bluuebunny/crossref_metadata_2025 huggingface dataset:
Cinnamamides: a review of research in the agrochemical field
Authors: Da Silva Adrielle Firmino , França Saraliny Bezerra , Costa Lucas Fernando De Lima , dos Santos Ricardo Alexandre , Pinheiro Natália De Araújo , Barros Maria Ester De Sá Barreto , Lima Dimas José Da Paz
Published: November 2024

The need for implementation of economically viable agrochemicals with lower toxicity and that are capable of overcoming resistance developed by insects, fungi and invasive plants has spurred the scientific community in the search for new active and selective substances and synthetic methodologies that adhere to the parameters of green chemistry. Cinnamamides, in turn, present a scaffold that has been a basis for various investigations due to their broad spectrum of biological activities. The agrochemical industry is a vast field in which these classes of compounds stand out, whether for their potential herbicidal, fungicidal, nematicidal, or insecticidal properties. Therefore, this review reports the progress of synthesis and the agrochemical potential of cinnamamides, their mechanism of action, and their structure–activity relationship (SAR), to provide insights for further research addressing the use of cinnamamides in crop protection. © 2024 Society of Chemical Industry.
Temperature‐driven cotton verticillium wilt: a beta model for risk assessment from laboratory insights to climate scenarios
Authors: Zhang Tianyi , Zheng Bangyou , Xie Zongming , Zhang Tao , Feng Hongjie , Zhou Jinglong , Ouyang Fang
Published: November 2024

BACKGROUND

Verticillium wilt is a critical disease affecting cotton in the Xinjiang province, a region producing 90% cotton in China. Defining the specific temperature thresholds for disease prevalence is essential but has remained unclear.

RESULTS

This study aimed to establish a model to quantify the relationship between temperature and cotton verticillium wilt disease risk. Through a controlled temperature experiment, we identified a nonlinear temperature relationship, with an optimal temperature of 26.5 °C. Then a beta model, parameterized from these findings, was validated against historical regional disease data, confirming its ability to accurately reflect interannual variations in disease occurrence and its direct applicability from laboratory to regional scales. We then utilized the model to project future disease risks under two Shared Socioeconomic Pathways (SSP) climate scenarios. The projections estimate a 4.8% to 10.1% increase in disease risks in Xinjiang by the 2080s under SSP1‐2.6 and SSP5‐8.5 scenarios, respectively.

CONCLUSION

This research offers a valuable predictive tool for cotton verticillium wilt risks, informing strategic decisions for cotton production in the face of climate change. The successful application of a laboratory‐derived model at a regional scale marks a significant advancement in plant disease risk assessment, underscoring temperature as a dominate factor in cotton disease dynamics. © 2024 Society of Chemical Industry.
Wastecraft and its multifaceted learning in Cuba
Authors: Lanzidei Claudia Marina
Published: November 2024

In Cuba, scarcity is an ever‐present reality due to more than six decades of socialist regime and consequent economic embargo. One of the coping strategies for people facing such adversity has been to develop great abilities to repair and reuse objects and materials. In a certain way, Cubans are like Lévi‐Straussian bricoleurs, or, better said, they are engineers who had to adjust their project because the universe of tools at their disposition was closed, leading them to make do with the less they are provided with. Indeed, they create objects by repairing and reusing parts and materials, and by doing so, they refer to specific concepts like inventing, innovating, adapting, and recycling. Many of the practices, apart from being a way of earning a living, directly depend on the recovery of discarded elements and are therefore part of a complex economy that involves waste, which, once recovered, becomes a resource again. This article focuses on how social actors regulate and negotiate access to remunerative knowledges related to waste, what I call wastecrafts. Drawing on anthropological literature about gift giving and sharing, I reflect on how the transmission of practices related to waste takes place in Havana. My argument is that practices of reciprocity, sharing, and, in some cases, stealing the art coexist and are all to understand within the emic ideas of inventar, luchar, and sobrevivir.
Graph Neural Networks and Molecular Docking as Two Complementary Approaches for Virtual Screening: A Case Study on Cruzain
Authors: Gómez Chávez José Leonardo , Luchi Adriano Martín , Villafañe Roxana Noelia , Conti Germán Andres , Perez Ernesto Rafael , Angelina Emilio Luis , Peruchena Nélida María
Published: November 2024

Molecular docking is one of the most widely used techniques for virtual screening (VS) of potential drug candidates. Despite its popularity, docking accuracy is often limited due to the trade‐off between speed and precision required for screening large compound libraries. In the present work, we leverage graph convolutional networks (GCNs), a state‐of‐the‐art deep neural network architecture, to enhance docking capacity for prioritizing active compounds from a library of ∼200,000 compounds screened against Cruzain. We propose strategies to integrate both techniques into a single VS pipeline. By applying the GCN as a pre‐docking filter, the compound library was enriched with active molecules, resulting in higher hit rates in subsequent docking screenings. Additionally, to further enhance the docking performance, the GCN‐learned atomic embeddings were directly incorporated into the docking process through pharmacophoric restraints. Unlike common approaches that use deep learning (DL) scoring functions to rank pre‐generated docking poses, the approaches we propose here have the advantage that only compounds that passed the DL filters need to be screened by the more computationally demanding docking method. This work might serve as a proof of concept for combining deep learning and classical docking in drug discovery.
Infrared PbS Quantum Dot–Lead Halide Perovskite Combinations for Breaking the Shockley–Queisser Limit
Authors: Jiang Yuhong , Zhang Yong , Zheng Jianghui , Gao Yijun , Xiang Chaoyu , Dong Beining , Lin Chun‐Ho , Chen Fandi , Guan Xinwei , Li Xiaoning , Wan Tao , Mei Tingting , Huang Shujuan , Hu Long , Chu Dewei
Published: November 2024

