bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultra‐processed food and non‐communicable diseases in the United Kingdom: A narrative review and thematic synthesis of literature
Authors: Henney Alex E. , Gillespie Conor S. , Alam Uazman , Hydes Theresa J. , Boyland Emma , Cuthbertson Daniel J.
Published: January 2024

The social and economic constructs of the United Kingdom (UK) provide a fertile food environment for the dramatic expansion in the ultra‐processed food (UPF) market, driving increased UPF consumption. This has coincided with the significant increase in the incidence and prevalence of non‐communicable diseases (NCDs) such as obesity, type 2 diabetes, cardiovascular disease, and cancer, with an inherent impact on morbidity and mortality. Our review aims to assess the current epidemiological and public health trends in the United Kingdom, specifically examining consumption of UPFs and subsequent development of NCDs, summarizing existing meta‐analytical and experimental approaches. First, we address important socioeconomic and psychosocial domains that may contribute to increased availability and consumption of UPF. Additionally, we explore the putative mechanistic basis for the association between UPFs and NCDs: partly attributable to their energy density, the macro‐ and micronutrient composition (including high refined carbohydrate, saturated, and trans fats composition, in addition to low fiber and protein content), and artificially engineered additives and other compounds that adversely affect health in inadequately researched pathophysiological pathways. This review highlights the importance of promoting minimally processed diets to both clinical and political decision makers.
How well does Invisalign ClinCheck predict actual results: A prospective study
Authors: Ghislanzoni Luis Huanca , Kalemaj Zamira , Manuelli Maurizio , Magni Cinzia , Polimeni Antonella , Lucchese Alessandra
Published: January 2024

Introduction

This study aimed to compare achieved movements with predicted movements after 28‐week use of Invisalign Lite aligners.

Settings and Sample Population

The digital impressions of 21 subjects treated with Invisalign Lite at a private practice and in the dental clinic (Milan, Italy) were taken and analysed. Subjects were Caucasian with a mean age of 20.1 years.

Methods

Patients were analysed at two time points: at T0, before starting therapy, and at T1, after 28 weeks of treatment with Invisalign clear aligners, with a 2‐week change interval. The changes that occurred between T0 and T1 were compared to the predicted changes between T0 and Ts (setup/ClinCheck). Tooth movement performance was estimated through variables calculated as the difference between obtained and planned movements.

Results

In both maxillary and mandibular arches, the teeth that exhibited the least accurate expression of torque were the central incisors. Tip was not accurate on maxillary central incisors and canines, mandibular central incisors, lateral incisors, first premolars, second premolars and first molars. Rotations were under‐expressed on maxillary lateral incisors, canines and second premolars and on mandibular central incisors, canines, first premolars, second premolars and first molars. The overall angular changes showed a tendency to underperformance. Transverse linear changes were accurate with a significant overperformance on maxillary and mandibular first molars.

Conclusions

Torque correction of maxillary central incisors, as well as rotational correction of most of the teeth, showed significant differences between what was planned and what was obtained.
Disentangling fine‐ and large‐scale colonization processes in metapopulation dynamics: a case study on a threatened epiphytic bryophyte
Authors: Percel Gwendoline , Bouget Christophe , Gosselin Marion , Dumas Yann , Laroche Fabien
Published: January 2024

Understanding the colonization process of species living in a dynamic fragmented habitat is essential to assess their persistence. In the metapopulation theory, the colonization of a species can be quantified using the turnover of occupancy in habitat patches. However, this approach is often limited by the feasible size of surveyed areas. Because many species are capable of long‐distance dispersal, such areas often constitute open systems undergoing colonization of propagules coming from outside, the ‘background deposition'. We focus on disentangling background deposition from local colonization among surveyed patches when analyzing turnover. We consider two spatial scales: 1) focal areas where all patches are monitored over time; 2) a larger extent, encompassing the focal areas, over which the distribution of the target species is quantified with a coarse spatial grain. Our key idea is to use the regional connectivity of focal areas within the larger scale as a covariate when analyzing colonization events within focal areas. A positive effect of regional connectivity on the colonization probability of patches may indicate background deposition. We applied this approach to the epiphytic bryophyte Dicranum viride in a managed temperate deciduous forest, considering phorophyte trees as patches, forest stands as focal areas and the whole forest as the larger scale. We combined a fine‐grained turnover survey of occupied trees within three forest stands (~ 3 ha) with a coarse‐grained snapshot of D. viride distribution over the forest (~ 15 000 ha). Regional connectivity came out as the most significant factor, with a strong positive effect on colonization probability within stands. However, it was attributed to sources in the immediate vicinity of focal stands, suggesting a short‐ranged colonization process occurring across stands' borders rather than long‐distance background deposition. Our results thus call for maintaining a stepping‐stone of habitat across the forest through time to improve D. viride persistence.
Oral lymphangioma: A clinicopathological analysis of 40 cases and review of the literature
Authors: da Cruz Lima Jabes Gennedyr , Gonçalo Rani Iani Costa , Pinheiro Juliana Campos , da Silva Gabriel Gomes , de Oliveira Costa Carla Samily , Queiroz Lélia Maria Guedes , de Oliveira Patricia Teixeira
Published: January 2024

Objective

This retrospective study aimed to perform a clinicopathological analysis of oral lymphangioma cases diagnosed at a reference service in oral pathology.

