bluuebunny/crossref_metadata_2025 huggingface dataset:
Betel‐quid addictive use disorders and Oral potentially malignant disorders and Oral cancer in south, southeast, and East Asia: A systematic review and meta‐analysis
Authors: Ko Albert Min‐Shan , Wu Pei‐Wen , Lin Wei‐Ting , Lee Chien‐Hung
Published: August 2024

Objective

This study aimed to provide a comprehensive assessment of the measurement and prevalence of betel‐quid (BQ) abuse, dependence, and BQ use disorder (BUD), as well as to evaluate the impact of BQ addiction on oral malignant diseases.

Methods

We used the PRISMA guidelines to perform a systematic review and meta‐analysis. We searched for relevant publications up to April 2024 in PubMed, Web of Science, and Embase. The articles were evaluated for BQ addiction and its relationship with oral potentially malignant disorders (OPMD) and oral cancer.

Results

The prevalence of BQ abuse, dependence, and BUD in South, Southeast, and East Asia varied between 0.8%–46.3%, 0.4%–43.5%, and 4.7%–39.2%, respectively. Among BQ chewers, the corresponding proportions of these disorders ranged from 40.5%–99.6%, 20.9%–99.6%, and 55.2%–99.3%. The pooled risks of OPMD associated with BQ abuse, dependence, and BUD were 16.3, 18.7, and 9.6–35.5, respectively. The risk of oral cancer for mild, moderate, and severe BUD was 8.5, 8.2, and 42.3, respectively.

Conclusions

BUD mediates the link between BQ use and an increased risk of oral malignant disorders. Addressing and treating BQ addiction is an important component of comprehensive OPMD and oral cancer preventive and intervention programs that go beyond simple cessation efforts.
Priapulid neoichnology, ecosystem engineering, and the Ediacaran–Cambrian transition
Authors: Turk Katherine A. , Wehrmann Achim , Laflamme Marc , Darroch Simon A. F.
Published: August 2024

The evolutionary rise of powerful new ecosystem engineering impacts is thought to have played an important role in driving waves of biospheric change across the Ediacaran–Cambrian transition (ECT; c. 574–538 Ma). Among the most heavily cited of these is bioturbation (organism‐driven sediment disturbance) as these activities have been shown to have critical downstream geobiological impacts. In this regard priapulid worms are crucial; trace fossils thought to have been left by priapulan‐grade animals are now recognized as appearing shortly before the base of the Cambrian and represent some of the earliest examples of bed‐penetrative bioturbation. Understanding the ecosystem engineering impacts of priapulids may thus be key to reconstructing drivers of the ECT. However, priapulids are rare in modern benthic ecosystems, and thus comparatively little is known about the behaviours and impacts associated with their burrowing. Here, we present the early results of neoichnological experiments focused on understanding the ecosystem engineering impacts of priapulid worms. We observe for the first time a variety of new burrowing behaviours (including the formation of linked burrow networks and long in‐burrow residence times) hinting at larger ecosystem engineering impacts in this group than previously thought. Finally, we identify means by which these results may contribute to our understanding of tracemakers across the ECT, and the role they may have had in shaping the latest Ediacaran and earliest Cambrian biosphere.
Editing and genome‐wide analysis upstream open reading frames contributes to enhancing salt tolerance in tomato
Authors: Jia Chunping , Wang Juan , Guo Bin , Yang Tao , Yang Haitao , Wang Baike , Yu Qinghui
Published: August 2024

The salinization of soil constitutes a substantial hindrance to the advancement of sustainable agriculture. Our research seeks to elucidate the role of a Rab GTPase‐activating protein (RabGAP) family member, SlRabGAP22, in salt tolerance and its translational regulation under salt stress in tomatoes, employing gene‐editing techniques and ribosome profiling methodologies. Findings demonstrate that SlRabGAP22 acts as a positive regulator of tomato salt tolerance, with four predicted upstream open reading frames (uORFs) classified into three categories. Functional uORFs were found to be negative regulation. Editing these uORFs along with altering their classifications and characteristics mitigated the inhibitory effects on primary ORFs and fine‐tuned gene expression. Enhanced tomato salt tolerance was attributed to improved scavenging of reactive oxygen species, reduced toxicity Na+, and diminished osmotic stress effects. Furthermore, we conducted genome‐wide analysis of ORFs to lay the foundation for further research on uORFs in tomatoes. In summary, our findings offer novel perspectives and important data for the enhancement of genetic traits via uORF‐based strategies and translational regulation against the backdrop of salt stress.
A case of congenital pili multigemini
Authors: Davidson Edan , Finkelstein Eve , Gold Jonathan , Molho‐Pessach Vered
Published: August 2024

