bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and characterization of the siderochelin biosynthetic gene cluster
via
coculture
Authors: Schaenzer Adam J. , Wang Wenliang , Hackenberger Dirk , Wright Gerard D.
Published: August 2024

Many microbial biosynthetic gene clusters (BGCs) are inactive under standard laboratory conditions, making characterization of their products difficult. Silent BGCs are likely activated by specific cues in their natural environment, such as the presence of competitors. Growth conditions such as coculture with other microbes, which more closely mimic natural environments, are practical strategies for inducing silent BGCs. Here, we utilize coculture to activate BGCs in nine actinobacteria strains. We observed increased production of the ferrous siderophores siderochelin A and B during coculture of
Amycolatopsis
strain WAC04611 and
Tsukamurella
strain WAC06889b. Furthermore, we identified the siderochelin BGC in WAC04611 and discovered that the GntR-family transcription factor
sidR3
represses siderochelin production. Deletion of the predicted aminotransferase
sidA
abolished production of the carboxamides siderochelin A/B and led to the accumulation of the carboxylate siderochelin D. Finally, we deleted the predicted hydroxylase
sidB
and established that it is essential for siderochelin production. Our findings show that microbial coculture can successfully activate silent BGCs and lead to the discovery and characterization of unknown BGCs for molecules like siderochelin.

IMPORTANCE

Siderophores are vital iron-acquisition elements required by microbes for survival in a variety of environments. Furthermore, many siderophores are essential for the virulence of various human pathogens, making them a possible target for antibacterials. The significance of our work is in the identification and characterization of the previously unknown BGC for the siderophore siderochelin. Our work adds to the growing knowledge of siderophore biosynthesis, which may aid in the future development of siderophore-targeting pharmaceuticals and inform on the ecological roles of these compounds. Furthermore, our work demonstrates that combining microbial coculture with metabolomics is a valuable strategy for identifying upregulated compounds and their BGCs.
Complete genome sequence of
Achromobacter
sp. strain E1, an endophyte from
Zea mays
L. cultivar (Zheng dan 958)
Authors: Li Hao , Wu Qingliu , Yu Pugang , Ni Bin
Published: August 2024

This announcement reports the complete genome sequence of
Achromobacter
sp. strain E1, which was isolated from the root of maize cultivar (Zheng dan 958) grown in Beijing, China.
Achromobacter
sp. strain E1 consists of a single, closed genome consisting of 5,975,307 bp, with GC content of 65.86%.
Genomic analysis of five antibiotic-resistant bacteria isolated from the environment
Authors: Bedore T. J. , Kumar Girish , McIntyre Cherish , Alvarez Anishka , Leslie Ariel , Snead Au'Nisha , Hudson André O.
Published: August 2024

Our study presents the whole-genome sequences and annotation of five bacteria isolates, each demonstrating distinct antibiotic resistance. These isolates include
Bacillus paranthracis
RIT 841,
Atlantibacter hermanii
RIT 842,
Pantoea leporis
RIT 844,
Enterococcus casseliflavus
RIT 845, and
Pseudomonas alkylphenolica
RIT 846, underscoring the importance of understanding antimicrobial resistance.
Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches
Authors: Nagy Gergely Ármin , Tombácz Dóra , Prazsák István , Csabai Zsolt , Dörmő Ákos , Gulyás Gábor , Kemenesi Gábor , Tóth Gábor E. , Holoubek Jiří , Růžek Daniel , Kakuk Balázs , Boldogkői Zsolt
Published: August 2024

In this study, we employed short- and long-read sequencing technologies to delineate the transcriptional architecture of the human monkeypox virus and to identify key regulatory elements that govern its gene expression. Specifically, we conducted a transcriptomic analysis to annotate the transcription start sites (TSSs) and transcription end sites (TESs) of the virus by utilizing Cap Analysis of gene expression sequencing on the Illumina platform and direct RNA sequencing on the Oxford Nanopore technology device. Our investigations uncovered significant complexity in the use of alternative TSSs and TESs in viral genes. In this research, we also detected the promoter elements and poly(A) signals associated with the viral genes. Additionally, we identified novel genes in both the left and right variable regions of the viral genome.

IMPORTANCE

Generally, gaining insight into how the transcription of a virus is regulated offers insights into the key mechanisms that control its life cycle. The recent outbreak of the human monkeypox virus has underscored the necessity of understanding the basic biology of its causative agent. Our results are pivotal for constructing a comprehensive transcriptomic atlas of the human monkeypox virus, providing valuable resources for future studies.
A nitrogenase-like enzyme is involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium
Rhodobacter capsulatus
Authors: Morimoto Yoshiki , Uesaka Kazuma , Fujita Yuichi , Yamamoto Haruki
Published: August 2024

