bluuebunny/crossref_metadata_2025 huggingface dataset:
Is plant acoustic communication fact or fiction?
Authors: Son Jin‐Soo , Jang Seonghan , Mathevon Nicolas , Ryu Choong‐Min
Published: March 2024

In recent years, the idea has flourished that plants emit and perceive sound and could even be capable of exchanging information through the acoustic channel. While research into plant bioacoustics is still in its infancy, with potentially fascinating discoveries awaiting ahead, here we show that the current knowledge is not conclusive. While plants do emit sounds under biotic and abiotic stresses such as drought, these sounds are high‐pitched, of low intensity, and propagate only to a short distance. Most studies suggesting plant sensitivity to airborne sound actually concern the perception of substrate vibrations from the soil or plant part. In short, while low‐frequency, high‐intensity sounds emitted by a loudspeaker close to the plant seem to have tangible effects on various plant processes such as growth – a finding with possible applications in agriculture – it is unlikely that plants can perceive the sounds they produce, at least over long distances. So far, there is no evidence of plants communicating with each other via the acoustic channel.
Exploring the frontier of rapid prototyping technologies for plant synthetic biology and what could lie beyond
Authors: Morey Kevin , Khakhar Arjun
Published: March 2024

Realizing the full potential of plant synthetic biology both to elucidate the relationship between genotype and phenotype and to apply these insights to engineer traits requires rapidly iterating through design‐build‐test cycles. However, the months‐long process of transgenesis, the long generation times, and the size‐based limitations on experimentation have stymied progress by limiting the speed and scale of these cycles. Herein, we review a representative sample of recent studies that demonstrate a variety of rapid prototyping technologies that overcome some of these bottlenecks and accelerate progress. However, each of them has caveats that limit their broad utility. Their complementary strengths and weaknesses point to the intriguing possibility that these strategies could be combined in the future to enable rapid and scalable deployment of synthetic biology in plants.
Assessing the immediate impact of Twin‐block appliance insertion on adolescents' sleep using a wearable device
Authors: Saifeldin Hatem , Negm Ibrahim M.
Published: March 2024

Objective

This prospective clinical study aimed to evaluate the immediate impact of Twin‐block appliance insertion on the sleep of adolescents using a wearable device.

Materials and Methods

A total of 24 girls, aged 11‐13 years, with Class II division 1 molar relationship, skeletal class 2 malocclusion (ANB ≥5) and overjet measuring ≥5 mm were selected. Exclusion criteria included a history of previous orthodontic treatment, systemic disease, irregular sleep pattern, obstructive sleep apnea, medical history of breathing disorders, or concurrent use of medications. Participants wore a wearable device to measure sleep parameters, including deep sleep, light sleep, minutes awake during sleep, wake‐up times, bedtimes and total sleep times. The participants wore the device for 10 days prior to Twin‐block insertion and sleep data were collected for another 10 days after insertion.

Results

Following the insertion of the Twin‐block appliance, there was a highly statistically significant shift in bedtime and wake‐up time to later hours (P < .001). All participants experienced a highly significant delay in bedtime compared to the recommended 10 pm time (P < .001). Additionally, there was a significant increase in the duration of light sleep (P < .05). However, the effect on deep sleep, minutes awake during sleep and sleep duration was not statistically significant. None of the sleep parameters tested showed statistically significant changes between the first 5 days after Twin‐block insertion with the subsequent 5 days.

Conclusion

The immediate insertion of the Twin‐block appliance disrupts sleep onset, wake‐up time and light sleep during the specified period of 10 days.
Short and long effects of the COVID‐19 context on oral health‐related quality of life of adolescents
Authors: Pohl Marina Blanco , Noronha‐Ramos Thais Gioda , Knorst Jessica Klöckner , Lito Marcia Farias Pereira , de Araujo Gabriela , Emmanuelli Bruno , Ardenghi Thiago Machado , Tomazoni Fernanda
Published: March 2024

Aim

To assess the immediate and late effects of the COVID‐19 pandemic on the oral health‐related quality of life (OHRQoL) of adolescents.

Design

This is a longitudinal study performed with adolescents (11–15 years old) from Southern Brazil who were evaluated before the COVID‐19 outbreak, and 3 (T2) and 15 (T3) months after the beginning of the pandemic. OHRQoL was assessed using the CPQ11‐14. Sociodemographic and clinical variables were also collected. Changes in OHRQoL before, 3 and 15 months after the start of the pandemic were analyzed through multilevel Poisson regression models for repeated measures.

Results

A total of 290 adolescents were evaluated at T1, 207 were re‐evaluated at T2, and 204 at T3. Overall CPQ11‐14 scores over follow‐ups were 11.0 (SD 8.0) at T1, 8.3 (SD 7.8) and 12.8 (SD 8.8) at T3. Compared to T1, adolescents presented 29% lower overall CPQ11‐14 scores (IRR 0.71 95% CI 0.66–0.75) at T2, and 11% higher scores at T3 (IRR 1.11 95% CI 1.05–1 0.17), especially for the emotional and social well‐being domains.