Lead sulfide (PbS) quantum dots (QDs) and lead halide perovskites (LHPs) have emerged as highly promising materials for high‐efficiency photovoltaics. PbS QDs offer size‐dependent bandgaps in the infrared region and the potential for multiple exciton generation, while LHPs feature tunable bandgaps, high absorption coefficients, and long carrier diffusion lengths in the visible spectrum. This review focuses on two primary approaches to breaking the Shockley–Queisser (S–Q) limit based on the combinations of these two semiconducting materials: 1) monolithic 2‐terminal tandem photovoltaics with complementary spectral absorption; and 2) intermediate‐band solar cells (IBSCs) leveraging PbS QDs within a LHP matrix. Due to the ideally complementary spectrum of PbS and LHPs, emphasis is placed on the prevailing strategies for enhancing efficiency, addressing the major challenges in rational materials designs and device optimizations. Then, key obstacles including surface passivation, solvent compatibility, and the limited performance of small‐bandgap PbS QD solar cells are analyzed, along with various potential solutions for tandem cells. For IBSCs, the evolution of materials and device architecture and the unique advantages of their combination are outlined in detail. Finally, this review provides a comprehensive outlook on future research directions to develop efficient tandem and IBSC devices for breaking the S–Q limit.
Introduction
Authors: Nair V. Parameswaran
Published: November 2024

The motivation for geometric quantization and how it relates to other approaches to quantization are briefly discussed.
A Comment on the Metaplectic Correction
Authors: Nair V. Parameswaran
Published: November 2024

This chapter is a comment on the metaplectic correction and how it enters into the realization of polarization-changing transformations.
Classical Dynamics
Authors: Nair V. Parameswaran
Published: November 2024

The Hamiltonian formulation of classical dynamics is outlined, including the relation between the action and the symplectic structure.
Geometric Quantization
Authors: Nair V. Parameswaran
Published: November 2024

This chapter gives the basic framework of geometric quantization. Prequantum operators, polarization and the integration measures for the inner product of wave functions are introduced.
Coherent States, the Two-Sphere and G/H Spaces
Authors: Nair V. Parameswaran
Published: November 2024

As examples of geometric quantization, we consider coherent states in flat space, on the two-sphere and on the complex projective space. These are treated using local coordinates, homogeneous coordinates and a group-theoretic formulation. Quantization of Kähler spaces of the G/H-type is also considered. We also outline the use of index theorems to calculate the dimension of the Hilbert space.
The Chern-Simons Theory in 2+1 Dimensions
Authors: Nair V. Parameswaran
Published: November 2024

The Chern-Simons theory is a field theory in 2+1 dimensions with applications to the quantum Hall effect, knot theory, gravity, etc. General features of the geometric quantization of this theory are considered here, with some details presented for $$S^2$$ and for the Abelian theory on the torus.
$$\theta $$-Vacua in a Nonabelian Gauge Theory
Authors: Nair V. Parameswaran
Published: November 2024

The $$\theta $$-vacuum in a nonabelian gauge theory, which is a prime example of nontrivial $$\mathcal {H}^{1} (M, \mathbb {R})$$, is discussed.
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution
Authors: Khurana Mridul , Daw Arka , Maruf M. , Uyeda Josef C. , Dahdul Wasila , Charpentier Caleb , Bakış Yasin , Bart Henry L. , Mabee Paula M. , Lapp Hilmar , Balhoff James P. , Chao Wei-Lun , Stewart Charles , Berger-Wolf Tanya , Karpatne Anuj
Published: November 2024

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)
Potential of the International Dispute Settlement Mechanisms as Established Under UNCLOS: Options for Improvement
Authors: Wolfrum Rüdiger
Published: November 2024

One of the major achievements of UNCLOS—there are many—is the establishment of a mandatory system for the settlement of maritime disputes. Since we are celebrating UNCLOS let me briefly mention some of the important issues, which distinguishes this regime from previous ones.
Quantum subsystem codes, CFTs and their ℤ2-gaugings
Authors: Ando Keiichi , Kawabata Kohki , Nishioka Tatsuma
Published: November 2024

Abstract

We construct Narain conformal field theories (CFTs) from quantum subsystem codes, a more comprehensive class of quantum error-correcting codes than quantum stabilizer codes, for qudit systems of prime dimensions. The resulting code CFTs exhibit a global ℤ2 symmetry, enabling us to perform the ℤ2-gauging to derive their orbifolded and fermionized theories when the symmetry is non-anomalous. We classify a subset of these subsystem code CFTs using weighted oriented graphs and enumerate those with small central charges. Consequently, we identify several bosonic code CFTs self-dual under the ℤ2-orbifold, new supersymmetric code CFTs, and a few fermionic code CFTs with spontaneously broken supersymmetry.
Inclusive $$ \overline{B}\to {X}_s{\ell}^{+}{\ell}^{-} $$ at the LHC: theory predictions and new-physics reach
Authors: Huber Tobias , Hurth Tobias , Jenkins Jack , Lunghi Enrico , Qin Qin , Vos K. Keri
Published: November 2024

Abstract

We present theoretical predictions for observables in inclusive $$ \overline{B}\to {X}_s{\ell}^{+}{\ell}^{-} $$

