bluuebunny/crossref_metadata_2025 huggingface dataset:
Histone H3.3 chaperone HIRA renders stress‐responsive genes poised for prospective lethal stresses in acquired tolerance
Authors: Nagagaki Yoshikazu , Kozakura Yuji , Mahandaran Theventhiran , Fumoto Yukiko , Nakato Ryuichiro , Shirahige Katsuhiko , Ishikawa Fuyuki
Published: July 2024

Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low‐dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low‐dose stress remains profoundly limited. Here we report that histone variant H3.3‐specific chaperone, HIRA, is required for acquired tolerance, where low‐dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress‐responsive genes, including HSP70, by depositing histone H3.3 following low‐dose stresses. These genes are also marked with histone H3 Lys‐4 trimethylation and H3 Lys‐9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.
Leprosy knowledge among primary care physicians in Southern Brazil: are we underdiagnosing?
Authors: de Cássia Francisco Priscila , Kliemann Breno Saty , Tarlé Roberto Gomes
Published: July 2024

Background

Leprosy is a chronic infection with high morbidity in Brazil. Primary care physicians' lack of knowledge about the disease may play a significant role in underdiagnosis. This study aimed to assess primary care physicians' ability to identify typical leprosy skin lesions and their knowledge of the subject.

Methods

This cross‐sectional study relied on a questionnaire in which participating doctors chose one main diagnostic hypothesis and two differential diagnoses for each skin lesion presented. Five leprosy lesions were included. Questions regarding management, follow‐up, and diagnostic workup for the disease were also included. The questionnaire was sent to primary care physicians working in Curitiba, in the Southern Brazilian state of Paraná, and dermatologists, who constituted the control group.

Results

Thirty‐two primary care physicians and 26 dermatologists agreed to participate in the study. Primary care physicians accurately identified a mean of 1.8 ± 1.2 of the five leprosy skin lesions, while dermatologists accurately identified 2.5 ± 0.9 (P = 0.009). The main misdiagnosed leprosy forms were the lepromatous and histoid variants. Among primary care physicians, 56.2% claimed to have little knowledge of the subject and a large share of participants was unaware of recent updates in treating paucibacillary forms, even within the dermatologist subgroup.

Conclusions

Primary care physicians in Curitiba have little information regarding the diagnosis, treatment, and follow‐up of leprosy. Even dermatologists had difficulties with treatment and patient management, emphasizing the constant need for education on this subject.
The role of group membership and culture in interpersonal distance regulation
Authors: Wei JuanJuan , Candini Michela , Frassinetti Francesca , Rubini Monica
Published: July 2024

The current study aims to examine the influence of group membership and cultural conceptions on the regulation of interpersonal distance (IPD) among Chinese and Italian adolescents. Two‐hundred forty participants completed an online computerized version of the Interpersonal Visual Analogue Scale to assess their preferred IPD. A greater distance was found in Chinese than Italian participants. Chinese participants also chose a larger distance from outgroup than ingroup members, whereas no such tendencies were found among Italian participants. Moreover, in the Chinese group, a larger distance from the male target was chosen by females compared to male participants. Finally, all participants maintained greater distance when outgroup members approached from the back than from the front. These findings not only provide evidence that nationality and group membership impact on how individuals regulate spatial boundaries, but also offer a new lens to understand intergroup dynamics shaping social interactions among individuals from diverse cultural backgrounds.
Could bi‐axial orientation explain range expansion in a migratory songbird?
Authors: Wynn Joe , Fandos Guillermo , Delmore Kira , Van Doren Benjamin M. , Fransson Thord , Liedvogel Miriam
Published: July 2024

The likelihood of a new migratory route emerging is presumably a function of 1) the associated fitness payoff and 2) the probability that the route arises in the first place. It has been suggested that diametrically opposed ‘reverse' migratory trajectories might be surprisingly common and, if such routes were heritable, it follows that they could underlie the rapid evolution of divergent migratory trajectories. Here, we used Eurasian blackcap (Sylvia atricapilla; ‘blackcap') ringing recoveries and geolocator trajectories to investigate whether a recently evolved northwards autumn migratory route – and accompanying rapid northerly wintering range expansion – could be explained by the reversal of each individual's population‐specific traditional southwards migratory direction. We found that northwards autumn migrants were recovered closer to the sites specified by an axis reversal than would be expected by chance, consistent with the rapid evolution of new migratory routes via bi‐axial variation in orientation. We suggest that the surprisingly high probability of axis reversal might explain why birds expand their wintering ranges rapidly and divergently, and propose that understanding how migratory direction is encoded is crucial when characterising the genetic component underlying migration.
Human papillomavirus (HPV) vaccination in Japan
Authors: Miyagi Etsuko
Published: July 2024

Aim

To review the status of human papillomavirus (HPV) vaccination in Japan from inception to the present, focusing on past and current challenges.

Methods

Published articles and website content related to HPV vaccination were reviewed.