Conclusion

COVID‐19 pandemic impacted the adolescents' OHRQoL differently over time, indicating a reduction in impacts immediately after the beginning and worsening over long term exposure to this scenario.
Awareness of dental complications with oral piercings
Authors: Masood Manal , Walsh Laurence J. , Zafar Sobia
Published: March 2024

Objectives

To investigate knowledge and awareness of dental complications with oral piercings among adults with oral piercings, a control population with no piercings and body‐piercing professionals in South‐East Queensland, Australia.

Methods

Participants recruited from public and private dental clinics and body‐piercing professionals from piercing centres in the same region completed questionnaires to assess knowledge and attitudes.

Results

Respondents comprised 54 pierced individuals, 54 controls and 35 body‐piercing professionals. Only 13% of the pierced group were informed about oral piercing‐related complications, and 14% of body‐piercing professionals did not warn their clients about long‐term complications. The latter included chipped teeth (26%) and gingival recession (15%). About 76% play with their piercing, developing teeth grinding (15%), jaw clenching (15%) and sleep disturbances (4%). Interestingly, 41% of those with oral piercings advised others against getting piercings.

Conclusions

There is a lack of awareness about dental‐related complications among pierced individuals and body‐piercing professionals. A significant proportion of pierced individuals advise others against getting piercings. Body piercers do not consistently advise clients about risks associated with oral piercings. Thus, it is recommended that programmes be developed to improve awareness of oral and dental complications associated with oral piercings.
A method of genetic transformation and gene editing of succulents without tissue culture
Authors: Lu Jinghua , Li Shanshan , Deng Shuai , Wang Mugui , Wu Yinghuang , Li Ming , Dong Jinsong , Lu Suhui , Su Chunli , Li Guofu , Lang Zhaobo , Zhu Jian‐Kang
Published: March 2024

Succulents, valued for their drought tolerance and ornamental appeal, are important in the floriculture market. However, only a handful of succulent species can be genetically transformed, making it difficult to improve these plants through genetic engineering. In this study, we adapted the recently developed cut‐dip‐budding (CDB) gene delivery system to transform three previously recalcitrant succulent varieties – the dicotyledonousKalanchoe blossfeldianaandCrassula arborescensand the monocotyledonousSansevieria trifasciata.Capitalizing on the robust ability of cut leaves to regenerate shoots, these plants were successfully transformed by directly infecting cut leaf segments with theAgrobacterium rhizogenesstrain K599. The transformation efficiencies were approximately 74%, 5% and 3.9%–7.8%, respectively, forK. blossfeldianaandC. arborescensandS. trifasciata. Using this modified CDB method to deliver the CRISPR/Cas9 construct, gene editing efficiency inK. blossfeldianaat thePDSlocus was approximately 70%. Our findings suggest that succulents with shoot regeneration ability from cut leaves can be genetically transformed using the CDB method, thus opening up an avenue for genetic engineering of these plants.
A dual pathway model of remote work intensity: A meta‐analysis of its simultaneous positive and negative effects
Authors: Gajendran Ravi S. , Ponnapalli Ajay R. , Wang Chen , Javalagi Anoop A.
Published: March 2024

As the COVID‐19 pandemic wanes, many organizations are asking employees to return to the office concerned that more extensive remote work could hurt employee morale and productivity. Employees, however, prefer to work remotely because of the flexibility it provides. In light of such competing perspectives, we conducted a meta‐analysis examining remote work intensity's (RWI) effects on employee outcomes. RWI refers to the extensiveness of remote work ranging from one or two days a week to full‐time remote work. We propose a dual pathway model linking RWI to employee outcomes arguing that it has indirect but opposing effects on the same outcomes via two mediators—perceived autonomy and isolation. Findings from a meta‐analysis of RWI's effects based on 108 studies (k = 110, N = 45,288) support the dual pathway model. Allaying organizational concerns about remote work, RWI had overall small but beneficial effects on multiple consequential employee outcomes including job satisfaction, organizational commitment, perceived organizational support, supervisor‐rated performance, and turnover intentions. We also conducted a meta‐analysis of the effects of remote work use (RWU), a binary construct taking on two values—remote workers (users) versus office‐based workers (non‐users of remote work). Findings from the RWU meta‐analysis based on 62 studies (k = 63, N = 41,904) suggest that remote workers generally have better outcomes than their office‐based colleagues. Altogether, findings suggest that remote work offers modest upsides with limited downsides—even for those who spend more time working away from the office.
The effect of human menopausal gonadotropin and equine chorionic gonadotropin on the reproductive performance of treated ewes with short‐term progesterone injections and sponge during the non‐breeding season
Authors: Sorkh Shahram Dehghani Ghale , Mirzaei Abdolah , Zeyghami Abbas
Published: March 2024

