bluuebunny/crossref_metadata_2025 huggingface dataset:
Two new species of Eriophyidae from China (Acari: Eriophyoidea) with a list of bamboo-associated eriophyoid mites
Authors: Han Xiao , Chen Ri-Zhao , Hong Xiao-Yue
Published: August 2023

This paper presents a list of the species, the host plants and distribution of eriophyoid mites on bamboo in the world. Seventy-two eriophyoid species from 32 genera, associated with bamboo species from 13 genera, are listed. Twelve of the reported species belong to Diptilomiopidae and 60 to Eriophyidae. Two new species of eriophyoid mites on bamboo from Yunnan and Hunan Provinces of China are described and illustrated: Calacarus bambusis sp. nov. on Bambusa sp. (Poaceae) and Tetra tessella sp. nov. on Indocalamus tessellatus (Munro) Keng f. (Poaceae). Both species are vagrants on leaf surfaces, causing no apparent damage.
Inconsistent Effect of Psychometric-Scale Familiarization on the Relationship Between Ratings of Perceived Exertion and External Load Measures in Elite Youth Soccer Players
Authors: Kyprianou Efthymios , Lolli Lorenzo , Weston Matthew , Gregson Warren
Published: August 2023

Objectives: To examine the moderating effect of familiarization on the relationship between external load and ratings of perceived exertion (RPEs) in elite youth soccer players. Methods: Thirty-five elite male youth soccer players were monitored over a 31-week period. Players had no previous experience using the centiMax scale (arbitrary units [AU]). The final sample included familiarized (blackness test; n = 20) and nonfamiliarized players (n = 15) with the Borg centiMax scale. Players recorded a global RPE and differential RPEs (dRPE) for breathlessness (RPE-B) and leg-muscle exertion (RPE-L) 15 to 30 minutes following training sessions and competitive matches. Separate multivariable-adjusted random-effects generalized additive models with restricted maximum likelihood quantified familiarization versus no-familiarization differences in actual perceived exertion score (in AU) by number of accelerations, decelerations, and high-speed running distance (in meters) as predictor variables, respectively. Results: Players improved their blackness test score from 39% to 78%. For explorations by number of accelerations, familiarization effects were not practically relevant for the RPE and RPE-B variables. The width and sign of the effects for the RPE-L variable at 30 efforts of 10 AU (95% CI, 4–16 AU) suggested that scores were lower for players who underwent familiarization versus players who did not. Familiarization effects were not practically relevant for any RPE variable irrespective of the number of deceleration efforts and high-speed running distance covered. Conclusion: Improved performance on the blackness test did not have a moderating effect on the relationship between proxy measures of external load and RPEs.
Evaluation of Within- and Between-Site Agreement for Direct Observation of Physical Behavior Across Four Research Groups
Authors: Keadle Sarah Kozey , Martinez Julian , Strath Scott J. , Sirard John , John Dinesh , Intille Stephen , Arguello Diego , Amalbert-Birriel Marcos , Barnett Rachel , Thapa-Chhetry Binod , Cox Melanna , Chase John , Dooley Erin , Marcotte Rob , Tolas Alexander , Staudemayer John W.
Published: August 2023

Direct observation (DO) is a widely accepted ground-truth measure, but the field lacks standard operational definitions. Research groups develop project-specific annotation platforms, limiting the utility of DO if labels are not consistent. Purpose: The purpose was to evaluate within- and between-site agreement for DO taxonomies (e.g., activity intensity category) across four independent research groups who have used video-recorded DO. Methods: Each site contributed video files (508 min) and had two trained research assistants annotate the shared video files according to their existing annotation protocols. The authors calculated (a) within-site agreement for the two coders at the same site expressed as intraclass correlation and (b) between-site agreement, the proportion of seconds that agree between any two coders regardless of site. Results: Within-site agreement at all sites was good–excellent for both activity intensity categories (intraclass correlation range: .82–.9) and posture/whole-body movement (intraclass correlation range: .77–.98). Between-site agreement for intensity categories was 94.6% for sedentary, 80.9% for light, and 82.8% for moderate–vigorous. Three of the four sites had common labels for eight posture/whole-body movements and had within-site agreements of 94.5% and between-site agreements of 86.1%. Conclusions: Distinct research groups can annotate key features of physical behavior with good-to-excellent interrater reliability. Operational definitions are provided for core metrics for researchers to consider in future studies to facilitate between-study comparisons and data pooling, enabling the deployment of deep learning approaches to wearable device algorithm calibration.
Daily Activity of Individuals With an Amputation Above the Knee as Recorded From the Nonamputated Limb and the Prosthetic Limb
Authors: Hagberg Kerstin , Zügner Roland , Thomsen Peter , Tranberg Roy
Published: August 2023