Results

The Ministry of Health, Labor and Welfare suspended proactive recommendations for HPV vaccination in June 2013 following repeated media reports of girls experiencing adverse events, including chronic pain and walking disturbances, after receiving the HPV vaccine. Despite later recognition of these symptoms as a functional somatic syndrome, HPV vaccine coverage of target girls aged 12 to 16 years in the National Immunization Program (NIP) rapidly decreased to near zero. This suspension of the proactive HPV vaccination recommendation ceased in fiscal year (f‐year) 2022, initiating a 3‐year catch‐up free HPV vaccination period from April 2022 to March 2025 for women born from f‐years 1997 to 2005. These drastic changes were driven by established evidence of the effectiveness and safety of HPV vaccines reported from both Japan and other countries, and a nine‐valent HPV vaccine has been included in the NIP since f‐year 2023. However, the estimated HPV vaccination rate in the NIP remains low at ≤30%.

Conclusions

To regain high coverage of HPV vaccination in Japan, it is essential that government, industry, and academic society work together to raise awareness and educate Japanese people about cervical cancer prevention and HPV‐related diseases.
Feedback, learning and becoming: Narratives of feedback in complex performance challenges
Authors: Bearman Margaret , Dracup Mary , Ajjawi Rola , Kirby Catherine , Brown James
Published: July 2024

Introduction

Becoming a general practitioner (or family medicine specialist) is challenging, as trainees learn to manage complex and ambiguous situations. Feedback is a key component of this learning. Although research has tended to focus on feedback's momentary processes and impacts, there is value in seeking to understand the work it does over time and how trainees position themselves across multiple feedback encounters. We ask: how do newly qualified GPs narrate themselves and their experiences with complex performance challenges? Within these narratives, what is the role of feedback?

Methods

The research adopts a holistic and sequential narrative analysis approach, with in‐depth narrative interviews of 16 general practice trainees who had just completed their training requirements. The analysis involved restorying the participant narratives chronologically. Each narrative formed a unit of analysis where narrative commonalities across plots, characters, emotions and the role of feedback were interpreted.

Results

Four plotlines within GP trainees' stories of complex performance challenges were identified: Journeyperson, Hero's Quest, Solo Journeyer and Endless Struggle. Trainees, supervisors and feedback are positioned differently within these plotlines. Narratives were saturated with emotions.

Discussion

The plotlines bring together an alternative way of understanding how feedback, learning and becoming are woven together. They illustrate how multiple interactions with patients, supervisors, peers and systems thread together into an overall trajectory. How a trainee positions themselves as protagonists and who they characterise as their antagonists can help direct the focus of supervisors' feedback conversations.
The induced defocus by Defocus Incorporated Soft Contact lenses is dependent on visual distance and ambient illuminance
Authors: Hao Jiangdong , Lin Zhenghua , Xi Xiaoyun , Yang Zhikuan , Artal Pablo , Lan Weizhong
Published: July 2024

Purpose

Defocus Incorporated Soft Contact (DISC) lenses, a commonly used type of multifocal lens in clinical practice, may slow down myopia progression by inducing myopic retinal defocus. The purpose of this study was to explore whether the induced defocus across the retina could be affected by visual environments encountered in the real world, such as differences in viewing distance and ambient illuminance.

Methods

In this cross‐over trial, 30 myopic adults wore both DISC lenses and single vision contact (SVC) lenses in random order. An open‐view Hartmann–Shack scanning wavefront sensor was used to measure defocus at different retinal locations along the horizontal meridian under four experimental conditions: far target (3 m) and near targets (0.33 m) under scotopic (<1 lux) or photopic (~300 lux) conditions.

Results

The results showed that DISC lenses induced more myopic retinal defocus than SVC lenses in all conditions (all p < 0.05), except for the scotopic near target. In addition, for DISC lenses, the defocus was greater in the photopic than the scotopic conditions for both the far and near targets (both p < 0.05).

Conclusion

In conclusion, the retinal defocus induced by these multifocal lenses was dependent on both visual distance and ambient illuminance, indicating that the visual conditions might affect the anti‐myopia efficacy of these devices.
India in Contested Regional Multilateralism: Between Seeking Institutional Balancing and Avoiding Rising Power Dilemmas
Authors: Jamali Ahmed Bux , Liu Hongsong
Published: July 2024

How does India navigate contested regional multilateral frameworks in the Asia‐Pacific? This question has important implications for India's multilateral foreign policy and diplomacy that seeks to emerge from regional to global power. The authors argue that India's foreign policy involves seeking institutional balancing and avoiding rising power dilemmas. Based on the conceptual framework of institutional balancing and rising power dilemma, the paper examines how seeking institutional balancing helps India advance its diplomatic prowess vis‐à‐vis rising China while simultaneously leveraging its multi‐alignment strategy against the United States. Furthermore, the paper discusses India's key priorities for avoiding the rising power dilemma, thus exhibiting its reluctance to conform to the US hegemony and addressing its internal and external dilemma concerning China. The evaluation suggests that India's foreign policy rationality navigates between obtaining comprehensive security and economic gains in dealing with contested regional multilateralism.
Pachyonychia congenita: A father and son with a novel variant in the KRT16 gene
Authors: Tran Tu Nguyen Anh , Vu Thao Thi Phuong , Pham Nguyen Nhat , Bui Chi‐Bao , Nguyen Hao Trong
Published: July 2024