Prokaryotes contribute to the global sulfur cycle by using diverse sulfur compounds as sulfur sources or electron acceptors. In this study, we report that a nitrogenase-like enzyme (NFL) and a radical SAM enzyme (RSE) are involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium
Rhodobacter capsulatus
. The
nflHDK
genes for NFL are localized at a locus containing genes for known sulfonate metabolism in the genome. A gene
nflB
encoding an RSE is present just upstream of
nflH
, forming a small gene cluster
nflBHDK
. Mutants lacking any
nflBHDK
genes are incapable of growing with isethionate as the sole sulfur source under anaerobic photosynthetic conditions, indicating that all four NflBHDK proteins are essential for the isethionate assimilation pathway. Heterologous expression of the
islAB
genes encoding a known isethionate lyase that degrades isethionate to sulfite and acetaldehyde restored the isethionate-dependent growth of a mutant lacking
nflDK
, indicating that the enzyme encoding
nflBHDK
is involved in an isethionate assimilation reaction to release sulfite. Furthermore, the heterologous expression of
nflBHDK
and
ssuCAB
encoding an isethionate transporter in the closely related species
R. sphaeroides
, which does not have
nflBHDK
and cannot grow with isethionate as the sole sulfur source, conferred isethionate-dependent growth ability to this species. We propose to rename
nflBHDK
as
isrBHDK
(
is
ethionate
r
eductase). The
isrBHDK
genes are widely distributed among various prokaryote phyla. Discovery of the isethionate assimilation pathway by IsrBHDK provides a missing piece for the anaerobic sulfur cycle and for understanding the evolution of ancient sulfur metabolism.

IMPORTANCE

Nitrogenase is an important enzyme found in prokaryotes that reduces atmospheric nitrogen to ammonia and plays a fundamental role in the global nitrogen cycle. It has been noted that nitrogenase-like enzymes (NFLs), which share an evolutionary origin with nitrogenase, have evolved to catalyze diverse reactions such as chlorophyll biosynthesis (photosynthesis), coenzyme F
430
biosynthesis (methanogenesis), and methionine biosynthesis. In this study, we discovered that an NFL with unknown function in the photosynthetic bacterium
Rhodobacter capsulatus
is a novel isethionate reductase (Isr), which catalyzes the assimilatory degradation of isethionate, a sulfonate, releasing sulfite used as the sulfur source under anaerobic conditions. Isr is widely distributed among various bacterial phyla, including intestinal bacteria, and is presumed to play an important role in sulfur metabolism in anaerobic environments such as animal guts and microbial mats. This finding provides a clue for understanding ancient metabolism that evolved under anaerobic environments at the dawn of life.
Microbial genotoxin-elicited host DNA mutations related to mitochondrial dysfunction, a momentous contributor for colorectal carcinogenesis
Authors: Yang Xue , Gan Yumeng , Zhang Yuting , Liu Zhongjian , Geng Jiawei , Wang Wenxue
Published: August 2024

Gut microbe dysbiosis increases repetitive inflammatory responses, leading to an increase in the incidence of colorectal cancer. Recent studies have revealed that specific microbial species directly instigate mutations in the host nucleus DNA, thereby accelerating the progression of colorectal cancer. Given the well-established role of mitochondrial dysfunction in promoting colorectal cancer, it is reasonable to postulate that gut microbes may induce mitochondrial gene mutations, thereby inducing mitochondrial dysfunction. In this review, we focus on gut microbial genotoxins and their known and potential targets in mitochondrial genes. Consequently, we propose that targeted disruption of genotoxin transport pathways may effectively reduce the rate of mitochondrial gene mutations and yield substantial benefits for the prevention of colorectal carcinogenesis.
Effective biofilm eradication in MRSA isolates with aminoglycoside-modifying enzyme genes using high-concentration and prolonged gentamicin treatment
Authors: Ando Kohei , Miyahara Satoshi , Hanada Shuhei , Fukuda Kazumasa , Saito Mitsumasa , Sakai Akinori , Maruo Akihiro , Zenke Yukichi
Published: August 2024

Bone and soft tissue infections caused by biofilm-forming bacteria, such as methicillin-resistant
Staphylococcus aureus
(MRSA), remain a significant clinical challenge. While the control of local infection is necessary, systemic treatment is also required, and biofilm eradication is a critical target for successful management. Topical antibiotic treatments, such as antibiotic-loaded bone cement (ALBC), have been used for some time, and continuous local antibiotic perfusion therapy, a less invasive method, has been developed by our group. However, the optimal antibiotics and concentrations for biofilms of clinical isolates are still not well understood. We examined the efficacy of high concentrations of gentamicin against MRSA biofilms and the role of gentamicin resistance genes in biofilm eradication. We collected 101 MRSA samples from a hospital in Japan and analyzed their gene properties, including methicillin and gentamicin resistance, and their minimum biofilm eradication concentration (MBEC) values. Our results showed that high concentrations of gentamicin are effective against MRSA biofilms and that even concentrations lower than the MBEC value could eliminate biofilms after prolonged exposure. We also identified three aminoglycoside/gentamicin resistance genes [
aac(6′)-aph(2″)
,
aph(3′)-III
, and
ant(4′)-IA
] and found that the presence or absence of these genes may inform the selection of treatments. It was also found that possession of the
aac(6′)-aph(2″
) gene correlated with the minimum inhibitory concentration/MBEC values of gentamicin. Although this study provides insight into the efficacy of gentamicin against MRSA biofilms and the role of gentamicin resistance genes, careful selection of the optimal treatment strategy is needed for clinical application.