Introduction: Mobility restriction following limb loss might lead to a sedentary lifestyle, impacting health. Daily activity monitoring of amputees has focused on prosthetic steps, neglecting overall activity. Purpose: To assess daily activity in individuals with an established amputation and to explore the amount of activity recorded from the prosthesis as compared to the overall activity. Methods: Individuals with a unilateral transfemoral amputation or knee disarticulation who had used a prosthesis in daily life for >1 year and could walk 100 m (unsupported or single aided) were recruited. Descriptive information and prosthetic mobility were collected. Two activPAL™ accelerometers were attached to the nonamputated thigh and the prosthesis, respectively. The mean daily activity over 7 days was compared between the nonamputated limb and the prosthesis. Results: Thirty-nine participants (22 men/17 women; mean age 54 [14.5] years) with amputation mainly due to trauma (59%) or tumor (28%) were included. Overall, participants took 6,125 steps and spent 10.2 hr sedentary, 5.0 hr upright, and 8.7 hr laying per day. Compared to recordings from the nonamputated limb, 85% of sit-to-stand transitions (32/38), 73% of steps (4,449/6,125), and 68% of walking time (1.0/1.5 hr) were recorded from the prosthesis. Recordings seemed to be less adequate for incidental prosthetic steps than for walks. Conclusions: Sedentary behavior accounted for most of the day demonstrating the importance to encourage physical activity among established prosthetic users. The prosthesis is used for daily activity to a great extent. However, noted pitfalls in the recordings call for further refinement of the measurements.
Evolution of a fatty acyl–CoA elongase underlies desert adaptation in
Drosophila
Authors: Wang Zinan , Pu Jian , Richards Cole , Giannetti Elaina , Cong Haosu , Lin Zhenguo , Chung Henry
Published: August 2023

Traits that allow species to survive in extreme environments such as hot-arid deserts have independently evolved in multiple taxa. However, the genetic and evolutionary mechanisms underlying these traits have thus far not been elucidated. Here, we show that
Drosophila mojavensis
, a desert-adapted fruit fly species, has evolved high desiccation resistance by producing long-chain methyl-branched cuticular hydrocarbons (mbCHCs) that contribute to a cuticular lipid layer reducing water loss. We show that the ability to synthesize these longer mbCHCs is due to evolutionary changes in a fatty acyl–CoA elongase (
mElo
).
mElo
knockout in
D. mojavensis
led to loss of longer mbCHCs and reduction of desiccation resistance at high temperatures but did not affect mortality at either high temperatures or desiccating conditions individually. Phylogenetic analysis showed that
mElo
is a
Drosophila
-specific gene, suggesting that while the physiological mechanisms underlying desert adaptation may be similar between species, the genes involved in these mechanisms may be species or lineage specific.
Lattice engineering for stabilized black FAPbI
3
perovskite single crystals for high-resolution x-ray imaging at the lowest dose
Authors: Chu Depeng , Jia Binxia , Liu Naiming , Zhang Yunxia , Li Xiaotong , Feng Jiangshan , Pi Jiacheng , Yang Zhou , Zhao Guangtao , Liu Yucheng , Liu Shengzhong (Frank) , Park Nam-Gyu
Published: August 2023

Preliminary theoretical analyses indicate that lattice relaxation may be used to release lattice strain in the FAPbI
3
perovskite to warrant both high x-ray detection performance and improved stability. Herein, we demonstrate stable black α-phase FAPbI
3
single crystals (SCs) realized by lattice engineering via annealing in the ambient atmosphere. The engineered α-FAPbI
3
SC detector shows almost all the best figures of merit including a high sensitivity of 4.15 × 10
5
μC Gy
air
−1
cm
−2
, a low detection limit of 1.1 nGy
air
s
−1
, a high resolution of 15.9 lp mm
−1
, and a short response time of 214 μs. We further demonstrate high-definition x-ray imaging at a dose rate below 10 nGy
air
s
−1
on the FAPbI
3
SC, indicating a minimal dose-area product of 0.048 mGy
air
cm
2
to the patient for one-time posteroanterior chest diagnosis, which is more than 3000 times lower than the international reference level of 150 mGy
air
cm
2
. In addition, the robust long-term stability enables the FAPbI
3
SC x-ray detector to work steadily for more than 40 years.
Structures of wild-type and selected CMT1X mutant connexin 32 gap junction channels and hemichannels
Authors: Qi Chao , Lavriha Pia , Bayraktar Erva , Vaithia Anand , Schuster Dina , Pannella Micaela , Sala Valentina , Picotti Paola , Bortolozzi Mario , Korkhov Volodymyr M.
Published: August 2023

In myelinating Schwann cells, connection between myelin layers is mediated by gap junction channels (GJCs) formed by docked connexin 32 (Cx32) hemichannels (HCs). Mutations in Cx32 cause the X-linked Charcot-Marie-Tooth disease (CMT1X), a degenerative neuropathy without a cure. A molecular link between Cx32 dysfunction and CMT1X pathogenesis is still missing. Here, we describe the high-resolution cryo-electron microscopy (cryo-EM) structures of the Cx32 GJC and HC, along with two CMT1X-linked mutants, W3S and R22G. While the structures of wild-type and mutant GJCs are virtually identical, the HCs show a major difference: In the W3S and R22G mutant HCs, the amino-terminal gating helix partially occludes the pore, consistent with a diminished HC activity. Our results suggest that HC dysfunction may be involved in the pathogenesis of CMT1X.
Influence of nuclear dynamics on molecular attosecond photoelectron interferometry
Authors: Ertel Dominik , Busto David , Makos Ioannis , Schmoll Marvin , Benda Jakub , Ahmadi Hamed , Moioli Matteo , Frassetto Fabio , Poletto Luca , Schröter Claus Dieter , Pfeifer Thomas , Moshammer Robert , Mašín Zdeněk , Patchkovskii Serguei , Sansone Giuseppe
Published: August 2023

