bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional analysis of salivary intercalated duct cells reveals a secretory phenotype
Authors: Wahl Amanda M. , Takano Takahiro , Su Shan , Warner Blake M. , Perez Paola , Sneyd James , Yule David I. 
Published: September 2023

AbstractCurrently, all salivary ducts (intercalated, striated and collecting) are assumed to function broadly in a similar manner, reclaiming ions that were secreted by the secretory acinar cells while preserving fluid volume and delivering saliva to the oral cavity. Nevertheless, there has been minimal investigation into the structural and functional differences between distinct types of salivary duct cells. Therefore, in this study, the expression profile of proteins involved in stimulus–secretion coupling, as well as the function of the intercalated duct (ID) and striated duct cells, was examined. Particular focus was placed on defining differences between distinct duct cell populations. To accomplish this, immunohistochemistry and in situ hybridization were utilized to examine the localization and expression of proteins involved in reabsorption and secretion of ions and fluid. Further, in vivo calcium imaging was employed to investigate cellular function. Based on the protein expression profile and functional data, marked differences between the IDs and striated ducts were observed. Specifically, the ID cells express proteins native to the secretory acinar cells while lacking proteins specifically expressed in the striated ducts. Further, the ID and striated duct cells display different calcium signalling characteristics, with the IDs responding to a neural stimulus in a manner similar to the acinar cells. Overall, our data suggest that the IDs have a distinct role in the secretory process, separate from the reabsorptive striated ducts. Instead, based on our evidence, the IDs express proteins found in secretory cells, generate calcium signals in a manner similar to acinar cells, and, therefore, are likely secretory cells.
imageKey points
Current studies examining salivary intercalated duct cells are limited, with minimal documentation of the ion transport machinery and the overall role of the cells in fluid generation.
Salivary intercalated duct cells are presumed to function in the same manner as other duct cells, reclaiming ions, maintaining fluid volume and delivering the final saliva to the oral cavity.
Here we systematically examine the structure and function of the salivary intercalated duct cells using immunohistochemistry, in situ hybridization and by monitoring in vivo Ca2+ dynamics.
Structural data revealed that the intercalated duct cells lack proteins vital for reabsorption and express proteins necessary for secretion.
Ca2+ dynamics in the intercalated duct cells were consistent with those observed in secretory cells and resulted from GPCR‐mediated IP3 production.
Early transcriptional responses to human enteric fever challenge
Authors: Barton Amber , Hill Jennifer , O'Connor Daniel , Jones Claire , Jones Elizabeth , Camara Susana , Shrestha Sonu , Jin Celina , Gibani Malick M. , Dobinson Hazel C. , Waddington Claire , Darton Thomas C. , Blohmke Christoph J. , Pollard Andrew J. 
Published: September 2023

ABSTRACT

Enteric fever, caused by oral infection with typhoidal
Salmonella
serovars, presents as a non-specific febrile illness preceded by an incubation period of 5 days or more. The enteric fever human challenge model provides a unique opportunity to investigate the innate immune response during this incubation period, and how this response is altered by vaccination with the Vi polysaccharide or conjugate vaccine. We find that on the same day as ingestion of typhoidal
Salmonella
, there is already evidence of an immune response, with 199 genes upregulated in the peripheral blood transcriptome 12 hours post-challenge (false discovery rate <0.05). Gene sets relating to neutrophils, monocytes, and innate immunity were over-represented (false discovery rate <0.05). Estimating cell proportions from gene expression data suggested a possible increase in activated monocytes 12 hours post-challenge (
P
= 0.036, paired Wilcoxon signed-rank test). Furthermore, plasma TNF-α rose following exposure (
P
= 0.011, paired Wilcoxon signed-rank test). There were no significant differences in gene expression (false discovery rate <0.05) in the 12 hours response between those who did and did not subsequently develop clinical or blood culture confirmed enteric fever or between vaccination groups. Together, these results demonstrate early perturbation of the peripheral blood transcriptome after enteric fever challenge and provide initial insight into early mechanisms of protection.
A procedure to harmonize the hydrodynamic force during microbial cultivation in shaking flasks
Authors: Simões Lúcia Chaves , Oliveira Isabel , Borges Anabela , Gomes Inês Bezerra , Simões Manuel 
Published: September 2023

