bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifunctional potentials of lactic acid bacterial isolates from Turkish traditional fermented foods
Authors: Sağiroğlu Ayşen , Özdemir Nilgün , Çon Ahmet Hilmi 
Published: April 2024

Abstract
This study aimed to isolate LAB strains with antimicrobial activity that can be used as bio-protective agents, from yogurt, pickle, and cheese samples, which are Turkish traditional fermented foods, and to reveal the potential probiotic properties of these isolates with antimicrobial activity. In addition, it was aimed for the first time to examine the potential and uniqueness of these domestic and local traditional fermented foods. In the study, a total of 682 LAB isolates from Turkish traditional fermented samples were isolated. Thirteen isolates with both high and antifungal activities were selected; four Lactiplantibacillus pentosus strains, six Lactiplantibacillus plantarum strains, and one each Enterococcus lactis, Enterococcus durans, and Enterococcus faecalis strains. Ten isolates of them were suggested as potential probiotics (excluding 1Y2-1, 1Y7-3, and 3Y12-4). It was thought that the L. pentosus 2Y7-1, which was slow to produce acid, could be used as a co-culture in fermented products with a long ripening stage, supported by enriching the product of its milk coagulation, β-galactosidase, proteolytic, and cholesterol assimilation abilities in terms of bioactive peptide and prebiotics. Another strain, E. faecalis 3Y4-3, which was high proteolytic activity, was suggested as a co-culture in fermented products to improve both organoleptic properties and increase bioactive peptides. On the other hand, among non-probiotics, L. plantarum 3Y12-4 can be used as a starter culture in fermented milk products in order to evaluate its milk coagulation, cholesterol assimilation, and proteolytic abilities. As a result, these three strains can be used in many areas, such as fermented and/or functional food production and enzyme production. In addition, this has been the first study to examine the potential and uniqueness of Turkish domestic and local traditional fermented foods in Samsun, Turkey, together, in terms of both antimicrobial and probiotic LAB isolate (multifunctional) potential and diversity.
Effect of seed biopriming with selected endophytes on the growth and chilling tolerance of rice plants
Authors: Lai Wei-An , Shen Fo-Ting , Ho Tuan-Hua David , Yu Su-May , Young Chiu-Chung 
Published: April 2024

Abstract
The aim of this study was to develop an efficient bioinoculant for amelioration of adverse effects from chilling stress (10°C), which are frequently occurred during rice seedling stage. Seed germination bioassay under chilling condition with rice (Oryza sativa L.) cv. Tainan 11 was performed to screen for plant growth-promoting (PGP) bacteria among 41 chilling-tolerant rice endophytes. And several agronomic traits were used to evaluate the effects of bacterial inoculation on rice seedling, which were experienced for 7-d chilling stress in walk-in growth chamber. The field trials were further used to verify the performance of potential PGP endophytes on rice growth. A total of three endophytes with multiple PGP traits were obtained. It was demonstrated that Pseudomonas sp. CC-LS37 inoculation led to 18% increase of maximal efficiency of Photosystem II (PSII) after 7-d chilling stress and 7% increase of chlorophyll a content, and 64% decline of malondialdehyde content in shoot after 10-d recovery at normal temperature in walk-in growth chamber. In field trial, biopriming of seeds with strain CC-LS37 caused rice plants to increase shoot chlorophyll soil plant analysis development values (by 2.9% and 2.5%, respectively) and tiller number (both by 61%) under natural climate and chilling stress during the end of tillering stage, afterward 30% more grain yield was achieved. In conclusion, strain CC-LS37 exerted its function in increase of tiller number of chilling stress-treated rice seedlings via improvement of photosynthetic characteristics, which in turn increases the rice grain yield. This study also proposed multiple indices used in the screening of potential endophytes for conferring chilling tolerance of rice plants.
Exposure to enrofloxacin affects the early development and metabolic system of juvenile American shad, as indicated by host metabolism and the environmental microbiome
Authors: Du Jia , Liu Qinghua , Zhang Ke-Qin 
Published: April 2024