In extreme ultraviolet spectroscopy, the photoionization process occurring in a molecule due to the absorption of a single photon can trigger an ultrafast nuclear motion in the cation. Taking advantage of attosecond photoelectron interferometry, where the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional infrared quantum of light, one can investigate the influence of nuclear dynamics by monitoring the characteristics of the photoelectron spectra generated by the two-color field. Here, we show that attosecond photoelectron interferometry is sensitive to the nuclear response by measuring the two-color photoionization spectra in a mixture of methane (CH
4
) and deuteromethane (CD
4
). The effect of the different nuclear evolution in the two isotopologues manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks. Our work indicates that nuclear dynamics can affect the coherence properties of the electronic wave packet emitted by photoionization on a time scale as short as a few femtoseconds.
Leaf metabolic traits reveal hidden dimensions of plant form and function
Authors: Walker Tom W. N. , Schrodt Franziska , Allard Pierre-Marie , Defossez Emmanuel , Jassey Vincent E. J. , Schuman Meredith C. , Alexander Jake M. , Baines Oliver , Baldy Virginie , Bardgett Richard D. , Capdevila Pol , Coley Phyllis D. , van Dam Nicole M. , David Bruno , Descombes Patrice , Endara María-José , Fernandez Catherine , Forrister Dale , Gargallo-Garriga Albert , Glauser Gaëtan , Marr Sue , Neumann Steffen , Pellissier Loïc , Peters Kristian , Rasmann Sergio , Roessner Ute , Salguero-Gómez Roberto , Sardans Jordi , Weckwerth Wolfram , Wolfender Jean-Luc , Peñuelas Josep
Published: August 2023

The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functional traits reveals that plants vary on two major axes of leaf metabolic specialization—a leaf chemical defense spectrum and an expression of leaf longevity. Axes are similar for tropical and temperate species, with many trait combinations being viable. However, metabolic traits vary orthogonally to life-history strategies described by widely used functional traits. The metabolome thus expands the functional trait concept by providing additional axes of metabolic specialization for examining plant form and function.
Human cerebrospinal fluid contains diverse lipoprotein subspecies enriched in proteins implicated in central nervous system health
Authors: Merrill Nathaniel J. , Davidson W. Sean , He Yi , Díaz Ludovico Ivo , Sarkar Snigdha , Berger Madelyn R. , McDermott Jason E. , Van Eldik Linda J. , Wilcock Donna M. , Monroe Matthew E. , Kyle Jennifer E. , Bruce Kimberley D. , Heinecke Jay W. , Vaisar Tomas , Raber Jacob , Quinn Joseph F. , Melchior John T.
Published: August 2023

Lipoproteins in cerebrospinal fluid (CSF) of the central nervous system (CNS) resemble plasma high-density lipoproteins (HDLs), which are a compositionally and structurally diverse spectrum of nanoparticles with pleiotropic functionality. Whether CSF lipoproteins (CSF-Lps) exhibit similar heterogeneity is poorly understood because they are present at 100-fold lower concentrations than plasma HDL. To investigate the diversity of CSF-Lps, we developed a sensitive fluorescent technology to characterize lipoprotein subspecies in small volumes of human CSF. We identified 10 distinctly sized populations of CSF-Lps, most of which were larger than plasma HDL. Mass spectrometric analysis identified 303 proteins across the populations, over half of which have not been reported in plasma HDL. Computational analysis revealed that CSF-Lps are enriched in proteins important for wound healing, inflammation, immune response, and both neuron generation and development. Network analysis indicated that different subpopulations of CSF-Lps contain unique combinations of these proteins. Our study demonstrates that CSF-Lp subspecies likely exist that contain compositional signatures related to CNS health.
Increasing the payload capacity of soft robot arms by localized stiffening
Authors: Bruder Daniel , Graule Moritz A. , Teeple Clark B. , Wood Robert J.
Published: August 2023

Soft robot arms offer safety and adaptability due to their passive compliance, but this compliance typically limits their payload capacity and prevents them from performing many tasks. This paper presents a model-based design approach to effectively increase the payload capacity of soft robot arms. The proposed approach uses localized body stiffening to decrease the compliance at the end effector without sacrificing the robot’s range of motion. This approach is validated on both a simulated and a real soft robot arm, where experiments show that increasing the stiffness of localized regions of their bodies reduces the compliance at the end effector and increases the height to which the arm can lift a payload. By increasing the payload capacity of soft robot arms, this approach has the potential to improve their efficacy in a variety of tasks including object manipulation and exploration of cluttered environments.
Farnesol prevents aging-related muscle weakness in mice through enhanced farnesylation of Parkin-interacting substrate
Authors: Bae Ju-Hyeon , Jo Areum , Cho Sung Chun , Lee Yun-Il , Kam Tae-In , You Chang-Lim , Jeong Hyeon-Ju , Kim Hyebeen , Jeong Myong-Ho , Jeong Yideul , Ha Young Wan , Kim Yu Seon , Kim Jiwoon , Woo Seung-Hwa , Kim Minseok S. , Shin Eui Seok , Song Sang Ok , Kang Hojin , Khang Rin , Park Soojeong , Park Joobae , Dawson Valina L. , Dawson Ted M. , Park Sang Chul , Shin Joo-Ho , Kang Jong-Sun
Published: August 2023