This study investigated the effect of human menopausal gonadotropin (hMG) on reproductive efficiency of synchronized ewes with the sponge and progesterone (P4) injection‐based protocols. In study 1, anoestrous ewes (n = 120) were used. Sixty ewes were treated with sponge (S) for 12 days. The injection of eCG (SeCG group, n = 30) or hMG (ShMG, n = 30) was given at the time of sponge removal. Thirty ewes received IM injection of P4, three times every 48 h and the injection of hMG was given 24 h after the third P4 injection (3PhMG group, n = 30), and 30 ewes were used as control group. Pregnancy was diagnosed on day 50 after the release of ram. In study 2, 60 ewes were randomly divided into two equal groups. In the treated group with antibiotics (n = 30), before inserting, the sponges were impregnated with the antibiotic penicillin G sodium (5,000,000 IU) and in the control group (n = 30), there was no added antibiotics. Before inserting and after removing sponges, a vaginal cytology sample was taken with a sterile cotton swab. The number of neutrophils in each sample was counted and analysed. The rate of oestrus and total pregnancy was greater in SeCG (96.7, 93.3%), ShMG (82.8, 93.1%) and 3PhMG (67.9, 89.3%) groups compared with the control group (13.8, 41.4%) (p < .05). No significant difference was found in single, twin and total lambing and pregnancy rates after injection of eCG and hMG during the non‐breeding season (p > .05). A higher percentage of control ewes had the vaginal smear with neutrophils more than 50% (96.7% vs. 76.7%; p < .05). In conclusion, a single dose of hMG can induce fertile oestrus in synchronized ewes with P4 administered by either injection or intravaginally. Purulent discharge and percentage of neutrophils were significantly reduced in the synchronized ewes by the impregnated sponges with the antibiotic penicillin.
Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data
Authors: Bayraktar Mervan , Cebeci Zeynel , Gökçe Gökhan
Published: March 2024

The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035–0.071) and Asian breeds (Fst = 0.025–0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.
Impact of China on commodity exporters
Authors: Chatterjee Arpita , Saraf Richa
Published: March 2024

We compare the effect of a domestic shock in China and the US on the real economy and financial markets of various commodity‐exporting countries. To obtain a reliable indicator for China's macroeconomic conditions, we estimate a Bayesian dynamic factor model using block‐exclusion restrictions to identify a China factor and a US factor from monthly macroeconomic data for China and the US. We, then, assess the implications of a negative shock to both factors on the macroeconomy of a commodity‐exporting nation using Bayesian FAVARs based on recursive identification. A negative China shock leads to output loss and a fall in stock prices in these countries. China shock affects the output of only a subset of countries in our sample compared to the US shock, which affects all countries. China shock has a larger, quicker and more persistent impact on the stock markets of commodity‐exporting countries compared to the US shock. Countries with weaker institutional or business environments experience a larger negative real effect of the China shock, whereas countries with less stable financial systems demonstrate stronger financial effects. Using historical decomposition, we establish a growing role of the China factor over time, in particular for large emerging economies such as Brazil and Russia.
Quality of life, sleep and anxiety status among patients with rosacea in the Yunnan plateau region: A 2‐year retrospective study
Authors: Yang Zhenghui , Zhao Wei , Hu Min , Wu Pan , Zhang Xin , Wang Tingyu , Yao Qiuyan , Hua Piyan , Gu Hua
Published: March 2024

Objective

To investigate the life, sleep quality and anxiety of rosacea patients in Yunnan and the improvement of these aspects after treatment.

Methods

A total of 141 patients with rosacea and 123 healthy controls were included in our study. The quality of life, sleep quality and anxiety of patients with rosacea and healthy controls were investigated by the Rosacea Severity Scores (RSSs), the Medical Outcomes Study 36‐item short‐form health survey (SF‐36), the Pittsburgh Sleep Quality Index (PSQI) and Self‐rating Anxiety Scale (SAS). The quality of life, sleep quality and anxiety of patients with rosacea were assessed again after treatment.

Results

Compared with healthy controls, patients with rosacea had significantly lower physical component scores (PCS) and mental component scores (MCS) but higher PSQI and SAS scores. After treatment, rosacea patients showed significantly higher MCS but lower PSQI and SAS scores. Correlation analysis showed a significant correlation between PCS, MCS, PSQI, SAS and RSSs.

Conclusions

Patients with rosacea have a lower quality of life and sleep quality and tend to be more anxious than healthy controls. In addition, the mental quality of life, sleep quality and anxiety of rosacea patients can be significantly improved after treatment. Therefore, it is important to pay attention to the psychological status of rosacea patients. Psychological counseling and intervention are necessary to better prevent and treat rosacea.
Genetic insights into the gut microbiota and risk of facial skin aging: A Mendelian randomization study
Authors: Chen Mulan , Che Yuhui , Liu Mengsong , Xiao Xinyu , Zhong Lin , Zhao Siqi , Zhang Xueer , Chen Anjing , Guo Jing
Published: March 2024

Background

A growing number of experimental studies have shown an association between the gut microbiota (GM) and facial skin aging. However, the causal relationship between GM and facial skin aging remains unclear to date.

Methods

We conducted a two‐sample Mendelian randomization (MR) analysis to investigate the potential causal relationship between GM and facial skin aging. MR analysis was mainly performed using the inverse‐variance weighting (IVW) method, complemented by the weighted median (MW) method, MR‐Egger regression, and weighted mode, and sensitivity analysis was used to test the reliability of MR analysis results.

Results

Eleven GM taxa associated with facial skin aging were identified by IVW method analysis, Family Victivallaceae (p = 0.010), Genus Eubacterium coprostanoligenes group (p = 0.038), and Genus Parasutterella (p = 0.011) were negatively associated with facial skin aging, while Phylum Verrucomicrobia (p = 0.034), Family Lactobacillaceae (p = 0.017) and its subgroups Genus Lactobacillus (p = 0.038), Genus Parabacteroides (p = 0.040), Genus Eggerthella (p = 0.049), Genus Family XIII UCG001 (p = 0.036), Genus Phascolarctobacterium (p = 0.027), and Genus Ruminococcaceae UCG005 (p = 0.012) were positively associated with facial skin aging. At Class and Order levels, we did not find a causal relationship between GM and facial skin aging. Results of sensitivity analyses did not show evidence of pleiotropy and heterogeneity.

