.
Published: November 2024

Xylella fastidiosa
(
Xf
) bacteria form biofilm on the cuticular surfaces of the functional foregut (precibarium and cibarium) of its vectors, xylem fluid-ingesting sharpshooter leafhoppers and spittlebugs. While much is known about
Xf
biofilm development and maturation
in vitro
, little is known about these processes in vectors. Real-time (RT)-PCR was used to quantify
Xf
genomes daily in the functional foreguts of blue-green sharpshooters,
Graphocephala atropunctata,
over 7 days of exposure to infected grapevines. Scanning electron microscopy (SEM) was used to examine
Xf
biofilm formation at 4 and 7 days of that time course. PCR showed populations building and reducing over a 4-day cycle. SEM revealed that foreguts at 4 days showed variability in quantity and location of bacterial attachment. Only early-stage biofilm formation occurred in low-turbulence areas of the cibarium, while high-turbulence areas of the cibarium and precibarium had rare but older, more developed macro-colonies. Biofilm was almost absent at 7 days but left behind adhesive material and remnants of prior colonization. Evidence supports the hypothesis that bacterial colonization was repeatedly interrupted and constrained by the vector. Behaviors such as egestion and enzymatic salivation likely can loosen and eject
Xf
biofilm, perhaps when profuse biofilm interferes with ingestion. Thus, vector acquisition of
Xf
is a dynamic and stochastic process of interactions between bacteria and insects. We further hypothesize for future testing that the insect can regulate this interaction. A deep understanding of
Xf
acquisition will aid the ongoing development of grapevine resistance to vector transmission of xylellae diseases.

IMPORTANCE

Xylella fastidiosa
(
Xf
) is one of the most destructive invasive plant pathogens in the world, able to hijack new vectors when it invades a region; yet the temporal interplay of bacterial colonization and insect behavior is unknown. This paper describes important findings about the process of
Xf
biofilm formation and maturation in a vector, contrasting similarities and differences with such formation
in vitro
. Results support the hypothesis that the behavior of the vector constrains and may regulate
Xf
biofilm formation, in dynamic competition with the bacterium. The data from this paper partly explain why
Xf
is so successful at invasion. Because the bacterium can be acquired and inoculated very quickly, it can move readily from old to new vectors and host plants in all-new environments. Our findings are relevant to biosecurity decisions because they demonstrate the importance of identifying potential vector species in the
Xylella
invasion front.
Assessing horizontal gene transfer in the rhizosphere of
Brachypodium distachyon
using fabricated ecosystems (EcoFABs)
Authors: Priya Shweta , Rossbach Silvia , Eng Thomas , Lin Hsiao-Han , Andeer Peter F. , Mortimer Jenny C. , Northen Trent R. , Mukhopadhyay Aindrila
Published: November 2024

Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the
Brachypodium distachyon
rhizosphere in an EcoFAB using
Pseudomonas putida
KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from
P. putida
to another
B. distachyon
root colonizer,
Burkholderia
sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.

IMPORTANCE

We report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.
Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023
Authors: Carella Arianna , Carroll Karen C. , Munson Erik
Published: November 2024

Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the
International Journal of Systematic and Evolutionary Microbiology
during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to
Aerococcus
spp., several
Corynebacterium
spp.,
Exercitatus varius
gen. nov., sp. nov., and
Mycoplasma phocimorsus
sp. nov. With respect to nomenclature revision, the
Bacillus
and
Clostridium
genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera
Hallella
,
Hoylesella
,
Leyella
,
Segatella
, and
Xylanibacter
impacted several
Bacteroides
spp. and
Prevotella
spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.
A human monoclonal antibody neutralizing SARS-CoV-2 Omicron variants containing the L452R mutation
Authors: Stein Saskia C. , Hansen Guido , Ssebyatika George , Ströh Luisa J. , Ochulor Okechukwu , Herold Elisabeth , Schwarzloh Britta , Mutschall Doris , Zischke Jasmin , Cordes Anne K. , Schneider Talia , Hinrichs Imke , Blasczyk Rainer , Kleine-Weber Hannah , Hoffmann Markus , Klein Florian , Kaiser Franziska K. , Gonzalez-Hernandez Mariana , Armando Federico , Ciurkiewicz Malgorzata , Beythien Georg , Pöhlmann Stefan , Baumgärtner Wolfgang , Osterhaus Albert , Schulz Thomas F. , Krey Thomas
Published: November 2024

The effectiveness of SARS-CoV-2 therapeutic antibodies targeting the spike (S) receptor-binding domain (RBD) has been hampered by the emergence of variants of concern (VOCs), which have acquired mutations to escape neutralizing antibodies (nAbs). These mutations are not evenly distributed on the RBD surface but cluster on several distinct surfaces, suggesting an influence of the targeted epitope on the capacity to neutralize a broad range of VOCs. Here, we identified a potent nAb from convalescent patients targeting the receptor-binding domain of a broad range of SARS-CoV-2 VOCs. Except for the Lambda and BA.2.86 variants, this nAb efficiently inhibited the entry of most tested VOCs, including Omicron subvariants BA.1, BA.2, XBB.1.5, and EG.5.1 and to a limited extent also BA.4/5, BA.4.6, and BQ.1.1. It bound recombinant S protein with picomolar affinity, reduced the viral load in the lung of infected hamsters, and prevented the severe lung pathology typical for SARS-CoV-2 infections. An X-ray structure of the nAb-RBD complex revealed an epitope that does not fall into any of the conventional classes and provided insights into its broad neutralization properties. Our findings highlight a conserved epitope within the SARS-CoV-2 RBD that should be preferably targeted by therapeutic antibodies and inform rational vaccine development.