Peroxisome proliferator–activated receptor-γ coactivator-1α (PGC-1α) is a master regulator of mitochondrial biogenesis. Reduced PGC-1α abundance is linked to skeletal muscle weakness in aging or pathological conditions, such as neurodegenerative diseases and diabetes; thus, elevating PGC-1α abundance might be a promising strategy to treat muscle aging. Here, we performed high-throughput screening and identified a natural compound, farnesol, as a potent inducer of PGC-1α. Farnesol administration enhanced oxidative muscle capacity and muscle strength, leading to metabolic rejuvenation in aged mice. Moreover, farnesol treatment accelerated the recovery of muscle injury associated with enhanced muscle stem cell function. The protein expression of Parkin-interacting substrate (PARIS/
Zfp746
), a transcriptional repressor of PGC-1α, was elevated in aged muscles, likely contributing to PGC-1α reduction. The beneficial effect of farnesol on aged muscle was mediated through enhanced PARIS farnesylation, thereby relieving PARIS-mediated PGC-1α suppression. Furthermore, short-term exercise increased PARIS farnesylation in the muscles of young and aged mice, whereas long-term exercise decreased PARIS expression in the muscles of aged mice, leading to the elevation of PGC-1α. Collectively, the current study demonstrated that the PARIS–PGC-1α pathway is linked to muscle aging and that farnesol treatment can restore muscle functionality in aged mice through increased farnesylation of PARIS.
Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion
Authors: Mirzakhanyan Yeva , Jankevics Andris , Scheltema Richard A. , Gershon Paul David
Published: August 2023

Vaccinia virus, the prototypical poxvirus and smallpox/monkeypox vaccine, has proven a challenging entity for structural biology, defying many of the approaches leading to molecular and atomic models for other viruses. Via a combination of deep learning and cross-linking mass spectrometry, we have developed an atomic-level model and an integrated processing/assembly pathway for a structural component of the vaccinia virion, protein P4a. Within the pathway, proteolytic separation of the C-terminal P4a-3 segment of P4a triggers a massive conformational rotation within the N-terminal P4a-1 segment that becomes fixed by disulfide-locking while removing a steric block to trimerization of the processing intermediate P4a-1+2. These events trigger the proteolytic separation of P4a-2, allowing the assembly of P4a-1 into a hexagonal lattice that encloses the nascent virion core.

IMPORTANCE

An outstanding problem in the understanding of poxvirus biology is the molecular structure of the mature virion. Via deep learning methods combined with chemical cross-linking mass spectrometry, we have addressed the structure and assembly pathway of P4a, a key poxvirus virion core component.
Selection for oligotrophy among bacteria inhabiting host microbiomes
Authors: Jackrel Sara L. , White Jeffrey D. , Perez-Coronel Elisabet , Koch Ryan Y.
Published: August 2023

Host microbiomes are important regulators of organismal fitness, physiology, and ecology. Microbiomes promote the fitness of their host in part by buffering the host from the full effects of fluctuating conditions and stressors imposed by the external environment. Whether the host conversely serves as a buffer for their associated microbes against variation in the external environment is less clear. Here, we test if bacteria inhabiting the microbiome of a host are locally adapted to nutrient levels in their surrounding external environment. We used a system in which the host, the phytoplankter
Microcystis aeruginosa
, has strains that are locally adapted to low-nutrient versus high-nutrient lakes. Assessing 40 metagenome-assembled genomes belonging to four taxonomic groups of heterotrophic bacteria residing within the host microbiome, we found consistent phylogenetic divergence between strains originating from low-nutrient versus high-nutrient environments. Bacteria found in association with low-nutrient host genotypes obtained from low-nutrient lakes demonstrated genome streamlining, including reduced genome size and fewer sigma factors. These bacterial genomes have features that would facilitate survival in low-nutrient lakes, including (i) greater number of alkaline phosphatase genes that are essential for phosphorus acquisition and (ii) positive selection within genes involved in phosphorus metabolism. Overall, our results demonstrate that despite living in close association with host organisms, bacteria residing within microbiomes may have evolved and undergone environmental selection to stressors external to their host, demonstrating similar patterns of adaptation to those that might be expected to develop among free-living bacteria.

IMPORTANCE

Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.
Rapid and strain-specific resistance evolution of
Staphylococcus aureus
against inhibitory molecules secreted by
Pseudomonas aeruginosa
Authors: Niggli Selina , Schwyter Lukas , Poveda Lucy , Grossmann Jonas , Kümmerli Rolf
Published: August 2023

Pseudomonas aeruginosa
and
Staphylococcus aureus
frequently occur together in polymicrobial infections, and there is evidence that their interactions negatively affect disease outcome in patients. At the molecular level, interactions between the two bacterial species are well-described, with
P. aeruginosa
usually being the dominant species suppressing
S. aureus
through a variety of inhibitory molecules. However, in chronic infections the two species interact over prolonged periods of time, and
S. aureus
might be able to evolve resistance against inhibitory molecules deployed by
P. aeruginosa
. Here, we used experimental evolution to test this hypothesis by exposing three different
S. aureus
strains (Cowan I, 6850, and JE2) to the growth-inhibitory supernatant of
P. aeruginosa
PAO1 over 30 days. Prior to evolution, we found that
S. aureus
strains were inhibited by secreted compounds regulatorily controlled by the
Pseudomonas
quinolone signal quorum-sensing system. Following evolution, inhibitory effects were significantly attenuated, and we observed that adaptations were
S. aureus
strain specific and involved the upregulation of virulence traits such as staphyloxanthin production and the formation of small colony variants. At the genetic level, mutations in membrane transporters (known to be involved in antibacterial uptake) were the most frequent evolutionary targets. Our work indicates that adaptations of
S. aureus
to
P. aeruginosa
occurs rapidly and affect both virulence trait expression and membrane transporter functionality. Thus, pathogen evolution could promote species co-existence and complicate treatment options in infections.