ABSTRACT
Shake flask cultivation is a routine technique in microbiology and biotechnology laboratories where cell growth can be affected by the hydrodynamic conditions, which depend on the agitation velocity, shaking diameter, and shake flask size. Liquid agitation is implemented inherently to increase aeration, substrate transfer to the cells, and prevent sedimentation, disregarding the role of hydrodynamics in microbial growth and metabolism. Here, we present a simple approach to help standardize the hydrodynamic forces in orbital shakers to increase the experimental accuracy and reproducibility and give students a better knowledge of the significance of the agitation process in microbial growth.
Molecular basis and evolutionary cost of a novel macrolides/lincosamides resistance phenotype in
Staphylococcus haemolyticus
Authors: Xu Ruilin , Wang Qiang , Wu Shuhua , Wang Hongqiu , Song Tianqiang , Zhao Chenhao , Wang Min , Du Hong , Zhang Haifang 
Published: September 2023

ABSTRACT

Staphylococcus haemolyticus
(
S. haemolyticus
) is a coagulase-negative
Staphylococcus
that has become one of the primary causes of nosocomial infection. After a long period of antibiotic use,
S. haemolyticus
has developed multiple resistance phenotypes for macrolides and lincosamides. Herein, we evaluated four
S
.
haemolyticus
clinical isolates, of which three had antibiotic resistance patterns reported previously. The fourth isolate was resistant to both erythromycin and clindamycin in the absence of erythromycin induction. This novel phenotype, known as constitutive macrolides-lincosamides-streptogramins resistance, has been reported in other bacteria but has not been previously reported in
S. haemolyticus
. Investigation of the isolate demonstrated a deletion in the methyltransferase gene
ermC,
upstream leader peptide. This deletion resulted in constitutive MLS resistance based on whole-genome sequencing and experimental verification. Continuous expression of
ermC
was shown to inhibit the growth of
S. haemolyticus
, which turned out to be the fitness cost with no MLS pressure. In summary, this study is the first to report constitutive MLS resistance in
S. haemolyticus
, which provides a better understanding of MLS resistance in clinical medicine.

Importance

This study identified a novel phenotype of macrolides/lincosamides resistance in
Staphylococcus haemolyticus
which improved a better guidance for clinical treatment. It also clarified the mechanistic basis for this form of antibiotic resistance that supplemented the drug resistance mechanism of
Staphylococcus
. In addition, this study elaborated on a possibility that continuous expression of some resistance genes was shown to inhibit the growth of bacteria themselves, which turned out to be the fitness cost in the absence of antibiotic pressure.
The distinct transcriptome of virulence-associated phylogenetic group B2
Escherichia coli
Authors: Hogins Jacob , Xuan Zhenyu , Zimmern Philippe E. , Reitzer Larry 
Published: September 2023

ABSTRACT

Escherichia coli
strains of phylogenetic group B2 are often associated with urinary tract infections (UTIs) and several other diseases. Recent genomic and transcriptomic analyses have not suggested or identified specific genes required for virulence, but have instead suggested multiple virulence strategies and complex host-pathogen interactions. Previous analyses have not compared core gene expression between phylogenetic groups or between pathogens and nonpathogens within phylogenetic groups. We compared the core gene expression of 35 strains from three phylogenetic groups that included both pathogens and nonpathogens after growth in a medium that allowed comparable growth of both types of strains. K-means clustering suggested a B2 cluster with 17 group B2 strains and two group A strains; an AD cluster with six group A strains, five group D strains and one B2 strain; and four outliers which included the highly studied model uropathogenic
E. coli
strains UTI89 and CFT073. Half of the core genes were differentially expressed between B2 and AD cluster strains, including transcripts of genes for all aspects of macromolecular synthesis—replication, transcription, translation, and peptidoglycan synthesis—energy metabolism, and environmental-sensing transcriptional regulators. Notably, core gene expression between nonpathogenic and uropathogenic transcriptomes within phylogenetic groups did not differ. If differences between pathogens and nonpathogens exist, then the differences do not require transcriptional reprogramming. In summary, B2 cluster strains have a distinct transcription pattern that involves hundreds of genes. We propose that this transcription pattern is one factor that contributes to virulence.