IMPORTANCE

Our analysis of 101 MRSA clinical isolates has provided valuable insights that could enhance treatment selection for biofilm infections in orthopedics. We found that high concentrations of gentamicin were effective against MRSA biofilms, and even prolonged exposure to concentrations lower than the minimum biofilm eradication concentration (MBEC) value could eliminate biofilms. The presence of the
aac(6′)-aph(2″)
gene, an aminoglycoside resistance gene, was found to correlate with the minimum inhibitory concentration (MIC) and MBEC values of gentamicin, providing a potential predictive tool for treatment susceptibility. These results suggest that extended high concentrations of local gentamicin treatment could effectively eliminate MRSA biofilms in orthopedic infections. Furthermore, testing for gentamicin MIC or the possession of the
aac(6′)-aph(2″)
gene could help select treatment, including topical gentamicin administration and surgical debridement.
Evaluation of human antibodies from vaccinated volunteers for protection against
Yersinia pestis
infection
Authors: Zhang Li , Zheng Binyang , Lu Jing , Wu Haisheng , Wu Hailian , Zhang Qi , Jiao Lei , Pan Hongxing , Zhou Jianfang
Published: August 2024

Yersinia pestis
has a broad host range and has caused lethal bubonic and pneumonic plague in humans. With the emergence of multiple resistant strains and the potential for biothreat use, there is an urgent need for new therapeutic strategies that can protect populations from natural or deliberate infection. Targeting F1 has been proven to be the main strategy for developing vaccines and therapeutic antibodies, but data on anti-F1 antibodies, especially in humans, are scarce. To date, three human anti-F1 monoclonal antibodies (m252, αF1Ig2, and αF1Ig8) from naive populations have been reported. Here, we constructed an antibody library from vaccinees immunized with the plague subunit vaccine IIa by phage display. The genetic basis, epitopes, and biological functions of the obtained mAbs were assessed and evaluated in plague-challenged mice. Three human mAbs, namely, F3, F19, and F23, were identified. Their biolayer responses were 0.4, 0.6, and 0.6 nm, respectively. The dissociation constants (K
D
) of the F1 antigen were 1 pM, 0.165 nM, and 1 pM, respectively. Although derived from distinct Ab lineages, that is, VH3-30-D3-10-JH4 (F3&F23) and VH3-43-D6-19-JH4 (F19), these mAbs share similar binding sites in F1 with some overlap with αF1Ig8 but are distinct from αF1Ig2. Each of them provided a significant protective effect for Balb/c mice against a 100 median lethal dose (MLD) challenge of a virulent
Y. pestis
strain when administered at a dose of 100 µg. No synergistic or antagonistic effects were observed among them. These mAbs are novel and excellent candidates for further drug development and use in clinical practice.

IMPORTANCE

In this study, we identified three human monoclonal antibodies with a high affinity to F1 protein of
Yersinia pestis
. We discovered that they have relatively lower somatic hypermutations compared with antibodies, m252, αF1Ig2, and αF1Ig8, derived from the naive library reported previously. We also observed that these mAbs share similar binding sites in F1 with some overlapping with αF1Ig8 but distinct from that of αF1Ig2. Furthermore, each of them could provide complete protection for mice against a lethal dose of
Yersinia pestis
challenge. Our data provided new insights into the anti-F1 Ab repertories and their associated epitopes during vaccination in humans. The findings support the additional novel protective human anti-F1Abs for potential therapeutics against plaque.
Functional characterization of two survival factor 1 genes in
Mucor lusitanicus
Authors: Jáger Olivér , Szebenyi Csilla , Abu Saleem Tammam Khaliefeh Siliman , Molnár Anna , Kovács Vanda , Kiss Karina , Homa Mónika , Vágó Bernadett , Kiss-Vetráb Sándor , Varga Mónika , Sinka Rita , Vágvölgyi Csaba , Nagy Gábor , Papp Tamás
Published: August 2024

Survival factor 1 (Svf1) protein has been described in some ascomycetous fungi where it was found to be contributing to several essential physiological processes, such as response to osmotic, oxidative and cold stresses, sphingolipid biosynthesis, morphogenesis, sporulation, antifungal resistance, and pathogenicity. It was also suggested that it can be a novel central regulator affecting the expression of various genes. In the present study, function of this protein and the encoding genes is described for the first time in a fungus (i.e., in
Mucor lusitanicus
) belonging to the order Mucorales.
M. lusitanicus
has two putative
svf1
genes named
svf1a
and
svf1b
. Expression of both genes was proven. Although the expression of
svf1a
was affected by several environmental stresses and knocking out the gene affected adaptation to low temperatures and the sporulation ability, the main survival factor functions, such as participation in the maintenance of the viability, the response to oxidative and cold stresses, and the sphingolipid biosynthesis, could be associated with Svf1b, suggesting a central regulatory role to this protein. Interestingly, knockout of both genes affected the pathogenicity of the fungus in a
Drosophila
model.