B
¯

→

X
s

ℓ
+

ℓ
−

suitable for measurements at hadron colliders through a sum-over-exclusive approach. At low q2 we calculate the branching ratio and three angular observables. At high q2 we provide the branching ratio and the ratio of the $$ \overline{B}\to {X}_s{\ell}^{+}{\ell}^{-} $$

B
¯

→

X
s

ℓ
+

ℓ
−

rate with respect to the inclusive $$ \overline{B}\to {X}_u\ell \overline{\nu} $$

B
¯

→

X
u

ℓ

ν
¯

rate with the same phase-space cut. We compare our predictions to the B factory measurements and also to an extraction of the experimental rate through a sum-over-exclusive method using branching ratios of the exclusive $$ \overline{B}\to {K}^{\left(\ast \right)}{\mu}^{+}{\mu}^{-} $$

B
¯

→

K

∗

μ
+

μ
−

modes measured at LHCb. We find a consistent picture comparing Standard Model theory and experiment. As such, our analysis does not support a recent claim about a deficit in the inclusive branching ratio in the high-q2 region. Finally, we present current model-independent bounds on new physics and emphasize the potential of complementary analyses of $$ \overline{B}\to {X}_s{\ell}^{+}{\ell}^{-} $$

B
¯

→

X
s

ℓ
+

ℓ
−

at Belle II and the LHC.
Deconstruction and surface defects in 6d CFTs
Authors: Conti Andrea , Dibitetto Giuseppe , Lozano Yolanda , Petri Nicolò , Ramírez Anayeli
Published: November 2024

Abstract

We study the two families of AdS3 × S3 × S2 × Σ2 solutions to massive Type IIA supergravity with small and large (0, 4) supersymmetries constructed recently in the literature, in connection with the AdS7 × S2 × I solutions to massive Type IIA, to which they asymptote locally. Based on our analysis of various observables, that we study holographically, we propose an interpretation of the first class of solutions as dual to deconstructed 6d (1,0) CFTs dual to AdS7, and of the second class as dual to surface defects in the same 6d theories. Among the observables that we study are baryon vertices and giant graviton configurations in quiver-like constructions.
Regulation of formin INF2 and its alteration in INF2-linked inherited disorders
Authors: Labat-de-Hoz Leticia , Jiménez M. Ángeles , Correas Isabel , Alonso Miguel A.
Published: November 2024

Formins are proteins that catalyze the formation of linear filaments made of actin. INF2, a formin, is crucial for correct vesicular transport, microtubule stability and mitochondrial division. Its activity is regulated by a complex of cyclase-associated protein and lysine-acetylated G-actin (KAc-actin), which helps INF2 adopt an inactive conformation through the association of its N-terminal diaphanous inhibitory domain (DID) with its C-terminal diaphanous autoinhibitory domain. INF2 activation can occur through calmodulin binding, KAc-actin deacetylation, G-actin binding, or association with the Cdc42 GTPase. Mutations in the INF2 DID are linked to focal segmental glomerulosclerosis (FSGS), affecting podocytes, and Charcot-Marie-Tooth disease, which affects Schwann cells and leads to axonal loss. At least 80 pathogenic DID variants of INF2 have been identified, with potential for many more. These mutations disrupt INF2 regulation, leading to excessive actin polymerization. This in turn causes altered intracellular trafficking, abnormal mitochondrial dynamics, and profound transcriptional reprogramming via the MRTF/SRF complex, resulting in mitotic abnormalities and p53-mediated cell death. This sequence of events could be responsible for progressive podocyte loss during glomerular degeneration in FSGS patients. Pharmacological targeting of INF2 or actin polymerization could offer the therapeutic potential to halt the progression of FSGS and improve outcomes for patients with INF2-linked disease.
Hawking-Type Singularity Theorems for Worldvolume Energy Inequalities
Authors: Graf Melanie , Kontou Eleni-Alexandra , Ohanyan Argam , Schinnerl Benedict
Published: November 2024

The classical singularity theorems of R. Penrose and S. Hawking from the 1960s show that, given a pointwise energy condition (and some causality as well as initial assumptions), spacetimes cannot be geodesically complete. Despite their great success, the theorems leave room for physically relevant improvements, especially regarding the classical energy conditions as essentially any quantum field theory necessarily violates them. While singularity theorems with weakened energy conditions exist for worldline integral bounds, so-called worldvolume bounds are in some cases more applicable than the worldline ones, such as the case of some massive free fields. In this paper, we study integral Ricci curvature bounds based on worldvolume quantum strong energy inequalities. Under the additional assumption of a—potentially very negative—global timelike Ricci curvature bound, a Hawking-type singularity theorem is proved. Finally, we apply the theorem to a cosmological scenario proving past geodesic incompleteness in cases where the worldline theorem was inconclusive.
Targeting RNA-protein interactions with small molecules: promise and therapeutic potential
Authors: Rhodes Curran , Balaratnam Sumirtha , Yazdani Kamyar , Seshadri Srinath , Schneekloth John S.
Published: November 2024