Conclusion

Our findings confirm the causal relationship between GM and facial skin aging, providing a new perspective on delaying facial aging.
An Analytical Framework for Cross‐border Regional Innovation Ecosystems: The Case of Shenzhen–Hong Kong Cross‐border Region
Authors: Zhao Yanan , Lyu Lachang , Grimes Seamus
Published: March 2024

In cross‐border regions (CBRs), especially in Cross‐Border Regional Innovation Systems (CBRISs) research, proximity has traditionally served as the primary framework for measuring cross‐border integration and supports the view that the closer the proximity on both sides of the border in terms of physical, functional, cognitive, institutional and other dimensions, the more integration is fostered. Recently, however, this view has been questioned, with both theoretical studies of ‘related varieties’ and empirical results from specific cross‐border cases challenging the adequacy of the proximity framework as a singular dimension for analysing CBR integration. To bridge this knowledge gap, this paper expands the proximity framework to four dimensions of relational proximity, innovation ecological environment integration, complementary advantages and common goals from the perspective of innovation ecosystem, builds an analytical assessment framework of cross‐border regional innovation ecosystem (CBRIE), and conducts an empirical analysis of the Shenzhen–Hong Kong CBR. The results show that the framework accounts well for the development of CBRIEs. Furthermore, the exchange of innovation factors between Shenzhen and Hong Kong has made greater progress and accelerated, and is moving towards building an innovation ecosystem. However, they have not yet formed a complete CBRIE.
The Bayliss–Starling Prize Lecture: The developmental physiology of spinal cord and cortical nociceptive circuits
Authors: Fitzgerald Maria
Published: March 2024

When do we first experience pain? To address this question, we need to know how the developing nervous system processes potential or real tissue‐damaging stimuli in early life. In the newborn, nociception preserves life through reflex avoidance of tissue damage and engagement of parental help. Importantly, nociception also forms the starting point for experiencing and learning about pain and for setting the level of adult pain sensitivity. This review, which arose from the Bayliss–Starling Prize Lecture, focuses on the basic developmental neurophysiology of early nociceptive circuits in the spinal cord, brainstem and cortex that form the building blocks of our first pain experience.

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Turbulent Pulsating Convective Flow in the Quasi-Steady and Low-Frequency Regimes
Authors: Banerjee Ayan Kumar
Published: March 2024

The instantaneous and time-averaged dynamics of turbulent pulsating convective pipe flow is investigated experimentally over Strouhal number, St=3.3×10−4−0.12 that falls in the quasi-steady and low-frequency regimes, pulsation amplitude, βb=0.05−0.2, and bulk Reynolds numbers, Reb=7528−10,920. The analytical expressions for pulsation amplitudes of centerline velocity, bulk velocity, and Nusselt number are derived. The time series of oscillating components of centerline velocity (Uc˜), cross-sectionally averaged bulk velocity (Ub˜), and Nusselt number (Nu˜) depicts that the phase differences between Uc˜, and Ub˜, and between Ub˜, and Nu˜ increase with St nonmonotonically with near zero phase difference at St→0. The time-averaged pulsating Nusselt number Nu¯ is invariant of St for St > 0.01. Nu¯ depends marginally on βb. The relative mean Nusselt number, Nur=Nu¯/Nus<1 for Reb≥8885 and Nur>1 for Reb = 7528. The general observations from this study is that, in the quasi-steady and low-frequency regimes, turbulent pulsating flows leads to marginal changes in the time-averaged Nusselt number Nu¯ compared to the time-averaged Nusselt number Nus in steady flow condition at any Reb.
Numerical Investigation of Elastomeric Solid Cutting: Enhancing Cut Initiation for Minimally Invasive Biological Tissue Cutting
Authors: Satake Urara , Sambe Ryutaro , Enomoto Toshiyuki
Published: March 2024

Minimizing tissue damage during blade cutting is vital for optimal surgical outcomes. However, the elastomeric properties of tissues require that they be considerably deformed before cut initiation, resulting in physical damage. Thus, the blade indentation depth required for cut initiation must be reduced by enhancing the cut-initiation ability of a process. In this study, factors that influence the cut initiation of elastomeric solids are identified by investigating the tensile stress states beneath the blade that trigger cut initiation. Finite element simulations are used to analyze interfacial interactions between the blade and workpiece and their relation to the stress states. Results show that the distribution of the in-plane stretch of the workpiece surface along the blade surface plays a key role in determining the stress states and the resulting cut-initiation ability. The effects of process parameters, including interfacial friction, blade tip geometry, blade motion, and workpiece size, are examined and discussed by analyzing the corresponding in-plane surface stretch distribution. This study offers a fundamental understanding of cut initiation in elastomeric solid cutting for improving surgical cutting tasks.
REVIEWS OF ACOUSTICAL PATENTS
Authors: Fulop Sean A.
Published: March 2024

