bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Paper: A Preliminary Study on the Dynamics of Modulated Turning (MT) With Spindle Speed Variation (SSV)
Authors: Ozdemir Mert , Sencer Burak 
Published: August 2024

Abstract
This paper proposes a novel strategy to enhance dynamic stability of turning processes. It presents a novel assistive strategy, which combines Spindle Speed Variation (SSV) and Sinusoidal Tool Modulations to dramatically improve chatter stability of high-speed turning. Chatter vibrations are a type of self-exiting vibrations that originate due to the dynamic flexibilities in the machine/workpiece/tool. Once chatter is triggered, it rapidly grows to destroy the surface finish, harms the tool and even the machine tool components. Chatter is the most limiting factor restricting productivity and attenable material removal rates (MRR) in most high-speed turning operations. A well-known strategy to improve chatter stability in turning is to use SSV. Continuously varying the spindle speed helps disturb and weaken the regenerative effect (regenerations) and thus improve chatter stability. Most recently, it is also reported that adding sinusoidal tool modulations also help improve chatter stability. This process is called the modulated turning (MT), and sinusoidal tool modulations cause the tool to disengage from the workpiece (cut) repeatedly introducing time for the regeneration effect to die out. This paper, for the first time, proposes to utilize sinusoidal tool modulations and SSV at the same time to assist and improve chatter stability of turning even further. The semi-discrete time domain approach is utilized to analyze chatter stability of this newly created turning process. It is observed, that jointly using tool modulations and SSV provides greater asymptotic chatter stability margins enabling average 10∼20% greater material removal rates to be achieved. Furthermore, it modifies existing stability lobes and helps create additional lobes, which may be utilized to maximize material removal rate at other desired target spindle speeds. Overall, joint application of SSV and tool modulations provide greater stability in turning.
CGRP inhibits SARS-CoV-2 infection of bronchial epithelial cells, and its pulmonary levels correlate with viral clearance in critical COVID-19 patients
Authors: Barbosa Bomfim Caio César , Génin Hugo , Cottoignies-Callamarte Andréa , Gallois-Montbrun Sarah , Murigneux Emilie , Sams Anette , Rosenberg Arielle R. , Belouzard Sandrine , Dubuisson Jean , Kosminder Olivier , Pène Frédéric , Terrier Benjamin , Bomsel Morgane , Ganor Yonatan 
Published: August 2024

ABSTRACT

Upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with critical coronavirus disease 2019 (COVID-19) present with life-threatening respiratory distress, pulmonary damage, and cytokine storm. One unexplored component in COVID-19 is the neuropeptide calcitonin gene-related peptide (CGRP), which is highly abundant in the airways and could converge in multiple aspects of COVID-19-related pulmonary pathophysiology. Whether CGRP affects SARS-CoV-2 infection directly remains elusive. We show that in critical COVID-19 patients, CGRP is increased in both plasma and lungs. Importantly, CGRP pulmonary levels are elevated in early SARS-CoV-2-positive patients and restored to baseline upon subsequent viral clearance in SARS-CoV-2-negative patients. We further show that CGRP and its stable analog SAX directly inhibit infection of bronchial Calu-3 epithelial cells with SARS-CoV-2 Omicron and Alpha variants in a dose-dependent manner. Both pre- and post-infection treatments with CGRP and/or SAX are enough to block SARS-CoV-2 productive infection of Calu-3 cells. CGRP-mediated inhibition occurs via activation of the CGRP receptor and involves down-regulation of both SARS-CoV-2 entry receptors at the surface of Calu-3 cells. Together, we propose that increased pulmonary CGRP mediates beneficial viral clearance in critical COVID-19 patients by directly inhibiting SARS-CoV-2 propagation. Hence, CGRP-based interventions could be harnessed for management of COVID-19.