Materials and Methods

A total of 40 cases with reviewed and confirmed histopathological diagnoses for oral lymphangioma were included in the study.

Results

It was found that Caucasian women represented most of the sample, with the tongue and lower lip being the most affected sites. The most frequent clinical presentation of the lesions was as an asymptomatic reddish nodule. As for morphological characteristics, there was a slight predominance of simple lymphangioma (55%). Surgical removal was the therapeutic approach adopted in most cases.

Conclusions

Despite OL being rare, it is essential that dentists and other professionals recognize variations in the clinical presentation and histopathological aspects of these lesions, differentiating them from other vascular lesions, and implementing correct treatment in each case.
Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society
Authors: Garg Vanika , Barmukh Rutwik , Chitikineni Annapurna , Roorkiwal Manish , Ojiewo Chris , Bohra Abhishek , Thudi Mahendar , Singh Vikas K. , Kudapa Himabindu , Saxena Rachit K. , Fountain Jake , Mir Reyazul Rouf , Bharadwaj Chellapilla , Chen Xiaoping , Xin Liu , Pandey Manish K.
Published: January 2024

Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground‐breaking work, especially his effort to list orphan tropical crops to genomic resource‐rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape.
Transcranial pulsed current stimulation: A scoping review of the current literature on scope, nature, underlying mechanisms, and gaps
Authors: Malekahmad Mona , Frazer Ashlyn , Zoghi Maryam , Jaberzadeh Shapour
Published: January 2024

Transcranial pulsed current stimulation (tPCS) is a noninvasive brain stimulation technique that has aroused considerable attention in recent years. This review aims to provide an overview of the existing literature on tPCS, examine the scope and nature of previous research, investigate its underlying mechanisms, and identify gaps in the literature. Searching online databases resulted in 36 published tPCS studies from inception until May 2023. These studies were categorized into three groups: human studies on healthy individuals, human studies on clinical conditions, and animal studies. The findings suggest that tPCS has the potential to modulate brain excitability by entraining neural oscillations and utilizing stochastic resonance. However, the underlying mechanisms of tPCS are not yet fully understood and require further investigation. Furthermore, the included studies indicate that tPCS may have therapeutic potential for neurological diseases. However, before tPCS can be applied in clinical settings, a better understanding of its mechanisms is crucial. Hence, the tPCS studies were categorized into four types of research: basic, strategic, applied, and experimental research, to identify the nature of the literature and gaps. Analysis of these categories revealed that tPCS, with its diverse parameters, effects, and mechanisms, presents a wide range of research opportunities for future investigations.
Performance assessment and indicators for agricultural water management—A review
Authors: Ahmad Muhammad Tajuri , Haie Naim , Gonçalves José Manuel , Pinho José , Yen Haw , Yakubu Mahadi Lawan , Mohammed Murtala Uba , Suleimana Aiuba
Published: January 2024

The complexity of irrigation systems and the need to adapt them to uncertainties requires developing approaches to synthesize their performances. This paper reviews performance assessment and indicators for agricultural water systems. It is aimed at finding various methods and indices used for irrigation performance assessment and standard classes for their characterization. The global application of the metrics was also documented. Adopting a systematic review approach, peer‐reviewed journal articles published in the English language in the last two decades (1 March 2001 to 31 December 2020) were surveyed. Case studies were presented demonstrating the application of the indicators. The study revealed a lack of standardization and the use of a wide range of indicators among others, and recommended representing certain indicators as single. However, this review considered one indicator as the best. Suggestions for further studies were made.
Rubidium-Strontium Isochron Study of the Grenville Front near Lake Timagami, Ontario
Authors: Grant James A.
Published: January 2024

Rubidium-strontium isotopic analyses of whole-rock samples and of constituent minerals from a suite of rocks taken across the Grenville Front demonstrate that granitic rocks of the Superior province, with a primary age of approximately 2.4 billion years, and older metasedimentary rocks were reconstituted during Grenville metamorphism, at approximately 930 million years, and now form part of the Grenville province.
Two thousand years of garden urbanism in the Upper Amazon
Authors: Rostain Stéphen , Dorison Antoine , de Saulieu Geoffroy , Prümers Heiko , Le Pennec Jean-Luc , Mejía Mejía Fernando , Freire Ana Maritza , Pagán-Jiménez Jaime R. , Descola Philippe
Published: January 2024