IMPORTANCE

Mucor lusitanicus
is a widely used model organism to study various biological processes in the basal fungal group Mucorales. Several members of this group can be agents of mucormycosis, an opportunistic fungal infection, which is associated with high mortality, rapid progression, and wide resistance to the commonly used antifungal agents. Svf1 proteins have so far only been identified in fungi, where they have been involved in pathogenicity and resistance to antifungal agents in many cases. Only a limited number of factors affecting the stress response, antifungal resistance, and virulence of Mucorales fungi have been revealed. Elucidating the function of a fungus-specific protein that may regulate these processes may bring us closer to understanding the pathogenesis of these fungi.
One-tube detection of
Salmonella
Typhimurium using LAMP and CRISPR-Cas12b
Authors: Gong Jiansen , Jiang Yi , Zhang Di , Li Tingting , Fu Lixia , Dou Xinhong
Published: August 2024

Salmonella enterica
serovar Typhimurium (ST) is a predominant serovar causing foodborne illnesses worldwide. Traditional detection methods often face challenges, including the need for specialized equipment, skilled operators, and lengthy procedures. To address these limitations, we developed a rapid, sensitive, and specific ST detection method by integrating loop-mediated isothermal amplification (LAMP) with the clustered regularly interspaced short palindromic repeats and associated protein 12b (CRISPR/Cas12b) system, all within a single tube. Our results indicate that the LAMP–CRISPR/Cas12b reaction can be completed isothermally in under 1 h without requiring specialized instruments. The platform’s limit of detection (LoD) is 12.5 copies per reaction. Additionally, the system demonstrated 100% inclusivity and exclusivity when tested against 30 reference strains, highlighting its specificity. In practical applications, the LoDs for ST in pure nucleic acid and contaminated fecal samples were 2.32 and 23.2 CFU/mL, respectively, with higher sensitivity observed in pure nucleic acid samples. Overall, our findings underscore the potential of the one-tube LAMP–CRISPR/Cas12b platform as a rapid, sensitive, and specific tool for ST detection, particularly in resource-limited settings.

IMPORTANCE

Here, we have provided a novel one-step method for
Salmonella
Typhimurium detection in one pot by integrating the LAMP assay with the CRISPR/Cas12b system, offering significant advantages in terms of simplicity, speed, and accuracy.
MALDI-TOF mass spectrometry from nucleic acid: development and evaluation of a novel platform for identification of mycobacteria and detection of genetic markers of resistance
Authors: DeCurtis Emily K. , Machado Iara , Kuss-Duerkop Sharon K. , Wang Yongbao , Khare Reeti
Published: August 2024

Complete identification methods are critical for evaluating nontuberculous mycobacteria (NTM). Here, we describe a novel diagnostic method for identification of eight NTM,
Mycobacterium tuberculosis
complex, and three drug resistance markers using PCR/matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) from cultured organisms. With this technology, a multiplex end-point PCR is performed for targets of interest. Detection probes that are extended in the presence of a target are added. The extended probes have greater molecular weight and can be detected by MALDI-TOF MS. An AFB Primary Panel was designed to differentiate
Mycobacterium avium
;
Mycobacterium intracellulare
subsp.
chimaera
;
Mycobacterium avium
complex (other);
Mycobacterium abscessus
subsp.
abscessus
,
bolletii
, and
massiliense
;
Mycobacterium kansasii
, and
M. tuberculosis
complex. This design should cover 90% (3,483/3,691) of mycobacteria seen onsite. A development set of unblinded isolates (
n
= 217) was used to develop PCR primers, detection probes, and probe barcodes. It demonstrated 99.1% (215/217) agreement with reference methods. An evaluation set using blinded isolates (
n
= 320) showed an overall sensitivity of 94.3% (range by target: 90.0–100%). Overall specificity from negative media, non-target mycobacteria, and bacteria was 99.1% (108/109; range by target: 94.4–100%). Three drug resistance markers
erm
(41),
rrl,
and
rrs
demonstrated 100%, 91%, and 100% sensitivity, respectively, and >99% specificity. Limit of detection per target ranged from 2.2 × 10
3
to 9.9 × 10
6
CFU/mL. The AFB Primary Panel allows for mycobacterial speciation, subspeciation, and resistance mutation detection, which is essential for diagnosis, appropriate therapy, identifying outbreaks, and managing treatment-refractory disease. It can perform with high-throughput and high specificity and sensitivity from isolates.

IMPORTANCE

Even closely related mycobacteria can have unique treatment patterns, but differentiating these organisms is a challenge. Here, we tested an innovative platform that combines two commonly used technologies and creates something new: matrix-assisted, laser-desorption ionization time-of flight mass spectrometry was performed on PCR amplicons instead of on proteins. This created a robust system with the advantages of PCR (high discriminatory power, high throughput, detection of resistance) with the advantages of mass spectrometry (more targets, lower operational cost) in order to identify closely related mycobacterial organisms.
Gut
Lactococcus garvieae
promotes protective immunity to foodborne
Clostridium perfringens
infection
Authors: Wang Xue-Yin , Meng Fan-Hua , Zhang Ming-Yue , Li Fen-Xin , Lei Yu-Xin , Ma Zhao-Guo , Li Jia-Qi , Lou Ya-Nan , Chu Yue-Feng , Ma Ke , Yu Shui-Xing
Published: August 2024