IMPORTANCE

Therapeutic antibodies are effective in preventing severe disease from SARS-CoV-2 infection and constitute an important option in pandemic preparedness, but mutations within the S protein of virus variants (e.g., a mutation of L452) confer resistance to many of such antibodies. Here, we identify a human antibody targeting the S protein receptor-binding domain (RBD) with an elevated escape barrier and characterize its interaction with the RBD functionally and structurally at the atomic level. A direct comparison with reported antibodies targeting the same epitope illustrates important differences in the interface, providing insights into the breadth of antibody binding. These findings highlight the relevance of an extended neutralization profiling in combination with biochemical and structural characterization of the antibody-RBD interaction for the selection of future therapeutic antibodies, which may accelerate the control of potential future pandemics.
Lipid nanoparticles as adjuvant of norovirus VLP vaccine augment cellular and humoral immune responses in a TLR9- and type I IFN-dependent pathway
Authors: Dai Weiqian , Xing Man , Sun Lingjin , Lv Lihui , Wang Xiang , Wang Yihan , Pang Xueyang , Guo Yingying , Ren Jiling , Zhou Dongming
Published: November 2024

Norovirus (NoV) virus-like particles (VLPs) adjuvanted with aluminum hydroxide (Alum) are common vaccine candidates in clinical studies. Alum adjuvants usually inefficiently assist recombinant proteins to induce cellular immune responses. Thus, novel adjuvants are required to develop NoV vaccines that could induce both efficient humoral and robust cellular immune responses. Lipid nanoparticles (LNPs) are well-known mRNA delivery vehicles. Increasing evidence suggests that LNPs may have intrinsic adjuvant activity and can be used as adjuvants for recombinant protein vaccines; however, the underlying mechanism remains poorly understood. In this study, we compared the adjuvant effect of LNPs and Alum for a bivalent GI.1/GII.4 NoV VLP vaccine. Compared with Alum, LNP-adjuvanted vaccines induced earlier production of binding, blocking, and neutralizing antibodies and promoted a more balanced IgG2a/IgG1 ratio. It is crucial that LNP-adjuvanted vaccines induced stronger Th1-type cytokine-producing CD4
+
T cell and CD8
+
T cell responses than Alum. The adjuvant activity of LNPs depended on the ionizable lipid components. Mechanistically, LNPs activated innate immune responses in a type I IFN-dependent manner and were partially dependent on Toll-like receptor (TLR) 9, thus affecting the adaptive immune responses of the vaccine. This conclusion was supported by RNA-seq analysis and
in vitro
cell experiments and by the deeply blunted T cell responses in IFNαR1
−/−
mice immunized with LNP-adjuvanted vaccines. This study not only identified LNPs as a high quality adjuvant for NoV VLP vaccines, but also clarified the underlying mechanism of LNPs as a potent immunostimulatory component for improving protein subunit vaccines.

IMPORTANCE

With the rapid development of mRNA vaccines, recurrent studies show that lipid nanoparticles (LNPs) have adjuvant activity. However, the mechanism of its adjuvant effect in protein vaccines remains unknown. In this study, we found that the LNP-adjuvanted norovirus bivalent virus-like particle vaccines led to durable antibody responses as well as Th1-type cytokine-producing CD4
+
T cell and CD8
+
T cell responses, which exceeded the efficiency of the conventional adjuvant aluminum hydroxide. Mechanistically, LNPs activated innate immune responses in a type I IFN-dependent manner and were partially dependent on Toll-like receptor 9, thus affecting the adaptive immune responses of the vaccine. This work unveils that LNPs as a potent immunostimulatory component may be ideal for generating CD8
+
T cell and B cell responses for recombinant protein vaccines.
Supplemental Material: Tracing carbonatite metasomatism in the source of arc magmatism using Li-Mg-Zn isotopes: Implications for deep carbon cycling
Authors: Yan Xiang-Yu , Yang De-Bin , al. et
Published: November 2024

Files included as Supplemental Material consist of Supplemental Text S1 (12 Figures and 5 Texts) and Supplemental Tables (11 Tables). They contain additional information regarding analytical methods and results.
Socioeconomic inequalities and dyslipidaemia in adult population of the Ravansar Non-Communicable Disease Cohort Study: the role of sex and age
Authors: Izadi Neda , Yari-Boroujeni Reza , Soofi Moslem , Niknam Mahdieh , Amiri Parisa , Najafi Farid
Published: November 2024

Objectives

This study represents a pioneering attempt to quantify the contribution of age, sex and socioeconomic status (SES) to the observed inequalities in lipid profile components.