Pili multigemini is an uncommon hair follicle disorder, where multiple hair shafts emerge from the same follicular opening. While it is commonly observed in men's facial hair, it has also been reported, albeit infrequently, in other areas of the body. Here we describe an unusual case of congenital pili multigemini presenting on the eyebrow of a female infant.
Investigating properties of sweet cherry (Prunus avium) flower buds that help promote freezing avoidance by supercooling
Authors: Houghton E. , Watanabe Y. , Neilsen D. , Nelson L. M. , Hannam K.
Published: August 2024

Mechanisms involved in the supercooling of plant tissues as a means of low temperature survival are still not fully understood. We investigated properties that may promote supercooling in overwintering sweet cherry (Prunus avium) flower buds.

We conducted experiments on sweet cherry flower buds using differential thermal analysis (DTA) and observed locations of ice formation in the bud structure. We also used anatomical development and water‐soluble dye uptake throughout the overwintering period to identify changes that correlate with gain and loss of supercooling capacity.

Our results revealed barriers to ice propagation are likely unique to each primordium, as inferred from exotherms produced from buds subjected to DTA, although multiple primordia may freeze simultaneously. Ice is accommodated between the bud scales and within the bud axis; however, full expression of supercooling was not dependent on the presence of scales. Anatomical and DTA studies revealed a correlation between vascular differentiation in primordia and loss of supercooling in the spring; these observations were at a higher temporal resolution than previously described for Prunus. Furthermore, disturbing tissues subtending the primordia interfered with typical patterns of supercooling, indicated more erratic and numerous exotherms produced during DTA.

In summary, sweet cherry flower buds undergo extra‐organ freezing. In winter, a barrier to ice propagation in the region directly subtending primordia protects the flower from freezing damage, but in the spring xylem differentiation in primordia provides a conduit for ice propagation that compromises supercooling.
Domain‐specific control for cognitive and emotional conflict: Evidence from the transfer of proportion congruency effects
Authors: Xiang Ling , Gao Yu , Yang Tingting , Clayson Peter Eugene , Wang Baoxi
Published: August 2024

There is ongoing debate about whether control‐related processing related to cognitive conflict and emotional conflict operate independently. This study manipulated the proportion of congruent to incongruent trials to determine the domain specificity or generality of these two types of conflict control. Two experiments were conducted in which spatial Simon conflict was combined with emotional face‐word conflict. In Experiment 1, the proportion congruency (PC) of spatial conflict was manipulated, and in Experiment 2, the PC of emotional conflict was manipulated. The aim was to determine whether control‐related processes elicited by cognitive or emotional conflict show domain‐specific (within cognitive or within emotional control‐related effects) or domain‐general effects, where control elicited by cognitive conflict benefits emotional control processes and vice versa. Behavioral findings indicated that spatial and emotional conflict exhibited within‐domain PC effects. For event‐related brain potential (ERP) activity, PC effects were primarily reflected in a late slow potential, rather than an early negativity, suggesting that control‐related adjustments impacted conflict resolution rather than conflict detection. Furthermore, the results did not show evidence of PC effects across domains for behavioral or ERP data, indicating that proactive control elicited by PC manipulation does not transfer across cognitive and emotional conflict. This study supports the modular nature of proactive control for processes related to cognitive and emotional control.
Educational inequality as a consequence and cause of race
Authors: Rochmes Jane
Published: August 2024

This review starts from the premise that racial inequality has become a normalized backdrop within U.S. education, in many ways following the prevailing racial hierarchy in society. While enduring racial stratification produces numerous educational disparities, I argue that these disparities, in turn, contribute to reinforcing the symbolic meanings associated with racial categories. Put simply, racial inequality in education is both a consequence and a cause of race itself. I review these “predictable” patterns of racial inequality in education, distilling some of the nuances that are most frequently misunderstood and summarizing trends through recent data. Next, I examine explanations for racial inequality in education, debunking some persistent misconceptions. Then I synthesize the patterns and explanations with literature highlighting how racial inequality in education re‐constructs durable notions of racial categories and racialization. All three of these areas have produced significant scholarship, but they are seldom fully in conversation with one another. Finally, I discuss the role of race and racism in the latest politicization of schools to argue that it can be understood as a new wave in the colorblind era, with significant implications for the social construction of whiteness and the potential to stall progress toward reducing racial inequality in education.
Introduction to the Debate: How Does Political Science Matter? The Relevance and Impact of the Discipline
Authors: Garzia Diego , Papadopoulos Yannis
Published: August 2024