IMPORTANCE

Polymicrobial infections are common. In chronic infections, the different pathogens may repeatedly interact, which could spur evolutionary dynamics with pathogens adapting to one another. Here, we explore the potential of
Staphylococcus aureus
to adapt to its competitor
Pseudomonas aeruginosa
. These two pathogens frequently co-occur, and
P. aeruginosa
is seen as the dominant species being able to displace
S. aureus
. We studied three different
S. aureus
strains and found that all became quickly resistant to inhibitory compounds secreted by
P. aeruginosa
. Our experimental evolution revealed strains-specific adaptations with three main factors contributing to resistance evolution: (i) overproduction of staphyloxanthin, a molecule protecting from oxidative stress; (ii) the formation of small colony variants also protecting from oxidative stress; and (iii) alterations of membrane transporters possibly reducing toxin uptake. Our results show that species interactions can change over time potentially favoring species co-existence, which in turn could affect disease progression and treatment options.
Spontaneous mutational patterns and novel mutations for bedaquiline and clofazimine resistance in
Mycobacterium tuberculosis
Authors: Shi Jin , Liu Yuanyuan , Wu Tuoya , Li Lu , Han Shujing , Peng Xiao , Shang Yuanyuan , Guo Yongli , Pang Yu , Gao Mengqiu , Lu Jie
Published: August 2023

The 2022 World Health Organization guidelines recommend use of two core anti-tuberculosis (TB) drugs, bedaquiline (BDQ) and clofazimine (CFZ), for treatment of drug-resistant (DR)-TB. However, several mutated
Mycobacterium tuberculosis
(MTB) genes, conferring BDQ and CFZ resistance, have been reported that predominantly arose from sporadic mutations that have not been comprehensively characterized. Herein, MTB clinical isolates collected from drug-susceptible (DS)-, multidrug-resistant (MDR)-, and extensively drug-resistant (XDR)-TB patients were cultured
in vitro
with BDQ or CFZ to generate progeny strains with resistance to these drugs. Progeny strains exposed to CFZ exhibited increased CFZ minimum inhibitory concentrations (MICs) that exceeded MIC increases of BDQ-exposed progeny strains. Notably,
mmpR
and
pepQ
mutations accounted for 83% and 17% of BDQ-induced spontaneous gene mutations, respectively, and 86% and 14% of CFZ-induced spontaneous gene mutations, respectively. Analyses of predicted mutation-induced changes in amino acid sequences and structures of MmpR and PepQ mutants revealed several point mutations affected sequence conversation and functionality as an underlying mechanism for observed acquired BDQ/CFZ resistance. Moreover, our results revealed differences in patterns of BDQ- and CFZ-induced acquired spontaneous mutations that may enhance our understanding of MTB BDQ/CFZ-resistance mechanisms.

IMPORTANCE

This study of MTB drug resistance mechanisms revealed patterns of spontaneous MTB mutations associated with acquired BDQ and CFZ resistance that arose after clinical MTB isolates were cultured
in vitro
with BDQ or CFZ. Results of protein sequence and structural analyses provided insights into potential mechanisms underlying associations between MTB gene mutations and DR phenotypes. Taken together, these results revealed differences in acquired BDQ and CFZ resistance mechanisms as a new perspective that may enhance our understanding of BDQ/CFZ resistance mechanisms and facilitate the development of new methods for detecting MTB drug resistance genes.
Staphylococcus aureus
susceptibility to complestatin and corbomycin depends on the VraSR two-component system
Authors: Gómez-Arrebola Carmen , Hernandez Sara B. , Culp Elizabeth J. , Wright Gerard D. , Solano Cristina , Cava Felipe , Lasa Iñigo
Published: August 2023

The overuse of antibiotics in humans and livestock has driven the emergence and spread of antimicrobial resistance and has therefore prompted research on the discovery of novel antibiotics. Complestatin (Cm) and corbomycin (Cb) are glycopeptide antibiotics with an unprecedented mechanism of action that is active even against methicillin-resistant and daptomycin-resistant
Staphylococcus aureus
. They bind to peptidoglycan and block the activity of peptidoglycan hydrolases required for remodeling the cell wall during growth. Bacterial signaling through two-component transduction systems (TCSs) has been associated with the development of
S. aureus
antimicrobial resistance. However, the role of TCSs in
S. aureus
susceptibility to Cm and Cb has not been previously addressed. In this study, we determined that, among all 16
S. aureus
TCSs, VraSR is the only one controlling the susceptibility to Cm and Cb. Deletion of
vraSR
increased bacterial susceptibility to both antibiotics. Epistasis analysis with members of the vraSR regulon revealed that deletion of spdC, which encodes a membrane protein that scaffolds SagB for cleavage of peptidoglycan strands to achieve physiological length, in the vraSR mutant restored Cm and Cb susceptibility to wild-type levels. Moreover, deletion of either
spdC
or
sagB
in the wild-type strain increased resistance to both antibiotics. Further analyses revealed a significant rise in the relative amount of peptidoglycan and its total degree of cross-linkage in
ΔspdC
and
ΔsagB
mutants compared to the wild-type strain, suggesting that these changes in the cell wall provide resistance to the damaging effect of Cm and Cb.