A dense system of pre-Hispanic urban centers has been found in the Upano Valley of Amazonian Ecuador, in the eastern foothills of the Andes. Fieldwork and light detection and ranging (LIDAR) analysis have revealed an anthropized landscape with clusters of monumental platforms, plazas, and streets following a specific pattern intertwined with extensive agricultural drainages and terraces as well as wide straight roads running over great distances. Archaeological excavations date the occupation from around 500 BCE to between 300 and 600 CE. The most notable landscape feature is the complex road system extending over tens of kilometers, connecting the different urban centers, thus creating a regional-scale network. Such extensive early development in the Upper Amazon is comparable to similar Maya urban systems recently highlighted in Mexico and Guatemala.
Envisioning artificial intelligence
R.U.R. and the Vision of Artificial Life
Karel Čapek, translated by Štěpán Šimek, edited by Jitka Čejková
MIT Press, 2024. 312 pp.
Authors: Finn Ed
Published: January 2024

Scholars consider a new translation of the prescient play that coined the term “robot”
The bumpy road to friction control
Authors: Slesarenko Viacheslav , Pastewka Lars
Published: January 2024

The frictional properties of material interfaces can be rationally designed
Fixing forest carbon credits
Authors: Pande Rohini
Published: January 2024

The world’s forests store an estimated 861 billion tonnes of carbon—equivalent to approximately 100 years worth of anthropogenic emissions, at current rates—and with good husbandry could potentially store up to 226 billion tonnes more. Clearly, preserving and repairing forests is a vital element of mitigating climate breakdown.
Rooting out scientific misconduct
Authors: Oransky Ivan , Redman Barbara
Published: January 2024

Scientific misconduct is an issue rife with controversy, from its forms and definitions to the policies that guide how allegations are handled. A survey published nearly 15 years ago reported that 2% of researchers said they had fabricated or falsified data in their published work. This is not just an academic issue. Fake data promote ineffective or even dangerous treatments, for example, and thwart the discovery of real solutions for society. In the United States, the Office of Research Integrity (ORI) is tasked with rooting out misconduct in research funded by the National Institutes of Health (NIH). Last October, ORI proposed changes to how it functions. The agency’s recommendations—the first since 2005—have evoked mixed reactions, but the real problem is that ORI is underfunded and lacks the resources and authority needed to make a difference. Unless its charter is revised by Congress, the ORI can sadly do little more than tinker at the edges of scientific fraud.
Targeting host tyrosine kinase receptor EphA2 signaling via small-molecule ALW-II-41-27 inhibits macrophage pro-inflammatory signaling responses to
Pneumocystis carinii
β-glucans
Authors: Kottom Theodore J. , Carmona Eva M. , Limper Andrew H.
Published: January 2024

Pneumocystis jirovecii,
the fungus that causes
Pneumocystis jirovecii
pneumonia (PJP), is a leading cause of morbidity and mortality in immunocompromised individuals. We have previously shown that lung epithelial cells can bind
Pneumocystis
spp. β-glucans via the EphA2 receptor, resulting in activation and release of proinflammatory cytokines. Herein, we show that
in vivo Pneumocystis
spp. β-glucans activation of the inflammatory signaling cascade in macrophages can be pharmacodynamically inhibited with the EphA2 receptor small-molecule inhibitor ALW-II-41-27.
In vitro
, when ALW-II-41-27 is administrated via intraperitoneal to mice prior to the administration of highly proinflammatory
Saccharomyces cerevisiae
β-glucans in the lung, a significant reduction in TNF-alpha release was noted in the ALW-II-41-27 pre-treated group. Taken together, our data suggest that targeting host lung macrophage activation via EphA2 receptor-fungal β-glucans interactions with ALW-II-41-27 or other EphA2 receptor kinase targeting inhibitors might be an attractive and viable strategy to reduce detrimental lung inflammation associated with PJP.
Evaluation of the VioOne HIV profile supplemental assay
Authors: Franz Brian J. , Register Heidi , Sullivan Vickie , Warber Kimbrough , Granade Timothy C. , Cornaby Caleb , Magee Mark E. , Denny Thomas N. , Lockwood Don , Schmitz John L.
Published: January 2024

We evaluated the reproducibility, sensitivity, and specificity data for two versions of the VioOne HIV Profile Supplemental Assay and compared these results back to similar results for the Geenius HIV 1/2 Supplemental Assay that are publicly available. Our study concluded that the VioOne HIV Profile Supplemental Assay compared favorably with the Geenius HIV 1/2 Supplemental Assay, thus providing an additional option for clinical laboratories to improve and expand their HIV testing capabilities.
Inhibiting influenza virus transmission using a broadly acting neuraminidase that targets host sialic acids in the upper respiratory tract
Authors: Ortigoza Mila B. , Mobini Catherina L. , Rocha Hedy L. , Bartlett Stacey , Loomis Cynthia A. , Weiser Jeffrey N.
Published: January 2024