This debate aims at discussing the broader social relevance of political science research, a debate that has not yet taken place in Switzerland although it has been ongoing internationally. In this introduction, we highlight the main questions raised by the debate and illustrate the various contributions. With this debate we hope to stimulate further contributions on the topic in the future.
The Swiss Approach to Societal Impact is Good, but Might Become Even Better: A Comment on Ochsner
Authors: Lepori Benedetto
Published: August 2024

In my comment to Michael Ochsner's essay on societal impact of research, I argue that Michael is right to point to the complexity of societal impact and to the pitfalls of overly simple measurement frameworks as the one introduced in the UK's Research Assessment Framework. I also convey with him that the lack of such framework does not mean that societal impact is not an important dimension of Swiss research policy. However, I observe that there is currently a stronger concern at the political and societal level for accountability and measuring more systematically societal impact, as related to the emergence of societal grand challenges. Accordingly, I suggest that political scientists should be more proactive and suggest novel ways of measuring impact and of integrating impact assessment in the evaluation of research programs, funding agencies and higher education institutions.
Beyond Social Impact: The Value of Science for Society (A Comment on Ochsner)
Authors: Bernardi Laura
Published: August 2024

The following text is a brief commentary on Michael Ochsner's article “The Mis‐conceptualisation of Societal Impact: Why the Swiss Approach to Societal Impact is Productive and not Inexistent” in this special issue. It makes three points about the concept of social impact. The first point questions the appropriateness of the concept of social impact for assessing the value of research to society. The second point concerns the balance between creativity and research limits and between research freedom and responsibility to society. Finally, I look at the implications of information and communication technologies and artificial intelligence in assessing the value of research to society.
Neutrophil extracellular trap related risk score exhibits crucial prognostic value in skin cutaneous melanoma, associating with distinct immune characteristics
Authors: Zhang Haiyang , Bi Xiaoqing , Yan Pengrong , Wang Congcong
Published: August 2024

Background

Neutrophil extracellular traps (NETs) are related to the prognosis of cancer patients. Nevertheless, the potential prognostic values of NETs in skin cutaneous melanoma (SKCM) remains largely unknown.

Materials and methods

The NET‐related gene signature was constructed by LASSO Cox regression analysis using the TCGA‐SKCM cohort. The overall survival (OS) and immune status in SKCM patients between the high‐ and low‐NET score (high‐score, low‐score) groups were explored. The scRNA‐seq dataset GSE115978 was used to understand the role of NET score in SKCM at single cell resolution.

Results

A five NET genes‐based signature (TLR2, CLEC6A, PDE4B, SLC22A4 and CYP4F3) was constructed as the NET‐related prognostic model for SKCM. The OS of SKCM patients with low‐score was better than that in patients with high‐score. Additionally, NET score was negatively associated with infiltration of some immune cells (e.g. type I Macrophages, CD8‐T cells, CD4‐T cells). Moreover, patients with high‐score had low stromal, immune and ESTIMATE scores. Furthermore, drug sensitivity analysis results showed that Lapatinib, Trametinib and Erlotinib may have better therapeutic advantages in patients with high‐score.

Conclusion

We established a NET‐related five gene signature in SKCM and found that the NET‐related signature may exhibit a good predictive ability for SKCM prognosis. The NET score may not only predict the survival outcome and drug sensitivity in SKCM, but also reflect the immune conditions of SKCM patients.
Differences in soil seed longevity for two subspecies of the invasive weed, Chrysanthemoides monilifera (Asteraceae)
Authors: French Kris , Ashcroft Michael B. , Panetta F. Dane , Raghu S. , Cherry Hillary
Published: August 2024

The persistence of a soil seed bank influences weed management options. However, for many species, the degree of persistence of a soil seed bank is unknown. We assessed how long seeds remain in the soil for two invasive weeds, Chrysanthemoides monilifera subsp. monilifera (boneseed) and C. monilifera subsp. rotundata (bitou bush), as seeds of these species were predicted to have different longevity in the soil associated with differences in seed coat thickness. Seeds of both subspecies were buried at two depths at two sites in eastern Australia. Seeds were tested for germinability and viability regularly over an 8‐year period. Freshly collected seeds had quite low viability, and there was a rapid decline in viability in the first couple of years after burial, with C. m. rotundata declining faster than C. m. monilifera. Some seeds, however, remained viable in the soil at some sites for up to 8 years, with high site‐to‐site variability. The variability in viability from site to site may be due to the length of time soils remain moist: a combination of rainfall quantity and humidity levels. The low numbers of seeds remaining viable at 8 years indicate progressively lower probabilities of recruitment at sites following weed control but also suggest that monitoring for both subspecies needs to occur for a long period to minimize the risk of reinfestation from the seed bank.
Construction of multi‐bubble blow‐up solutions to the L2$L^2$‐critical half‐wave equation
Authors: Cao Daomin , Su Yiming , Zhang Deng
Published: August 2024