IMPORTANCE
The neuropeptide CGRP is highly abundant in the airways. Due to its immunomodulatory, vasodilatory, and anti-viral functions, CGRP could affect multiple aspects of COVID-19-related pulmonary pathophysiology. Yet, the interplay between CGRP and SARS-CoV-2 during COVID-19 remains elusive. Herein, we show that pulmonary levels of CGRP are increased in critical COVID-19 patients, at an early stage of their disease when patients are SARS-CoV-2-positive. Upon subsequent viral clearance, CGRP levels are restored to baseline in SARS-CoV-2-negative patients. We further show that pre- and post-infection treatments with CGRP directly inhibit infection of Calu-3 bronchial epithelial cells with SARS -CoV-2, via activation of the CGRP receptor leading to decreased expression of both SARS-CoV-2 entry receptors. Together, we propose that increased pulmonary CGRP is beneficial in COVID-19, as CGRP-mediated inhibition of SARS-CoV-2 infection could contribute to viral clearance in critical COVID-19 patients. Accordingly, CGRP-based formulations could be useful for COVID-19 management.
Draft genomes of one
Staphylococcus haemolyticus
and five
Staphylococcus lugdunensis
strains isolated from catheterized urine samples of females
Authors: Appleberry Helen , Anjum Haaris , Cage Taleah , Jarm Kayla , Khan Haashir , Proctor Lizzie , Saroca Junelle , Wolfe Alan J. , Putonti Catherine , Kula Alex 
Published: August 2024

ABSTRACT

Although
Staphylococcus haemolyticus
and
Staphylococcus lugdunensis
are members of the normal human flora, they also can cause infection. Here, we present the draft genomes of five strains of
S. lugdunensis
and one strain of
S. haemolyticus
isolated from transurethral catheterized urine samples from different females experiencing lower urinary tract symptoms.
New
Cydia pomonella
granulovirus strain with high entomopathogenic activity
Authors: Tsygichko Aleksandra A. , Asaturova Anzhela M. , Vasiliev Gennady V. , Klimenko Alexandra I. , Lashin Sergey A. , Lakhova Tatiana N. 
Published: August 2024

ABSTRACT

We report a genome of CpGV from the bioresource collection of the Federal Research Center of Biological Plant Protection “State Collection of Entomoacariphages and Microorganisms.” Its sequence is 123,862 bp. The genome under study demonstrates a degree of similarity of more than 99% with reference
NC_002816
from the NCBI RefSeq database.
Oxford Nanopore long read-based shotgun metagenomic data sets of simulated bacterial communities originating from fresh spinach and surface water
Authors: Chen Zhao , Grim Christopher J. , Ramachandran Padmini , Meng Jianghong 
Published: August 2024

ABSTRACT

Oxford Nanopore long reads of simulated bacterial communities from fresh spinach and surface water were generated (R9.4.1+SQK-LSK109 and R10.4+SQK-LSK112; 0.5, one, and two million reads).
Salmonella enterica
serotype Heidelberg, Montevideo, or Typhimurium was included alone or in combination in the spinach community, while the water community harbored
Pseudomonas aeruginosa
.
Ruminal microbial metagenomes and host transcriptomes shed light on individual variability in the growth rate of lambs before weaning: the regulated mechanism and potential long-term effect on the host
Authors: Hu Fan , Cheng Yan , Fan Bing , Li Wei , Ye Bingsen , Wu Zhiwu , Tan Zhiliang , He Zhixiong 
Published: August 2024

ABSTRACT

Weaning weight is a reflection of management during the breastfeeding phase and will influence animal performance in subsequent phases, considered important indicators within production systems. The aims of this study were as follows: (i) to investigate variability in the growth rate among individual lambs from ewes rearing single or twin lambs fed with two different diets and (ii) to explore the molecular mechanisms regulating the growth rate and the potential long-term effects on the host. No significant change in lamb average daily gain (ADG) was observed in litter size and diet treatment, and there were large variations among individual lambs (ranging from 0.13 to 0.41 kg/day). Further analysis was conducted on serum amino acids, rumen fermentation characteristics, rumen metagenomics and transcriptome, and hepatic transcriptome of lambs with extremely high (HA;
n
= 6) and low (LA;
n
= 6) ADG. We observed significant increases in serum lysine, leucine, alanine, and phenylalanine in the HA group. The metagenome revealed that the HA group presented a higher rumen propionate molar proportion via increasing gene abundance in the succinate pathway for propionate synthesis. For the rumen transcriptome, higher expressed gene sets in the HA group were mainly related to rumen epithelial growth, including cytokine–cytokine receptor interaction, Jak-STAT signaling pathway, and adherens junction. For the liver transcriptome, the upregulated KEGG pathways in the HA group were primarily associated with fatty acid degradation, glyoxylate and dicarboxylate metabolism, cholesterol metabolism, and the immune system. This research suggests that preweaning lambs with high ADG may benefit from rumen development and enhanced liver metabolic and immune function.