The gut microbiota, a pivotal component of the intestinal mucosal barrier, is critical for host resistance to enteric pathogen infection. Here, we report a novel function of the potentially probiotic
Lactococcus garvieae
strain LG1 (
L. garvieae
strain LG1) in maintaining intestinal mucosal barrier integrity and protecting against foodborne
Clostridium perfringens
(
C. perfringens
) infection.
L. garvieae
was isolated from the intestinal contents of Chinese Mongolian sheep (MS) and exhibited potential probiotic properties. In a
C. perfringens
enterocolitis model,
L. garvieae-
pretreated mice were less susceptible to
C. perfringens
infection compared with Phosphate buffered solution (PBS)
-
pretreated mice, which manifested as higher survival rates, lower pathogen loads, less weight loss, mild clinical symptoms and intestinal damage, and minor inflammation. Further mechanistic analysis showed that
L. garvieae
could ameliorate the disruption of intestinal permeability and maintain the integrity of the intestinal mucosal barrier by promoting the expression of tight junction proteins and mucoproteins. Moreover,
L. garvieae
was also able to facilitate antimicrobial peptide expression and ameliorate dysbiosis of the gut microbiota caused by
C. perfringens
. Together, these findings highlight the prospect of immunomodulatory potentially probiotic
L. garvieae
and might offer valuable strategies for prophylaxis and/or treatment of pathogenic
C. perfringens
mucosal infection.

IMPORTANCE

C. perfringens
necrotic enteritis leads to losses of about US $2 billion to the poultry industry worldwide every year. Worse, US Centers for Disease Control and Prevention (CDC) has estimated that
C. perfringens
causes nearly 1 million foodborne illnesses in the United States annually. Nowadays, the treatment recommendation is a combination of a broad-spectrum synergistic penicillin with clindamycin or a carbapenem, despite growing scientific concern over antibiotic resistance. The global understanding of the gut microbiome for
C. perfringens
infection may provide important insights into the intervention.
L. garvieae
originated from Mongolian sheep intestine, exhibited potentially probiotic properties, and was able to limit
C. perfringens
enterocolitis and pathogenic colonization. Importantly, we found that
L. garvieae
limits
C. perfringens
invasion via improving intestinal mucosal barrier function. Also,
L. garvieae
alleviates
C. perfringens
-induced gut microbiota dysbiosis. It allowed us to convince that utilization of probiotics to promote protective immunity against pathogens infection is of pivotal importance.
Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese
Authors: Ali Qasim , Ma Sen , Farooq Umar , Liu Boshuai , Wang Zhichang , Sun Hao , Cui Yalei , Li Defeng , Shi Yinghua
Published: August 2024

It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days),
Clostridia_UCG-014
,
RF39
(at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.

IMPORTANCE

Low dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.
Supplemental Material: The South Purulia Shear Zone, eastern India: Its anatomy and implication for timing the Rodinia-age collision in the eastern part of the Central Indian Tectonic Zone
Authors: Banerjee Anwesa , Sequeira Nicole
Published: August 2024

Figure S1: Field photo in southern North Singhbhum Mobile Belt showing fabric relations in mica schists interleaved with quartzite and south-down shear sense during D3 deformation. Text S1: Summary of instrumentation and analytical details for whole-rock geochemistry, laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) U-Pb zircon dating, and electron probe micro-analysis monazite chemical dating. Table S1: Data table for LA-ICP-MS U-Pb zircon analyses. Text S2: Lithological description and textural characteristics of monazite with dates in Ma. Table S2: Chemical compositions of monazites and spot dates. Figure S2: Probability density plots of monazite dates (<10% error) in individual samples.
Utilising the Ipzo parameter for more reliable estimates of undrained shear strength directly from CPTU data in saturated natural clay-like soils
Authors: Ramsey N. , Tho K.K.
Published: August 2024

Ramsey and Tho illustrated the ability of the Ipzo parameter to estimate plasticity index in a wide range of saturated natural soils and highlighted the potential of the Ipzo parameter for improving the reliability of estimations of other soil properties affected by plasticity index. In this note, an improved method is proposed for estimating undrained shear strength in clay-like soils using CPTU data, where clay-like is defined as Ipzo ≥ 12%. The improved method is validated using a geographically and geologically diverse “Nkt1-database” comprising 54 anisotropically consolidated undrained triaxial compression tests, with complementary CPTU measurements from 36 geological units at 18 globally distributed marine sites.
Prospect for measurement of the CP-violating phase $$\phi _s$$ in the $$B_{s}\rightarrow J/\psi \phi $$ channel at a future Z factory
Authors: Li Xiaomei , Ruan Manqi , Zhao Mingrui
Published: August 2024

The CP-violating phase $$\phi _s$$

ϕ
s

, the $$B_{s}$$

B
s

decay width ($$\varGamma _s$$

Γ
s

), and the $$B_{s}$$

B
s

decay width difference ($$\varDelta \varGamma _s$$

Δ

Γ
s

) are sensitive probes to new physics and can constrain the heavy quark expansion theory. The potential for the measurement at future Z factories is studied in this manuscript. It is found that operating at Tera-Z mode, the expected precision can reach: $$\sigma (\phi _s) = 4.6~\textrm{mrad}$$

σ
(

ϕ
s

)
=
4.6

mrad

, $$\sigma (\varDelta \varGamma _s) = 2.4~\mathrm {ns^{-1}}$$

σ

(
Δ

Γ
s

)

=
2.4

ns

-
1

and $$\sigma (\varGamma _s) = 0.72~\mathrm {ns^{-1}}$$

σ

(

Γ
s

)