This paper concerns the bubbling phenomena for the ‐critical half‐wave equation in dimension one. Given arbitrarily finitely many distinct singularities, we construct blow‐up solutions concentrating exactly at these singularities. This provides the first examples of multi‐bubble solutions for the half‐wave equation. In particular, the solutions exhibit the mass quantization property. Our proof strategy draws upon the modulation method in Krieger, Lenzmann and Raphaël [Arch. Ration. Mech. Anal. 209 (2013), no. 1, 61–129] for the single‐bubble case, and explores the localization techniques in Cao, Su and Zhang [Arch. Ration. Mech. Anal. 247 (2023), no. 1, Paper No. 4] and Röckner, Su and Zhang [Trans. Amer. Math. Soc., 377 (2024), no. 1, 517–588] for bubbling solutions to non‐linear Schrödinger equations (NLS). However, unlike the single‐bubble or NLS cases, different bubbles exhibit the strongest interactions in dimension one. In order to get sharp estimates to control these interactions, as well as non‐local effects on localization functions, we utilize the Carlderón estimate and the integration representation formula of the half‐wave operator, and find that there exists a narrow room between the orders and for the remainder in the geometrical decomposition. Based on this, a novel bootstrap scheme is introduced to address the multi‐bubble non‐local structure.
Schauder and Cordes–Nirenberg estimates for nonlocal elliptic equations with singular kernels
Authors: Fernández‐Real Xavier , Ros‐Oton Xavier
Published: August 2024

We study integro‐differential elliptic equations (of order ) with variable coefficients, and prove the natural and most general Schauder‐type estimates that can hold in this setting, both in divergence and non–divergence form. Furthermore, we also establish Hölder estimates for general elliptic equations with no regularity assumption on , including for the first‐time operators like , provided that the coefficients have “small oscillation.”
Stated SL(n$n$)‐skein modules and algebras
Authors: Lê Thang T. Q. , Sikora Adam S.
Published: August 2024

We develop a theory of stated SL()‐skein modules, , of 3‐manifolds marked with intervals in their boundaries. These skein modules, generalizing stated SL(2)‐modules of the first author, stated SL(3)‐modules of Higgins', and SU(n)‐skein modules of the second author, consist of linear combinations of framed, oriented graphs, called ‐webs, with ends in , considered up to skein relations of the ‐Reshetikhin–Turaev functor on tangles, involving coupons representing the anti‐symmetrizer and its dual. We prove the Splitting Theorem asserting that cutting of a marked 3‐manifold along a disk resulting in a 3‐manifold yields a homomorphism for all . That result allows to analyze the skein modules of 3‐manifolds through the skein modules of their pieces. The theory of stated skein modules is particularly rich for thickened surfaces , in whose case, is an algebra, denoted by . One of the main results of this paper asserts that the skein algebra of the ideal bigon is isomorphic with and it provides simple geometric interpretations of the product, coproduct, counit, the antipode, and the cobraided structure on . (In particular, the coproduct is given by a splitting homomorphism.) We show that for surfaces with boundary every splitting homomorphism is injective and that is a free module with a basis induced from the Kashiwara–Lusztig canonical bases. Additionally, we show that a splitting of a thickened bigon near a marking defines a right ‐comodule structure on , or dually, a left ‐module structure. Furthermore, we show that the skein algebra of surfaces glued along two sides of a triangle is isomorphic with the braided tensor product of Majid. These results allow for geometric interpretation of further concepts in the theory of quantum groups, for example, of the braided products and of Majid's transmutation operation. Building upon the above results, we prove that the factorization homology with coefficients in the category of representations of is equivalent to the category of left modules over for surfaces with . We also establish isomorphisms of our skein algebras with the quantum moduli spaces of Alekseev–Schomerus and with the internal algebras of the skein categories for these surfaces and .
Development of High-Temperature, Interlaminar Tension Test Methodology for Ceramic Matrix Composites
Authors: Mattison Jacob T. , Faucett D. Calvin , Choi Sung R.
Published: August 2024