The therapeutic potential of targeting protein-RNA interactions has not been fully explored. While several approaches to block the interactions between various RNA and protein partners have been developed, rational efforts to target pre-assembled complexes have not been broadly pursued. This is despite the recent commercial success of risdiplam, and the high-resolution structure of the EIF4A-polypurine-Rocaglamide A ternary complex, which elucidates how compounds may recognize these pockets. These prominent examples indicate the viability of this approach, but important questions remain. For example, how abundant are these pockets in other protein-RNA complexes? Do such pockets have properties suitable for small molecule recognition? A broad analysis of 160 previously published RNP complexes confirmed that interfacial pockets in RNA-protein complexes are both abundant and have favorable properties that would make them good candidates for rational screening campaigns. These conclusions are expected to have important implications especially for those working on developing small molecules that bind directly to RNA structural elements.
Boundary Behavior of Limit-Interfaces for the Allen–Cahn Equation on Riemannian Manifolds with Neumann Boundary Condition
Authors: Li Martin Man-chun , Parise Davide , Sarnataro Lorenzo
Published: November 2024

We study the boundary behavior of any limit-interface arising from a sequence of general critical points of the Allen–Cahn energy functionals on a smooth bounded domain. Given any such sequence with uniform energy bounds, we prove that the limit-interface is a free boundary varifold which is integer rectifiable up to the boundary. This extends earlier work of Hutchinson and Tonegawa on the interior regularity of the limit-interface. A key novelty in our result is that no convexity assumption of the boundary is required and it is valid even when the limit-interface clusters near the boundary. Moreover, our arguments are local and thus work in the Riemannian setting. This work provides the first step towards the regularity theory for the Allen–Cahn min-max theory for free boundary minimal hypersurfaces, which was developed in the Almgren–Pitts setting by the first-named author and Zhou.
On the Boltzmann equation with strong kinetic singularity and its grazing limit from a new perspective
Authors: Yang Tong , Zhou Yu-Long
Published: November 2024

For the inverse power law potential $$U(r)=r^{-p}$$

U

(
r
)

=

r

-
p

, the Boltzmann kernel has the asymptotic behavior $$B(v-v_{*}, \sigma ) \sim \theta ^{-2-2s} |v-v_{*}|^{\gamma }$$

B

(
v
-

v

∗

,
σ
)

∼

θ

-
2
-
2
s

|
v
-

v

∗

|

γ

as the deviation angle tends to 0. Global well-posedness of the Boltzmann equation with such singular kernels has been built in the parameter range $$\gamma >-3, 0<s<1$$

γ
>
-
3
,
0
<
s
<
1

independently by Gressman and Strain (J Am Math Soc 24:771–847, 2011), Alexandre et al. (J Funct Anal 262:915–1010, 2012), triggering many other theoretical developments thereafter. In this work, we consider stronger kinetic singularity and extend the global well-posedness theory to the range $$\gamma >-2s -3, 0<s<1$$

γ
>
-
2
s
-
3
,
0
<
s
<
1

. This range is optimal by recalling that the dominant part of the Boltzmann operator behaves like the factional Laplace operator $$(-\Delta )^{s}$$

(
-
Δ
)

s

which allows a singularity with exponent $$-2s -3$$

-
2
s
-
3

in 3-dimensional space. Based on the global well-posedness result, we prove the grazing limit of the Boltzmann equation to the Landau equation as $$s \rightarrow 1^{-}$$

s
→

1
-

from a new perspective for any $$\gamma >-5$$

γ
>
-
5

that includes the Coulomb potential $$\gamma =-3$$

γ
=
-
3

. As a byproduct, the Landau equation is globally well-posed for any $$\gamma >-5$$

γ
>
-
5

.
Activation of sirtuin 3 and maintenance of mitochondrial homeostasis by artemisinin protect against diclofenac-induced kidney injury in rats
Authors: Hellal Doaa , El-Khalik Sarah Ragab Abd , Arakeep Heba M. , Radwan Doaa A. , Abo Safia Hend S. , Farrag Eman A. E.
Published: November 2024

Nonsteroidal anti-inflammatory drug (NSAID)-induced kidney injury is one of the most common causes of renal failure. The exact pathogenesis of NSAID induced kidney injury is not fully known and the treatment is still challenging. Artemisinin (ART) gains more attention by its potent biological activities in addition to its antimalarial effect. In our research, we evaluated the preventive and therapeutic effects of ART in Diclofenac (DIC) induced kidney injury through its effect on mitochondria and regulation of sirtuin 3 (SIRT3). Thirty adult male Sprague Dawley rats were divided into five groups: control, ART, DIC, DIC + ART prophylactic, and DIC followed + ART therapeutic groups. At the end of the study, animals were scarified and the following parameters were evaluated: serum urea and creatinine, renal malondialdehyde (MDA), superoxide dismutase (SOD) and nitrate. SIRT3 was detected by western blotting and real-time PCR. Mitochondrial related markers (PGC-1α, Drp1, and mitochondrial ATP) were detected by immunoassay. Caspase-3 and LC3 II expression in kidney tissues were demonstrated by immune-histochemical staining. The kidney specimens were stained for H&E and PAS special stain. Electron microscopy was done to detect mitochondrial morphology. ART improved renal function test, oxidative stress, SIRT3 level, mitochondrial function, LC3 II expression and decrease caspase-3. Histopathological examination confirmed ART alleviation as determined by light or electron microscopy. ART can modulate biochemical and pathological changes in DIC-induced kidney injury and can be considered a new possible therapeutic approach for DIC-induced kidney injury through its effect on SIR3 and maintenance of mitochondrial homeostasis.
Protective effect of Dulaglutide, a GLP1 agonist, on acetic acid-induced ulcerative colitis in rats: involvement of GLP-1, TFF-3, and TGF-β/PI3K/NF-κB signaling pathway
Authors: Mahdy Raghda N. El , Nader Manar A. , Helal Manar G. , Abu-Risha Sally E. , Abdelmageed Marwa E.
Published: November 2024