=
0.72

ns

-
1

. The precision of $$\phi _s $$

ϕ
s

is 40% larger than the expected precision with the LHCb experiment at HL-LHC. If operating at 10-Tera-Z mode, the precision of $$\phi _s $$

ϕ
s

can be measured at 45% of the precision obtained from the LHCb experiment at HL-LHC. However, the measurement of $$\varGamma _s$$

Γ
s

and $$\varDelta \varGamma _s$$

Δ

Γ
s

cannot benefit from the excellent time resolution and tagging power of the future Z-factories. Only operating at 10-Tera-Z mode can the $$\varGamma _s$$

Γ
s

and $$\varDelta \varGamma _s$$

Δ

Γ
s

reach an 18% larger precision than the precision expected to be obtained from LHCb at HL-LHC. The control of penguin contamination at the future Z-factories is also discussed.
Efficient computation of Fourier–Bessel transforms for transverse-momentum dependent parton distributions and other functions
Authors: Diehl Markus , Grocholski Oskar
Published: August 2024

We present a method for the numerical computation of Fourier–Bessel transforms on a finite or infinite interval. The function to be transformed needs to be evaluated on a grid of points that is independent of the argument of the Bessel function. We demonstrate the accuracy of the algorithm for a wide range of functions, including those that appear in the context of transverse-momentum dependent parton distributions in Quantum Chromodynamics.
Inquisition of optical soliton structure and qualitative analysis for the complex-coupled Kuralay system
Authors: Kopçasız Bahadır , Yaşar Emrullah
Published: August 2024

This study seeks to explore the integrable dynamics of induced curves through the utilization of the complex-coupled Kuralay system. The importance of the coupled complex Kuralay equation lies in its role as a fundamental model that contributes to the understanding of intricate physical and mathematical concepts, making it a valuable tool in scientific research and applications. The soliton solutions originating from the Kuralay equations are believed to encapsulate cutting-edge research in various important domains such as optical fibers, nonlinear optics, and ferromagnetic materials. Analytical techniques are employed to derive traveling wave solutions for this model, given that the Cauchy problem cannot be resolved using the inverse scattering transform. In the quest for solitary wave solutions, the extended modified auxiliary equation mapping (EMAEM) method is employed. We derive several novel families of precise traveling wave solutions, encompassing trigonometric, hyperbolic, and exponential forms. Moreover, the planar dynamical system of the concerned equation is created, all probable phase portraits are given, and sensitive inspection is applied to check the sensitivity of the considered equation. Furthermore, after adding a perturbed term, chaotic and quasi-periodic behaviors have been observed for different values of parameters, and multistability is reported at the end. Numerical simulations of the solutions are incorporated alongside the analytical results to enhance comprehension of the dynamic characteristics of the solutions obtained. This study’s outcomes can offer valuable insights for addressing other nonlinear partial differential equations (NLPDEs). The soliton solutions obtained in this study offer important insights into the intricate nonlinear equation being examined.
Evaluation of OEE at Lifelong India Using Lean Practices: A Case Study
Authors: Surya Amit , Kumar Rakesh , Trehan Rajeev
Published: August 2024

Today, the industry is facing issues related to nonvalue-added activities (NVA). By integrating lean practices, industries can systematically evaluate and enhance their overall equipment effectiveness (OEE), leading to more efficient and effective production processes. This alignment not only boosts productivity by eliminating nonvalue activities but also contributes to higher quality outputs and reduced operational costs as well. Manufacturers are required to use value-added approaches in their manufacturing management due to the intense rivalry in real-world markets and growing client needs. Through continuous improvement, lean manufacturing (LM) has been demonstrated to be a significant technique for getting rid of nonvalue-added operations in manufacturing organizations. OEE at Lifelong India is assessed using lean tools and techniques, including Pareto analysis, Why–Why analysis, Kaizen concept and evaluation of Kaizen ideas, as well as before-and-after comparison, in order to assess the operational performance of the organization. A questionnaire was designed with data collection in mind, and business professionals in the field were surveyed and contacted personally. This study indicates that widespread implementation of lean principles leads to an increase in OEE of 95.89%, a level of OEE that is unmatched in the industry and ensures flawless output.
A generalization of prime ideals in MV-algebras
Authors: Bedrood Mahta , Sajadian Farhad , Lenzi Giacomo , Saeid Arsham Borumand
Published: August 2024

In this paper, we introduce a special type of prime ideals in [Formula: see text]-algebras. We define the concept of a [Formula: see text]-prime ideal, which is a proper ideal [Formula: see text] that preserves the property of being prime with respect to the ideal [Formula: see text]. If [Formula: see text] is not a subset of [Formula: see text], then we call the [Formula: see text]-prime ideal an [Formula: see text]-prime ideal. We investigate the relationships between these ideals and their connections to minimal prime ideals and maximal ideals. Additionally, we explore various properties such as extension, transitivity, meet, join, and annihilator. Finally, we study prime ideals in [Formula: see text]-algebras of continuous functions.
Pac-Sim: Simulation of Multi-threaded Workloads using Intelligent, Live Sampling
Authors: Liu Changxi , Sabu Alen , Chaudhari Akanksha , Kang Qingxuan , Carlson Trevor E.
Published: August 2024

High-performance, multi-core processors are the key to accelerating workloads in several application domains. To continue to scale performance at the limit of Moore’s Law and Dennard scaling, software and hardware designers have turned to dynamic solutions that adapt to the needs of applications in a transparent, automatic way. For example, modern hardware improves its performance and power efficiency by changing the hardware configuration, like the frequency and voltage of cores, according to a number of parameters, such as the technology used or the workload running at the time. With this level of dynamism, it is essential to simulate next-generation multi-core processors in a way that can both respond to system changes and accurately determine system performance metrics. Currently, no sampled simulation platform can achieve these goals of dynamic, fast, and accurate simulation of multi-threaded workloads.