The purpose of these acoustical patent reviews is to provide enough information for a Journal reader to decide whether to seek more information from the patent itself. Any opinions expressed here are those of the reviewers as individuals and are not legal opinions. Patents are available via the internet at the USPTO website.
Numerical study of the scattering of acoustic waves by an elliptic vortex
Authors: Martin-Martin L. , Clair V. , Bogey C. , Gabard G.
Published: March 2024

The scattering of the acoustic waves generated by a monopolar source propagating through a two-dimensional elliptic vortex, fixed or convected by a uniform flow, is studied by solving the Linearized Euler Equations in Cartesian coordinates using the Discontinuous Galerkin Method. For a fixed vortex position, the number, amplitudes, and angular spreads of the acoustic interference beams resulting from the sound scattering are found to significantly depend on the orientation of the vortex major axis with respect to the direction of the incident waves and on the vortex maximum tangential velocity. In particular, additional interference beams are obtained at large observation angles for a more elliptical vortex. For a convected elliptic vortex, the interference beams are curved as the angle between the incident acoustic wave and the vortex major axis varies when the vortex travels in the downstream direction. As expected, the scattering of the acoustic waves leads to spectral broadening in this case. Moreover, the widths and the frequencies of the lateral lobes obtained in the spectra on both sides of the peak at the source frequency are different for elliptic and round vortices.
Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density
Authors: Nakanoh Shota , Sham Kendig , Ghimire Sabitri , Mohorianu Irina , Rayon Teresa , Vallier Ludovic
Published: March 2024

Mechanisms specifying amniotic ectoderm and surface ectoderm are unresolved in humans due to their close similarities in expression patterns and signal requirements. This lack of knowledge hinders the development of protocols to accurately model human embryogenesis. Here, we developed a human pluripotent stem cell model to investigate the divergence between amniotic and surface ectoderms. In the established culture system, cells differentiated into functional amnioblast-like cells. Single-cell RNA sequencing analyses of amnioblast differentiation revealed an intermediate cell state with enhanced surface ectoderm gene expression. Furthermore, when the differentiation started at the confluent condition, cells retained the expression profile of surface ectoderm. Collectively, we propose that human amniotic ectoderm and surface ectoderm are specified along a common nonneural ectoderm trajectory based on cell density. Our culture system also generated extraembryonic mesoderm–like cells from the primed pluripotent state. Together, this study provides an integrative understanding of the human nonneural ectoderm development and a model for embryonic and extraembryonic human development around gastrulation.
Improving potential energy surfaces using measured Feshbach resonance states
Authors: Horn Karl P. , Vazquez-Salazar Luis Itza , Koch Christiane P. , Meuwly Markus
Published: March 2024

The structure and dynamics of a molecular system is governed by its potential energy surface (PES), representing the total energy as a function of the nuclear coordinates. Obtaining accurate potential energy surfaces is limited by the exponential scaling of Hilbert space, restricting quantitative predictions of experimental observables from first principles to small molecules with just a few electrons. Here, we present an explicitly physics-informed approach for improving and assessing the quality of families of PESs by modifying them through linear coordinate transformations based on experimental data. We demonstrate this “morphing” of the PES for the He ‐ H
2
+
complex using recent comprehensive Feshbach resonance (FR) measurements for reference PESs at three different levels of quantum chemistry. In all cases, the positions and intensities of peaks in the energy distributions are improved. We find these observables to be mainly sensitive to the long-range part of the PES.
On-fault earthquake energy density partitioning from shocked garnet in an exhumed seismic midcrustal fault
Authors: Toffol Giovanni , Pennacchioni Giorgio , Menegon Luca , Wallis David , Faccenda Manuele , Camacho Alfredo , Bestmann Michel
Published: March 2024

The energy released during an earthquake is mostly dissipated in the fault zone and subordinately as radiated seismic waves. The on-fault energy budget is partitioned into frictional heat, generation of new grain surface by microfracturing, and crystal-lattice distortion associated with dislocation defects. The relative contribution of these components is debated and difficult to assess, but this energy partitioning strongly influences earthquake mechanics. We use high-resolution scanning-electron-microscopy techniques, especially to analyze shocked garnet in a fault wall-rock, to provide the first estimate of all three energy components for a seismic fault patch exhumed from midcrustal conditions. Fault single-jerk seismicity is recorded by the presence of pristine quenched frictional melt. The estimated value of energy per unit fault surface is ~13 megajoules per square meter for heat, which is predominant with respect to both surface energy (up to 0.29 megajoules per square meter) and energy associated with crystal lattice distortion (0.02 megajoules per square meter).
Speed of thermal adaptation of terrestrial vegetation alters Earth’s long-term climate
Authors: Rogger Julian , Mills Benjamin J. W. , Gerya Taras V. , Pellissier Loïc
Published: March 2024