A chronic inflammatory condition of the colon called ulcerative colitis (UC) is characterized by mucosal surface irritation that extends from the rectum to the near proximal colon portions. The rationale of this work was to conclude if dulaglutide (Dula) could protect rats from developing colitis caused by exposure to acetic acid (AA). Rats were randomly divided into seven groups (each with eight rats): Normal control, Dula control, AA (received 2 milliliters of 3% v/v AA through the rectum), Sulfasalazine (SLZ); given SLZ (100 mg/kg) orally from day 11 to day 21 then AA intrarectally on day 22 and Dula groups ( pretreated with 50, 100 or 150 μg/kg subcutaneous injection of Dula - once weekly for three weeks and AA on day 22 to induce ulcerative colitis, colon tissues and blood samples were taken on day 23. By generating colonic histological deviations such as inflammatory processes, goblet cell death, glandular hyperplasia, and mucosa ulcers, Dula dropped AA-induced colitis. Additionally, these modifications diminished blood lactate dehydrogenase (LDH), C-reactive protein (CRP), colon weight, and the weight/length ratio of the colon. In addition, Dula decreased the oxidative stress biomarker malondialdehyde (MDA) and increased the antioxidant enzymes (total antioxidant capacity (TAC), reduced glutathione (GSH), and superoxide dismutase (SOD) concentrations). Dula also significantly reduced the expression of transforming growth factor-1 (TGF-β1), phosphatidylinositol-3-kinase (PI3K), protein kinase B (AKT) signaling pathway, and the inflammatory cytokines: nuclear factor kappa B (NF-κB), interleukin-6 (IL-6), and interferon-γ (IFN-γ) in colonic cellular structures. In addition, Dula enforced the levels of glucagon-like peptide-1 (GLP-1) and trefoil factor-3 (TFF-3) that were crucial to intestinal mucosa regeneration and healing of wounds. By modulating TGF-β1 in conjunction with other inflammatory pathways like PI3K/AKT and NF-κB, regulating the oxidant/antioxidant balance, and improving the integrity of the intestinal barrier, Dula prevented AA-induced colitis in rats.
Xenorhabdus bharatensis sp. nov., Xenorhabdus entomophaga sp. nov., Xenorhabdus siamensis sp. nov., and Xenorhabdus thailandensis sp. nov. Isolated from Steinernema Entomopathogenic Nematodes
Authors: Thanwisai Aunchalee , Machado Ricardo A. R. , Bhat Aashaq Hussain , Pidot Sacha J. , Tandhavanant Sarunporn , Subkrasae Chanakan , Meesil Wipanee , Ardpairin Jiranun , Pansri Supawan , Vitta Apichat
Published: November 2024

Four Gram-stain-negative bacterial strains, CS20T, AUT15.5T, XENO-11T, and CCN3.3T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel species within the genus Xenorhabdus (Gammaproteobacteria, Morganellaceae). In this study, we described these new species using whole-genome phylogenomic reconstructions, sequence identity values from core genome sequences, and phenotypic characterization. Phylogenetic reconstructions based on 16S rRNA gene sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T, (ii) strain AUT15.5T is closely related to X. budapestensis DSM 16342T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The 16S rRNA gene sequence similarity value between strain CS20T and X. stockiae DSM 17904T is 97.8%, between strain AUT15.5T and X. budapestensis DSM 16342T is 98.1%, between strain XENO-11T and X. khoisanae DSM 25463T is 97.8%, and between strain CCN3.3T and X. griffiniae DSM 17911T is 98.6%. Phylogenomic reconstructions using whole-genome sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T and X. innexi DSM 16336T, (ii) strain AUT15.5T is closely related to X. indica DSM 17382T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains CS20T, AUT15.5T, XENO-11T, and CCN3.3T and the type strains of their more closely related species are below the 70% and the 95–96% divergence thresholds, respectively, used for prokaryotic species delineation. Hence, we propose the following four new species: Xenorhabdus bharatensis sp. nov. (the type strain is CS20T=CCM 9320T=CCOS 2070T), X. entomophaga sp. nov. (the type strain is XENO-11T=CCM 9389T=CCOS 2111T), X. siamensis sp. nov. (the type strain is AUT15.5T=CCM 9405T=CCOS 2116T), and X. thailandensis sp. nov. (the type strain is CCN3.3T=CCM 9406T=CCOS 2115T). The following biochemical tests may be useful for differentiating the novel species from their more closely related taxa: acetoin production, arginine dihydrolase, citrate utilization, gelatinase, glucose oxidation, indole production, and tryptophan deaminase. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.
Flexible colorimetric sensor for ammonia detection based on polyurethane and bromocresol green
Authors: Abilevitch Lihi , Otorgust Gilad , Mizrahi Limor , Dotan Ana , Amir Elizabeth
Published: November 2024

Ammonia (NH3) is a highly toxic, colorless gas with the potential to cause severe health damage and even fatality. This study aims to develop an inexpensive, flexible, and reversible colorimetric thin film based on thermoplastic polyurethane (TPU), poly (vinyl alcohol) (PVOH) and bromocresol green (BCG) as a colorimetric gas sensor reagent. The fabrication of the sensor films process involves a two-step procedure consisting of melt compounding and compression molding on a laboratory scale. Optimization of the materials composition of the sensor film revealed the optimal concentrations of 0.5 wt% of BCG and 1 wt% of PVOH in the TPU matrix. A visible transition from yellow-orange to green upon exposure to gaseous and liquid ammonia was attributed to the deprotonation of BCG by ammonia nitrogen atom. Furthermore, the sensor exhibited an efficient gas detection limit of 25 ppm and good reversibility for at least 10 exposure cycles. Additionally, the sensor exhibits outstanding selectivity in detecting ammonia over various basic solutions. This study also demonstrates the feasibility of using the proposed system for industrial-scale production as exemplified by the fabrication of filament by continuous extrusion process. The colorimetric filament with diameter of 0.8 mm was successfully weaved onto different cotton fabrics to show their applicability as smart ammonia textile sensors.