This study underscores the significance of identifying the clinical manifestations of pachyonychia congenita (PC) and emphasizes the patterns of genetic inheritance. A 12‐month‐old boy presented with a “white hairy tongue” and, following a comprehensive evaluation, was diagnosed with PC. His father exhibited similar symptoms. Genetic testing revealed a KRT16 pathogenic variant (c.616 T > G) in both the patient and his father, marking it as a novel variant in the PC literature. This case contributes to a broader understanding of PC's genetic diversity and its clinical presentations.
Seed germination requirements of the rare Helosciadium repens (aka Apium repens) determine persistence of seeds in the soil seed bank
Authors: Ronse A. , Van de Vyver A. , Vandelook F.
Published: July 2024

The rare and threatened Heliosciadium repens grows in moist grasslands and has a distinct life cycle. Plants reproduce both clonally, although ramets tend to be short‐lived, and sexually, with seeds that can form a persistent soil seed bank. The germination requirements of H. repens were investigated, yielding important information for its habitat management and conservation.

We examined the soil seed bank in three populations and carried out germination experiments and embryo growth measurements with fresh seeds in laboratory, greenhouse and outdoor conditions. We also investigated the effects of storage and burial of seeds.

H. repens formed a long‐term persistent (>6 years) soil seed bank with very pronounced primary dormancy, but no secondary dormancy or dormancy cycles. Seeds can germinate throughout the growing season when temperatures are sufficiently high. Embryo growth and seed germination are triggered by light and, to a lesser extent, daily temperature fluctuations.

Seeds of H. repens seem to have developed a unique germination syndrome with several strategies to remain dormant in the soil until optimal conditions are present for seedling establishment and survival. Both sexual reproduction and seed bank formation are crucial for the long‐term survival of the populations.
Stress, burnout and coping among nurses working on acute medical wards and in the community: A quantitative study
Authors: Hjörleifsdóttir Elísabet , Sigurðardóttir Þórhalla , Óskarsson Guðmundur Kristján , Halapi Eva Charlotte
Published: July 2024

Background

Psychological distress can cause burnout, which affects mental and physical well‐being. It is important to identify factors associated with psychological distress and physical discomfort and how nurses deal with these problems.

Aim

The aim was to investigate distress, burnout and coping among community nurses (CN) and hospital nurses (HN).

Approach and Methods

In this cross‐sectional study, 409 nurses completed three questionnaires: Perceived Stress Scale (PSS), Copenhagen Burnout Inventory (CBI) and Ways of Coping (WOC).

Findings

Participants younger than 40 demonstrated significantly more distress and burnout than those older than 40 years. Participants who had moderate and high distress on the PSS were significantly more at risk for experiencing personal, work‐related and patient‐related burnout. A significant positive correlation was found between distress and behavioural escape‐avoidance, cognitive escape‐avoidance and distancing. Significant positive correlations were also seen between all the subscales of the CBI and behavioural escape‐avoidance, cognitive escape‐avoidance and distancing. Positive significant correlation was also obtained between staff resources and distress and personal‐related and work‐related burnout. Negative correlation was demonstrated between staff resources and patient‐related burnout. Participants with longer work experience were less likely to report moderate or high distress, and those who scored higher on personal burnout and behavioural escape‐avoidance were more likely to have moderate or high distress.

Conclusion

The results of this study call for increased attention to the younger generation in the nursing profession. The results also validate the need to investigate further the correlation between distress, burnout and coping and how these issues might influence each other among nurses working in the community and hospitals. Findings should be taken with precaution, they do not describe in detail what underlying factors contribute to distress and discomfort found in this study, they do, however, indicate certain coping strategies nurses use to deal with distress and burnout.
The immigrant linguistic maturation of Asian American and Latinx language brokers
Authors: Higuera Kimberly
Published: July 2024

Immigrant children in the U.S. often learn English before their caretakers, leading them to take on the role of day‐to‐day translators (“language brokers”). This study explores the familial socialization of immigrant, linguistic‐minority families in the U.S. by drawing on deductive‐inductive thematic analysis of 14 semi‐structured interviews with Asian American and Latinx young adult language brokers reflecting on how this role shaped their childhoods and prepared them for adulthood. The bulk of interviewees experienced working‐class childhoods. Despite this, respondents seem to have experienced a family socialization model that reflects elements of both middle‐class and working‐class models. “Immigrant Linguistic Maturation” (ILM) consists of linguistic scaffolding in English and heritage languages, verbal airtime, and engagement with authority figures, while also leading children to hold adult knowledge, roles, and responsibilities. Racial and ethnic differences primarily lie in the actors involved in ILM socialization processes. Extended family, and especially grandparents, played a more active role in the ILM socialization of Asian American brokers, while ILM socialization of Latinx brokers was primarily driven by parents, particularly mothers. The case of Asian American and Latinx language brokers calls attention to the importance of factors like immigrant background and linguistic marginalization in shaping familial socialization.
Finding ‘Home’ and Navigating ‘Cultural Precarity’: Grey Areas Between Racism and ‘Hate Crime’ Victimization Among Korean Businesses
Authors: Lee Claire Seungeun , Lee Hannarae , Park Insun
Published: July 2024