Abstract
Enrofloxacin as a special fish medicine is widely used in aquaculture fishes in China. But the effect of enrofloxacin exposure to the gut of aquatic animals is still unclear. In our investigation, enrofloxacin (300 mg/kg feed) was experimentally exposed to the juvenile American shad for 7 days and monitored for alterations in metabolomic and transcriptomic responses. The results showed the similar subset of affected pathways (P-value &lt; 0.05), but there were still many differences in the number of identified biomarkers (520 differentially expressed genes genes and 230 metabolites). Most gut metabolic profiles were related to oxidative stress, inflammation, and lipid metabolism. These multiomic results reveal the specific metabolic disruption by enrofloxacin altering many signaling pathways (P-value &lt; 0.05), such as arginine and proline metabolism pathways, pyrimidine metabolism, the FoxO signaling pathway, and purine metabolism. In addition, the predicted functions of proteins analysis showed that enrofloxacin exposure in an aquaculture environment could prevent the occurrence of organic diseases, including Vibrio cholerae infection and bacterial toxins, in aquatic systems. This is the first research indicating that enrofloxacin affects the relationship between environmental microorganisms and intestinal metabolism, and a study of the ecotoxicity of enrofloxacin occurrences in the aquatic system is warranted.
Chemical composition, antioxidant, and antimicrobial activities of six commercial essential oils
Authors: Coimbra Alexandra , Miguel Sónia , Ribeiro Maximiano , Coutinho Paula , Silva Lúcia A , Ferreira Susana , Duarte Ana Paula 
Published: April 2024

Abstract
Essential oils (EOs) and their components extracted from medicinal and aromatic plants are used in several areas, such as perfumery and chemical, cosmetic, food, and pharmaceutical industries. Considering the different applications of EOs, this work aimed to screen the composition and the bioactivities properties of the EOs of Foeniculum vulgare, Helichrysum stoechas, Mentha pulegium, Pinus pinaster, Ruta graveolens, and Thymus mastichina. Gas chromatography–mass spectrometry revealed the presence of different compounds in EOs F. vulgare (12), H. stoechas (27), M. pulegium (8), P. pinaster (24), R. graveolens (8), and T. mastichina (16). All the EOs showed antioxidant activity acting through inhibition of lipid peroxidation, while only two EOs (H. stoechas and M. pulegium) scavenged the free radicals of DPPH. Mentha pulegium and T. mastichina EOs showed the strongest antimicrobial activity. Also, the effect on the fibroblast’s viability was directly proportional to the EOs concentration, and the highest cytotoxic effect was registered with R. graveolens EO. The present study revealed significant bioactive properties of different EOs, highlighting M. pulegium and T. mastichina EOs to be considered in further studies for potential use in the food and pharmaceutical industries, due to their antioxidant and antimicrobial properties.
Study of dependence of ram pressure stripping on the orbital parameters of the galaxies
Authors: Singh Ankit , Davessar Shreya , Gulati Mamta , Bagla Jasjeet Singh , Prajapati Meenu 
Published: April 2024

ABSTRACT
Comprehensive observations of galaxy clusters suggest that gas deficiency in the galaxies could be due to ram pressure stripping due to the high-pressure intra-cluster medium acting on the galactic discs. The presence of gas in galaxies is essential for star formation. The net force due to ram pressure is dependent on the ambient medium and the orbit followed by the galaxy as it moves past the cluster medium. This work deals with the effect of non-radial orbits of galaxies and the inclination of the disc plane of galaxies with the orbital plane on the mass of gas removed due to ram pressure. This gives a realistic approach to understanding the process of ram pressure stripping. The orbital parameters are extracted from eagle simulation data set along with the mass distribution of the galaxies. The analytical model proposed by Singh et. al. is modified appropriately to include the effect of the inclination angle. The non-radial orbits and infalling galaxies not being face-on decrease the amount of gas removed. Moreover, the inclination angle has a pronounced effect on the stripping of gas in low-mass galaxies as compared to high-mass galaxies with similar inclinations. The results show that the efficiency of the ram pressure stripping can be much lower in some cases, and hence gas in infalling galaxies can survive for much longer than expected from a simple analysis.
A model-independent precision test of general relativity using bright standard sirens from ongoing and upcoming detectors
Authors: Afroz Samsuzzaman , Mukherjee Suvodip 
Published: April 2024