Graphical abstract
Plant ways in Middle Bronze Age Anatolia—an archaeological interpretation of phytoliths and other plant remains from Zincirli Höyük, Türkiye
Authors: Öğüt Birgül , Karakaya Doğa
Published: November 2024

This paper presents the results of phytolith analysis from Middle Bronze Age II (1800–1600 bce) Zincirli Höyük, Türkiye. The study area was destroyed by a single fire event resulting in the preservation and recovery of several food processing installations (archaeological features) and restorable vessels (broken pots) in situ. The archaeological contexts were only slightly disturbed by later sedimentary and human activities. In this paper, we focus on the interpretation of the phytolith assemblages from samples collected from various archaeological features and destruction debris, including potential Phragmites (reed) matting, pottery contents and various kinds of installations. Complementary evidence from diatoms, dung spherulites and macrobotanical remains from this study and a previous one are also evaluated to add to the contextual significance of the phytolith record.
Fitted Fv/Fm temperature response curves: applying lessons from plant ecophysiology to acute thermal stress experiments in coral holobionts
Authors: Gomez-Campo Kelly , Baums Iliana B.
Published: November 2024

Maximum photochemical efficiency, F

v

/F

m
, is the preferred metric for quantifying the loss of photosystem II (PSII) function in photosynthetic algal symbionts (Symbiodiniaceae) of reef-building corals exposed to heat stress, particularly at the early stages of coral bleaching. Loss of PSII function can be quantified as the temperature at which a holobiont loses 50% of maximum photochemical efficiency (50% effective dose, or ED50) when exposed to a range of experimental temperatures. Here, we demonstrate that dose–response curves can be substantially more informative about a coral’s stress response by including ED5 (5% effective dose), ED95 (95% effective dose), and decline width (ED95–ED5) values in summary statistics. These parameters are commonly used in plant ecophysiology and can be extracted from fitted F

v

/F

m
temperature response curves. This suite of metrics provides a broader understanding of the loss of PSII function in acute thermal stress experiments in corals and could enhance comparability among coral and plant studies.
Coral reef attributes associated with microplastic exposure
Authors: Hankins Cheryl , Lasseigne Danielle , Davis Sarah M. , Edwards Kimberly , Paul Jenny S.
Published: November 2024

Coral reef declines have been documented since the 1980’s from a variety of global and local stressors. Management resource tools are needed to preserve these fragile ecosystems from stressors, both known and unknown. Laboratory studies have shown microplastics (MP) to have negative effects on coral physiology, but their effects in a natural environment are not well understood. Thus, our primary objectives were to explore associations between MPs and coral reef attributes. We measured MP concentrations from sub-surface water and coral tissue samples from two Caribbean/Atlantic scleractinian coral species, Montastraea cavernosa and Orbicella faveolata, from St. John, U.S. Virgin Islands and Florida’s Coral Reef in 2017 and 2018, respectively. Polymer identification yielded mostly cotton or polyester fibers for both water and coral tissue samples. This study is the first to document MPs in coral tissues from either the U.S. Virgin Islands or Florida’s Coral Reef and is the first to explore how MPs relate to coral reef attributes. Significant, positive relationships were seen between MPs in coral tissue and coral density, rugosity, and percent coral cover, indicating MPs may not have immediate adverse effects on coral reef health.
Using underwater mini-ROV for coral eDNA survey: a case study in Okinawan mesophotic ecosystems
Authors: Satoh Noriyuki , Sinniger Frederic , Narisoko Haruhi , Nagahama Shinichiro , Okada Nobuhiro , Shimizu Yuki , Yoshioka Yuki , Hisata Kanako , Harii Saki
Published: November 2024

Mesophotic coral ecosystems (MCEs) are light-dependent communities occurring at depths of 30–150 m. They have been suggested to serve as refuge against thermal stress during heat waves for some coral species. Recent studies on MCEs have revealed a high diversity of communities, some unique, and that these ecosystems are far from being immune to anthropogenic threats. However, the depths at which these ecosystems are found make their exploration and study challenging. Consequently, most suitable environments for MCEs remain unexplored. To facilitate the detection and characterization of MCEs, we improved the methodology for mesophotic scleractinian survey by environmental DNA (eDNA) metabarcoding analysis using seawater collected by underwater mini-Remote Operated Vehicle (mini-ROV). We tested this improved approach at upper mesophotic sites in Okinawa, Japan, with different corals dominating the communities (i.e., Alveopora-dominated, Seriatopora-dominated, and Acropora-dominated communities). Despite the proximity of the different sites, our eDNA metabarcoding analyses detected the dominant coral genera specific to each site. In addition, this study detected numerous other genera present at these sites, including Acropora, Pachyseris, Galaxea, Lobophyllia, Montipora, Pocillopora, Porites, and others. Therefore, this study might support a new technical gate for comprehensive survey of MCEs using eDNA samples collected by underwater mini-ROV, although further technical improvement is required for quantitative estimation.
Effect of ventricular fibrillation on infarct size after myocardial infarction: a translational study
Authors: Stevic Neven , Pinède Alexandre , Mewton Nathan , Ovize Michel , Argaud Laurent , Lecour Sandrine , Boiteux Clément , Bochaton Thomas , Cour Martin
Published: November 2024