The United States has often been lauded for its reputation as a melting pot, embracing diverse cultures and backgrounds. However, beneath this outward display of diversity lies a more intricate reality illuminated by the experiences of immigrants. This study, which involved 19 interviews with first‐generation Korean immigrants operating small businesses in the United States, examines the diverse forms of discrimination and hate crime encountered by participants from various demographic backgrounds and immigration histories. These diverse perspectives, influenced by factors such as duration in the United States, gender, and age, contribute to a nuanced understanding of the challenges faced by immigrants before and during the COVID‐19 pandemic. The study also explores participants' experiences attributing the sources of challenges to neighborhood safety, grappling with issues related to racial background and language barriers, and contending with cultural precarity. The narratives vividly depict the multifaceted challenges within the business setting and daily lives of Korean immigrants. Significantly, these occurrences transcend differences in residency duration, age, gender, and personal experiences, emphasizing the need for nuanced and inclusive approaches to address discrimination effectively. Recognizing the shared impact of discriminatory practices across diverse individuals fosters a collective understanding, informing targeted interventions for a more inclusive and equitable society for Asian immigrants. Based on firsthand accounts and perceptions, the study discerns policy implications to comprehensively address these challenges among Korean/Asian immigrants in the United States.
Protocol biopsy of kidney allograft enables early detection of BK virus nephropathy to preserve kidney allograft function
Authors: Iwahara Naoya , Hotta Kiyohiko , Hirose Takayuki , Okada Hiromi , Shinohara Nobuo
Published: July 2024

Background

The Banff Working Group has updated the histological classification of BK virus nephropathy (BKVN), highlighting the importance of early detection. However, an early detection strategy for BKVN using biopsy has not yet been established. Our investigation aimed to assess the efficacy of protocol biopsy for the diagnosis of BKVN.

Methods

We performed a retrospective cohort study of 314 patients who had undergone kidney transplantation between 2006 and 2021. Kidney allograft biopsies were performed as part of a protocol biopsy at 3 months and 1 year post‐transplantation. Following the diagnosis of BKVN, the immunosuppressant dose was reduced.

Results

Twelve patients (3.8%) were diagnosed with BKVN by biopsy. Most diagnoses are established during the early stages of BKVN (polyomavirus nephropathy class 1 in six, class 2 in five, and class 3 in one). Following the reduction in immunosuppressant dose, kidney allograft function did not deteriorate in any patients. Additionally, test for BK virus DNA in the blood was negative. All but one patient demonstrated histological resolution of BKVN, and the other had a very slight positivity for the simian virus 40 large T antigen. The median follow‐up time after BKVN diagnosis was 6 years. One patient developed de novo donor‐specific antibody and subclinical acute antibody‐mediated rejection that was successfully cured.

Conclusions

Our analysis indicates that protocol biopsy may enable the early detection of BKVN, resulting in the preservation of kidney function.

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Trehalose along with ABA promotes the salt tolerance of Avicennia marina by regulating Na+ transport
Authors: Song Ling‐Yu , Xu Chao‐Qun , Zhang Lu‐Dan , Li Jing , Jiang Li‐Wei , Ma Dong‐Na , Guo Ze‐Jun , Wang Qian , Wang Xiu‐Xiu , Zheng Hai‐Lei
Published: July 2024

Mangroves grow in tropical/subtropical intertidal habitats with extremely high salt tolerance. Trehalose and trehalose‐6‐phosphate (T6P) have an alleviating function against abiotic stress. However, the roles of trehalose in the salt tolerance of salt‐secreting mangrove Avicennia marina is not documented. Here, we found that trehalose was significantly accumulated in A. marina under salt treatment. Furthermore, exogenous trehalose can enhance salt tolerance by promoting the Na+ efflux from leaf salt gland and root to reduce the Na+ content in root and leaf. Subsequently, eighteen trehalose‐6‐phosphate synthase (AmTPS) and 11 trehalose‐6‐phosphate phosphatase (AmTPP) genes were identified from A. marina genome. Abscisic acid (ABA) responsive elements were predicted in AmTPS and AmTPP promoters by cis‐acting elements analysis. We further identified AmTPS9A, as an important positive regulator, that increased the salt tolerance of AmTPS9A‐overexpressing Arabidopsis thaliana by altering the expressions of ion transport genes and mediating Na+ efflux from the roots of transgenic A. thaliana under NaCl treatments. In addition, we also found that ABA could promote the accumulation of trehalose, and the application of exogenous trehalose significantly promoted the biosynthesis of ABA in both roots and leaves of A. marina. Ultimately, we confirmed that AmABF2 directly binds to the AmTPS9A promoter in vitro and in vivo. Taken together, we speculated that there was a positive feedback loop between trehalose and ABA in regulating the salt tolerance of A. marina. These findings provide new understanding to the salt tolerance of A. marina in adapting to high saline environment at trehalose and ABA aspects.
Auditory brainstem response audiometry in tauopathy mouse model of human Alzheimer's disease
Authors: Burke Kali , Screven Laurel A. , Vicencio-Jimenez Sergio , Lauer Amanda M.
Published: July 2024

