bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in sleep effort mediate insomnia severity in older adults following online cognitive behavioural therapy
Authors: Kutzer Yvonne , Whitehead Lisa , Quigley Eimear , Stanley Mandy 
Published: January 2024

AbstractBackgroundTo examine treatment mechanisms of digitally delivered cognitive behavioural therapy for insomnia (CBT‐I), this study assessed the mediating effects of dysfunctional beliefs, hyperarousal, locus of control, self‐efficacy, sleep effort, and safety behaviours on self‐reported insomnia severity in older adults before and following the completion of a self‐guided, online CBT‐I program.MethodsThe baseline and follow‐up measurements were completed by 62 older adults (55 female, 89%). This was a two‐condition within‐participant design. Mediation analysis using a parallel mediation model was conducted using the MEMORE macro for repeated measure designs.ResultsOut of all the included mediator variables, only a reduction in sleep effort scores (0.88; SE 0.51; 95% CI 0.001–2.00) significantly mediated changes in insomnia severity scores following the intervention. Insomnia severity scores significantly reduced following the intervention (Mpre = 9.84, SD = 5.89, Mpost = 6.87, SD = 4.90); t(61) = 5.19, P = <0.001; d = 0.55 95% CI 0.38–0.93.ConclusionsSleep in older adults improved following digitally delivered CBT‐I, and these changes were influenced by a reduction in sleep control efforts exerted by participants. These findings highlight possible treatment pathways of CBT‐I. Further investigation of CBT‐I as a strategy to prevent sleep problems is warranted.Trial RegistrationAustralian New Zealand Clinical Trials Registry (ANZCTR), ACTRN 12619001509156; http://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=378451.
A pilot study of antimicrobial effects and ototoxicity of a Norway spruce (Picea abies) resin‐based canine otic rinse product
Authors: Aimo‐Koivisto Elina , Punakallio Laura , Järvinen Riikka , Junnila Jouni , Grönthal Thomas , Rantala Merja 
Published: January 2024

AbstractBackgroundNorway spruce (Picea abies) resin‐based products are used in human medicine. A resin‐based otic rinse also could be useful in supportive care of canine otitis externa (COE), yet information on its antimicrobial effect against canine pathogens or ototoxicity is lacking.ObjectivesTo investigate the antimicrobial properties and ototoxicity of a commercial resin‐based otic product.Materials and MethodsAntimicrobial effect was evaluated using a standardised challenge test on Staphylococcus pseudintermedius, Corynebacterium auriscanis, Pseudomonas aeruginosa, Escherichia coli, Malassezia pachydermatis, and Streptococcus halichoeri strains to measure reduction in growth after 24 h exposure to the product. Effect on cell morphology was investigated by exposing S. pseudintermedius, C. auriscanis, P. aeruginosa and M. pachydermatis to the product in 20% and 100% (v/v) concentrations for 6, 24 and 48 h, and evaluating cells by transmission (TEM) and scanning (SEM) electron microscopy. An in vitro microbial kill–rate assay also was performed. Auditory brain stem response test, clinical evaluation and postmortem histological evaluation of ear canals were undertaken on experimental guinea pigs treated with the test product or saline controls.ResultsThe product showed >log 5 growth reduction for all strains in the challenge test. TEM and SEM images showed clear changes in the cells' inner structures and deterioration of cells, and 100% (v/v) test product exposure induced microbial killing in 1–2 h. Ototoxicity was not detected in guinea pigs.Conclusions and Clinical RelevanceThe product may be an option in supportive care of COE because of antimicrobial effects and lack of ototoxic properties in a guinea pig model.
Alopecia X in a cloned Pomeranian dog
Authors: Deleporte Sébastien , Prelaud Pascal , Laffort Catherine 
Published: January 2024

AbstractA two‐year‐old Pomeranian dog with Alopecia X was cloned after accidental death. Despite earlier castration, the cloned animal developed the same lesions of Alopecia X at the same age. This observation suggests that the disease is due to genetically programmed hair cycle arrest without strong environmental influences.
Discrepancy of arithmetic progressions in grids
Authors: Fox Jacob , Xu Max Wenqiang , Zhou Yunkun 
Published: January 2024