Earth’s long-term climate is driven by the cycling of carbon between geologic reservoirs and the atmosphere-ocean system. Our understanding of carbon-climate regulation remains incomplete, with large discrepancies remaining between biogeochemical model predictions and the geologic record. Here, we evaluate the importance of the continuous biological climate adaptation of vegetation as a regulation mechanism in the geologic carbon cycle since the establishment of forest ecosystems. Using a model, we show that the vegetation’s speed of adaptation to temperature changes through eco-evolutionary processes can strongly influence global rates of organic carbon burial and silicate weathering. Considering a limited thermal adaptation capacity of the vegetation results in a closer balance of reconstructed carbon fluxes into and out of the atmosphere-ocean system, which is a prerequisite to maintain habitable conditions on Earth’s surface on a multimillion-year timescale. We conclude that the long-term carbon-climate system is more sensitive to biological dynamics than previously expected, which may help to explain large shifts in Phanerozoic climate.
Aberrant RNA sensing in regulatory T cells causes systemic autoimmunity
Authors: Luca Domnica , Lee Sumin , Hirota Keiji , Okabe Yasutaka , Uehori Junji , Izawa Kazushi , Lanz Anna-Lisa , Schütte Verena , Sivri Burcu , Tsukamoto Yuta , Hauck Fabian , Behrendt Rayk , Roers Axel , Fujita Takashi , Nishikomori Ryuta , Lee-Kirsch Min Ae , Kato Hiroki
Published: March 2024

Chronic and aberrant nucleic acid sensing causes type I IFN–driven autoimmune diseases, designated type I interferonopathies. We found a significant reduction of regulatory T cells (T
regs
) in patients with type I interferonopathies caused by mutations in
ADAR1
or
IFIH1
(encoding MDA5). We analyzed the underlying mechanisms using murine models and found that T
reg
-specific deletion of
Adar1
caused peripheral T
reg
loss and
scurfy
-like lethal autoimmune disorders. Similarly, knock-in mice with T
reg
-specific expression of an MDA5 gain-of-function mutant caused apoptosis of peripheral T
regs
and severe autoimmunity. Moreover, the impact of ADAR1 deficiency on T
regs
is multifaceted, involving both MDA5 and PKR sensing. Together, our results highlight the dysregulation of T
reg
homeostasis by intrinsic aberrant RNA sensing as a potential determinant for type I interferonopathies.
TGF-β specifies T
FH
versus T
H
17 cell fates in murine CD4
+
T cells through c-Maf
Authors: Chang Yinshui , Bach Luisa , Hasiuk Marko , Wen Lifen , Elmzzahi Tarek , Tsui Carlson , Gutiérrez-Melo Nicolás , Steffen Teresa , Utzschneider Daniel T. , Raj Timsse , Jost Paul Jonas , Heink Sylvia , Cheng Jingyuan , Burton Oliver T. , Zeiträg Julia , Alterauge Dominik , Dahlström Frank , Becker Jennifer-Christin , Kastl Melanie , Symeonidis Konstantinos , van Uelft Martina , Becker Matthias , Reschke Sarah , Krebs Stefan , Blum Helmut , Abdullah Zeinab , Paeschke Katrin , Ohnmacht Caspar , Neumann Christian , Liston Adrian , Meissner Felix , Korn Thomas , Hasenauer Jan , Heissmeyer Vigo , Beyer Marc , Kallies Axel , Jeker Lukas T. , Baumjohann Dirk
Published: March 2024

T follicular helper (T
FH
) cells are essential for effective antibody responses, but deciphering the intrinsic wiring of mouse T
FH
cells has long been hampered by the lack of a reliable protocol for their generation in vitro. We report that transforming growth factor–β (TGF-β) induces robust expression of T
FH
hallmark molecules CXCR5 and Bcl6 in activated mouse CD4
+
T cells in vitro. TGF-β–induced mouse CXCR5
+
T
FH
cells are phenotypically, transcriptionally, and functionally similar to in vivo–generated T
FH
cells and provide critical help to B cells. The study further reveals that TGF-β–induced CXCR5 expression is independent of Bcl6 but requires the transcription factor c-Maf. Classical TGF-β–containing T helper 17 (T
H
17)–inducing conditions also yield separate CXCR5
+
and IL-17A–producing cells, highlighting shared and distinct cell fate trajectories of T
FH
and T
H
17 cells. We demonstrate that excess IL-2 in high-density T cell cultures interferes with the TGF-β–induced T
FH
cell program, that T
FH
and T
H
17 cells share a common developmental stage, and that c-Maf acts as a switch factor for T
FH
versus T
H
17 cell fates in TGF-β–rich environments in vitro and in vivo.
Reduced peptidoglycan synthesis capacity impairs growth of
E. coli
at high salt concentration
Authors: Alodaini Dema , Hernandez-Rocamora Victor , Boelter Gabriela , Ma Xuyu , Alao Micheal B. , Doherty Hannah M. , Bryant Jack A. , Moynihan Patrick , Moradigaravand Danesh , Glinkowska Monika , Vollmer Waldemar , Banzhaf Manuel
Published: March 2024

Gram-negative bacteria have a thin peptidoglycan layer between the cytoplasmic and outer membranes protecting the cell from osmotic challenges. Hydrolases of this structure are needed to cleave bonds to allow the newly synthesized peptidoglycan strands to be inserted by synthases. These enzymes need to be tightly regulated and their activities coordinated to prevent cell lysis. To better understand this process in
Escherichia coli
, we probed the genetic interactions of
mrcA
(encodes PBP1A) and
mrcB
(encodes PBP1B) with genes encoding peptidoglycan amidases and endopeptidases in envelope stress conditions. Our extensive genetic interaction network analysis revealed relatively few combinations of hydrolase gene deletions with reduced fitness in the absence of PBP1A or PBP1B, showing that none of the amidases or endopeptidases is strictly required for the functioning of one of the class A PBPs. This illustrates the robustness of the peptidoglycan growth mechanism. However, we discovered that the fitness of ∆
mrcB
cells is significantly reduced under high salt stress and
in vitro
activity assays suggest that this phenotype is caused by a reduced peptidoglycan synthesis activity of PBP1A at high salt concentration.