Alzheimer's disease (AD) is a progressive neurodegenerative disorder in which changes in hearing sensitivity precede cognitive decline. Despite a well-known link between dementia and hearing loss, few AD model mouse lines have hearing characterized. We screened for hearing loss using auditory brainstem responses (ABR) in young (3–4 months) and aging (9–10 months) mice with a P301S tauopathy (PS19 mice). Compared to wild types, aging PS19 mice did not show accelerated hearing loss but did show latency differences in centrally generated ABR waveform components. These results suggest that tauopathy causes mild central auditory dysfunction in the absence of overt hearing loss.
Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs in
Escherichia coli
Authors: Bianco Colleen M. , Caballero-Rothar Nancy N. , Ma Xiangqian , Farley Kristen R. , Vanderpool Carin K.
Published: July 2024

The small RNA (sRNA) RydC strongly activates
cfa
, which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation of
cfa
increases the conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The regulators that control RydC synthesis had not previously been identified. In this study, we identify a GntR-family transcription factor, YieP, that represses
rydC
transcription. YieP positively autoregulates its own transcription and indirectly regulates
cfa
through RydC. We further identify additional sRNA regulatory inputs that contribute to the control of RydC and
cfa
. The translation of
yieP
is repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator of
rydC
and
cfa
. Conversely, RydC activity on
cfa
is antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link the control of membrane biophysical properties to multiple environmental signals.

IMPORTANCE

Bacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.
Seasonal metabolic dynamics of microeukaryotic plankton: a year-long metatranscriptomic study in a temperate sea
Authors: Perneel Michiel , Lagaisse Rune , Mortelmans Jonas , Maere Steven , Hablützel Pascal I.
Published: July 2024

Seasonal fluctuations profoundly affect marine microeukaryotic plankton composition and metabolism, but accurately tracking these changes has been a long-standing challenge. In this study, we present a year-long metatranscriptomic data set from the Southern Bight of the North Sea, shedding light on the seasonal dynamics in temperate plankton ecosystems. We observe distinct shifts in active plankton species and their metabolic processes in response to seasonal changes. We characterized the metabolic signatures of different seasonal phases in detail, thereby revealing the metabolic versatility of dinoflagellates, the heterotrophic dietary strategy of
Phaeocystis
during its late-stage blooms, and stark variations in summer and fall diatom abundance and metabolic activity across nearby sampling stations. Our data illuminate the varied contributions of microeukaryotic taxa to biomass production and nutrient cycling at different times of the year and allow delineation of their ecological niches.

IMPORTANCE

Ecosystem composition and metabolic functions of temperate marine microeukaryote plankton are strongly influenced by seasonal dynamics. Although monitoring of species composition of microeukaryotes has expanded recently, few methods also contain seasonally resolved information on ecosystem functioning. We generated a year-long spatially resolved metatranscriptomic data set to assess seasonal dynamics of microeukaryote species and their associated metabolic functions in the Southern Bight of the North Sea. Our study underscores the potential of metatranscriptomics as a powerful tool for advancing our understanding of marine ecosystem functionality and resilience in response to environmental changes, emphasizing its potential in continuous marine ecosystem monitoring to enhance our ecological understanding of the ocean's eukaryotic microbiome.
A network of acetyl phosphate-dependent modification modulates c-di-AMP homeostasis in
Actinobacteria
Authors: Fu Yu , Zhao Liu-Chang , Shen Jin-Long , Zhou Shi-Yu , Yin Bin-Cheng , Ye Bang-Ce , You Di
Published: July 2024

Cyclic purine nucleotides are important signal transduction molecules across all domains of life. 3′,5′-cyclic di-adenosine monophosphate (c-di-AMP) has roles in both prokaryotes and eukaryotes, while the signals that adjust intracellular c-di-AMP and the molecular machinery enabling a network-wide homeostatic response remain largely unknown. Here, we present evidence for an acetyl phosphate (AcP)-governed network responsible for c-di-AMP homeostasis through two distinct substrates, the diadenylate cyclase
D
NA
i
ntegrity
s
canning protein (DisA) and its newly identified transcriptional repressor, DasR. Correspondingly, we found that AcP-induced acetylation exerts these regulatory actions by disrupting protein multimerization, thus impairing c-di-AMP synthesis via K66 acetylation of DisA. Conversely, the transcriptional inhibition of
disA
was relieved during DasR acetylation at K78. These findings establish a pivotal physiological role for AcP as a mediator to balance c-di-AMP homeostasis. Further studies revealed that acetylated DisA and DasR undergo conformational changes that play crucial roles in differentiation. Considering the broad distribution of AcP-induced acetylation in response to environmental stress, as well as the high conservation of the identified key sites, we propose that this unique regulation of c-di-AMP homeostasis may constitute a fundamental property of central circuits in
Actinobacteria
and thus the global control of cellular physiology.