Design

Cross-sectional study.

Setting

The data from the Ravansar Non-Communicable Disease (RaNCD) Cohort Study were used.

Participants

10 000 individuals aged 35–65 years.

Main outcome measures

Principal component analysis was used to determine the SES of individuals. Using the concentration index (C-index) and curves, the study assessed socioeconomic inequalities in dyslipidaemia in different age groups and genders. Decomposition analysis was used to determine the contribution of sex, age and SES to the observed inequality in the prevalence of dyslipidaemia components between the wealthiest and poorest groups.

Results

The prevalence of dyslipidaemia was 72.39% of the population and was significantly higher in women than in men (excluding hypertriglyceridaemia). Overall, no significant SES-based inequality in dyslipidaemia was observed (C-index=−0.045, p=0.116), but after adjustment for age and sex, individuals with high SES had increased odds of dyslipidaemia (OR=1.16, 95% CI: 1.03 to 1.31). Hypercholesterolaemia and hyper-low-density lipoprotein (LDL) were more common in individuals with lower SES (C-index=−0.117 and −0.105), while hypo-high-density lipoprotein (HDL) was more prevalent in individuals with higher SES (C-index=0.029), regardless of adjustment for age, sex and confounding factors. SES played a significant role in hypercholesterolaemia and hyper-LDL (322.11% and 400.14%), while sex dominated in hypertriglyceridaemia and hypo-HDL (814.05% and −615.26%) and contributed to the existing inequalities.

Conclusion

The results highlight the existing inequalities in lipid profiles due to SES, sex and age. Consideration of these factors in interventions and policy decisions is critical to reduce abnormalities and inform future interventions.
Fasting plasma glucose trends in the elderly living with HIV/AIDS on combination antiretroviral therapy regimens
Authors: Shang Menglin , Zhang Jing , Chen Mingyu , Chen Xiuyuan , Liu Cong , Zhong Haidan , Du Peishan , Li Quanmin , Cai Weiping , Li Linghua , Gu Jing
Published: November 2024

Background

With the ageing of people living with HIV/AIDS (PLWHA), the prevalence of chronic comorbidities, especially hyperglycaemia, is increasing among elderly PLWHA. Antiretroviral therapy (ART) is associated with fasting plasma glucose (FPG) levels. This study aimed to investigate both short-term and long-term FPG characteristics and trends across different ART regimens in elderly Chinese PLWHA.

Methods

This retrospective cohort study, based on hospital treatment information, classified ART regimens as this retrospective cohort study used hospital treatment data. ART regimens are classified into three categories: non-nucleoside reverse transcriptase inhibitors (NNRTIs) based, protease inhibitors (PIs) based and integrase strand transfer inhibitor (INSTIs) based. Propensity score matching was applied to control for confounding factors. Follow-up FPG characteristics were then described, and a generalised linear mixed model was employed to estimate FPG trends under different regimens within 1-year and 5-year periods following ART initiation.

Results

Participants had an average age of 58.28 years, with 75.02% male. FPG increased following ART initiation, with the most significant rise within 1 year of ART, followed by stabilisation. The FPG increase within 1 year was slower in the PIs-based group compared with the NNRTIs-based group (β=−0.08, 95% CI −0.15 to –0.01), while there was a higher prevalence of diabetes within 5 years of ART (31.55% vs 22.33%, standardised difference=0.357). The FPG increase within 1 year of ART did not differ between NNRTIs-based and INSTIs-based groups (β=−0.01, 95% CI −0.20, 0.18).

Conclusion

Our study highlights that elderly Chinese PLWHA experience an increase in FPG levels, particularly during the first year of ART, with variations observed across different ART regimens. The higher long-term prevalence of diabetes in the PIs-based regimen group emphasises the need for tailored glucose management strategies. Routine glucose monitoring and proactive management are crucial for preventing and controlling diabetes in this population, particularly given the long-term metabolic risks associated with ART.
Telehealth service use and quality of care among US adults with diabetes: A cross-sectional study of the 2022 health information national trends survey
Authors: Hong Young-Rock , Xie Zhigang , Nguyen Oliver T , Turner Kea , Walker Ashby F
Published: November 2024

Objective

To characterise telehealth use, reasons for using or not using telehealth and the factors associated with telehealth use among US adults with diabetes.

Design

A cross-sectional study.

Setting

Data were sourced from the 2022 Health Information National Trends Survey.

Participants

US adults aged 18 years or older with self-reported diagnosis of diabetes (both type 1 and type 2).

Primary and secondary outcomes

Past 12-month utilisation of telehealth services, modality (eg, video, voice only), overall perception of quality of care, perceived trust in healthcare system and patient-centred communication score.