IMPORTANCE

Although
Staphylococcus aureus
is a common colonizer of the skin and digestive tract of humans and many animals, it is also a versatile pathogen responsible for causing a wide variety and number of infections. Treatment of these infections requires the bacteria to be constantly exposed to antibiotic treatment, which facilitates the selection of antibiotic-resistant strains. The development of new antibiotics is, therefore, urgently needed. In this paper, we investigated the role of the sensory system of
S. aureus
in susceptibility to two new antibiotics: corbomycin and complestatin. The results shed light on the cell-wall synthesis processes that are affected by the presence of the antibiotic and the sensory system responsible for coordinating their activity.
A type I-F CRISPRi system unveils the novel role of CzcR in modulating multidrug resistance of
Pseudomonas aeruginosa
Authors: Chen Shuzhen , Cao Huiluo , Xu Zirui , Huang Jiahui , Liu Zhiqing , Li Ting , Duan Cheng , Wu Weiyan , Wen Yongqi , Zhang Lian-Hui , Xu Zeling
Published: August 2023

Pseudomonas aeruginosa
has abundant signaling systems that exquisitely control its antibiotic resistance in response to different environmental cues. Understanding the regulation of antibiotic resistance will provide important implications for precise antimicrobial interventions. However, efficient genetic tools for functional gene characterizations are sometimes not available, particularly, in clinically isolated strains. Here, we established a type I-F CRISPRi (CSYi) system for programmable gene silencing. By incorporating anti-CRISPR proteins, this system was even applicable to bacterial hosts encoding a native type I-F CRISPR-Cas system. With the newly developed gene-silencing system, we revealed that the response regulator CzcR from the zinc (Zn
2+
)-responsive two-component system CzcS/CzcR is a repressor of efflux pumps MexAB-OprM and MexGHI-OpmD, which inhibits the expression of both operons by directly interacting with their promoters. Repression of MexAB-OprM consequently increases the susceptibility of
P. aeruginosa
to multiple antibiotics such as levofloxacin and amikacin. Together, this study provided a simple approach to study gene functions, which enabled us to unveil the novel role of CzcR in modulating efflux pump genes and multidrug resistance in
P. aeruginosa
.

IMPORTANCE

P. aeruginosa
is a ubiquitous opportunistic pathogen frequently causing chronic infections. In addition to being an important model organism for antibiotic-resistant research, this species is also important for understanding and exploiting CRISPR-Cas systems. In this study, we established a gene-silencing system based on the most abundant type I-F CRISPR-Cas system in this species, which can be readily employed to achieve targeted gene repression in multiple bacterial species. Using this gene-silencing system, the physiological role of Zn
2+
and its responsive regulator CzcR in modulating multidrug resistance was unveiled with great convenience. This study not only displayed a new framework to expand the abundant CRISPR-Cas and anti-CRISPR systems for functional gene characterizations but also provided new insights into the regulation of multidrug resistance in
P. aeruginosa
and important clues for precise anti-pseudomonal therapies.
The IQ-1S JNK (c-Jun N-Terminal Kinase) Inhibitor Suppresses Premature Aging of OXYS Rat Brain
Authors: Zhdankina A. A. , Osipenko A. N. , Tikhonov D. I. , Logvinov S. V. , Plotnikov M. B. , Khlebnikov A. I. , Kolosova N. G.
Published: August 2023

Abstract—According to the Alzheimer’s Disease International (ADI) international organization about 50 million people in the world suffer from Alzheimer’s disease (AD). However, there are no effective methods for preventing or slowing the progression of AD. Inhibition of the c-Jun N-terminal kinase (JNK) signaling pathway is discussed below as an alternative way to prevent the development of AD and other neurodegenerative diseases. In the present study, we evaluated the ability of a recently synthesized selective JNK3 inhibitor, 11H-indeno[1,2-b]quinoxalin-11-one oxime sodium salt (IQ-1S), to suppress neurodegenerative processes in OXYS rats at an early stage of development of AD at the ages of 4.5 to 6 months. Treatment with IQ-1S (50 mg/kg intragastrically) led to the suppression of the development of neurodegenerative processes in the cerebral cortex of OXYS rats: an increase in the proportion of unchanged neurons, a decrease in the proportion of neurons with signs of destruction and irreversible damage, and a normalization of the glioneuronal index, which was facilitated by a decrease in the severity of hyperviscosity syndrome blood in OXYS rats. The use of the IQ-1S JNK3 inhibitor may be a promising strategy for the prevention of early neurodegenerative disorders and, possibly, the treatment of AD.
Castleman disease masquerading as a paraganglioma showing uptake on DOTATATE PET
Authors: Sachan Ankit , Singh Prashant , Kaushal Seema , Kumar Rajeev
Published: August 2023