IMPORTANCE

Since the identification of c-di-AMP is required for bacterial growth and cellular physiology, a major challenge is the cell signals and stimuli that feed into the decision-making process of c-di-AMP concentration and how that information is integrated into the regulatory pathways. Using the bacterium
Saccharopolyspora erythraea
as a model, we established that AcP-dependent acetylation of the diadenylate cyclase DisA and its newly identified transcriptional repressor DasR is involved in coordinating environmental and intracellular signals, which are crucial for c-di-AMP homeostasis. Specifically, DisA acetylated at K66 directly inactivates its diadenylate cyclase activity, hence the production of c-di-AMP, whereas DasR acetylation at K78 leads to increased
disA
expression and c-di-AMP levels. Thus, AcP represents an essential molecular switch in c-di-AMP maintenance, responding to environmental changes and possibly hampering efficient development. Therefore, AcP-mediated posttranslational processes constitute a network beyond the usual and well-characterized synthetase/hydrolase governing c-di-AMP homeostasis.
The coding complete genomic sequence of a feline panleukopenia virus detected from a domestic cat (
Felis catus
) in Chattogram, Bangladesh
Authors: Akter Jesmin , Nath Chandan , Hossain Md Saddam , Ahaduzzaman Md
Published: July 2024

The coding complete genome sequence of the feline panleukopenia virus (FPLV), detected from an indigenous cat in Bangladesh, has been determined. The genome spans 4,842 bp and contains four protein-coding genes. The genome will contribute to a comprehensive understanding of the genetic traits and evolutionary trends of FPLV.
Microbiological and functional traits of peri-implant mucositis and correlation with disease severity
Authors: Feng Ziying , Zhu Jinzan , Zhang Limin , Li Chunchun , Su Duyao , Wang Huihui , Yu Youcheng , Song Liang
Published: July 2024

Osseointegrated dental implants replace missing teeth and create an artificial surface for biofilms of complex microbial communities to grow. These biofilms on implants and dental surfaces can trigger infection and inflammation in the surrounding tissue. This study investigated the microbial characteristics of peri-implant mucositis (PM) and explored the correlation between microbial ecological imbalance, community function, and disease severity by comparing the submucosal microflora from PM with those of healthy inter-subject implants and intra-subject gingivitis (G) within a group of 32 individuals. We analyzed submucosal plaques from PM, healthy implant (HI), and G sites using metagenome shotgun sequencing. The bacterial diversity of HIs was higher than that of PM, according to the Simpson index. Beta diversity revealed differences in taxonomic and functional compositions across the groups. Linear discriminant analysis of the effect size identified 15 genera and 37 species as biomarkers that distinguished PM from HIs. Pathways involving cell motility and protein processing in the endoplasmic reticulum were upregulated in PM, while pathways related to the metabolism of cofactors and vitamins were downregulated. Microbial dysbiosis correlated positively with the severity of clinical inflammation measured by the sulcus bleeding index (SBI) in PM.
Prevotella
and protein processing in the endoplasmic reticulum also correlated positively with the SBI. Our study revealed PM’s microbiological and functional traits and suggested the importance of certain functions in disease severity.

IMPORTANCE

Peri-implant mucositis is an early stage in the progression of peri-implantitis. The high prevalence of it has been a threat to the widespread use of implant prosthodontics. The link between the submucosal microbiome and peri-implant mucositis was demonstrated previously. Nevertheless, the taxonomic and functional composition of the peri-implant mucositis microbiome remains controversial. In this study, we comprehensively characterize the microbial signature of peri-implant mucositis and for the first time, we investigate the correlations between microbial dysbiosis, functional potential, and disease severity. With the help of metagenomic sequencing, we find the positive correlations between microbial dysbiosis, genus
Prevotella
, pathway of protein processing in the endoplasmic reticulum, and more severe mucosal bleeding in the peri-implant mucositis. Our studies offer insight into the pathogenesis of peri-implant mucositis by providing information on the relationships between community function and disease severity.
Antibacterial potential of
Stenotrophomonas maltophilia
complex cystic fibrosis isolates
Authors: Crisan Cristian V. , Pettis Morgan L. , Goldberg Joanna B.
Published: July 2024

Over 160,000 people worldwide suffer from cystic fibrosis (CF), a genetic condition that causes mucus to accumulate in internal organs. Lung decline is a significant health burden for people with CF (pwCF), and chronic bacterial pulmonary infections are a major cause of death.
Stenotrophomonas maltophilia
complex (Smc) is an emerging, multidrug-resistant CF pathogen that can cause pulmonary exacerbations and result in higher mortality. However, little is known about the antagonistic interactions that occur between Smc isolates from pwCF and competitor bacteria. We obtained 13 Smc isolates from adult and pediatric pwCF located in the United States or Australia. We co-cultured these isolates with
Pseudomonas aeruginosa
,
Staphylococcus aureus,
and
Escherichia coli
. We also performed whole-genome sequencing of these Smc isolates and compared their genomes using average nucleotide identity analyses. We observed that some Smc CF isolates can engage in antagonistic interactions with
P. aeruginosa
and
S. aureus
but recovered a substantial number of
P. aeruginosa
and
S. aureus
cells following co-cultures with all tested Smc isolates. By contrast, we discovered that most Smc CF isolates display strong antibacterial properties against
E. coli
cells and reduce recovery below detectable limits. Finally, we demonstrate that Smc CF strains from this study belong to diverse phylogenetic lineages.