This paper was to present how an affordable, high-temperature, interlaminar tension (ILT) strength testing method was explored and developed for ceramic matrix composites (CMCs), leading to development of a diametral-compression test methodology. The test methodology was first delved and verified at ambient temperature by employing a model, 2D-woven polymer matrix composite (PMC) with various test-specimen configurations. The test method was then applied to and confirmed with two different gas-turbine grade CMCs of 2D melt-infiltrated (MI) SiC/SiC and 2D N720/alumina oxide/oxide at both ambient and elevated temperatures. Life prediction testing was also conducted at 1316 °C for the MI SiC/SiC to validate the effectiveness of test method for a long-term life prediction testing. All of the results on strength and life prediction testing indicated an applicability and feasibility as an appropriate high-temperature ILT test methodology in CMCs with provisions of simplicity, affordability, and technical soundness.
Acoustic Metamaterial Plates With Interlinked Octuple-Action Vibration Absorbers for Multistopband Elastic Wave Mitigation
Authors: Althamer Saeed
Published: August 2024

This article explores an innovative vibration suppression design, termed octuple-action (OA), for acoustic metamaterial plates, aimed at mitigating the propagation of acoustic waves. The design's goal is to create broad frequency stopbands, which can be configured by adjusting passive parameters governing the locally resonant subsystems of the OA absorber. The metamaterial plate is structured with a sequence of evenly spaced OA vibration absorbers that are attached to an isotropic plate. Each OA vibration absorber is composed of two separate spring-mass-damper subsystems, interlinked to each segment of the isotropic plate at eight uniformly distributed locations through elastic couplers. An analytical methodology is developed, utilizing finite element modeling (FEM) and Bloch's theorem, to elucidate the presence of stopbands, resulting in the formation of a single configurable and unified frequency stopband, or two broad stopbands. A comprehensive analysis and illustration of the proposed metamaterial plate's OA vibration absorber are presented. The OA vibration absorber effectively impedes the propagation of acoustic waves through the metamaterial plate by generating a set of eight internal forces. These forces act in a manner that counteracts any incoming wave with a frequency residing within the designated stopband ranges. Furthermore, by optimally manipulating the effective material properties of the OA, the internal forces can be tailored, enabling the creation of configurable and broad stopbands. To comprehensively examine the influence of the OA vibration absorber's subsystem parameters on the characteristics of the stopbands, a rigorous parametric investigation is undertaken. This investigation focuses on how variations in mass densities and stiffness coefficients impact the stopband locations and widths. The excellent agreement observed between the FEM simulation results and the dispersion curves across a wide range of prescribed configurations and patterns serves as robust validation for the efficacy of the proposed metamaterial design incorporating the OA vibration absorber.
No Combined Effect of Caffeinated Chewing Gum and Priming Exercise on Oxygen Uptake and Muscle Near-Infrared Spectroscopy-Derived Kinetics: A Double-Blind Randomized Crossover Placebo-Controlled Trial in Cyclists
Authors: Nascimento Eduardo Marcel Fernandes , Borszcz Fernando Klitzke , Ventura Thiago Pereira , Boaventura Brunna Cristina Bremer , do Nascimento Salvador Paulo Cesar , Guglielmo Luiz Guilherme Antonacci , Dantas de Lucas Ricardo
Published: August 2024

This study aimed to investigate the effects of caffeine ingestion by chewing gum (GUMCAF) combined with priming exercise on pulmonary oxygen uptake () and near-infrared spectroscopy-derived muscle oxygen extraction (HHb + Mb) kinetics during cycling performed in a severe-intensity domain. Fifteen trained cyclists completed four visits: two under a placebo gum (GUMPLA) and two under GUMCAF ingestion. Each visit consisted of two square-wave cycling bouts at Δ70 intensity (70% of difference between the at first ventilatory threshold and ) with duration of 6 min each and 5 min of passive rest between the bouts. The GUMPLA or GUMCAF (400 mg) was chewed for 5 min, 12 min before the first Δ70 bout in a randomized double-blind procedure. The fundamental phase and slow component of HHb + Mb and kinetics were evaluated. For HHb + Mb kinetics, regardless of ingested gum, priming exercise effects occurred on the time constant (GUMCAF 16.0 ± 4.0 vs. 13.9 ± 2.9 s; GUMPLA 15.7 ± 6.1 vs. 13.2 ± 2.5 s), amplitude, slow component, time delay, and mean response time parameters (p ≤ .032). For kinetics, there were significant effects of bouts on the amplitude, slow component, end , and the gain kinetics parameters (p < .017). Baseline was higher during GUMCAF than GUMPLA (p = .020). No significant effects occurred for the interaction between gum and bout in any parameter of or HHb + Mb kinetics. Therefore, unlike the priming exercise in severe-intensity exercise, GUMCAF is not an effective strategy for improving or HHb + Mb kinetics acceleration.
Dual-initiation ruptures in the 2024 Noto earthquake encircling a fault asperity at a swarm edge
Authors: Xu Liuwei , Ji Chen , Meng Lingsen , Ampuero Jean-Paul , Yunjun Zhang , Mohanna Saeed , Aoki Yosuke
Published: August 2024