IMPORTANCE
There is accumulating evidence indicating that the early-life rumen microbiome plays vital roles in rumen development and microbial fermentation, which subsequently affects the growth of young ruminants. The liver is also vital to regulate the metabolism and distribution of nutrients. Our results demonstrate that lambs with high average daily gain (ADG) enhanced microbial volatile fatty acid (VFA) metabolism toward rumen propionate and serum amino acid (AA) production to support host growth. The study highlights that high ADG in the preweaning period is beneficial for the rumen development and liver energy metabolism, leading to better growth later in life. Overall, this study explores the molecular mechanisms regulating the growth rate and the potential long-term effects of increased growth rate on the host metabolism, providing fundamental knowledge about nutrient manipulation in pre-weaning.
The core microbiome of cultured Pacific oyster spat is affected by age but not mortality
Authors: Cho Anna , Finke Jan F. , Zhong Kevin X. , Chan Amy M. , Saunders Rob , Schulze Angela , Warne Snehal , Miller Kristina M. , Suttle Curtis A. 
Published: August 2024

ABSTRACT

The Pacific oyster is the most widely cultured shellfish worldwide, but production has been affected by mortality events, including in hatcheries that supply the seed for growers. Several pathogens cause disease in oysters, but in many cases, mortality events cannot be attributed to a single agent and appear to be multifactorial, involving environmental variables and microbial interactions. As an organism’s microbiome can provide resilience against pathogens and environmental stressors, we investigated the microbiomes in cohorts of freshly settled oyster spat, some of which experienced notable mortality. Deep sequencing of 16S rRNA gene fragments did not show a significant difference among the microbiomes of cohorts experiencing different mortality levels, but revealed a characteristic core microbiome comprising 74 taxa. Irrespective of mortality, the relative abundance of taxa in the core microbiomes changed significantly as the spat aged, yet remained distinct from the microbial community in the surrounding water. The core microbiome was dominated by bacteria in the families
Rhodobacteraceae
,
Nitrosomonadaceae
,
Flavobacteriaceae, Pirellulaeceae,
and
Saprospiraceae
. Within these families, 14 taxa designated as the “Hard-Core Microbiome” were indicative of changes in the core microbiome as the spat aged. The variability in diversity and richness of the core taxa decreased with age, implying niche occupation. As well, there was exchange of microbes with surrounding water during development of the core microbiome. The shift in the core microbiome demonstrates the dynamic nature of the microbiome as oyster spat age.

IMPORTANCE

The Pacific oyster (
Magallana gigas
, also known as
Crassostrea gigas
) is the most widely cultivated shellfish and is important to the economy of many coastal communities. However, high mortality of spat during the first few days following metamorphosis can affect the seed supply to oyster growers. Here, we show that the microbiome composition of recently settled oyster spat experiencing low or high mortality was not significantly different. Instead, development of the core microbiome was associated with spat aging and was partially driven by dispersal through the water. These findings imply the importance of early-stage rearing conditions for spat microbiome development in aquaculture facilities. Furthermore, shellfish growers could gain information about the developmental state of the oyster spat microbiome by assessing key taxa. Additionally, the study provides a baseline microbiome for future hypothesis testing and potential probiotic applications on developing spat.
Nuclear reorganization by NPM1-mediated phase separation triggered by adenovirus core protein VII
Authors: Genoveso Michelle Jane , Okuwaki Mitsuru , Kato Kohsuke , Nagata Kyosuke , Kawaguchi Atsushi 
Published: August 2024