In this work, we propose a solution that allows for fast, accurate simulation in the presence of both hardware and software dynamism. To accomplish this goal, we present Pac-Sim, a novel sampled simulation methodology for fast, accurate sampled simulation that requires no upfront analysis of the workload. With our proposed methodology, it is now possible to simulate long-running dynamically scheduled multi-threaded programs with significant simulation speedups, even in the presence of dynamic hardware events. We evaluate Pac-Sim using the SPEC CPU2017, NPB, and PARSEC multi-threaded benchmarks with both static and dynamic thread scheduling. The experimental results show that Pac-Sim achieves a very low sampling error of 1.63% and 3.81% on average for statically and dynamically scheduled benchmarks, respectively. Pac-Sim also demonstrates significant simulation speedups as high as 523.5× (210.3× on average) for the training input set of SPEC CPU2017 running eight threads.
Adversarial Missingness Attacks on Causal Structure Learning
Authors: Koyuncu Deniz , Gittens Alex , Yener Bülent , Yung Moti
Published: August 2024

Causality-informed machine learning has been proposed as an avenue for achieving many of the goals of modern machine learning, from ensuring generalization under domain shifts to attaining fairness, robustness, and interpretability. A key component of causal machine learning is the inference of causal structures from observational data; in practice, this data may be incompletely observed. Prior work has demonstrated that adversarial perturbations of completely observed training data may be used to force the learning of inaccurate structural causal models (SCMs). However, when the data can be audited for correctness (e.g., it is cryptographically signed by its source), this adversarial mechanism is invalidated. This work introduces a novel attack methodology wherein the adversary deceptively omits a portion of the true training data to bias the learned causal structures in a desired manner (under strong signed sample input validation, this behavior seems to be the only strategy available to the adversary). Under this model, theoretically sound attack mechanisms are derived for the case of arbitrary SCMs, and a sample-efficient learning-based heuristic is given. Experimental validation of these approaches on real and synthetic datasets, across a range of SCMs from the family of additive noise models (linear Gaussian, linear non-Gaussian, and non-linear Gaussian), demonstrates the effectiveness of adversarial missingness attacks at deceiving popular causal structure learning algorithms.
Case 328: Brown Tumor in Hyperparathyroidism Due to Parathyroid Adenoma
Authors: Agostinis Cristina , Lupi Elide
Published: August 2024

History

A 45-year-old female patient with diffuse osteoarticular pain, particularly low back pain, was referred by a rheumatologist for an updated radiologic evaluation. The patient had experienced these symptoms for many years and was diagnosed with human leukocyte antigen B27–negative spondyloarthritis approximately 11 years prior, based on findings of bilateral erosive sacroiliitis at pelvic radiography and bone scintigraphy with technetium 99m (99mTc) methylene diphosphonate. After 3 years of treatment with a tumor necrosis factor–α inhibitor (adalimumab), which was effective for pain, the patient was lost to follow-up. At the current presentation, approximately 8 years after being lost to follow-up, the patient presented with worsening low back pain. The presence of nonobstructing kidney stones on US images confounded the underlying cause of worsening pain. The patient also experienced fatigue and depressed mood. Routine blood tests revealed a normal blood cell count, creatinine level of 0.64 mg/dL (56.58 μmol/L) (normal range, 0.30–1.1 mg/dL [26.52–97.24 μmol/L]), C-reactive protein level of 1.1 mg/dL (normal, <1 mg/dL), and vitamin D level of 21 ng/mL (52.42 nmol/L) (normal range, 30–100 ng/mL [74.88–249.60 nmol/L]). Noncontrast MRI of the thoracic and lumbar spine, MRI of the sacroiliac joints, and CT of the abdomen and pelvis were performed.
Case 332
Authors: Adler Cameron , Menias Christine
Published: August 2024