Influenza virus transmission studies have historically focused on viral mutations that alter hemagglutinin binding to sialic acid (SA) receptors
in vitro
. However, SA binding preference does not fully account for the complexities of influenza A virus transmission in humans. Our previous findings reveal that viruses that are known to bind α2,6-SA
in vitro
have different transmission kinetics
in vivo
, suggesting that diverse SA interactions may occur during their life cycle. In this study, we examine the role of host SA on viral replication, shedding, and transmission
in vivo
. We highlight the critical role of SA presence during virus shedding, such that attachment to SA during virion egress is equally important as detachment from SA during virion release. These insights support the potential of broadly acting neuraminidases as therapeutic agents capable of restraining viral transmission
in vivo
. Our study unveils intricate virus-host interactions during shedding, highlighting the necessity to develop innovative strategies to effectively target transmission.
The cost of adaptability: resource availability constrains functional stability under pulsed disturbances
Authors: Rain-Franco Angel , Peter Hannes , Pavan de Moraes Guilherme , Beier Sara
Published: January 2024

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.

IMPORTANCE

Understanding the communities’ responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.
Canine
Staphylococcaceae
circulating in a Kenyan animal shelter
Authors: Akarsu Hatice , Liljander Anne M. , Lacasta Anna , Ssajjakambwe Paul , Brodard Isabelle , Cherbuin Jérémy D. R. , Torres-Puig Sergi , Perreten Vincent , Kuhnert Peter , Labroussaa Fabien , Jores Joerg
Published: January 2024

Animal shelters, especially in resource-poor countries, bring together pets from different regions and with different backgrounds. The crowding of such animals often results in infectious diseases, such as respiratory infections. This study characterized
Staphylococcaceae
from diseased and apparently healthy dogs housed in an animal shelter in Kenya, to determine their antibiotic resistance profiles, their genetic relatedness, and the presence of dominant clones. Therefore, bacteria were collected from all 167 dogs present in the shelter in June 2015 and screened for
Staphylococcaceae
using standard cultivation techniques. In all, 92 strains were isolated from 85 dogs and subsequently sequenced by PacBio long-read sequencing. Strains encompassed nine validated species, while
S. aureus
(
n
= 47),
S. pseudintermedius
(
n
= 21), and
Mammaliicoccus (M.) sciuri
(
n
= 16) were the three most dominant species. Two
S
.
aureus
clones of ST15 (CC15) and ST1292 (CC1) were isolated from 7 and 37 dogs, respectively. All 92 strains isolated were tested for their antimicrobial susceptibility by determining the minimum inhibitory concentrations. In all, 86 strains had resistance-associated minimal inhibitory concentrations to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, kanamycin/gentamicin, or streptomycin. Many virulence-encoding genes were detected in the
S. aureus
strains, other
Staphylococcaceae
contained a different set of homologs of such genes. The presence of mobile genetic elements, such as plasmids and prophages, known to facilitate the dissemination of virulence- and resistance-encoding genes, was also assessed. The unsuspected high presence of two
S
.
aureus
clones in about 50% of dogs suggests dissemination within the shelter and a human source.

IMPORTANCE

Microbiological data from sub-Saharan Africa are scarce compared to data from North America, Europe, or Asia, and data derived from dogs, the man’s best friend, kept in sub-Saharan Africa are largely missing. This work presents data on
Staphylococcaceae
mainly isolated from the nasal cavity of dogs stationed at a Kenyan shelter in 2015. We characterized 92 strains isolated from 85 dogs, diseased and apparently healthy ones. The strains isolated covered nine validated species and we determined their phenotypic resistance and characterized their complete genomes. Interestingly,
Staphylococcus aureus
of two predominant genetic lineages, likely to be acquired from humans, colonized many dogs. We also detected 15 novel sequence types of
Mammaliicoccus sciuri
and
S. pseudintermedius
indicating sub-Saharan-specific phylogenetic lineages. The data presented are baseline data that guide antimicrobial treatment for dogs in the region.
Supplemental Material: A temporal dissection of late Quaternary volcanism and related hazards within the Rio Grande rift and along the Jemez lineament of New Mexico, USA
Authors: Zimmerer Matthew J.
Published: January 2024

40Ar/39Ar data tables and related figures.  
Effect of Risk Mitigation Guidance for opioid and stimulant dispensations on mortality and acute care visits during dual public health emergencies: retrospective cohort study
Authors: Slaunwhite Amanda , Min Jeong Eun , Palis Heather , Urbanoski Karen , Pauly Bernie , Barker Brittany , Crabtree Alexis , Bach Paxton , Krebs Emmanuel , Dale Laura , Meilleur Louise , Nosyk Bohdan
Published: January 2024

Objective

To determine the effect of opioid and stimulant Risk Mitigation Guidance (RMG) dispensations on mortality and acute care visits during the dual public health emergencies of overdose and covid-19.