A man in his 50s presented with shortness of breath and was found to have a large paracaval mass, which on further evaluation with CT, showed a large heterogeneously enhancing mass lesion adjacent to right renal hilum. His 24-hour urinary metanephrines and nor-metanephrines were normal. In view of location and features on CT, paraganglioma was considered as a possibility. A68Ga-DOTATATE positron emission tomography/CT demonstrated avidity in the lesion with maximum standardised uptake value of 16.5. He underwent right laparoscopic converted to open mass excision along with nephrectomy. Histopathological examination was suggestive of hyaline vascular Castleman disease.
Piloting a new method to estimate action thresholds in medicine through intuitive weighing
Authors: Jacobs Bart K M , Keter Alfred Kipyegon , Henriquez-Trujillo Aquiles Rodrigo , Trinchan Paco , de Rooij Madeleine L , Decroo Tom , Lynen Lutgarde
Published: August 2023

Objectives

In clinical decision-making, physicians take actions such as prescribing treatment only when the probability of disease is sufficiently high. The lowest probability at which the action will be considered, is the action threshold. Such thresholds play an important role whenever decisions have to be taken under uncertainty. However, while several methods to estimate action thresholds exist, few methods give satisfactory results or have been adopted in clinical practice. We piloted the adapted nominal group technique (aNGT), a new prescriptive method based on a formal consensus technique adapted for use in clinical decision-making.

Design, setting and participants

We applied this method in groups of postgraduate students using three scenarios: treat for rifampicin-resistant tuberculosis (RR-TB), switch to second-line HIV treatment and isolate for SARS-CoV-2 infection.

Interventions

The participants first summarise all harms of wrongly taking action when none is required and wrongly not taking action when it would have been useful. Then they rate the statements on these harms, discuss their importance in the decision-making process, and finally weigh the statements against each other.

Main outcome measures

The resulting consensus threshold is estimated as the relative weights of the harms of the false positives divided by the total harm, and averaged out over participants. In some applications, the thresholds are compared with an existing method based on clinical vignettes.

Results

The resulting action thresholds were just over 50% for RR-TB treatment, between 20% and 50% for switching HIV treatment and 43% for COVID-19 isolation. These results were considered acceptable to all participants. Between sessions variation was low for RR-TB and moderate for HIV. Threshold estimates were moderately lower with the method based on clinical vignettes.

Conclusions

The aNGT gives sensible results in our pilot and has the potential to estimate action thresholds, in an efficient manner, while involving all relevant stakeholders. Further research is needed to study the value of the method in clinical decision-making and its ability to generate acceptable thresholds that stakeholders can agree on.
Expansion of non-invasive prenatal screening to the screening of 10 types of chromosomal anomalies: a cost-effectiveness analysis
Authors: Soukkhaphone Bounhome , Baradaran Mohammad , Nguyen Ba Diep , Nshimyumukiza Leon , Little Julian , Rousseau Francois , Audibert Francois , Langlois Sylvie , Reinharz Daniel
Published: August 2023

Objectives

To determine the cost-effectiveness of the addition of chromosomal anomalies detectable by non-invasive prenatal screening (NIPS), in a prenatal screening programme targeting common aneuploidies.

Design, setting and participants

A simulation study was conducted to study the addition of chromosomal anomalies detectable by NIPS (sex chromosome aneuploidies, 22q11.2 deletion syndrome, large deletion/duplication >7 Mb and rare autosomal trisomies) to five basic strategies currently aiming the common trisomies: three strategies currently offered by the public healthcare systems in Canada, whose first-tier test is performed with biochemical markers, and two programmes whose first-tier test consists of NIPS-based methods.

Outcome measures

The total number of cases of chromosomal anomalies detected and the costs related to the consumption of medical services.

Results

The most effective and the most cost-effective option in almost all prenatal screening strategies is the option that includes all targeted additional conditions. In the strategies where NIPS is used as first-tier testing, the cost per additional case detected by adding all possible additional anomalies to a programme that currently targets only common trisomies is $C25 710 (95% CI $C25 489 to $C25 934) for massively parallel shotgun sequencing and $C57 711 (95% CI $C57 141 to $C58 292) for targeted massively parallel sequencing, respectively. The acceptability curves show that at a willingness-to-pay of $C50 000 per one additional case detected, the expansion of NIPS-based methods for the detection of all possible additional conditions has a 90% probability of being cost-effective.

Conclusion

From an economic perspective, in strategies that use NIPS as a first-tier screening test, expanding the programmes to detect any considered chromosomal anomalies other than the three common trisomies would be cost-effective. However, the potential expansion of prenatal screening programmes also requires consideration of societal issues, including ethical ones.
Prognostic factors associated with failure of total elbow replacement: a protocol for a systematic review
Authors: Hamoodi Zaid , Gehringer Celina K , Bull Lucy M , Hughes Tom , Kearsley-Fleet Lianne , Sergeant Jamie C , Watts Adam C
Published: August 2023

Introduction

Total elbow replacement (TER) has higher failure rates requiring revision surgery compared with the replacement of other joints. Understanding the factors associated with failure is essential for informed decision-making between patients and clinicians, and for reducing the failure rate. This review aims to identify, describe and appraise the literature examining prognostic factors for failure of TER.