ABSTRACT
Gravitational waves (GWs) provide a new avenue to test Einstein’s General Relativity (GR) using the ongoing and upcoming GW detectors by measuring the redshift evolution of the effective Planck mass proposed by several modified theories of gravity. We propose a model-independent, data-driven approach to measure any deviation from GR in the GW propagation effect by combining multimessenger observations of GW sources accompanied by EM counterparts, commonly known as bright sirens [Binary Neutron Star (BNS) and Neutron Star Black Hole systems (NSBH)]. We show that by combining the GW luminosity distance measurements from bright sirens with the Baryon Acoustic Oscillation (BAO) measurements derived from galaxy clustering, and the sound horizon measurements from the Cosmic Microwave Background (CMB), we can make a data-driven reconstruction of deviation of the variation of the effective Planck mass (jointly with the Hubble constant) as a function of cosmic redshift. Using this technique, we achieve a precise measurement of GR with redshift (z) with a precision of approximately 7.9 per cent for BNSs at redshift z = 0.075 and 10 per cent for NSBHs at redshift z = 0.225 with 5 yr of observation from LIGO-Virgo-KAGRA network of detectors. Employing Cosmic Explorer and Einstein Telescope for just 1 yr yields the best precision of about 1.62 per cent for BNSs and 2 per cent for NSBHs at redshift z = 0.5 on the evolution of the frictional term, and a similar precision up to z = 1. This measurement can discover potential deviation from any kind of model that impacts GW propagation with ongoing and upcoming observations.
EC 19529−4430: SALT identifies the most carbon- and metal-poor extreme helium star
Authors: Jeffery C S , Scott L J A , Philip Monai A , Miszalski B , Woolf V M 
Published: April 2024

ABSTRACT
EC 19529−4430 was identified as a helium-rich star in the Edinburgh–Cape (EC) Survey of faint-blue objects and subsequently resolved as a metal-poor extreme helium (EHe) star in the Southern African Large Telescope (SALT) survey of chemically peculiar hot subdwarfs. This paper presents a fine analysis of the SALT high-resolution spectrum. EC 19529−4430 has $T_{\rm eff} = 20\, 700 \pm 250$ K, $\log g /{\rm cm\, s^{-2}} = 3.49\pm 0.03$, and an overall metallicity some 1.3 dex below solar; surface hydrogen is $\approx 0.5~{{\ \rm per\ cent}}$ by number. The surface CNO ratio 1:100:8 implies that the surface consists principally of CNO-processed helium and makes EC 19529−4430 the coolest known carbon-poor and nitrogen-rich EHe star. Metal-rich analogues include V652 Her and GALEX J184559.8−413827. Kinematically, its retrograde orbit indicates membership of the Galactic halo. No pulsations were detected in TESS photometry and there is no evidence for a binary companion. EC 19529−4430 most likely formed from the merging of two helium white dwarfs, which themselves formed as a binary system some 11 Gyr ago.
Cloud-by-cloud multiphase investigation of the circumgalactic medium of low-redshift galaxies
Authors: Sameer  , Charlton Jane C , Wakker Bart P , Kacprzak Glenn G , Nielsen Nikole M , Churchill Christopher W , Richter Philipp , Muzahid Sowgat , Ho Stephanie H , Nateghi Hasti , Rosenwasser Benjamin , Narayanan Anand , Ganguly Rajib 
Published: April 2024

ABSTRACT
The pervasive presence of warm gas in galaxy haloes suggests that the circumgalactic medium (CGM) is multiphase in its ionization structure and complex in its kinematics. Some recent state-of-the-art cosmological galaxy simulations predict an azimuthal dependence of CGM metallicities. We investigate the presence of such a trend by analysing the distribution of gas properties in the CGM around 47 z &lt; 0.7 galaxies from the Multiphase Galaxy Halos Survey determined using a cloud-by-cloud, multiphase, ionization modelling approach. We identify three distinct populations of absorbers: cool clouds (T ∼ 104.1 K) in photoionization equilibrium, warm–hot collisionally ionized clouds (T ∼ 104.5–105 K) affected by time-dependent photoionization, and hotter clouds (T ∼ 105.4–106 K) with broad O vi and Ly α absorption consistent with collisional ionization. We find that fragmentation can play a role in the origin of cool clouds, that warm–hot clouds are out of equilibrium due to rapid cooling, and that hotter clouds are representative of virialized halo gas in all but the lowest mass galaxies. The metallicities of clouds do not depend on the azimuthal angle or other galaxy properties for any of these populations. At face value, this disagrees with the simplistic model of the CGM with bipolar outflows and cold-mode planar accretion. However, the number of clouds per sightline is significantly larger close to the minor and major axes. This implies that the processes of outflows and accretion are contributing to these CGM cloud populations, and our sightlines are probing gas of mixed origins at all azimuthal angles in these low-redshift galaxies.
ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency
Authors: Saunders Scott H , Ahmed Ayesha M 
Published: April 2024