Results

In an analysis of 1116 US adults with diabetes, representing 33.6 million individuals, 48.1% reported telehealth use in the past year. Telehealth users were likely to be younger, women, with higher income, and urban dwellers. Older adults (≥65 years) were less likely to use telehealth compared with those aged 18–49 years (OR 0.43, 95% CI 0.20 to 0.90). Higher income and more frequent healthcare visits were predictors of telehealth usage, with no significant differences across race, education or location. Across respondents with telehealth usage, 39.3% reported having video-only, 35.0% having phone (voice)-only and 25.7% having both modalities. The main motivations included provider recommendation, convenience, COVID-19 avoidance and guidance on in-person care needs. Non-users cited preferences for in-person visits, privacy concerns and technology challenges. Patient-reported quality-of-care outcomes were comparable between telehealth users and non-users, with no significant differences observed by telehealth modality or area of residence (metro status).

Conclusions

Around half of US adults with diabetes used telehealth services in the past year. Patient-reported care quality was similar for telehealth and in-person visits. However, further efforts are needed to address key barriers to telehealth adoption, including privacy concern, technology difficulties, and care coordination issues.
Long-term effects of pelvic floor training in male chronic pelvic pain, correlation between subjective and objective outcomes: a study protocol for a randomised controlled trial
Authors: Hallencreutz Grape Helena , Nordgren Birgitta , Renström Koskela Lotta
Published: November 2024

Introduction

Chronic primary pelvic pain syndrome (CPPPS) is a condition characterised by pain in the pelvic area together with lower urinary tract symptoms. Pathophysiology remains largely unclear. Common treatment modalities show unsatisfactory results. This randomised controlled trial aims to establish the long-term effect of pelvic floor re-education using biofeedback and home training for men with CPPPS evaluated with the National Institute of Health–Chronic Prostatitis Symptom Index (NIH-CPSI) and to explore if outcomes can be correlated to changes in objective urodynamic measures.

Methods and analysis

After inclusion all study participants will go through baseline testing consisting of urodynamic evaluation, assessment of the pelvic floor muscles and the NIH-CPSI questionnaire, thereafter, randomised to intervention or control group. Intervention consists of short daily session of pelvic floor muscle training, during 6 months. Parallelly with starting up, the intervention group will attend four bio-feedback sessions, to guide and facilitate the training. The training will initially aim on how to correctly activate and relax the pelvic floor muscles with functional enhancement further on. The control group will be offered to enter the intervention group after the 6-month assessment. The outcome will be assessed by repeating the baseline tests at 3, 6 and 12 months.

To compare the primary outcome, the NIH-CPSI questionnaire between and within the two groups will be analysed. Secondary outcomes are the differences in sub-score reduction according to the domains in the NIH-CPSI questionnaire, the manual assessment of the pelvic floor muscles and numerical results from the urodynamic testing. The correlation between subjective and objective outcomes will be analysed.

Ethics and dissemination

The study obtained ethical approval from the Swedish Ethical Review Authority (2023-00286-01). The study result will be published in a peer-reviewed medical journal and presented at an international conference.

Trial registration number

This trial is registered at Clinicaltrials.gov (NCT06115083).
Thresholds for the value judgement of health technologies in the United Arab Emirates: a consensus approach through voting sessions
Authors: Aldallal Sara , Farghaly Mohamed , Fahmy Sahar , Alnaqbi Khalid A , Al Naeem Wael , Alsaadi Mouza , Moukarzel Marleine , Nader Fasseeh Ahmad , Korra Nada , Abaza Sherif , Kaló Zoltán
Published: November 2024

Background

In the evolving healthcare landscape of the United Arab Emirates (UAE), establishing cost-effectiveness thresholds (CETs) is pivotal to informing decision-makers about the value of health technologies.

Objective

This study aimed to establish CETs for the UAE that harmonise with international standards while reflecting the nation’s unique healthcare needs and economic context.

Setting

United Arab Emirates.

Methods

A multitiered methodology was employed, involving a literature review, a panel of national experts and workshops with key stakeholders, including healthcare providers, government health departments and healthcare payers. The panel and workshops were integral in assessing global CET practices and their applicability to the UAE providing a preliminary framework for CET in the UAE. Structured voting sessions were then conducted allowing voting on crucial aspects of CET to determine the baseline threshold, multipliers for severity, rarity and health gain, and methodologies for quantifying disease severity.

Results

CETs were linked to the economic status of the UAE, with a baseline threshold of 0.75 times the gross domestic product per capita for one quality-adjusted life year gained. A multiplier system was introduced to reflect societal views on disease severity, disease rarity and the relative health benefit of health technologies. Based on the voting results, disease rarity was deemed the most crucial factor, receiving a maximum multiplier of 3X, while severity and health gain were assigned a maximum of 2X. The multiplier values for both disease severity and relative health gain would be determined on a continuous scale. The proportional or relative shortfall method would be used to assess disease severity.