To reveal the connections between the 2024 moment magnitude (
M
w
) 7.5 Noto earthquake in Japan and the seismicity swarms that preceded it, we investigated its rupture process through near-source waveform analysis and source imaging techniques, combining seismic and geodetic datasets. We found notable complexity in the initial rupture stages. A strong fault asperity, which remained unbroken in preceding seismic swarms, slowed down the rupture. Then, a second rupture initiated at the opposite edge of the asperity, and the asperity succumbed to double-pincer rupture fronts. The failure of this high-stress drop asperity drove the earthquake into a large-scale event. Our observations help unravel the crucial role of fault asperities in controlling swarm migration and rupture propagation and underscore the need for detailed seismological and interdisciplinary studies to assess seismic risk in swarm-prone regions.
T6SS in plant pathogens: unique mechanisms in complex hosts
Authors: Matte Lexie M. , Genal Abigail V. , Landolt Emily F. , Danka Elizabeth S.
Published: August 2024

Type VI secretion systems (T6SSs) are complex molecular machines that allow bacteria to deliver toxic effector proteins to neighboring bacterial and eukaryotic cells. Although initial work focused on the T6SS as a virulence mechanism of human pathogens, the field shifted to examine the use of T6SSs for interbacterial competition in various environments, including in the plant rhizosphere. Genes encoding the T6SS are estimated to be found in a quarter of all Gram-negative bacteria and are especially highly represented in
Proteobacteria
, a group which includes the most important bacterial phytopathogens. Many of these pathogens encode multiple distinct T6SS gene clusters which can include the core components of the apparatus as well as effector proteins. The T6SS is deployed by pathogens at multiple points as they colonize their hosts and establish an infection. In this review, we describe what is known about the use of T6SS by phytopathogens against plant hosts and non-plant organisms, keeping in mind that the structure of plants requires unique mechanisms of attack that are distinct from the mechanisms used for interbacterial interactions and against animal hosts. While the interactions of specific effectors (such as phospholipases, endonucleases, peptidases, and amidases) with targets have been well described in the context of interbacterial competition and in some eukaryotic interactions, this review highlights the need for future studies to assess the activity of phytobacterial T6SS effectors against plant cells.
Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes
Authors: Kwan Suet-Ying , Sabotta Caroline M. , Cruz Lorenzo R. , Wong Matthew C. , Ajami Nadim J. , McCormick Joseph B. , Fisher-Hoch Susan P. , Beretta Laura
Published: August 2024

Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of
Inoviridae
was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate
Escherichia
phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of
Lactococcus
phages r1t and BK5-T, and enrichment of the globally prevalent
Crassvirales
phages, including members of genus cluster IX (
Burzaovirus coli
,
Burzaovirus faecalis
) and VI (
Kahnovirus oralis
). The
Lactococcus
phages showed strong correlations and co-occurrence with
Lactococcus lactis
, while the
Crassvirales
phages,
B. coli
,
B. faecalis
, and UAG-readthrough crAss clade correlated and co-occurred with
Prevotella copri
. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.

IMPORTANCE

Phages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of
Inoviridae
, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of
Escherichia coli
-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of
Lactococcus lactis
-infecting phages, and enrichment of
Crassvirales
phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.
Pangenomic landscapes shape performances of a synthetic genetic circuit across
Stutzerimonas
species
Authors: Chan Dennis Tin Chat , Bernstein Hans C.
Published: August 2024

Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the “chassis-effect” or "context-dependency". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related
Stutzerimonas
hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.

IMPORTANCE

Contemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as
Escherichia coli
serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.
Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study
Authors: Wilson Rebecca , Margelyte Ruta , Redaniel Maria Theresa , Eyles Emily , Jones Tim , Penfold Chris , Blom Ashley , Elliott Andrew , Harper Alison , Keen Tim , Pitt Martin , Judge Andrew
Published: August 2024

Objectives

Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.

Design

Longitudinal, observational study used routinely collected data.