IMPORTANCE

Escherichia coli
and many other bacteria have a surprisingly high number of peptidoglycan hydrolases. These enzymes function in concert with synthases to facilitate the expansion of the peptidoglycan sacculus under a range of growth and stress conditions. The synthases PBP1A and PBP1B both contribute to peptidoglycan expansion during cell division and growth. Our genetic interaction analysis revealed that these two penicillin-binding proteins (PBPs) do not need specific amidases, endopeptidases, or lytic transglycosylases for function. We show that PBP1A and PBP1B do not work equally well when cells encounter high salt stress and demonstrate that PBP1A alone cannot provide sufficient PG synthesis activity under this condition. These results show how the two class A PBPs and peptidoglycan hydrolases govern cell envelope integrity in
E. coli
in response to environmental challenges and particularly highlight the importance of PBP1B in maintaining cell fitness under high salt conditions.
Interferon lambda restricts herpes simplex virus skin disease by suppressing neutrophil-mediated pathology
Authors: Philip Drake T. , Goins Nigel M. , Catanzaro Nicholas J. , Misumi Ichiro , Whitmire Jason K. , Atkins Hannah M. , Lazear Helen M.
Published: March 2024

Type III interferons (IFN-λ) are antiviral and immunomodulatory cytokines that have been best characterized in respiratory and gastrointestinal infections, but the effects of IFN-λ against skin infections have not been extensively investigated. We sought to define the skin-specific effects of IFN-λ against the highly prevalent human pathogen, herpes simplex virus (HSV). We infected mice lacking the IFN-λ receptor (
Ifnlr1
−/−
), both the IFN-λ and the IFN-α/β receptors (
Ifnar1
−/−
Ifnlr1
−/−
), or IFN-λ cytokines (
Ifnl2/3
−/−
) and found that IFN-λ restricts the severity of HSV-1 and HSV-2 skin lesions without affecting viral loads. We used RNAseq to define IFN-λ- and IFN-β-induced transcriptional responses in primary mouse keratinocytes. Using conditional knockout mice, we found that IFN-λ signaling in both keratinocytes and neutrophils was necessary to control HSV-1 skin lesion severity and that IFN-λ signaling in keratinocytes suppressed CXCL9-mediated neutrophil recruitment to the skin. Furthermore, depleting neutrophils or blocking CXCL9 protected against severe HSV-1 skin lesions in
Ifnlr1
−/−
mice. Altogether, our results suggest that IFN-λ plays an immunomodulatory role in the skin that restricts neutrophil-mediated pathology during HSV infection and suggests potential applications for IFN-λ in treating viral skin infections.

IMPORTANCE

Type III interferons (IFN-λ) have been shown to have antiviral and immunomodulatory effects at epithelial barriers such as the respiratory and gastrointestinal tracts, but their effects on the skin have not been extensively investigated. We used mice lacking IFN-λ signaling to investigate the skin-specific effects of IFN-λ against the herpes simplex virus (HSV), which targets epithelial tissues to cause cold sores and genital herpes. We found that IFN-λ limited the severity of HSV skin lesions without affecting viral load and that this protective effect required IFN-λ signaling in both keratinocytes and neutrophils. We found that IFN-λ signaling in keratinocytes suppressed neutrophil recruitment to the skin and that depleting neutrophils protected against severe HSV skin lesions in the absence of IFN-λ. Altogether, our results suggest that IFN-λ plays an immunomodulatory role in the skin that restricts neutrophil-mediated pathology during HSV infection and suggests potential applications for IFN-λ in treating viral skin infections.
How
P. aeruginosa
cells with diverse stator composition collectively swarm
Authors: de Anda Jaime , Kuchma Sherry L. , Webster Shanice S. , Boromand Arman , Lewis Kimberley A. , Lee Calvin K. , Contreras Maria , Medeiros Pereira Victor F. , Schmidt William , Hogan Deborah A. , O’Hern Corey S. , O’Toole George A. , Wong Gerard C. L.
Published: March 2024

Swarming is a macroscopic phenomenon in which surface bacteria organize into a motile population. The flagellar motor that drives swarming in
Pseudomonas aeruginosa
is powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion of the MotAB stator enhances swarming. Interestingly, we measured a strongly asymmetric stator availability in the wild-type (WT) strain, with MotAB stators produced at an approximately 40-fold higher level than MotCD stators. However, utilization of MotCD stators in free swimming cells requires higher liquid viscosities, while MotAB stators are readily utilized at low viscosities. Importantly, we find that cells with MotCD stators are ~10× more likely to have an active motor compared to cells uses the MotAB stators. The spectrum of motility intermittency can either cooperatively shut down or promote flagellum motility in WT populations. In
P. aeruginosa
, transition from a static solid-like biofilm to a dynamic liquid-like swarm is not achieved at a single critical value of flagellum torque or stator fraction but is collectively controlled by diverse combinations of flagellum activities and motor intermittencies via dynamic stator utilization. Experimental and computational results indicate that the initiation or arrest of flagellum-driven swarming motility does not occur from individual fitness or motility performance but rather related to concepts from the “jamming transition” in active granular matter.