IMPORTANCE

Escherichia coli
is a diverse species and an opportunistic pathogen that is associated with various diseases, such as urinary tract infections. When examined, phylogenetic group B2 strains are more often associated with these diseases, but the specific properties that contribute to their virulence are not known. From a comparative transcriptomic analysis, we found that group B2 strains grown in a nutrient-rich medium had a distinct transcription pattern, which is the first evidence that core gene expression differs between phylogenetic groups. Understanding the consequences of group B2 transcription pattern will provide important information on basic
E. coli
biology, the basis for
E. coli
virulence, and possibly for developing therapies for a majority of urinary tract infections and other group B2-associated diseases.
A stochastic evaluation of quantum Fisher information matrix with generic Hamiltonians
Authors: Ho Le Bin 
Published: September 2023

AbstractQuantum Fisher information matrix (QFIM) is a fundamental quantity in quantum physics, which closely links to diverse fields such as quantum metrology, phase transitions, entanglement witness, and quantum speed limit. It is crucial in quantum parameter estimation, central to the ultimate Cramér-Rao bound. Recently, the evaluation of QFIM using quantum circuit algorithms has been proposed for systems with multiplicative parameters Hamiltonian. However, systems with generic Hamiltonians still lack these proposed schemes. This work introduces a quantum-circuit-based approach for evaluating QFIM with generic Hamiltonians. We present a time-dependent stochastic parameter-shift rule for the derivatives of evolved quantum states, whereby the QFIM can be obtained. The scheme can be executed in universal quantum computers under the family of parameterized gates. In magnetic field estimations, we demonstrate the consistency between the results obtained from the stochastic parameter-shift rule and the exact results, while the results obtained from a standard parameter-shift rule slightly deviate from the exact ones. Our work sheds new light on studying QFIM with generic Hamiltonians using quantum circuit algorithms.
(Invited) Intra- and Intermolecular Fano Resonances in Doped Semiconducting Carbon Nanotubes
Authors: Hertel Tobias , Eckstein Klaus , Müller Daniel 
Published: September 2023

Electron-phonon coupling plays a key role for understanding physical phenomena such as carrier transport and superconductivity [1]. The Fano-like line shape of vibrational resonance signals in the mid infrared, sheds light on the interactions of lattice vibrations with low-energy states of the electronic absorption continuum in doped semiconducting single-wall carbon nanotubes (s-SWNTs). [2,3]. Here, we present a systematic investigation of such Fano resonances in intrinsic and doped, polymer-wrapped monochiral s-SWNT thin-films. We observe distinct resonance signals for the Raman active D- and G-bands, which acquire IR oscillator strength via coupling to the dipole-allowed Drude-like intraband continuum in doped s-SWNTs [2]. We also observe two IR-active bands in the 800 cm-1 range which are discussed in terms of the coherent intra- as well as intermolecular superposition of coupled, harmonic oscillations of electronic intraband- and different vibrational modes.
[1] M. Lazzeri et al., Phys. Rev. B, 2006, 73(15), 155426.
[2] K. H. Eckstein et al., J. Phys. Chem C, 2021, 125(10), 5700-5707.
[3] U. Fano, Phys. Rev. 1961, 124, 1866-1878.
(Invited) Electroluminescence from Single-Walled Carbon Nanotubes with Quantum Defects
Authors: Li Min-Ken , Riaz Adnan , Wederhake Martina , Fink Karin , Saha Avishek , Dehm Simone , He Xiaowei , Schoeppler Friedrich , Kappes Manfred , Htoon Han , Popov Valentin , Doorn Stephen , Hertel Tobias , Hennrich Frank , Krupke Ralph 
Published: September 2023

Individual single-walled carbon nanotubes with covalent sidewall defects have emerged as a new class of photon sources whose photoluminescence spectra can be tailored by the carbon nanotube chirality and the attached functional group/molecule. Here we present electroluminescence spectroscopy data from single-tube devices based on (7,5) carbon nanotubes, functionalized with dichlorobenzene molecules, and wired to graphene electrodes. We observe electrically generated, defect-induced emissions that are controllable by electrostatic gating and strongly red-shifted compared to emissions from pristine nanotubes. The defect-induced emissions are assigned to excitonic and trionic recombination processes by correlating electroluminescence excitation maps with electrical transport and photoluminescence data. At cryogenic conditions additional, gate-dependent emission lines appear which are assigned to phonon-assisted hot-exciton electroluminescence from quasi-levels. Similar results were obtained with functionalized (6,5) nanotubes. We also compare functionalized (7,5) electroluminescence data with photoluminescence of pristine and functionalized (7,5) nanotubes redox-doped using gold(III) chloride solution. This work shows that electroluminescence excitation is selective toward neutral defect-state configurations with the lowest transition energy, which in combination with gate-control over neutral versus charged defect-state emission leads to high spectral purity.
Reference: Min-Ken Li et al., ACS Nano 2022 (doi: 10.1021/acsnano.2c03083)