AbstractWe prove that the discrepancy of arithmetic progressions in the d‐dimensional grid is within a constant factor depending only on d of . This extends the case , which is a celebrated result of Roth and of Matoušek and Spencer, and removes the polylogarithmic factor from the previous upper bound of Valkó from about two decades ago. We further prove similarly tight bounds for grids of differing side lengths in many cases.
Quick, Effective Screening Tasks Identify Children With Medical Conditions or Disabilities Needing Physical Literacy Support
Authors: Longmuir Patricia E. , Chubbs Payne Adam , Beshara Natalie , Brandão Leonardo R. , Wright F. Virginia , Pohl Daniela , Katz Sherri Lynne , McCormick Anna , De Laat Denise , Klaassen Robert J. , Johnston Donna L. , Lougheed Jane , Roth Johannes , McMillan Hugh J. , Venkateswaran Sunita , Sell Erick , Doja Asif , Boafo Addo , Macartney Gail , Matheson Katherine , Feldman Brian M. 
Published: January 2024

Purpose: This study evaluated screening tasks able to identify children with medical conditions or disabilities who may benefit from physical literacy. Method: Children completed ≤20 screening tasks during their clinic visit and then the Canadian Assessment of Physical Literacy (2nd edition) at a separate visit. Total Canadian Assessment of Physical Literacy scores <30th percentile were categorized as potentially needing physical literacy support. Receiver operator characteristic curves identified assessment cut points with 80% sensitivity and 40% specificity relative to total physical literacy scores. Results: 223 children (97 girls; 10.1 [2.6] y) participated. Physical activity adequacy, predilection, and physical competence achieved ≥80% sensitivity and ≥40% specificity in both data sets. Adequacy ≤ 6.5 had 86% to 100% sensitivity and 48% to 49% specificity. Daily screen time >4.9 hours combined with Adequacy ≤6.15 had 88% to 10% sensitivity and 53% to 56% specificity. Conclusions: Activity adequacy, alone or with screen time, most effectively identified children likely to benefit from physical literacy support. Adequacy and screen time questionnaires are suitable for clinical use. Similar results regardless of diagnosis suggest physical competence deficits are not primary determinants of active lifestyles. Research to enhance screening specificity is required.
The military gear microbiome: risk factors surrounding the warfighter
Authors: Kok Car Reen , Bram Zakariae , Thissen James B. , Horseman Timothy S. , Fong Keith S. K. , Reichert-Scrivner Susan A. , Paguirigan Carmen , O'Connor Kelsey , Thompson Kristina , Scheiber Alexander E. , Mabery Shalini , Ngauy Viseth , Uyehara Catherine F. , Be Nicholas A. 
Published: January 2024

ABSTRACT

Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditions of deployment or training is relatively unexplored. Opportunistic pathogens that can survive on gear represent risk factors for infection following injury, especially following combat blasts, where fibers and other materials are embedded in wounded tissue. We utilized 16S rRNA sequencing to assess the microbiome composition of different military gear types (boot, trouser, coat, and canteen) from two operational environments (training in Hawai’i and deployed in Indonesia) across time (days 0 and 14). We found that microbiome diversity, stability, and composition were dependent on gear type, training location, and sampling timepoint. At day 14, species diversity was significantly higher in Hawai’i samples compared to Indonesia samples for boot, coat, and trouser swabs. In addition, we observed the presence of potential microbial risk factors, as opportunistic pathogenic species, such as
Acinetobacter
,
Pseudomonas,
and
Staphylococcus
, were found to be present in all sample types and in both study sites. These study outcomes will be used to guide the design of antimicrobial materials and uniforms and for infection control efforts following combat blasts and other injuries, thereby improving treatment guidance during military training and deployment.

IMPORTANCE
Combat extremity wounds are vulnerable to contamination from environments of proximity to the warfighter, leading to potential detrimental outcomes such as infection and delayed wound healing. Therefore, microbial surveillance of such environments is necessary to aid the advancement of military safety and preparedness through clinical diagnostics, treatment protocols, and uniform material design.
Marinomonas mediterranea
synthesizes an R-type bacteriocin
Authors: Lucas-Elío Patricia , ElAlami Tarik , Martínez Alicia , Sanchez-Amat Antonio 
Published: January 2024