ABSTRACT

Recent evidence has revealed that the reorganization of nuclear domains is largely mediated by liquid-liquid phase separation (LLPS). During viral infection, numerous nuclear domains undergo significant changes through LLPS for and against the replication of the virus. However, the regulatory mechanism of LLPS in response to viral infection and its detailed functions in viral replication remain unclear. In this study, we found that the activity of the nucleolar protein NPM1, a remodeling factor for the chromatin-like structure of adenovirus DNA, to induce LLPS is required for deposition of adenovirus core protein VII in a subnuclear domain, the virus-induced post-replication (ViPR) body, in the late phases of infection. The interaction between NPM1 and protein VII was responsible for initiating LLPS. The inhibition of LLPS by 1,6-hexanediol treatment resulted in the dispersion of protein VII from the ViPR bodies. These findings suggest that protein VII accumulates in the ViPR bodies in concert with the LLPS formation of NPM1 triggered by protein VII. After photobleaching of EGFP-NPM1 in the ViPR bodies, EGFP-NPM1 showed a relatively fast recovery half-time, indicating the fluid-like properties of NPM1 in this compartment. Importantly, NPM1 depletion decreased the genome packaging in the viral capsids, possibly owing to the formation of a defective adenovirus core. This study highlights the dynamic interplay between viral pathogens and the host nucleus for the reorganization of membrane-less compartments that facilitate their replication.

IMPORTANCE
In this study, we explored how adenoviruses utilize a process known as liquid-liquid phase separation (LLPS) to enhance their replication. We focused on a cellular chromatin remodeling protein, NPM1, which plays a crucial role in nucleolar formation through LLPS. NPM1 facilitates LLPS by interacting with adenovirus protein VII, effectively accumulating protein VII into membrane-less compartments called virus-induced post-replication bodies. NPM1 functions as a molecular chaperone of protein VII to assemble viral chromatin by transferring protein VII to viral DNA. Remarkably, when NPM1 was depleted, this process was disrupted, decreasing viral genome packaging. These findings shed light on a critical aspect of virus-host interactions, illustrating how adenovirus utilizes NPM1-mediated LLPS activity. Our findings provide valuable insights into the dynamic interplay between viruses and the host nucleus.
PmrB Y358N, E123D amino acid substitutions are not associated with colistin resistance but with phylogeny in
Escherichia coli
Authors: Butters Alyssa , Jovel Juan , Gow Sheryl , Liljebjelke Karen , Waldner Cheryl , Checkley Sylvia L. 
Published: August 2024

ABSTRACT

Colistin resistance in
Escherichia coli
is of public health significance for its use to treat multidrug-resistant Gram-negative infections. Amino acid variations in PmrB have been implicated in colistin resistance in
E. coli
. In this cross-sectional study, 288 generic
E. coli
isolates from surveillance of broiler chicken and feedlot cattle feces, retail meat, wastewater, and well water were whole-genome sequenced. Phylogroup designation and screening for two amino acid substitutions in PmrB putatively linked to colistin resistance (Y358N, E123D) were performed
in silico
. Three additional data sets of publicly available
E. coli
assemblies were similarly scrutinized: (i)
E. coli
isolates from studies identifying the Y358N or E123D substitutions, (ii) colistin-susceptible
E. coli
isolates reported in the literature, and (iii) a random sampling of 14,700
E. coli
assemblies available in the National Center for Biotechnology Information public database. Within all data sets, ≥95% of phylogroup B1 and C isolates have the PmrB Y358N variation. The PmrB E123D amino acid substitution was only identified in phylogroup B2 isolates, of which 94%–100% demonstrate the substitution. Both PmrB amino acid variations were infrequent in other phylogroups. Among published colistin susceptible isolates, colistin minimum inhibitory concentrations (MICs) were not higher in isolates bearing the E123D and Y358N amino acid variations than in isolates without these PmrB substitutions. The E123D and Y358N PmrB amino acid substitutions in
E. coli
appear strongly associated with phylogroup. The previously observed associations between Y358N and E123D amino acid substitutions in PmrB and colistin resistance in
E. coli
may be spurious.