Figure 1
(Invited) Optical Properties and Device Application of One-Dimensional Vdw Heterostructures Based on Single-Walled Carbon Nanotubes
Authors: Maruyama Shigeo 
Published: September 2023

A typical one-dimensional (1D) van der Waals (vdW) heterostructure consists of SWCNT, boron nitride nanotube (BNNT), and molybdenum disulfide nanotube (MoS2NT), grown coaxially by successive chemical vapor deposition (CVD) steps [1, 2]. The coaxially nested structure based on SWCNTs, which has diverse electronic properties (metallic or semiconducting), can expand the board application possibilities of 1D vdW heterostructures [3]. By comparing the optical properties of films of BNNT@MoS2NT and SWCNT@BNNT@MoS2NT, we found strong photoluminescence (PL) from monolayer MoS2NT and quenching of PL by coupling to SWCNT through thin BNNT [4]. The inter-tube excitons are demonstrated by ultrafast optical spectroscopy [5]. The inter-tube excitons, the counterpart of inter-layer excitons for 2D heterostructures, suggest a possibility of efficient photovoltaic applications of the 1D heterostructure [6]. In addition to MoS2 nanotubes, we will discuss the growth control of WS2 and NbS2 nanotubes. A general strategy we can tune the CVD condition from 2D flake to 1D tube is proposed. The junctions of MoS2 and WS2 nanotube are also realized as the outermost layer. More specific optical properties are studied for semiconductor SWCNTs and chirality-sorted SWCNTs [7,8]. Semiconductor SWCNT or chirality-sorted SWCNT wrapped with BNNT can be regarded as the ideal building blocks of field-effect transistors (FET) [9]. We have demonstrated the radial semiconductor–insulator–semiconductor (S-I-S) tunneling heterojunction diode by using a micrometer long 1D vdW heterostructure SWCNT@BNNT@MoS2NT [10]. We will discuss a more recent array of 1D heterostructure FET devices.
Part of this work was supported by JSPS KAKENHI Grant Number JP20H00220, and by JST, CREST Grant Number JPMJCR20B5, Japan.
References:
[1] R. Xiang et al., Science
367, 537 (2020).
[2] Y. Zheng, et al, P. Natl. Acad. Sci., 118, e2107295118 (2021).
[3] S. Cambré, et al., Small, 17, 2102585 (2021).
[4] M. Liu et al., ACS Nano
15, 8418 (2021).
[5] M. G. Burdanova et al., Adv. Funct. Mater.
32, 2104969 (2022).
[6] R. Xiang, Y. Li, S. Maruyama, National Science Open, 1, 20220016 (2022).
[7] R. Zhang et al., Carbon
199, 407 (2022).
[8] C. Zhang et al., ACS Nano
16, 18630 (2022).
[9] R. Xiang, S. Maruyama, Small Sci., 1, 2000039 (2021).
[10] Y. Feng, et al., ACS Nano, 15, 5600 (2021).
(Invited) Discussion on Preparation of Single-Walled Carbon Nanotubes for High-Performance Electronics
Authors: Li Yan 
Published: September 2023

The unique structure and outstanding properties of single-walled carbon nanotubes (SWCNTs) make them top candidates for future high-performance electronics. Highly pure (>99.9999%) and dense (>125tubes/micron) SWCNTs are desired to present performance surpassing silicon-based devices and chips. Material preparation is the prerequisite of electronic applications. Selective synthesis, purification/sorting, and controlled assembling are procedures that associated with pathways to obtain SWCNT materials for high-performance electronics. However, it’s still not clear that what is the feasible strategy. More discussions and critical thinkings are in urgent need. I will try to review some of the recent developments in the field and discuss the possible directions in future study.
References:

A. D. Franklin. The road to carbon nanotube transistors. Nature 2013, 498, 443.

F. Yang, M. Wang, D. Zhang, J. Yang, M. Zheng, Y. Li. Chirality Pure Carbon Nanotubes: Growth, Sorting, and Characterization. Chemical Reviews 2020, 120 (5), 2693.

Y. Chen, M. Lyu, Z. Zhang, F Yang, Y. Li. Controlled preparation of single-walled carbon nanotubes as material for electronics. ACS Central Science 2022, 8, 1490.

A. D. Franklin, M. C. Hersam, H.-S. P. Wong. Carbon nanotube transistors: Making electronics from molecules. Science 2022, 378, 726.