Setting

Data were collected from an NHS Trust in South-West England between 2016 and 2019.

Participants

2352 hip replacement patients had complete data and were included in analysis.

Primary and secondary outcome measures

Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of ≤7 days/>7 days in hospital and a binary measure of remaining in hospital when medically fit for discharge.

Results

The mean length of stay was 5.4 days following surgery, with 18% in hospital for more than 7 days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95% CI 1.05 to 1.08), being female (OR=1.42, 95% CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95% CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95% CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95% CI 1.37 to 3.16).

Conclusions

Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.
Clinical decision-making on lung cancer investigations in primary care: a vignette study
Authors: Mitchinson Lucy , von Wagner Christian , Blyth Alexandra , Shah Heer , Rafiq Meena , Merriel Samuel William David , Barclay Matthew , Lyratzopoulos Georgios , Hamilton Willie , Abel Gary A , Renzi Cristina
Published: August 2024

Objectives

To investigate the role of comorbid chronic obstructive pulmonary disease (COPD) and symptom type on general practitioners’ (GP’s) symptom attribution and clinical decision-making in relation to lung cancer diagnosis.

Design

Vignette survey with a 2×2 mixed factorial design.

Setting

A nationwide online survey exploring clinical decision-making in primary care.

Participants

109 GPs based in the United Kingdom (UK) who were registered as responders on Dynata (an online survey platform).

Interventions

GPs were presented with four vignettes which described a patient aged 75 with a smoking history presenting with worsening symptoms (either general or respiratory) and with or without a pre-existing diagnosis of COPD.

Primary and secondary outcome measures

GPs indicated the three most likely diagnoses (free-text) and selected four management approaches (20 pre-coded options). Attribution of symptoms to lung cancer and referral for urgent chest X-ray were primary outcomes. Alternative diagnoses and management approaches were explored as secondary outcomes. Multivariable mixed-effects logistic regression was used, including random intercepts for individual GPs.

Results

422 vignettes were completed. There was no evidence for COPD status as a predictor of lung cancer attribution (OR=1.1, 95% CI=0.5–2.4, p=0.914). There was no evidence for COPD status as a predictor of urgent chest X-ray referral (OR=0.6, 95% CI=0.3–1.2, p=0.12) or as a predictor when in combination with symptom type (OR=0.9, 95% CI=0.5–1.8, p=0.767).

Conclusions

Lung cancer was identified as a possible diagnosis for persistent respiratory by only one out of five GPs, irrespective of the patients’ COPD status. Increasing awareness among GPs of the link between COPD and lung cancer may increase the propensity for performing chest X-rays and referral for diagnostic testing for symptomatic patients.
Growing–finishing pigs do not need additional zinc in a phytase-supplemented wheat–barley–soybean meal-based diet
Authors: Nielsen Tina Skau , Hansen Sally Veronika , Woyengo Tofuko Awori
Published: August 2024

Focus remains on reducing the excretion of surplus zinc (Zn) from pigs through manure due to environmental and public health concerns. Growing–finishing pigs may need less dietary Zn than current EU legislation allows and what is typically applied on farms. The aim of this study was to evaluate the effect of three dietary Zn levels on productivity, Zn homeostasis, and health status in growing pigs fed a grain and soybean meal-based diet with a high inclusion of phytase (1000 phytase units). Ninety pigs were offered a diet with 1431 and 83 ppm total Zn from weeks 0–2 and 2–6 post-weaning, respectively, followed by one of three dietary Zn levels (31 (unsupplemented), 69, or 102 ppm total Zn, n = 30/Zn level) from weeks 6–16 post-weaning (30–110 kg). Productivity and health were unaffected by dietary Zn level. Despite differences in serum Zn according to dietary Zn level in week 10, serum Zn remained above the assumed sufficient level following all dietary Zn levels through the experiment. No signs of parakeratosis were observed, and we conclude that growing–finishing pigs produce and stay healthy without added Zn to a phytase supplemented grain–soybean meal-based diet when optimal dietary Zn levels are applied up to 30 kg.
Basis-independent quantum coherence and its distribution under relativistic motion
Authors: Du Ming-Ming , Li Hong-Wei , Tao Zhen , Shen Shu-Ting , Yan Xiao-Jing , Li Xi-Yun , Zhong Wei , Sheng Yu-Bo , Zhou Lan
Published: August 2024