Ventricular fibrillation (VF)-induced cardiac arrest frequently complicates ST-segment elevation myocardial infarction (STEMI). Although larger infarct sizes (IS) correlate with a higher risk of VF, the influence of VF itself on IS has remained poorly investigated. To address this knowledge gap, we analyzed the effect of VF on IS in patients and two experimental models. From a prospective cohort, 30 STEMI patients with VF were matched 1:2 with STEMI patients without VF on the common determinants of IS. The primary endpoint was IS, assessed using the 48-h area under the curve (AUC) for troponin. We also compared IS in pigs with/without spontaneous VF during STEMI (n = 15/group), and in an isolated rat heart model of myocardial infarction with/without electrically induced VF (n = 7/group). After matching, the patient characteristics, including the area at risk (AR), were similar. IS was 33% lower in the VF group compared to the control group (troponin AUC 1.6 [0.5–3.3] 106 arbitrary units vs. 2.4 [0.9–4.1] 106 arbitrary units; p < 0.05), but infarct scar size (assessed using MRI and ECG) did not differ between the groups at 1 and 6 months. In both experimental models, IS, expressed as a percentage of AR, was lower (p < 0.05) in the VF group than in the control group. When common determinants of IS are comparable, VF occurring prior to myocardial infarction reperfusion appears to be associated with smaller IS. Nevertheless, this finding, observed under specific experimental conditions and in a highly selected group of patients, was not associated with reduced infarct scar size.

Registration (HIBISCUS-STEMI cohort): ClinicalTrials.gov NCT05794022.
SMOC1 colocalizes with Alzheimer’s disease neuropathology and delays Aβ aggregation
Authors: Balcomb Kaleah , Johnston Caitlin , Kavanagh Tomas , Leitner Dominique , Schneider Julie , Halliday Glenda , Wisniewski Thomas , Sunde Margaret , Drummond Eleanor
Published: November 2024

SMOC1 has emerged as one of the most significant and consistent new biomarkers of early Alzheimer’s disease (AD). Recent studies show that SMOC1 is one of the earliest changing proteins in AD, with levels in the cerebrospinal fluid increasing many years before symptom onset. Despite this clear association with disease, little is known about the role of SMOC1 in AD or its function in the brain. Therefore, the aim of this study was to examine the distribution of SMOC1 in human AD brain tissue and to determine if SMOC1 influenced amyloid beta (Aβ) aggregation. The distribution of SMOC1 in human brain tissue was assessed in 3 brain regions (temporal cortex, hippocampus, and frontal cortex) using immunohistochemistry in a cohort of 73 cases encompassing advanced AD, mild cognitive impairment (MCI), preclinical AD, and cognitively normal controls. The Aβ- and phosphorylated tau-interaction with SMOC1 was assessed in control, MCI, and advanced AD human brain tissue using co-immunoprecipitation, and the influence of SMOC1 on Aβ aggregation kinetics was assessed using Thioflavin-T assays and electron microscopy. SMOC1 strongly colocalized with a subpopulation of amyloid plaques in AD (43.8 ± 2.4%), MCI (32.8 ± 5.4%), and preclinical AD (28.3 ± 6.4%). SMOC1 levels in the brain strongly correlated with plaque load, irrespective of disease stage. SMOC1 also colocalized with a subpopulation of phosphorylated tau aggregates in AD (9.6 ± 2.6%). Co-immunoprecipitation studies showed that SMOC1 strongly interacted with Aβ in human MCI and AD brain tissue and with phosphorylated tau in human AD brain tissue. Thioflavin-T aggregation assays showed that SMOC1 significantly delayed Aβ aggregation in a dose-dependent manner, and electron microscopy confirmed that the Aβ fibrils generated in the presence of SMOC1 had an altered morphology. Overall, our results emphasize the importance of SMOC1 in the onset and progression of AD and suggest that SMOC1 may influence pathology development in AD.
Long-term results of Roux-en-Y gastric bypass (RYGB) versus single anastomosis duodeno-ileal bypass (SADI) as revisional procedures after failed sleeve gastrectomy: a systematic literature review and pooled analysis
Authors: Thomopoulos Theodoros , Mantziari Styliani , Joliat Gaëtan-Romain
Published: November 2024

Purpose

Revisional bariatric surgery (RBS) has flourished during the last decades in many countries, due to suboptimal weight loss or long-term complications of primary bariatric surgery. Restrictive procedures, and in particular sleeve gastrectomy (SG), although widely performed as primary bariatric surgery, seems particularly prone to need surgical revision for the above-mentioned reasons during long-term follow-up. The aim of this systematic review was to compare the long-term (5-year) safety and efficacy between Roux-en-Y gastric bypass (RYGB) and single anastomosis duodeno-ileal bypass (SADI) after ‘failed’ SG.

Methods

A systematic review was performed from 2007 to September 2024. Articles were included if SADI or RYGB were performed as RBS after ‘failed SG’ with follow-up at least 5 years. Pooled analysis was performed to summarize the data.

Results

Among the seven studies eligible and included in this review, the SADI procedure showed comparable results to RYGB in terms of weight loss, nutritional deficiencies, and resolution of comorbidities during the long-term follow-up. However, RYGB proved superior in terms of remission of reflux disease and other functional problems after SG.