Design

Population based retrospective cohort study.

Setting

British Columbia, Canada.

Participants

5882 people with opioid or stimulant use disorder who received RMG prescriptions for opioids (n=5356) and/or stimulants (n=1061) (535 received both) from 27 March 2020 to 31 August 2021.

Main outcome measures

All cause and overdose specific mortality and acute care visits in the week after RMG opioid or stimulant dispensation. RMG recipients were matched 1:1 with controls through use of high dimensional propensity score matching. Marginal structural models, executed on weekly time steps, were used to measure the effect of dispensations on outcomes.

Results

RMG opioid dispensations of one day or more were associated with reduced all cause mortality (adjusted hazard ratio 0.39, 95% confidence interval 0.25 to 0.60) and overdose related mortality (0.45, 0.27 to 0.75) in the subsequent week. Dispensations of RMG stimulants (≥1 days) were not significantly associated with reduced all cause mortality (adjusted hazard ratio 0.50, 0.20 to 1.23) or overdose related mortality (0.53, 0.18 to 1.56). The protective effect of RMG opioid dispensations increased with the number of days the medications were dispensed in a given week. People who received four or more days of RMG opioid dispensations had reduced all cause mortality (adjusted hazard ratio 0.09, 0.04 to 0.21) and overdose related mortality (0.11, 0.04 to 0.32) compared with the control group. Opioid RMG dispensations did not significantly modify the odds of all cause or overdose related acute care visits. Dispensations of RMG stimulants were associated with a significant decrease in the odds of acute care visits for any cause but did not affect the odds of overdose related acute care visits.

Conclusions

RMG opioid dispensations were associated with reduced overdose related and all cause mortality among a sample of people with opioid use disorder. Pharmaceutical alternatives to the illegal drug supply are promising interventions to reduce mortality in people with opioid use disorder.
Early treatment effects on plantation growth and biodiversity in mature ponderosa pine forest
Authors: Zhang Jianwei , Finley Kaelyn
Published: January 2024

We address the concerns that managed forest plantations may cause reductions of diversity of understory vegetation. We performed inventories of two mature ponderosa pine plantations in which multiple treatments were applied during plantation establishment. At stand age 35, we measured tree heights and diameters, understory plant cover and diversity, soil nutrients and chemical properties, and soil microbial biomass and diversity with phospholipid fatty acid. We found a significant, positive effect from both herbicide (H) and fertilizer (F) applications on subsequent overstory tree growth and development ( P < 0.05); insecticide (I) effect was minimal. We observed negative effects on understory plant diversity decades later when herbicide was applied during stand establishment. However, lower plant diversity and ground cover appeared to have been caused primarily from overstory canopy closure, supported by the increased understory cover and diversity observed in the HI and HFI plots that had been thinned at age 12. Similarly, while fertilizer increased tree growth at both sites, it only negatively affected understory plants at the higher quality site. We did not find significant influence of treatment effects on soil nutrients and microbial communities. Therefore, to mitigate the potential loss of understory biodiversity in plantations, foresters can manage overstory trees with traditional pre-commercial thinning techniques and early tending.
The river model of gravitational collapse
Authors: Chakrabarti Soumya
Published: January 2024

We show that the transformation of a time-evolving spherically symmetric metric tensor into a Painlevé–Gullstrand–Lemaître form brings forth a few curious consequences. The time evolution describes a non-singular gravitational collapse, leading to a bounce and dispersal of all the clustered matter, or a wormhole geometry for certain initial conditions. The null convergence condition is violated only at the onset of bounce or the wormhole formation. As an example, the requirements to develop a Simpson–Visser wormhole/regular black-hole geometry is discussed. The solution can be regarded as a new time-evolving twin of sonic dumb holes found in analog gravity.
Improved parameter targeting in 3D-integrated superconducting circuits through a polymer spacer process
Authors: Norris Graham J. , Michaud Laurent , Pahl David , Kerschbaum Michael , Eichler Christopher , Besse Jean-Claude , Wallraff Andreas
Published: January 2024

Three-dimensional device integration facilitates the construction of superconducting quantum information processors with more than several tens of qubits by distributing elements such as control wires, qubits, and resonators between multiple layers. The frequencies of resonators and qubits in flip-chip-bonded multi-chip modules depend on the details of their electromagnetic environment defined by the conductors and dielectrics in their vicinity. Accurate frequency targeting therefore requires precise control of the separation between chips and minimization of their relative tilt. Here, we describe a method to control the inter-chip separation by using polymer spacers. With the spacers, we measure a mean tilt of (76 ± 36) μrad, and a mean deviation of (0.4 ± 0.8) μm from the target inter-chip separation of 10 μm. We apply this process to coplanar waveguide resonator samples and observe chip-to-chip resonator frequency variations below 50 MHz ($\approx 1\%$
≈
1
%
). We measure internal quality factors of $5\times10^{5}$
5
×