History

A 65-year-old male patient with a history of sarcomatoid renal cell carcinoma and prior right nephrectomy developed recurrent disease adjacent to the inferior vena cava. The patient underwent surveillance imaging 7 months after initiation of treatment with maximum-dose pazopanib and less than 1 month after completing a 2-month regimen of palliative stereotactic body radiation therapy to the right nephrectomy bed and site of recurrence. (Stereotactic body radiation therapy was initiated 5 months after pazopanib treatment was initiated.) One month after initiating treatment with pazopanib and 6 months before the surveillance imaging, the patient developed diarrhea and required ongoing treatment with loperamide to control symptoms. He denied any fatigue, mouth sores, or extremity pain, but described some abdominal pain and discomfort associated with the diarrhea. He was not experiencing any fevers, and vital signs were normal. White blood cell count was normal at 5100/μL (5.1 ×109/L) (normal range, 4200–10 200/μL [4.2–10.2 ×109/L]), with all components of the differential count also being normal. A normal serum albumin level of 3.9 g/dL (39 g/L) (normal range, 3.5–5.0 g/dL [35–50 g/L]) and low serum total protein level of 6.1 g/dL (61 g/L) (normal range, 6.3–7.9 g/dL [63–79 g/L]) were noted. A comprehensive metabolic panel was performed, indicating a serum chloride level of 98 mmol/L (normal, 100–108 mmol/L) and alkaline phosphatase level of 121 U/L (2.02 μkat/L) (normal, 45–115 U/L [0.75–1.92 μkat/L]). The patient underwent surveillance imaging with contrast-enhanced CT of the abdomen and pelvis in the venous phase ( Figure ).
Framework Integrated with Flow Cell Experiments and Simulations for Understanding Etching in Chemical Conversion Treatments
Authors: Kwon Junam , Amaya Kenji
Published: August 2024

In this study, a new framework integrates simulations and flow cell experimentation to quantitatively understand the mechanism of chemical treatment reactions. Using this framework, the mechanisms of etching reactions induced by weak and strong acids were specifically investigated. A flow cell system experiment was developed for the etching experiment. Two acids (HNO3 and HF) were used, along with HNO3 without electrolytes. Average flow velocities were measured, and the molar flux of Fe2+ ions was determined by sampling the solution passing through the flow cell and measuring the iron content by using inductively coupled plasma. A concentration field simulation of the etching reaction in the flow cell was conducted. The concentration field within the boundary layer was visualized to understand the mechanism of H+ ion supply to the metal surface. In the case of weak acid solutions, H+ ions are primarily supplied by dissociation. In contrast, they were supplied by diffusion in strong acid solutions. A boundary layer formed within 100 μm from the metal surface. The experimental and simulated molar flux of Fe2+ ions were compared. The molar flux attributed to weak acid etching was more than 10 times that attributed to strong acids. The reaction rate constant of the H+ reduction reaction was evaluated through a parameter study. The influence of spectator ions on the etching process was investigated. An experiment was conducted to compare the etching of iron plates using HNO3 solutions with different concentrations of spectator ion. The results confirmed that the higher the concentration of the spectator ion, the greater the etching amount. Numerical analysis revealed that the electric field in the electric migration term acts in a direction that impedes the movement of H+ ions to the metal surface. While it is already known that electric migration inhibits electrode reactions, this study enabled its quantitative visualization and evaluation.
Effects of Dietary Yeast, Saccharomyces cerevisiae, and Costmary, Tanacetum balsamita, Essential Oil on Growth Performance, Digestive Enzymes, Biochemical Parameters, and Disease Resistance in Nile Tilapia, Oreochromis niloticus
Authors: Adineh Hossein , Yousefi Morteza , Al Sulivany Basim S. A. , Ahmadifar Ehsan , Farhangi Mohammad , Hoseini Seyyed Morteza
Published: August 2024

The present study assessed the effects of dietary yeast, Saccharomyces cerevisiae, and costmary, Tanacetum balsamita, essential oil on growth performance, biochemical parameters, and disease resistance of Nile tilapia, Oreochromis niloticus. Four diets containing 1 g/kg yeast (Sc), 0.1 g/kg costmary essential oil (Tb), 1 g/kg yeast + 0.1 g/kg costmary essential oil (Sc + Tb), and without Sc and Tb (control) were formulated and fed (2.5% per day) to triplicate groups of fish (average: 9.8 g; SD : 0.12) for 8 weeks. Each replicate was a 70‐L tank, stocked with 25 fish. Then, the fish were intraperitoneally challenged by Aeromonas hydrophila, and blood samples were taken from the fish before and 12 hr postinfection. All experimental groups showed significantly higher growth performance and feed efficiency, compared to the control, and the highest values were related to Sc + Tb treatment (P  < 0.001). Sc group showed significant elevations in the intestinal amylase, lipase, and protease activities, but Tb group showed only elevation in lipase activity. The highest amylase (P = 0.026), lipase (P = 0.036), and protease (P = 0.009) activities were observed in Sc + Tb treatment. The postchallenge survival of Sc (70.0%), Tb (73.3%), and Sc + Tb (76.6%) treatments were significantly (P = 0.038) higher than the control (56.6%). Bacterial challenge significantly increased plasma cortisol, glucose, malondialdehyde, glutathione peroxidase, and superoxide dismutase, but decreased lysozyme, alternative complement, albumin, globulin, and catalase (P  < 0.001). The Tb treatment showed improvements in plasma antioxidant, immunological, and biochemical parameters, compared to the Sc treatment. The Sc + Tb treatment showed the highest albumin, globulin, lysozyme, total immunoglobulin, alternative complement, glutathione peroxidase, and superoxide dismutase, but the lowest cortisol, glucose, malondialdehyde, and catalase, before/after the challenge (P  < 0.001). In conclusion, dietary Sc + Tb supplementation positively affects growth performance, antioxidant, and immunological responses, thereby augments resistance of Nile tilapia to A. hydrophila infection.