Figure 1
(Invited) Diameter-Dependent Stacking of Squaraine Dye Molecules inside Chirality-Sorted Single-Wall Carbon Nanotubes
Authors: Wenseleers Wim , Forel Salome , van Bezouw Stein , Campo Jochen , Cambre Sofie , Li Han , Wieland Laura , Flavel Benjamin S 
Published: September 2023

Filling of single-wall carbon nanotubes (SWCNTs) with organic dye molecules is a promising strategy to add new functionalities, for instance by aligning dipolar dyes in a one-dimensional (1D) head-to-tail coupled chain to obtain a giant enhancement of their nonlinear optical response,[1] or by photo-sensitizing the tubes in new wavelength ranges by excitation energy transfer (EET) from the dye to the SWCNTs, useful for photo-conversion applications.[2] The 1D stacking of molecules inside SWCNTs modulates both the properties of the molecules and of the SWCNTs. We found that the EET of squaraine-dye-filled SWCNTs reveals a pronounced SWCNT-diameter-dependence of the dye absorption, indicating a diameter-dependent stacking. By performing IR fluorescence excitation spectroscopy on a range of chirality-enriched samples of dye-filled SWCNTs with different chirality distributions, each shifted dye absorption wavelength observed through the EET can be unambiguously assigned to a specific encapsulating SWCNT chirality.[3] This reveals a systematic trend with diameter that can be associated with the J-aggregate- and H-aggregate-like interactions expected in close-packed single- and double-file stackings, as corroborated by a simple geometric model, and enables tuning of the optical properties of the 1D molecular arrays through the selection of proper SWCNT diameters.
[1] S. Cambré, J. Campo, C. Beirnaert, C. Verlackt, P. Cool, W. Wenseleers, Nature Nanotechnol.
10(3) 248-252 (2015).
[2] S. van Bezouw, D.H. Arias, R. Ihly, S. Cambré, A.J. Ferguson, J. Campo, J.C. Johnson, J. Defillet, W. Wenseleers, J.L. Blackburn, ACS Nano
12(7) 6881-6894 (2018).
[3] S. Forel, H. Li, S. van Bezouw, J. Campo, L. Wieland, W. Wenseleers, B.S. Flavel, S. Cambré, Nanoscale
14, 8385-8397 (2022).
(Invited) Efficient Inner-to-Outer Wall Energy Transfer in Highly Pure Double-Wall Carbon Nanotubes Revealed by Detailed Spectroscopy
Authors: Cambre Sofie , Erkens Maksiem , Levshov Dmitry , Avramenko Marina , Forel Salome , Wenseleers Wim , Li Han , Flavel Benjamin S , Fagan Jeffrey , Popov Valentin , Flahaut Emmanuel 
Published: September 2023

The coaxial stacking of two single-wall carbon nanotubes (SWCNTs) into a double-wall carbon nanotube (DWCNT), forming a so-called one-dimensional van der Waals structure, leads to synergetic effects that dramatically affect the optical and electronic properties of both layers [1]. In this work, we explore these effects in purified DWCNT samples by combining absorption, wavelength-dependent infrared fluorescence−excitation (PLE), and wavelength-dependent resonant Raman scattering (RRS) spectroscopy. Purified DWCNTs are obtained by careful solubilization that strictly avoids ultrasonication [2] or by electronic-type sorting [3], both followed by a density gradient ultracentrifugation to remove unwanted SWCNTs that could obscure the DWCNT characterization [2]. Chirality-dependent shifts of the radial breathing mode vibrational frequencies and transition energies of the inner and outer DWCNT walls with respect to their SWCNT analogues are determined by advanced two-dimensional fitting of RRS and PLE data of DWCNT and their reference SWCNT samples. This exhaustive data set verifies that fluorescence from the inner DWCNT walls of well-purified samples is severely quenched, as previously evidenced in single-tube experiments [4]. Moreover, we find that this quenching occurs through efficient energy transfer from the inner to the outer DWCNT walls [5]. Combined analysis of the PLE and RRS results further reveals that this transfer is dependent on the inner and outer wall chirality, and we identify the specific combinations dominant in our DWCNT samples. These obtained results demonstrate the necessity and value of a combined structural characterization approach including PLE and RRS spectroscopy for bulk DWCNT samples.
[1] S. Cambré et al, Small 2021, 17, 2102585
[2] M. Erkens et al, Carbon 2021, 185, 113
[3] H. Li et al, Nature Nanotechnol. 2017, 12, 1176
[4] D. Levshov et al, Phys. Rev. B 2017, 96, 195410
[5] M. Erkens et al, ACS Nano 2022, 16, 16038