Conclusions

The proposed CET framework for the UAE will be dependent on local generation of cost-effectiveness evidence. Periodic review of CETs based on initial experiences ensures the responsiveness of policymakers to the changing healthcare and economic environment.
Closed-form solution for a mathematical extension of the multi-term fractional Bateman equations via Mikusiński operational method
Authors: Jornet Marc
Published: November 2024

We give a closed-form solution, in terms of multivariate Mittag–Leffler functions, for a lower triangular linear fractional system consisting of Riemann–Liouville derivatives. For such a task, we use Mikusiński algebraic calculus, while solving a certain difference equation. The system is motivated by an extension of the multi-order fractional Bateman model in nuclear physics. Thus, the paper contributes to the theory of operational analysis in physics.
Trajectory Prediction Analysis of Basketball Players’ Movements Based on DSM Optimization Algorithm
Authors: Liu Yang , Zhang Wei , Liu Shaohua , Lyu Hang
Published: November 2024

In this paper, the action trajectory of basketball players is predicted and analyzed by the DSM optimization algorithm. Data on the movements of basketball players, including position, speed and acceleration are collected. The motion trajectory is predicted by the DSM optimization algorithm. At present, computer technology is more and more applied in sports training. Based on this, this paper studies the simulation of basketball players’ motion trajectory prediction. After describing the research background and significance, this paper constructs a human joint model and then proposes the motion process DSM algorithm to simulate the jump shot action of basketball players. In this paper, the algorithm and model are tested, and the experiment adopts the run-jump fatigue model to produce fatigue. The infrared high-speed motion capture system and three-dimensional force measuring table are used to collect the kinematics and dynamics data of the sudden stop jump shot before and after fatigue. The experimental results show that the trajectory prediction simulation proposed in this paper is feasible.
Question Embedding on Weighted Heterogeneous Information Network for Knowledge Tracing
Authors: Sun Jianwen , Du Shangheng , Zhou Jianpeng , Yuan Xin , Shen Xiaoxuan , Liang Ruxia
Published: November 2024

Knowledge Tracing (KT) aims to predict students’ future performance on answering questions based on their historical exercise sequences. To alleviate the problem of data sparsity in KT, recent works have introduced auxiliary information to mine question similarity, resulting in the enhancement of question embeddings. Nonetheless, there remains a gap in developing an approach that effectively incorporates various forms of auxiliary information, including relational information (e.g.,
question–student
,
question–skill
relation), relationship attributes (e.g.,
correctness
indicating a student's performance on a question), and node attributes (e.g.,
student ability
). To tackle this challenge, the Similarity-enhanced Question Embedding (SimQE) method for KT is proposed, with its central feature being the utilization of weighted and attributed meta-paths for extracting question similarity. To capture multi-dimensional question similarity semantics by integrating multiple relations, various meta-paths are constructed for learning question embeddings separately. These embeddings, each encoding different similarity semantics, are then fused to serve the task of KT. To capture finer-grained similarity by leveraging the relationship attributes and node attributes on the meta-paths, the
biased random walk algorithm
is designed. In addition, the
auxiliary node generation method
is proposed to capture high-order question similarity. Finally, extensive experiments conducted on six datasets demonstrate that SimQE performs the best among 10 representative question embedding methods. Furthermore, SimQE proves to be more effective in alleviating the problem of data sparsity.
Effects of Phenology on Plant Community Assembly and Structure
Authors: Cleland Elsa E. , Wolkovich E.M.
Published: November 2024

Phenology—the timing of critical stages of growth and reproduction and the transitions between them—determines environmental conditions and biotic interactions. Hence, phenology is a key functional trait influencing organisms’ survival and fitness; however, the role of phenology in community assembly processes has been less considered. Here we review the importance of phenology in environmental and biotic filtering, structuring priority effects, and species coexistence in the context of the assembly of native communities, as well as in invasions and restoration. We highlight the complexity of the life-history aspect of phenology, which makes simple trade-offs—such as between growth timing and competitive ability—part of larger plant strategies shaped by a framework of risk, reward, and investment over multiple timescales. Embracing this complexity could yield insights into how phenology shapes communities.
Contemporary Management of Acute Ischemic Stroke
Authors: Ho James P. , Powers William J.
Published: November 2024

In the past decade, adding mechanical thrombectomy (MT) of intracranial arterial occlusions to intravenous (IV) thrombolysis has revolutionized the treatment of acute ischemic stroke (AIS) by expanding the therapeutic window to 24 h. Treatment decisions require establishing a high probability of AIS; confirming time since last known well (LKW); assessing severity of the neurological deficit; determining any contraindications to IV thrombolysis; and performing neuroimaging, usually noncontrast computed tomography (NCCT), to exclude intracerebral hemorrhage. If time since LKW is less than 4.5 h, patients with disabling stroke without contraindications can proceed immediately to IV thrombolysis while the decision about MT is under way. For some patients, the MT decision can be made on the basis of clinical assessment, NCCT, and CT angiography showing a large vessel occlusion. Others may require additional neuroimaging. Patients who are not candidates for IV thrombolysis within 4.5 h or MT should be immediately evaluated for eligibility for extended-window IV thrombolysis or early antiplatelet treatment.
The fate of neuronal synapse homeostasis in aging, infection, and inflammation
Authors: Tacke Charlotte , Landgraf Peter , Dieterich Daniela C. , Kröger Andrea
Published: November 2024