Conclusions

The present review found that SADI seems to be a promising and suitable method for suboptimal weight loss after SG, with comparable or even better results to RYGB after 5-year follow-up.
A comparison of formulations and non-linear solvers for computational modelling of semiconductor devices
Authors: Pérez-Escudero Sergi , Codony David , Arias Irene , Fernández-Méndez Sonia
Published: November 2024

The drift-diffusion formulation, modelling semiconductor materials in terms of carrier densities and electric potential, is considered together with an alternative formulation in terms of dimensionless logarithmic quantities. Stability of both formulations in presence of sharp variations with a Galerkin Finite Element discretisation is assessed in two realistic problems: a p-n junction and an n-MOSFET device. The robustness with respect to the initial guess and the computational efficiency of the Newton-Raphson and Gummel non-linear solvers are also compared.
Saline versus balanced crystalloids for hydration post-kidney biopsy
Authors: Tanaka Yu , Horinouchi Tomoko , Inoki Yuta , Ichikawa Yuta , Ueda Chika , Kitakado Hideaki , Kondo Atsushi , Sakakibara Nana , Ishimori Shingo , Yamamura Tomohiko , Nagano China , Nozu Kandai
Published: November 2024

Background

Isotonic fluids are becoming the standard for hydration and maintenance fluid therapy, but there is no consensus on the optional choice among the different types of isotonic solution.

Methods

This study is a single-center, non-randomized controlled trial at Kobe University Hospital, Japan, between April 2021 and March 2023. The study included pediatric patients aged 1–19 years who underwent kidney biopsies. From April 2021 to March 2022, 0.9% sodium chloride (saline) was administered, and from April 2022 to March 2023, balanced crystalloids were used. The primary outcome was the occurrence of hyponatremia (< 137 mEq/L) after a kidney biopsy. Secondary outcomes included other electrolyte balances, blood gas parameters, creatinine-based estimated glomerular filtration rate (Cr-eGFR), and arginine vasopressin concentrations (UMIN Clinical Trial Registry: UMIN 000044330).

Results

Of 61 patients enrolled, 2 were excluded, leaving 34 in the saline group and 25 in the balanced crystalloid group. No hyponatremia occurred, and serum sodium concentrations were similar between both groups (138.7 vs. 138.9 mEq/L, P = 0.08). The saline group showed a greater increase in serum chloride (+ 1.7 vs. + 0.2, P < 0.01) and a greater decrease in HCO3− concentrations (− 0.6 vs. + 0.9, P < 0.01). There were minimal changes in pH (− 0.01 vs. − 0.01, P = 0.99) and Cr-eGFR (− 1.5 vs. + 1.1 mL/min/1.73 m2, P = 0.96) in both groups.

Conclusions

During pediatric kidney biopsy, both saline and balanced crystalloids were effective in preventing hyponatremia. Although saline infusion results in higher serum chloride concentrations and lower blood HCO3− concentrations than balanced crystalloids infusion, the clinical significance was minimal.

Graphical abstract
Application of stochastic storm transposition for hydrologic modeling in the mountainous western US
Authors: Lawler Seth , Deshotel Matthew , Dietrich Alyssa Hendricks , Zhang Lan , Karlovits Gregory , Ferreira Celso
Published: November 2024

Recent studies have shown that stochastic storm transposition (SST) is an effective method for flood frequency analysis in small to medium sized watersheds. The effectiveness of this method has not been evaluated in larger watersheds in mountainous regions where snowmelt is the primary driver for peak flow events. In the western United States, several watersheds fall in an area where NOAA Atlas-14 precipitation frequency estimates do not exist. This data sparsity limits the available methods for developing flood frequency estimates. In this research, we present a case study for exploring the use of SST in the high desert of Wyoming, with challenges of scale, regulation, and snowmelt. Building on existing methods, a framework for performing SST in cold mountain regions is proposed, including incorporation of snowmelt functions, normalization fields in high altitude locations, and techniques for hydrologic model adjustment to account for epistemic uncertainty due to regulation. Results show that the foundational processes in the SST framework provide a valuable alternative for peak flow analysis in locations where frequency-based precipitation is not available.
Partial Plateau’s problem with H-mass
Authors: Alvarado Enrique , Xia Qinglan
Published: November 2024

Classically, Plateau’s problem asks to find a surface of the least area with a given boundary B. In this article, we investigate a version of Plateau’s problem, where the boundary of an admissible surface is only required to partially span B. Our boundary data is given by a flat

$$(m-1)$$

(
m
-
1
)

-chain B and a smooth compactly supported differential

$$(m-1)$$

(
m
-
1
)

-form

$$\Phi $$

Φ

. We are interested in minimizing

$$ \textbf{M}(T) - \int _{\partial T} \Phi $$

M

(
T
)

-

∫

∂
T

Φ

over all m-dimensional rectifiable currents T in

$$\mathbb {R}^n$$

R

n

such that

$$\partial T$$

∂
T

is a subcurrent of the given boundary B. The existence of a rectifiable minimizer is proven with Federer and Fleming’s compactness theorem. We generalize this problem by replacing the mass

$$\textbf{M}$$

M

with the H-mass of rectifiable currents. By minimizing over a larger class of objects, called scans with boundary, and by defining their H-mass as a type of lower-semicontinuous envelope over the H-mass of rectifiable currents, we prove an existence result for this problem by using Hardt and De Pauw’s BV compactness theorem.