Methods and analysis

This systematic review will be conducted and reported in line with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols guidelines. Electronic literature searches will be conducted using Medline, EMBASE, PubMed and Cochrane. The search strategy will be broad, including a combination of subject headings (MESH) and free text search. This search will be supplemented with a screening of reference lists of the included studies and relevant reviews. Two independent reviewers will screen all search results in two stages (title and abstract, and full text) based on the Population, Index prognostic factor, Comparator prognostic factor, Outcome, Time and Setting criteria. The types of evidence included will be randomised trials, non-randomised trials, prospective and retrospective cohort studies, registry studies and case–control studies. If the literature lacks enough studies, then case series with 50 or more TERs will be considered for inclusion. Data extraction and risk of bias assessment for included studies will be performed by two independent reviewers using the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies for Prognostic Factors and Quality In Prognostic Studies tools.

Meta-analyses of prognostic estimates for each factor will be undertaken for studies that are deemed to be sufficiently robust and comparable. Several challenges are likely to arise due to heterogeneity between studies, therefore, subgroup and sensitivity analyses will be performed to account for the differences between studies. Heterogeneity will be assessed using Q and I2statistics. If I2>40% then pooled estimates will not be reported. When quantitative synthesis is not possible, a narrative synthesis will be undertaken. The quality of the evidence for each prognostic factor will be assessed using the Grades of Recommendation Assessment, Development and Evaluation tool.

PROSPERO registration number

CRD42023384756.
Gender-based discrimination and son preference in Punjabi-Canadian families: a community-based participatory qualitative research study
Authors: Wanigaratne Susitha , Januwalla Alia , Bhangu Manvir , Uppal Pamela , Kumar-Ratta Amrita , Brar Amanpreet , Dennis Cindy-Lee , Urquia Marcelo
Published: August 2023

Objectives

To conduct a qualitative study, guided by the principles of community-based participatory research, with the following objectives: (1) to provide a conceptual framework describing the drivers of son preference; (2) to understand experiences of son preference among Punjabi-Canadians and (3) with this understanding, identify and co-design an appropriate educational tool.

Design, setting, participants, methods

Qualitative study consisting of four bilingual (Punjabi and English) focus group discussions with 11 mothers, 4 fathers and 17 grandmothers in Toronto and Brampton, Canada. Participants were queried about experiences and perspectives related to reproductive decision-making, gender equity and son preference, and for appropriate approaches to reducing inequities. Transcripts were simultaneously translated and written in English and thematic analysis was conducted. An infoposter was identified as a feasible educational tool and was co-designed by researchers and community partners.

Results

Participants identified patrilocality (ie, married sons reside with parents, married daughters with in-laws) and patrilineality (ie, sons inherit assets, daughters’ husband receives a dowry) as structural precursors to proximal drivers (ie, old-age security) of son preference. Mothers’ and grandmothers’ value to their families depended strongly on having a son but did not guarantee security. Pressures (ie, internalised discrimination, reproductive coercion) to conceive a son were common after the birth of at least one daughter in the absence of sons. Participants did not know anyone who had a sex selective abortion in Canada; however, traditional sex selection methods (eg, herbal medicines) were mentioned. Our co-designed infoposter entitled ‘Truths About Son Preference’ addressed three misconceptions identified in discussions.

Conclusion

This study may be useful to health and social care providers in providing structurally competent and culturally humble counselling and care, particularly after the birth of daughters in the absence of sons. Community engagement is necessary for future intervention development.
Development of a risk prediction tool for patients with locally advanced and recurrent rectal cancer undergoing pelvic exenteration: protocol for a mixed-methods study
Authors: Brown Kilian , Solomon Michael , Ng Kheng-Seong , Sutton Paul , Koh Cherry , White Kate , Steffens Daniel
Published: August 2023

Introduction

Pelvic exenteration (PE) surgery represents the only potentially curative treatment option for patients with locally advanced or recurrent rectal cancer (LARRC). Given the potential morbidity, whether or not PE should be recommended for an individual patient presents a major decisional conflict. This study aims to identify the outcomes of PE for which there is consensus among patients, carers and clinicians regarding their importance in guiding treatment decision-making, and to develop a risk prediction tool which predicts these outcomes.

Methods and analysis

This study will be conducted at a specialist PE centre, and employ a mixed-methods study design, divided into three distinct phases. In phase 1, outcomes of PE will be identified through a comprehensive systematic review of the literature (phase 1a), followed by exploration of the experiences of individuals who have undergone PE for LARRC and their carers (phase 1b, target sample size 10–20 patients and 5–10 carers). In phase 2, a survey of patients, their carers and clinicians will be conducted using Delphi methodology to explore consensus around the outcomes of highest priority and the level of influence each outcome should have on treatment decision-making. In phase 3 a, risk prediction tool will be developed using data from a single PE referral centre (estimated sample size 500 patients) to predict priority outcomes using multivariate modelling, and externally validated using data from an international PE collaboration.

Ethics and dissemination

Ethical approval has been granted for phases 1 and 2 (X22-0422 and 2022/ETH02659) and for maintenance of the database used in phase 3 (X13-0283 and HREC/13/RPAH/504). Informed consent will be obtained from participants in phases 1b and 2; a waiver of consent for secondary use of data in phase 3 will be sought. Study results will be submitted for publication in international and/or national peer reviewed journals.

PROSPERO registration number

CRD42022351909.