IMPORTANCE

It is now known that there exist multifactorial influences on swarming motility for
P. aeruginosa
, but it is not clear precisely why stator selection in the flagellum motor is so important. We show differential production and utilization of the stators. Moreover, we find the unanticipated result that the two motor configurations have significantly different motor intermittencies: the fraction of flagellum-active cells in a population on average with MotCD is active ~10× more often than with MotAB. What emerges from this complex landscape of stator utilization and resultant motor output is an intrinsically heterogeneous population of motile cells. We show how consequences of stator recruitment led to swarming motility and how the stators potentially relate to surface sensing circuitry.
Draft genome sequence of
Klebsiella pneumoniae
KLEB-33: a convergent biofilm hyperforming multiresistant strain belonging to the emerging ST16 lineage harboring multiple hypervirulence genes
Authors: Silva-Bea Sergio , García-Meniño Isidro , Rey Sonia , Romero Manuel , Fernández Javier , Hammerl Jens A. , Mora Azucena , Otero Ana
Published: March 2024

The emergence of convergent
Klebsiella pneumoniae
strains showing multiresistance, characteristic of nosocomial pathotypes and hypervirulent traits typical of community-acquired isolates, makes them important models for studying
K. pneumoniae
pathogenesis. Here, we describe the convergent, multidrug-resistant KLEB-33 strain harboring several hypervirulence genes and make its genome available to the scientific community.
Human Vγ9Vδ2 T cells exhibit antifungal activity against
Aspergillus fumigatus
and other filamentous fungi
Authors: Koga Satoru , Takazono Takahiro , Namie Hodaka , Okuno Daisuke , Ito Yuya , Nakada Nana , Hirayama Tatsuro , Takeda Kazuaki , Ide Shotaro , Iwanaga Naoki , Tashiro Masato , Sakamoto Noriho , Watanabe Akira , Izumikawa Koichi , Yanagihara Katsunori , Tanaka Yoshimasa , Mukae Hiroshi
Published: March 2024

Invasive aspergillosis (IA) and mucormycosis are life-threatening diseases, especially among immunocompromised patients. Drug-resistant
Aspergillus fumigatus
strains have been isolated worldwide, which can pose a serious clinical problem. As IA mainly occurs in patients with compromised immune systems, the ideal therapeutic approach should aim to bolster the immune system. In this study, we focused on Vγ9Vδ2 T cells that exhibit immune effector functions and examined the possibility of harnessing this unconventional T cell subset as a novel therapeutic modality for IA. A potent antifungal effect was observed when
A. fumigatus
(
Af293
) hyphae were challenged by Vγ9Vδ2 T cells derived from peripheral blood. In addition, Vγ9Vδ2 T cells exhibited antifungal activity against hyphae of all
Aspergillus
spp.,
Cunninghamella bertholletiae
, and
Rhizopus microsporus
but not against their conidia. Furthermore, Vγ9Vδ2 T cells also exhibited antifungal activity against azole-resistant
A. fumigatus
, indicating that Vγ9Vδ2 T cells could be used for treating drug-resistant
A. fumigatus
. The antifungal activity of Vγ9Vδ2 T cells depended on cell-to-cell contact with
A. fumigatus
hyphae, and degranulation characterized by CD107a mobilization seems essential for this activity against
A. fumigatus
. Vγ9Vδ2 T cells could be developed as a novel modality for treating IA or mucormycosis.

IMPORTANCE

Invasive aspergillosis (IA) and mucormycosis are often resistant to treatment with conventional antifungal agents and have a high mortality rate. Additionally, effective antifungal treatment is hindered by drug toxicity, given that both fungal and human cells are eukaryotic, and antifungal agents are also likely to act on human cells, resulting in adverse effects. Therefore, the development of novel therapeutic agents specifically targeting fungi is challenging. This study demonstrated the antifungal activity of Vγ9Vδ2 T cells against various
Aspergillus
spp. and several
Mucorales in vitro
and discussed the mechanism underlying their antifungal activity. We indicate that adoptive immunotherapy using Vγ9Vδ2 T cells may offer a new therapeutic approach to IA.
Organic Matter in the Ocean: Indicators of Biogeochemical Processes
Authors: Romankevich E. A. , Vetrov A. A. , Ulyantsev A. S.
Published: March 2024

The article presents informative organogeochemical indicators used in oceanology to characterize biogeochemical processes. A classification based on data on suspended particulate matter, plankton, benthos, bottom sediments, and sea, river, and pore water has been developed. Clusters have been identified that include the elemental and isotopic composition of organic matter (OM), the group composition of lipids, aliphatic and alicyclic hydrocarbons, higher alcohols, macromolecular acids and ketones, isoprenoids, lignin and its structural monomers, and PAHs. The most informative indices are considered, which make it possible to assess the genesis of the original OM, the degree of its transformation, sources, and the ratio of aquatic and terrigenous components. These indices reflect the influx of riverine and aeolian material and permafrost thawing and make it possible to reconstruct the temperature of river waters and coastal upwellings. They significantly complement biooceanological, lithological, and geochemical studies and expand the biogeochemical methodology for studying the carbon cycle.