bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractWe 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

AbstractFor 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

AbstractNonsteroidal 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

AbstractA 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

AbstractFour 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

AbstractAmmonia (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

AbstractThis 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

Abstract
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

Abstract
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

Abstract
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

AbstractVentricular 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

AbstractSMOC1 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.