Neuroplasticity is the brain’s ability to reorganize and modify its neuronal connections in response to environmental stimuli, experiences, learning, and disease processes. This encompasses a variety of mechanisms, including changes in synaptic strength and connectivity, the formation of new synapses, alterations in neuronal structure and function, and the generation of new neurons. Proper functioning of synapses, which facilitate neuron-to-neuron communication, is crucial for brain activity. Neuronal synapse homeostasis, which involves regulating and maintaining synaptic strength and function in the central nervous system (CNS), is vital for this process. Disruptions in synaptic balance, due to factors like inflammation, aging, or infection, can lead to impaired brain function. This review highlights the main aspects and mechanisms underlying synaptic homeostasis, particularly in the context of aging, infection, and inflammation.
A Heuristic Motion Planning Algorithm for a Mobile Robot With Nonholonomic Constraints
Authors: Tran Duc Thien , Pham Duc Huy , Nguyen Quang Chien
Published: November 2024

This paper proposes a heuristic motion planning algorithm to enhance optimal path determination and tracking for a differential drive mobile robot within a global environment. The proposed method uses the A‐star search algorithm to discover the optimal path between the start and goal vertices. This algorithm employs precise distance values and heuristic distance values to compute and expand the vertex for identifying a suitable path. When the path is generated, the movement of the robot is regulated by an attractive potential field (APF) and a repulsive potential field (RPF). The APF assists the robot in following its designed path, while the RPF is employed to avoid obstacles. Subsequently, the APF plays a role in helping the robot return to its trajectory. In case of obstacles obstruct the path, the A‐star algorithm identifies a new alternative route starting from the current position to the goal, and the robot navigates along this path. During a series of scenario evaluation, the algorithm demonstrates the ability to present optimal solutions in complex environments. To validate the effectiveness of the system, the simulation is executed with the Webots R2021a software. Then, experimental verification for the designed robot demonstrates the system’s high accuracy in tracking and obstacle avoidance on a specific map.
Alterations in the Gut Microbiota in Chinese Patients With Intrahepatic Cholestasis of Pregnancy
Authors: Lei Xiaozhen , Yu Jiangyan , Huang Yan , Lai Hua , Xin Siming , Zeng Xiaoming
Published: November 2024

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy‐specific liver disease and the second most frequent cause of jaundice in pregnancy, but the etiology of it is poorly understood. By collecting blood and fecal samples from 12 healthy pregnant women (CON group) and 32 ICP patients (ICP group) in China, we performed 16s rRNA gene sequencing and analyzed microbial diversity. The results showed a decrease in species richness of the ICP group compared to that in the CON group, with a significant difference in species diversity between the two groups. Differential analysis revealed the following biomarkers: s__unclassified__Megamonas, g__Megamonas, f__Selenomonadaceae, c__Bacilli, and o__Lactobacillales. Importantly, we found a decrease in species richness of Selenomonadaceae at the family level and decreased bacilli at the class level in ICP patients. Correlation network analysis and functional gene prediction were performed accordingly. Our data provided new information linking microbiota and ICP, and are possibly helpful for further exploration of the disease.
Laparoscopic Cholecystectomy for Gall Bladder Volvulus: A Report of an Original Case With Review of Literature
Authors: Mohammed Ayad Ahmad
Published: November 2024

Background: Volvulus of gallbladder is defined as a rotation of the gallbladder on its mesentery along the axis of the cystic duct and cystic artery. Many factors are postulated to be the causes such as anatomical, mechanical, physiological, and hormonal risk factors but the presence of a distended gallbladder with a redundant mesentery is thought to be an important cause.

Case presentation: A 68‐year‐old woman presented with right hypochondrial pain and vomiting for 2 days that was radiated to the interscapular region and associated with nausea and vomiting. The patient had no jaundice and the abdominal examination showed severe tenderness with guarding during palpation of the right upper abdomen with no palpable mass. The WBCs were elevated, with normal liver enzymes, bilirubin, and alkaline phosphatase. The ultrasound showed a single gallstone with increased wall thickness. There was no significant clinical improvement with antibiotics and analgesics. During laparoscopy, volvulus of the gallbladder was discovered causing gangrene of the gallbladder. Laparoscopic detorsion and successful laparoscopic cholecystectomy were performed. The patient was discharged on the third postoperative day with dramatic improvement with no postoperative complications.