Abstract
Microbiology and synthetic biology depend on reverse genetic approaches to manipulate bacterial genomes; however, existing methods require molecular biology to generate genomic homology, suffer from low efficiency, and are not easily scaled to high throughput. To overcome these limitations, we developed a system for creating kilobase-scale genomic modifications that uses DNA oligonucleotides to direct the integration of a non-replicating plasmid. This method, Oligonucleotide Recombineering followed by Bxb-1 Integrase Targeting (ORBIT) was pioneered in Mycobacteria, and here we adapt and expand it for Escherichia coli. Our redesigned plasmid toolkit for oligonucleotide recombineering achieved significantly higher efficiency than λ Red double-stranded DNA recombineering and enabled precise, stable knockouts (≤134 kb) and integrations (≤11 kb) of various sizes. Additionally, we constructed multi-mutants in a single transformation, using orthogonal attachment sites. At high throughput, we used pools of targeting oligonucleotides to knock out nearly all known transcription factor and small RNA genes, yielding accurate, genome-wide, single mutant libraries. By counting genomic barcodes, we also show ORBIT libraries can scale to thousands of unique members (&gt;30k). This work demonstrates that ORBIT for E. coli is a flexible reverse genetic system that facilitates rapid construction of complex strains and readily scales to create sophisticated mutant libraries.
The DNA Damage Response (DDR) landscape of endometrial cancer defines discrete disease subtypes and reveals therapeutic opportunities
Authors: Zhang Xingyuan , Joseph Sayali , Wu Di , Bowser Jessica L , Vaziri Cyrus 
Published: April 2024

Abstract
Genome maintenance is an enabling characteristic that allows neoplastic cells to tolerate the inherent stresses of tumorigenesis and evade therapy-induced genotoxicity. Neoplastic cells also deploy many mis-expressed germ cell proteins termed Cancer Testes Antigens (CTAs) to promote genome maintenance and survival. Here, we present the first comprehensive characterization of the DNA Damage Response (DDR) and CTA transcriptional landscapes of endometrial cancer in relation to conventional histological and molecular subtypes. We show endometrial serous carcinoma (ESC), an aggressive endometrial cancer subtype, is defined by gene expression signatures comprising members of the Replication Fork Protection Complex (RFPC) and Fanconi Anemia (FA) pathway and CTAs with mitotic functions. DDR and CTA-based profiling also defines a subset of highly aggressive endometrioid endometrial carcinomas (EEC) with poor clinical outcomes that share similar profiles to ESC yet have distinct characteristics based on conventional histological and genomic features. Using an unbiased CRISPR-based genetic screen and a candidate gene approach, we confirm that DDR and CTA genes that constitute the ESC and related EEC gene signatures are required for proliferation and therapy-resistance of cultured endometrial cancer cells. Our study validates the use of DDR and CTA-based tumor classifiers and reveals new vulnerabilities of aggressive endometrial cancer where none currently exist.
TDP2 is a regulator of estrogen-responsive oncogene expression
Authors: Manguso Nicholas , Kim Minhyung , Joshi Neeraj , Al Mahmud Md Rasel , Aldaco Juan , Suzuki Ryusuke , Cortes-Ledesma Felipe , Cui Xiaojiang , Yamada Shintaro , Takeda Shunichi , Giuliano Armando , You Sungyong , Tanaka Hisashi 
Published: April 2024

Abstract
With its ligand estrogen, the estrogen receptor (ER) initiates a global transcriptional program, promoting cell growth. This process involves topoisomerase 2 (TOP2), a key protein in resolving topological issues during transcription by cleaving a DNA duplex, passing another duplex through the break, and repairing the break. Recent studies revealed the involvement of various DNA repair proteins in the repair of TOP2-induced breaks, suggesting potential alternative repair pathways in cases where TOP2 is halted after cleavage. However, the contribution of these proteins in ER-induced transcriptional regulation remains unclear. We investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme for the removal of halted TOP2 from the DNA ends, in the estrogen-induced transcriptome using both targeted and global transcription analyses. MYC activation by estrogen, a TOP2-dependent and transient event, became prolonged in the absence of TDP2 in both TDP2-deficient cells and mice. Bulk and single-cell RNA-seq analyses defined MYC and CCND1 as oncogenes whose estrogen response is tightly regulated by TDP2. These results suggest that TDP2 may inherently participate in the repair of estrogen-induced breaks at specific genomic loci, exerting precise control over oncogenic gene expression.
Antifungal Treatment Duration in Hematology Patients With Invasive Mold Infections: A Real-life Update
Authors: Portillo Vera , Ragozzino Silvio , Stavropoulou Elisavet , El-Khoury Celine , Bochud Pierre-Yves , Lamoth Frederic , Khanna Nina , Neofytos Dionysios 
Published: April 2024

Abstract

Background
Limited data exist on when and how to stop antifungal treatment (AFT) in patients with invasive mold infections (IMIs) who are immunocompromised.