10

5

at the single-photon level, suggesting that the added spacers are compatible with low-loss device fabrication.
Beyond the curriculum: unveiling medical students’ drivers and barriers to research participation at Alfaisal University
Authors: Sabbah Belal Nedal , Shah Hassan Yousaf , Baqal Eman Javed , Arabi Tarek Ziad , Shakir Ismail Mohammed , Obeidat Akef , AlKattan Khaled , Sajid Muhammad Raihan
Published: January 2024

This article examines the motivating factors and obstacles of extracurricular research in Alfaisal University, Saudi Arabia. The study utilizes a mixed methodology of online surveys and in-person group interviews to gain insights from the medical students of the university. We revealed several extrinsic and intrinsic motivators that drove the students; however, there remain several challenges to students during their research journey. Addressing these challenges will help the students obtain a more fruitful, educational research experience.
Edelman Gamblegrams: a tool to teach and learn disorders of water/plasma tonicity homeostasis
Authors: Rondon-Berrios Helbert
Published: January 2024

This article introduces a new teaching tool called “Edelman Gamblegrams,” modeled after the conventional Gamblegrams used in acid-base disorder analysis and using the independent physiological variables that determine the plasma sodium concentration (Edelman equation), that aims to help medical learners understand disorders related to water/plasma tonicity homeostasis.
A New Divergence Based on the Belief Bhattacharyya Coefficient with an Application in Risk Evaluation of Aircraft Turbine Rotor Blades
Authors: Yin Zhu , Ma Xiaojian , Wang Hang
Published: January 2024

Belief divergence is a significant measure to quantify the discrepancy between evidence, which is beneficial for conflict information management in Dempster–Shafer evidence theory. In this article, three new concepts are given, namely, the belief Bhattacharyya coefficient, adjustment function, and enhancement factor. And based on them, a novel enhanced belief divergence, called EBD, is proposed, which can assess the correlation of subsets and fully reflect the uncertainty of multielement sets. The important properties of the EBD have been studied. In particular, a new EBD-based multisource information fusion method is designed to handle evidence conflict, where the weight of evidence is decided by the EBD between evidence and the information volume of each evidence. Compared with other methods, the proposed method in the applications of target recognition and iris classification can produce more rational and telling outcomes when dealing with conflict information. Finally, an application in risk priority evaluation of the failure modes of rotor blades of an aircraft turbine is provided to validate that the proposed method has the extensive applicability.
Method Validation and Measurement Uncertainty Estimation for Determination of Multiclass Pesticide Residues in Tomato by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)
Authors: Shrestha Suraj , Lamichhane Bandana , Chaudhary Nibedita
Published: January 2024

Method validation is an essential technique for ensuring the reliability and accuracy of an analytical method. This study aimed to optimize and validate a fast, reliable, and accurate method for quantitatively determining pesticide residues of diverse chemical classes in the tomato matrix. Various method performance characteristics were tested and compared with predefined criteria. Twenty-six different pesticides of diverse chemical classes were selected based on their use in tomato cultivation and the availability of reference materials. The pesticide residues in tomato samples were extracted with the QuEChERS technique with some modifications, followed by injection into an LC-MS/MS system operating in an optimized method. The validated method demonstrated reasonable specificity, as there were no interferences from matrix components at the retention times of pesticides. The calibration curves for all pesticides exhibited excellent linearities, with correlation coefficients exceeding 0.99. No significant matrix effect was observed for all pesticides in tomatoes, as the values fell within the range of ±20%. All pesticides were quantified successfully at a concentration of 5 μg/kg except for carbaryl, with an average recovery of more than 70% and a relative standard deviation of less than 20%. Similarly, measurement uncertainties were also estimated based on the validation data, and the values were found below the default limit of 50%. Subsequently, the validated method was applied to analyze 52 locally collected tomato samples. Study findings revealed that only four of the studied pesticides were detected in these samples, and their concentrations were below the maximum residue limits (500 µg/kg each for carbendazim, imidacloprid, and metalaxyl) established for tomatoes by the Government of Nepal and the Codex Alimentarius Commission.
Keyframe Extraction Algorithm for Continuous Sign-Language Videos Using Angular Displacement and Sequence Check Metrics
Authors: Aiswarya M. S. , Arockia Xavier Annie R.
Published: January 2024