Conclusion: Gall bladder volvulus is an acute surgical emergency that is usually seen in the elderly population. It required a high index of suspicion especially in the absence of gallstones and must be differentiated from acalculous cholecystitis. Most cases are discovered at surgery. It must be managed with immediate detorsion and cholecystectomy, and the prognosis is excellent in most cases after an appropriate surgical intervention.
Supplementary Table S3 from KHSRP Stabilizes m6A-Modified Transcripts to Activate FAK Signaling and Promote Pancreatic Ductal Adenocarcinoma Progression
Authors: Xu Zilan , Zhou Yifan , Liu Shaoqiu , Zhao Hongzhe , Chen Ziming , Li Rui , Li Mei , Huang Xudong , Deng Shuang , Zeng Lingxing , Zhao Sihan , Zhang Shaoping , He Xiaowei , Liu Ji , Xue Chunling , Bai Ruihong , Zhuang Lisha , Zhou Quanbo , Chen Rufu , Lin Dongxin , Zheng Jian , Zhang Jialiang
Published: November 2024

Supplementary Table S3
Supplementary Table S6 from NQO1 Triggers Neutrophil Recruitment and NET Formation to Drive Lung Metastasis of Invasive Breast Cancer
Authors: Wang Xinzhi , Qu Yi , Xu Qianqian , Jiang Zeyu , Wang Hang , Lin Binyan , Cao Zehong , Pan Yuqi , Li Sheng , Hu Yili , Yang Hui , He Li , Chang Hang , Hang Bo , Wen Hongmei , Wu Hao , Mao Jian-Hua
Published: November 2024

Supplementary Table S6
Supplementary Video S1 from Targeting Catechol-O-Methyltransferase Induces Mitochondrial Dysfunction and Enhances the Efficacy of Radiotherapy in Glioma
Authors: Jiao Meng , Pirozzi Christopher J. , Yu Chen , Bao Xuhui , Hu Mengjie , Pan Dong , Littleton Sejiro , Reynolds Nathan , Saban Daniel R. , Li Fang , Li Chuan-Yuan
Published: November 2024

Supplementary video 1
Figure S2 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S2
Figure S13 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S13
Figure S1 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S1
Supplementary Data Figure S3 from Neuroendocrine Differentiation in Prostate Cancer Requires ASCL1
Authors: Rodarte Kathia E. , Nir Heyman Shaked , Guo Lei , Flores Lydia , Savage Trisha K. , Villarreal Juan , Deng Su , Xu Lin , Shah Rajal B. , Oliver Trudy G. , Johnson Jane E.
Published: November 2024

Castration does not alter growth or heterogeneity of RPM and RPMA allograft tumors
Data from Neuroendocrine Differentiation in Prostate Cancer Requires ASCL1
Authors: Rodarte Kathia E. , Nir Heyman Shaked , Guo Lei , Flores Lydia , Savage Trisha K. , Villarreal Juan , Deng Su , Xu Lin , Shah Rajal B. , Oliver Trudy G. , Johnson Jane E.
Published: November 2024

Abstract
Most patients with prostate adenocarcinoma develop resistance to therapies targeting the androgen receptor (AR). Consequently, a portion of these patients develop AR-independent neuroendocrine (NE) prostate cancer (NEPC), a rapidly progressing cancer with limited therapies and poor survival outcomes. Current research to understand the progression to NEPC suggests a model of lineage plasticity whereby AR-dependent luminal-like tumors progress toward an AR-independent NEPC state. Genetic analysis of human NEPC identified frequent loss of RB1 and TP53, and the loss of both genes in experimental models mediates the transition to a NE lineage. Transcriptomics studies have shown that lineage transcription factors ASCL1 and NEUROD1 are present in NEPC. In this study, we modeled the progression of prostate adenocarcinoma to NEPC by establishing prostate organoids and subsequently generating subcutaneous allograft tumors from genetically engineered mouse models harboring Cre-induced loss of Rb1 and Trp53 with Myc overexpression (RPM). These tumors were heterogeneous and displayed adenocarcinoma, squamous, and NE features. ASCL1 and NEUROD1 were expressed within NE-defined regions, with ASCL1 being predominant. Genetic loss of Ascl1 in this model did not decrease tumor incidence, growth, or metastasis; however, there was a notable decrease in NE identity and an increase in basal-like identity. This study provides an in vivo model to study progression to NEPC and establishes the requirement for ASCL1 in driving NE differentiation in prostate cancer.

Significance: Modeling lineage transitions in prostate cancer and testing dependencies of lineage transcription factors have therapeutic implications, given the emergence of treatment-resistant, aggressive forms of neuroendocrine prostate cancer.