IMPORTANCE

Antagonism toward competitor bacteria may be important for the survival of
Stenotrophomonas maltophilia
complex (Smc) in external environments, for the elimination of commensal species and colonization of upper respiratory tracts to enable early infections, and for competition against other pathogens after establishing chronic infections. These intermicrobial interactions could facilitate the acquisition of Smc by people with cystic fibrosis from environmental or nosocomial sources. Elucidating the mechanisms used by Smc to eliminate other bacteria could lead to new insights into the development of novel treatments.
A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics
Authors: Ahmadi Atiyeh , Courtney Matthew , Ren Carolyn , Ingalls Brian
Published: July 2024

Time-lapse microscopy offers a powerful approach for analyzing cellular activity. In particular, this technique is valuable for assessing the behavior of bacterial populations, which can exhibit growth and intercellular interactions in a monolayer. Such time-lapse imaging typically generates large quantities of data, limiting the options for manual investigation. Several image-processing software packages have been developed to facilitate analysis. It can thus be a challenge to identify the software package best suited to a particular research goal. Here, we compare four software packages that support the analysis of 2D time-lapse images of cellular populations: CellProfiler, SuperSegger-Omnipose, DeLTA, and FAST. We compare their performance against benchmarked results on time-lapse observations of
Escherichia coli
populations. Performance varies across the packages, with each of the four outperforming the others in at least one aspect of the analysis. Not surprisingly, the packages that have been in development for longer showed the strongest performance. We found that deep learning-based approaches to object segmentation outperformed traditional approaches, but the opposite was true for frame-to-frame object tracking. We offer these comparisons, together with insight into usability, computational efficiency, and feature availability, as a guide to researchers seeking image-processing solutions.

IMPORTANCE

Time-lapse microscopy provides a detailed window into the world of bacterial behavior. However, the vast amount of data produced by these techniques is difficult to analyze manually. We have analyzed four software tools designed to process such data and compared their performance, using populations of commonly studied bacterial species as our test subjects. Our findings offer a roadmap to scientists, helping them choose the right tool for their research. This comparison bridges a gap between microbiology and computational analysis, streamlining research efforts.
Supplemental Material: Updating the Upper Cretaceous (Campanian) Two Medicine Formation of Montana (USA): Lithostratigraphic revisions, new CA-ID-TIMS U-Pb ages, and a calibrated framework for dinosaur occurrences
Authors: Rogers Raymond R. , et al.
Published: July 2024

Table S1: U-Pb isotopic data for zircon analyses from Campanian bentonites of the Two Medicine Formation, Montana, USA.
Prevalence of therapeutic use exemptions at the Olympic Games and Paralympic Games: an analysis of data from 2016 to 2022
Authors: Vernec Alan , Healy David , Banon Tamar , Petroczi Andrea
Published: July 2024

Objectives

The objectives of this study are to describe the prevalence of therapeutic use exemptions (TUEs) among athletes competing in four Olympic and four Paralympic games. The secondary objective was to present the prohibited substance and methods classes associated with TUEs.

Methods

Data from the Anti-Doping Administration and Management System were extracted for this cross-sectional observation study. Eight cohorts were created to include athletes with TUEs who competed in the Rio 2016, Pyeongchang 2018, Tokyo 2020 and Beijing 2022 Olympic and Paralympic games. Prevalence of TUEs and proportion of prohibited substance and methods classes were defined as percentages among all athletes competing at each games.

Results

28 583 athletes competed in four editions of the Olympic games. Total prevalence of athletes with TUEs was 0.90% among all competitors. At the four Paralympic games, a total of 9852 athletes competed and the total TUE prevalence was 2.76%. The most frequently observed substances associated with TUEs at the Summer Olympics were glucocorticoids (0.50% in Rio) and stimulants (0.39% in Tokyo). At the Summer Paralympics, diuretics (0.79% in Rio) and stimulants (0.75% in Tokyo) were the most common. Winter games had somewhat similar trends, although TUE numbers were very low.

Conclusions

The number of athletes competing with valid TUEs at the Olympic and Paralympic games was <1% and <3%, respectively. Variations in substances and methods associated with TUEs for different medical conditions were identified. Nevertheless, numbers were low, further reaffirming that TUEs are not widespread in elite sport.
Oblique subcostal transverse abdominis plane block for postoperative pain control in patients undergoing open sublay mesh hernia repair: a prospective double-blind randomized placebo-controlled clinical trial
Authors: Keller Marius , Dinkel Friederike , Jacoby Johann , Kraft Barbara , Haas Anne , Rosenberger Peter , Meierhenrich Rainer
Published: July 2024

Background

A bilateral oblique subcostal transverse abdominis plane block may help provide perioperative analgesia and reduce opioid use in patients undergoing sublay mesh hernia repair, but its clinical value is unclear.