Dynamic signs in the sentence form are conveyed in continuous sign-language videos. A series of frames are used to depict a single sign or a phrase in sign videos. Most of these frames are noninformational and they hardly effect on sign recognition. By removing them from the frameset, the recognition algorithm will only need to input a minimal number of frames for each sign. This reduces the time and spatial complexity of such systems. The algorithm deals with the challenge of identifying tiny motion frames such as tapping, stroking, and caressing as keyframes on continuous sign-language videos with a high reduction ratio and accuracy. The proposed method maintains the continuity of sign motion instead of isolating signs, unlike previous studies. It also supports the scalability and stability of the dataset. The algorithm measures angular displacements between adjacent frames to identify potential keyframes. Then, noninformational frames are discarded using the sequence check technique. Pheonix14, a German continuous sign-language benchmark dataset, has been reduced to 74.9% with an accuracy of 83.1%, and American sign language (ASL) How2Sign is reduced to 76.9% with 84.2% accuracy. A low word error rate (WER) is also achieved on the Phoenix14 dataset.
Generation of Smoke Dataset for Power Equipment and Study of Image Semantic Segmentation
Authors: Chang Rong , Mao Zhengxiong , Hu Jian , Bai Haicheng , Pan Anning , Yang Yang , Gao Shan
Published: January 2024

Fire in power equipment has always been one of the main hazards of power equipment. Smoke detection and recognition have always been extremely important in power equipment, as they can provide early warning before a fire breaks out. Compared to relying on smoke concentration for recognition, image-based smoke recognition has the advantage of being unaffected by indoor and outdoor environments. This paper addresses the problems of limited smoke data, difficult labeling, and insufficient research on recognition algorithms in power systems. We propose using three-dimensional virtual technology to generate smoke and image masks and using environmental backgrounds such as HDR (high dynamic range imaging) lighting to realistically combine smoke and background. In addition, to address the characteristics of smoke in power equipment, a dual UNet model named DS-UNet is proposed. The model consists of a deep and a shallow network structure, which can effectively segment the details of smoke in power equipment and handle partial occlusion. Finally, DS-UNet is compared with other smoke segmentation networks with similar structures, and it demonstrates better smoke segmentation performance.
Data from MYC in Chronic Myeloid Leukemia: Induction of Aberrant DNA Synthesis and Association with Poor Response to Imatinib
Authors: Albajar Marta , Gómez-Casares M. Teresa , Llorca Javier , Mauleon Itsaso , Vaqué Jose P. , Acosta Juan C. , Bermúdez Arancha , Donato Nicholas , Delgado M. Dolores , León Javier
Published: January 2024

Abstract
Untreated chronic myeloid leukemia (CML) progresses from chronic phase to blastic crisis (BC). Increased genomic instability, deregulated proliferation, and loss of differentiation appear associated to BC, but the molecular alterations underlying the progression of CML are poorly characterized. MYC oncogene is frequently deregulated in human cancer, often associated with tumor progression. Genomic instability and induction of aberrant DNA replication are described as effects of MYC. In this report, we studied MYC activities in CML cell lines with conditional MYC expression with and without exposure to imatinib, the front-line drug in CML therapy. In cells with conditional MYC expression, MYC did not rescue the proliferation arrest mediated by imatinib but provoked aberrant DNA synthesis and accumulation of cells with 4C content. We studied MYC mRNA expression in 66 CML patients at different phases of the disease, and we found that MYC expression was higher in CML patients at diagnosis than control bone marrows or in patients responding to imatinib. Further, high MYC levels at diagnosis correlated with a poor response to imatinib. MYC expression did not directly correlate with BCR-ABL levels in patients treated with imatinib. Overall our study suggests that, as in other tumor models, MYC-induced aberrant DNA synthesis in CML cells is consistent with MYC overexpression in untreated CML patients and nonresponding patients and supports a role for MYC in CML progression, possibly through promotion of genomic instability. Mol Cancer Res; 9(5); 564–76. ©2011 AACR.
Data from p53-Dependent Induction of Prostate Cancer Cell Senescence by the PIM1 Protein Kinase
Authors: Zemskova Marina , Lilly Michael B. , Lin Ying-Wei , Song Jin H. , Kraft Andrew S.
Published: January 2024