Recent studies have increasingly focused on the effect of relativistic motion on quantum coherence. Prior research predominantly examined the influence of relative motion on basis-dependent quantum coherence, underscoring its susceptibility to decoherence under accelerated conditions. Yet, the effect of relativistic motion on basis-independent quantum coherence, which is critical for understanding the intrinsic quantum features of a system, remains an interesting open question. This paper addresses this question by examining how total, collective, and localized coherence are affected by acceleration and coupling strength. Our analysis reveals that both total and collective coherence significantly decrease with increasing acceleration and coupling strength, ultimately vanishing at high levels of acceleration. This underscores the profound impact of Unruh thermal noise. Conversely, localized coherence exhibits relative stability, decreasing to zero only under the extreme condition of infinite acceleration. Moreover, we demonstrate that collective, localized, and basis-independent coherence collectively satisfy the triangle inequality. These findings are crucial for enhancing our understanding of quantum information dynamics in environments subjected to high acceleration and offer valuable insights on the behavior of quantum coherence under relativistic conditions.
Synthesis, characterization and correlation studies on the Ni–Zn–Mn ferrite as a photocatalyst
Authors: Elmekawy Ahmed , Abdel-Hakim M. , El Hussiny F. , Farag G. , Hemeda O. M. , Mosaad M. M. , Sharshar T. , Henaish A. M. A.
Published: August 2024

Samples of Ni0.3Zn0.7−xMnxFe2O4(x = 0, 0.15, 0.25, 0.35, 0.45, 0.55) nanoparticles (NPs) were synthesized by auto-combustion flash method. These ferrites were used as catalysts for photodegradation of methylene blue (MB) dye utilizing visible light energy. Structural analysis was carried out using the X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, while nanoparticle dimensions were elucidated through transmission electron microscopy (TEM). The magnetic and optical behaviours were unveiled via vibrating sample magnetometer and UV–VIS spectroscopy, respectively. The XRD outcomes established the presence of a cubic spinel-type structure for the studied ferrite samples. The FTIR spectra unveiled two absorption characteristic bands of the spinel ferrite. TEM images revealed nanoscale dimensions of ferrite NPs with the range from 21.1 to 51.8 nm. The optical features exhibited an indirect band gap energy spanning from 4.25 to 4.36 eV. Magnetization behaviour displayed a sinusoidal trend corresponding to varying Mn concentrations. The ferrite NPs catalyst (10 mg) yield photodegradation efficiency ranged from 22.8 to 33.9% for 100 ml MB dye solution after 120 min of light irradiation. The effects of dye concentration and catalyst dose on the degradation efficiency were examined using the Ni0.3Zn0.35Mn0.35Fe2O4catalyst with highest degradation (= 33.9%). On the other hand, the dependence of the degradation efficiency on the structure, morphological, magnetic and optical properties of the photocatalyst was investigated. The findings of this study underscore the potential of the prepared ferrite nanoparticles for advanced applications in environmental restoration.

Graphical abstract
A Data-Loader Tunable Knob to Shorten GPU Idleness for Distributed Deep Learning
Authors: Jia Danlin , Yuan Geng , Xie Yiming , Lin Xue , Mi Ningfang
Published: August 2024

Deep Neural Networks (DNNs) have been applied as an effective machine learning algorithm to tackle problems in different domains. However, the endeavor to train sophisticated DNN models can stretch from days into weeks, presenting substantial obstacles in the realm of research focused on large-scale DNN architectures. Distributed Deep Learning (DDL) contributes to accelerating DNN training by distributing training workloads across multiple computation accelerators, for example, graphics processing units (GPUs). Despite the considerable amount of research directed toward enhancing DDL training, the influence of data loading on GPU utilization and overall training efficacy remains relatively overlooked. It is non-trivial to optimize data-loading in DDL applications that need intensive central processing unit (CPU) and input/output (I/O) resources to process enormous training data. When multiple DDL applications are deployed on a system (e.g., Cloud and High-Performance Computing (HPC) system), the lack of a practical and efficient technique for data-loader allocation incurs GPU idleness and degrades the training throughput. Therefore, our work first focuses on investigating the impact of data-loading on the global training throughput. We then propose a throughput prediction model to predict the maximum throughput for an individual DDL training application. By leveraging the predicted results, A-Dloader is designed to dynamically allocate CPU and I/O resources to concurrently running DDL applications and use the data-loader allocation as a knob to reduce GPU idle intervals and thus improve the overall training throughput. We implement and evaluate A-Dloader in a DDL framework for a series of DDL applications arriving and completing across the runtime. Our experimental results show that A-Dloader can achieve a 28.9% throughput improvement and a 10% makespan improvement compared with allocating resources evenly across applications.