Methods

In a single-centre, prospective, placebo-controlled, double-blind study, patients scheduled for sublay mesh hernia repair were randomized to receive oblique subcostal transverse abdominis plane blocks with either 60 ml of 0.375% ropivacaine (n=19) or isotonic saline (placebo, n=17). The primary outcome was patient-controlled total morphine consumption at 8:00 p.m. on the second postoperative day (POD), while secondary outcomes included the total morphine consumption during the post-anesthesia care unit stay and the occurrence of adverse events.

Results

Total morphine consumption at 8:00 p.m. on the second POD was higher in patients receiving ropivacaine (39 mg, IQR 22, 62) compared with placebo (24 mg, IQR 7, 39), p value = 0.04. In contrast, the ropivacaine group received 2 mg less morphine during the post-anesthesia care unit stay (4 mg, IQR: 4, 9 mg vs 2 mg, IQR: 2,6 mg, p = 0.04). Patients receiving ropivacaine used more morphine (8:00 p.m. on the first POD until 8:00 a.m. on the second POD: 8 mg, IQR: 4, 18 mg vs 2 mg, IQR: 0, 9 mg, p = 0.01) and reported higher maximum pain scores since the last assessment (8:00 a.m. on the second POD: 5, IQR: 4, 7 vs 4, IQR: 3, 5, p = 0.03). There were no differences in adverse events between groups.

Conclusions

Bilateral oblique subcostal transverse abdominis plane blocks in patients undergoing sublay mesh hernia repair were not associated with a prolonged reduction in patient-controlled total morphine consumption in the evening of the second POD in this study. Rebound pain might explain the additional excess opioid required by the ropivacaine group.
Development of an age-adjusted, activity-based contact probability model for infectious diseases
Authors: Hoffman Bryn , Gaas Brian , McPhee-Knowles Sara , Guillouzic Steve , Kanary Lisa
Published: July 2024

The COVID-19 pandemic highlighted the importance of gathering restrictions in slowing the spread of communicable disease. Many restrictions on activities were applied without identifying how effective the restrictions might be in curtailing disease spread. We present a model that estimates the probability of contacting an infected individual as a function of prevalence and self-reported or hypothesized activities. The model incorporates an age adjustment factor to account for differences between the age demographics of infected versus activity participants. The age adjustment factor was important to include when the difference in prevalence between age groups was sufficiently large, and prevalence and activity group sizes were moderate. We applied our contact probability model to two scenarios to demonstrate how the model may inform the development of public health measures. Our model presents a method for estimating contact probability that could be adopted by jurisdictions considering facility closures or group size limits, or for individuals evaluating their own behaviours in future outbreaks or pandemics.
Modeling Sequences as Star Graphs to Address Over-Smoothing in Self-Attentive Sequential Recommendation
Authors: Peng Bo , Chen Ziqi , Parthasarathy Srinivasan , Ning Xia
Published: July 2024

Self-attention (SA) mechanisms have been widely used in developing sequential recommendation (SR) methods, and demonstrated state-of-the-art performance. However, in this article, we show that self-attentive SR methods substantially suffer from the over-smoothing issue that item embeddings within a sequence become increasingly similar across attention blocks. As widely demonstrated in the literature, this issue could lead to a loss of information in individual items, and significantly degrade models’ scalability and performance. To address the over-smoothing issue, in this article, we view items within a sequence constituting a star graph and develop a method, denoted as

\(\mathop{\mathtt{MSSG}}\limits\)

, for SR. Different from existing self-attentive methods,

\(\mathop{\mathtt{MSSG}}\limits\)

introduces an additional internal node to specifically capture the global information within the sequence, and does not require information propagation among items. This design fundamentally addresses the over-smoothing issue and enables

\(\mathop{\mathtt{MSSG}}\limits\)

a linear time complexity with respect to the sequence length. We compare

\(\mathop{\mathtt{MSSG}}\limits\)

with eleven state-of-the-art baseline methods on six public benchmark datasets. Our experimental results demonstrate that

\(\mathop{\mathtt{MSSG}}\limits\)

significantly outperforms the baseline methods, with an improvement of as much as 10.10%. Our analysis shows the superior scalability of

\(\mathop{\mathtt{MSSG}}\limits\)

over the state-of-the-art self-attentive methods. Our complexity analysis and runtime performance comparison together show that

\(\mathop{\mathtt{MSSG}}\limits\)

is both theoretically and practically more efficient than self-attentive methods. Our analysis of the attention weights learned in SA-based methods indicates that on sparse recommendation data, modeling dependencies in all item pairs using the SA mechanism yields limited information gain, and thus, might not benefit the recommendation performance. Our source code and data are publicly accessible through
GitHub
.