Methods
This retrospective multicenter study included adult patients with acute myelogenous leukemia and proven/probable IMI (1 January 2010–31 December 2022) in 3 university hospitals. The primary objective was to describe AFT duration and adaptation. Secondary objectives were to investigate the reasons for AFT adjustments and prolongation.

Results
In total 71 patients with 73 IMIs were identified; 51 (71.8%) had an allogeneic hematopoietic cell transplant. Most infections were invasive aspergillosis (IA; 49/71, 69%), followed by mucormycosis (12, 16.9%) and other (12, 16.9%); there were 2 mixed infections. Median treatment duration was 227 days (IQR, 115.5–348.5). There was no difference in AFT duration between patients with IA and non-IA IMI (P = .85) or by center (P = .92). Treatment was longer in patients with an allogeneic hematopoietic cell transplant vs not (P = .004). Sixteen patients (22.5%) had no therapy modifications. In 55 patients (77.5%), a median 2 changes (IQR, 1–3; range, 1–8) were observed. There were 182 reasons leading to 165 changes, associated with clinical efficacy (82/182, 44.5%), toxicity (47, 25.8%), and logistical reasons (22, 12.1%); no reason was documented in 32 changes (18.8%). AFT was continued beyond days 90 and 180 in 59 (83%) and 39 (54.9%) patients, respectively, mostly due to persistence of immunosuppression.

Conclusions
AFT in patients with acute myelogenous leukemia and IMI is longer than that recommended by guidelines and is frequently associated with treatment adjustments due to variable reasons. More data and better guidance are required to optimize AFT duration and secondary prophylaxis administration according to immunosuppression.
TP53-specific mutations serve as a potential biomarker for homologous recombination deficiency in breast cancer: a clinical next-generation sequencing study
Authors: Huang Yongsheng , Ren Shuwei , Ding Linxiaoxiao , Jiang Yuanling , Luo Jiahuan , Huang Jinghua , Yin Xinke , Zhao Jianli , Fu Sha , Liao Jianwei 
Published: April 2024

Abstract

Background
TP53 mutations and homologous recombination deficiency (HRD) occur frequently in breast cancer. However, the characteristics of TP53 pathogenic mutations in breast cancer patients with/without HRD are not clear.

Methods
Clinical next-generation sequencing (NGS) of both tumor and paired blood DNA from 119 breast cancer patients (BRCA-119 cohort) was performed with a 520-gene panel. Mutations, tumor mutation burden (TMB), and genomic HRD scores were assessed from NGS data. NGS data from 47 breast cancer patients in the HRD test cohort were analyzed for further verification.

Results
All TP53 pathogenic mutations in patients had somatic origin, which was associated with the protein expression of estrogen receptor and progestogen receptor. Compared to patients without TP53 pathologic mutations, patients with TP53 pathologic mutations had higher levels of HRD scores and different genomic alterations. The frequency of TP53 pathologic mutation was higher in the HRD-high group (HRD score ≥ 42) relative to that in the HRD-low group (HRD score &lt; 42). TP53 has different mutational characteristics between the HRD-low and HRD-high groups. TP53-specific mutation subgroups had diverse genomic features and TMB. Notably, TP53 pathogenic mutations predicted the HRD status of breast cancer patients with an area under the curve (AUC) of 0.61. TP53-specific mutations, namely HRD-low mutation, HRD-high mutation, and HRD common mutation, predicted the HRD status of breast cancer patients with AUC values of 0.32, 0.72, and 0.58, respectively. Interestingly, TP53 HRD-high mutation and HRD common mutation combinations showed the highest AUC values (0.80) in predicting HRD status.

Conclusions
TP53-specific mutation combinations predict the HRD status of patients, indicating that TP53 pathogenic mutations could serve as a potential biomarker for poly-ADP-ribose polymerase (PARP) inhibitors in breast cancer patients .