See related commentary by McQuillen and Brady, p. 3499
Supplementary Figure S7 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: November 2024

Subgroup analysis of confirmed ORR by tTMB for (A) durvalumab plus tremelimumab plus EP versus EP and (B) durvalumab plus EP versus EP. In each panel, the shaded band shows the confidence interval for the ITT population; circle sizes are proportional to the number of responses.
Supplementary Figure 1 from GEN-1 in Combination with Neoadjuvant Chemotherapy for Patients with Advanced Epithelial Ovarian Cancer: A Phase I Dose-escalation Study
Authors: Thaker Premal H. , Bradley William H. , Leath Charles A. , Gunderson Jackson Camille , Borys Nicholas , Anwer Khursheed , Musso Lauren , Matsuzaki Junko , Bshara Wiam , Odunsi Kunle , Alvarez Ronald D.
Published: November 2024

Changes in IL-12 and IFN-γ levels in blood samples
Supplementary Figure 2 from Circulating Tumor DNA Analysis Detects FGFR2 Amplification and Concurrent Genomic Alterations Associated with FGFR Inhibitor Efficacy in Advanced Gastric Cancer
Authors: Jogo Tomoko , Nakamura Yoshiaki , Shitara Kohei , Bando Hideaki , Yasui Hisateru , Esaki Taito , Terazawa Tetsuji , Satoh Taroh , Shinozaki Eiji , Nishina Tomohiro , Sunakawa Yu , Komatsu Yoshito , Hara Hiroki , Oki Eiji , Matsuhashi Nobuhisa , Ohta Takashi , Kato Takeshi , Ohtsubo Koushiro , Kawakami Takeshi , Okano Naohiro , Yamamoto Yoshiyuki , Yamada Takanobu , Tsuji Akihito , Odegaard Justin I. , Taniguchi Hiroya , Doi Toshihiko , Fujii Satoshi , Yoshino Takayuki
Published: November 2024

Box plots show max VAF in the tissue+ctDNA+ and tissue-ctDNA+ groups
Supplementary Figure 1 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Supplementary Figure 1: A; Immunoblot analysis of MEC-1 cells showing expression of total and phospho-ERK1/2 and AKT in untreated control (NA), ibrutinib or dasatinib-pre-treated cells (both at 500 nM for 60 minutes). Actin was analyzed as an additional loading control. B; Venn diagrams showing overlap of kinases isolated by the different KI used to create kinobeads during this study. C; Correlation graphs comparing intensities (Log10 scale) for kinases isolated from MEC-1 lysates by Ki-NET beads in untreated, ibrutinib-and dasatinib pre-treated cells.
Supplementary Dataset 1 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Large kinome signature gained from experiments using MEC-1 cells, showing changes in response to ibrutinib and dasatinib treatment.
Figure 5 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Longitudinal kinobead profiling of sIgM response in patients undergoing ibrutinib therapy. A, Heatmap comparing sIgM activation kinome fingerprints for IcICLLe clinical trial patients (n = 4) using their baseline (pre-therapy) sample and samples taken 1 month following commencement of ibrutinib therapy. Grey boxes denote loss of kinase binding. B, Graph comparing changes in KEGG pathways between baseline (BL) and 1-month (1M) samples. C, Graph comparing relative change of binding for kinases found to demonstrate significant change within 1-month samples in response to sIgM stimulation. D, Representative immunoblotting corroborating changes to kinases found by kinobead-MS.
Supplementary Information from A Phase I Study of LSZ102, an Oral Selective Estrogen Receptor Degrader, with or without Ribociclib or Alpelisib, in Patients with Estrogen Receptor–Positive Breast Cancer
Authors: Jhaveri Komal , Juric Dejan , Yap Yoon-Sim , Cresta Sara , Layman Rachel M. , Duhoux Francois P. , Terret Catherine , Takahashi Shunji , Huober Jens , Kundamal Nicole , Sheng Qing , Balbin Alejandro , Ji Yan , He Wei , Crystal Adam , De Vita Serena , Curigliano Giuseppe
Published: November 2024

The supplementary information describes the procedures used to assess circulating tumor DNA using the Novartis PanCancer gene panel.
Supplementary Figure 6 from A Phase I Study of LSZ102, an Oral Selective Estrogen Receptor Degrader, with or without Ribociclib or Alpelisib, in Patients with Estrogen Receptor–Positive Breast Cancer
Authors: Jhaveri Komal , Juric Dejan , Yap Yoon-Sim , Cresta Sara , Layman Rachel M. , Duhoux Francois P. , Terret Catherine , Takahashi Shunji , Huober Jens , Kundamal Nicole , Sheng Qing , Balbin Alejandro , Ji Yan , He Wei , Crystal Adam , De Vita Serena , Curigliano Giuseppe
Published: November 2024

Supplementary figure 6 shows exploratory multivariable predictors of disease progression in each treatment arm.
Supplement 1 from A Phase I Study of LSZ102, an Oral Selective Estrogen Receptor Degrader, with or without Ribociclib or Alpelisib, in Patients with Estrogen Receptor–Positive Breast Cancer
Authors: Jhaveri Komal , Juric Dejan , Yap Yoon-Sim , Cresta Sara , Layman Rachel M. , Duhoux Francois P. , Terret Catherine , Takahashi Shunji , Huober Jens , Kundamal Nicole , Sheng Qing , Balbin Alejandro , Ji Yan , He Wei , Crystal Adam , De Vita Serena , Curigliano Giuseppe
Published: November 2024

Supplement 1 contains the trial protocol.