IMPORTANCE

Colistin is a critical last-resort treatment for extensively drug-resistant Gram-negative infections in humans. Therefore, accurate identification of the genetic mechanisms of resistance to this antimicrobial is crucial to effectively monitor and mitigate the spread of resistance. Examining over 16,000 whole-genome sequenced
Escherichia coli
isolates, this study identifies that PmrB E123D and Y358N amino acid substitutions previously associated with colistin resistance in
E. coli
are strongly associated with phylogroup and are alone not sufficient to confer a colistin-resistant phenotype. This is a critical clarification, as both substitutions are identified as putative mechanisms of colistin resistance in many publications and a common bioinformatic tool. Given the potential spurious nature of initial associations of these substitutions with colistin resistance, this study's findings emphasize the importance of appropriate experimental design and consideration of relevant biological factors such as phylogroup when ascribing causal mechanisms of resistance to chromosomal variations.
The emergence of metronidazole-resistant
Prevotella bivia
harboring
nimK
gene in Japan
Authors: Ito Yukitaka , Hashimoto Yusuke , Suzuki Masato , Kaneko Naomi , Yoshida Mieko , Nakayama Haruo , Tomita Haruyoshi 
Published: August 2024

ABSTRACT

We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant
Prevotella bivia
strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn
6456
, where
nimK
was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where
tet
(Q) and
ermF
were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTn
DOT
-family transposons, where
ermF
and
tet
(Q) are located. A search of public databases revealed that
nimK
was present in
Prevotella
spp., including
P. bivia
, and was partially composed of a Tn
6456
-like element lacking the efflux transporter gene
qacE
and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in
Prevotella
spp. and
Bacteroides
spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of
P. bivia
(TOH-2715) with Tn
6456
encoding
nimK
. Other submitted genomes have described the presence of
nimK
, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus
Prevotella
and among anaerobes, raising concerns about the future spread of
nimK
among anaerobes.

IMPORTANCE

Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the
nim
gene (nitro-imidazole reductase) is one of the resistance mechanisms.
Prevotella bivia
is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the
nim
genes,
nimK
, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of
nimK
-positive
P. bivia
derived from clinical specimens based on comparisons with other anaerobic genomes.
P. bivia
was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the
nimK
gene is a concern.
Calcium-binding protein TgpCaBP regulates calcium storage of the zoonotic parasite
Toxoplasma gondii
Authors: Sun Weisong , Jiang Ning , Li Qilong , Liu Yize , Zhang Yiwei , Chen Ran , Feng Ying , Sang Xiaoyu , Long Shaojun , Chen Qijun 
Published: August 2024

ABSTRACT

Toxoplasma gondii
, the causative parasite of toxoplasmosis, is an apicomplexan parasite that infects warm-blooded mammals. The ability of the calcium-binding proteins (CBPs) to transport large amounts of Ca
2+
appears to be critical for the biological activity of
T. gondii
. However, the functions of some members of the CBP family have not yet been deciphered. Here, we characterized a putative CBP of
T. gondii
, TgpCaBP (TGME49_229480), which is composed of four EF-hand motifs with Ca
2+
-binding capability. TgpCaBP was localized in the cytosol and ER of
T. gondii
, and parasites lacking the
TgpCaBP
gene exhibited diminished abilities in cell invasion, intracellular growth, egress, and motility. These phenomena were due to the abnormalities in intracellular Ca
2+
efflux and ER Ca
2+
storage, and the reduction in motility was associated with a decrease in the discharge of secretory proteins. Therefore, we propose that TgpCaBP is a Ca
2+
transporter and signaling molecule involved in Ca
2+
regulation and parasitization in the hosts.

IMPORTANCE

Ca
2+
signaling is essential in the development of
T. gondii
. In this study, we identified a calcium-binding protein in
T. gondii
, named TgpCaBP, which actively regulates intracellular Ca
2+
levels in the parasite. Deletion of the gene coding for TgpCaBP caused serious deficits in the parasite’s ability to maintain a stable intracellular calcium environment, which also impaired the secretory protein discharged from the parasite, and its capacity of gliding motility, cell invasion, intracellular growth, and egress from host cells. In summary, we have identified a novel calcium-binding protein, TgpCaBP, in the zoonotic parasite
T. gondii
, which is a potential therapeutic target for toxoplasmosis.