Abstract
The PIM family of serine threonine protein kinases plays an important role in regulating both the growth and transformation of malignant cells. However, in a cell line–dependent manner, overexpression of PIM1 can inhibit cell and tumor growth. In 22Rv1 human prostate cells, but not in Du145 or RWPE-2, PIM1 overexpression was associated with marked increases in cellular senescence, as shown by changes in the levels of β-galactosidase (SA-β-Gal), p21, interleukin (IL)-6 and IL-8 mRNA and protein. During early cell passages, PIM1 induced cellular polyploidy. As the passage number increased, markers of DNA damage, including the level of γH2AX and CHK2 phosphorylation, were seen. Coincident with these DNA damage markers, the level of p53 protein and genes transcriptionally activated by p53, such as p21, TP53INP1, and DDIT4, increased. In these 22Rv1 cells, the induction of p53 protein was associated not only with senescence but also with a significant level of apoptosis. The importance of the p53 pathway to PIM1-driven cellular senescence was further shown by the observation that expression of dominant-negative p53 or shRNA targeting p21 blocked the PIM1-induced changes in the DNA damage response and increases in SA-β-Gal activity. Likewise, in a subcutaneous tumor model, PIM1-induced senescence was rescued when the p53-p21 pathways are inactivated. Based on these results, PIM1 will have its most profound effects on tumorigenesis in situations where the senescence response is inactivated. Mol Cancer Res; 8(8); 1126–41. ©2010 AACR.
Data from FOXM1 Confers Acquired Cisplatin Resistance in Breast Cancer Cells
Authors: Kwok Jimmy M.-M. , Peck Barrie , Monteiro Lara J. , Schwenen Helma D.C. , Millour Julie , Coombes R. Charles , Myatt Stephen S. , Lam Eric W.-F.
Published: January 2024

Abstract
The transcription factor Forkhead box M1 (FOXM1) is a key regulator of cell proliferation and is overexpressed in many forms of primary cancers, leading to uncontrolled cell division and genomic instability. To address the role of FOXM1 in chemoresistance, we generated a cisplatin-resistant breast cancer cell line (MCF-7-CISR), which had an elevated level of FOXM1 protein and mRNA expression relative to the parental MCF-7 cells. A close correlation was observed between FOXM1 and the expression of its proposed downstream targets that are involved in DNA repair; breast cancer–associated gene 2 (BRCA2) and X-ray cross-complementing group 1 (XRCC1) were expressed at higher levels in the resistant cell lines compared with the sensitive MCF-7 cells. Moreover, cisplatin treatment induced DNA damage repair in MCF-7-CISR and not in MCF-7 cells. Furthermore, the expression of a constitutively active FOXM1 (ΔN-FOXM1) in MCF-7 cells alone was sufficient to confer cisplatin resistance. Crucially, the impairment of DNA damage repair pathways through the small interfering RNA knockdown inhibition of either FOXM1 or BRCA2/XRCC1 showed that only the silencing of FOXM1 could significantly reduce the rate of proliferation in response to cisplatin treatment in the resistant cells. This suggests that the targeting of FOXM1 is a viable strategy in circumventing acquired cisplatin resistance. Consistently, the FOXM1 inhibitor thiostrepton also showed efficacy in causing cell death and proliferative arrest in the cisplatin-resistant cells through the downregulation of FOXM1 expression. Taken together, we have identified a novel mechanism of acquired cisplatin resistance in breast cancer cells through the induction of FOXM1. Mol Cancer Res; 8(1); 24–34
Data from Regulation of Cell Cycle Genes and Induction of Senescence by Overexpression of OTX2 in Medulloblastoma Cell Lines
Authors: Bunt Jens , de Haas Talitha G. , Hasselt Nancy E. , Zwijnenburg Danny A. , Koster Jan , Versteeg Rogier , Kool Marcel
Published: January 2024

Abstract
The transcription factor orthodenticle homeobox 2 (OTX2) has been implicated in the pathogenesis of medulloblastoma, as it is often highly expressed and sometimes amplified in these tumors. Little is known of the downstream pathways regulated by OTX2. We therefore generated MED8A and DAOY medulloblastoma cell lines with doxycycline-inducible OTX2 expression. In both cell lines, OTX2 inhibited proliferation and induced a senescence-like phenotype with senescence-associated β-galactosidase activity. Expression profiles of time series after OTX2 induction in MED8A showed early upregulation of cell cycle genes related to the G2-M phase, such as AURKA, CDC25C, and CCNG2. Paradoxically, G1-S phase genes such as MYC, CDK4, CDK6, CCND1, and CCND2 were strongly downregulated, in line with the observed G1 arrest. ChIP-on-chip analyses of OTX2 binding to promoter regions in MED8A and DAOY showed a strong enrichment for binding to the G2-M genes, suggesting a direct activation. Their mRNA expression correlated with OTX2 expression in primary tumors, underscoring the in vivo relevance of this regulation. OTX2 induction activated the P53 pathway in MED8A, but not in DAOY, which carries a mutated P53 gene. In DAOY cells, senescence-associated secretory factors, such as interleukin-6 and insulin-like growth factor binding protein 7, were strongly upregulated after OTX2 induction. We hypothesize that the imbalance in cell cycle stimulation by OTX2 leads to cellular senescence either by activating the P53 pathway or through the induction of secretory factors. Our data indicate that OTX2 directly induces a series of cell cycle genes but requires cooperating genes for an oncogenic acceleration of the cell cycle. Mol Cancer Res; 8(10); 1344–57. ©2010 AACR.