ABSTRACT

Prophages integrated into bacterial genomes can become cryptic or defective prophages, which may evolve to provide various traits to bacterial cells. Previous research on
Marinomonas mediterranea
MMB-1 demonstrated the production of defective particles. In this study, an analysis of the genomes of three different strains (MMB-1, MMB-2, and MMB-3) revealed the presence of a region named MEDPRO1, spanning approximately 52 kb, coding for a defective prophage in strains MMB-1 and MMB-2. This prophage seems to have been lost in strain MMB-3, possibly due to the presence of spacers recognizing this region in an I-F CRISPR array in this strain. However, all three strains produce remarkably similar defective particles. Using strain MMB-1 as a model, mass spectrometry analyses indicated that the structural proteins of the defective particles are encoded by a second defective prophage situated within the MEDPRO2 region, spanning approximately 13 kb. This finding was further validated through the deletion of this second defective prophage. Genomic region analyses and the detection of antimicrobial activity of the defective prophage against other
Marinomonas
species suggest that it is an R-type bacteriocin.
Marinomonas mediterranea
synthesizes antimicrobial proteins with lysine oxidase activity, and the synthesis of an R-type bacteriocin constitutes an additional mechanism in microbial competition for the colonization of habitats such as the surface of marine plants.

IMPORTANCE

The interactions between bacterial strains inhabiting the same environment determine the final composition of the microbiome. In this study, it is shown that some extracellular defective phage particles previously observed in
Marinomonas mediterranea
are in fact R-type bacteriocins showing antimicrobial activity against other
Marinomonas
strains. The operon coding for the R-type bacteriocin has been identified.
Rho-dependent termination enables cellular pH homeostasis
Authors: Bhardwaj Kanika , Kalita Arunima , Verma Neha , Prakash Anand , Thakur Ruchika , Dutta Dipak 
Published: January 2024

ABSTRACT

The termination factor Rho, an ATP-dependent RNA translocase, preempts pervasive transcription processes, thereby rendering genome integrity in bacteria. Here, we show that the loss of Rho function raised the intracellular pH to >8.0 in
Escherichia coli
. The loss of Rho function upregulates tryptophanase-A (TnaA), an enzyme that catabolizes tryptophan to produce indole, pyruvate, and ammonia. We demonstrate that the enhanced TnaA function had produced the conjugate base ammonia, raising the cellular pH in the Rho-dependent termination defective strains. On the other hand, the constitutively overexpressed Rho lowered the cellular pH to about 6.2, independent of cellular ammonia levels. Since Rho overexpression may increase termination activities, the decrease in cellular pH could result from an excess H
+
ion production during ATP hydrolysis by overproduced Rho. Furthermore, we performed
in vivo
termination assays to show that the efficiency of Rho-dependent termination was increased at both acidic and basic pH ranges. Given that the Rho level remained unchanged, the alkaline pH increases the termination efficiency by stimulating Rho’s catalytic activity. We conducted the Rho-mediated RNA release assay from a stalled elongation complex to show an efficient RNA release at alkaline pH, compared to the neutral or acidic pH, that supports our
in vivo
observation. Whereas acidic pH appeared to increase the termination function by elevating the cellular level of Rho. This study is the first to link Rho function to the cellular pH homeostasis in bacteria.

IMPORTANCE

The current study shows that the loss or gain of Rho-dependent termination alkalizes or acidifies the cytoplasm, respectively. In the case of loss of Rho function, the tryptophanase-A enzyme is upregulated, and degrades tryptophan, producing ammonia to alkalize cytoplasm. We hypothesize that Rho overproduction by deleting its autoregulatory DNA portion increases termination function, causing excessive ATP hydrolysis to produce H
+
ions and cytoplasmic acidification. Therefore, this study is the first to unravel a relationship between Rho function and intrinsic cellular pH homeostasis. Furthermore, the Rho level increases in the absence of autoregulation, causing cytoplasmic acidification. As intracellular pH plays a critical role in enzyme function, such a connection between Rho function and alkalization will have far-reaching implications for bacterial physiology.
N-acetyltransferase 10 regulates alphavirus replication via N4-acetylcytidine (ac4C) modiﬁcation of the lymphocyte antigen six family member E (LY6E) mRNA
Authors: Dang Yamei , Li Jia , Li Yuchang , Wang Yuan , Zhao Yajing , Zhao Ningbo , Li Wanying , Zhang Hui , Ye Chuantao , Ma Hongwei , Zhang Liang , Liu He , Dong Yangchao , Yao Min , Lei Yingfeng , Xu Zhikai , Zhang Fanglin , Ye Wei 
Published: January 2024

ABSTRACT
Epitranscriptomic RNA modifications can regulate the stability of mRNA and affect cellular and viral RNA functions. The N4-acetylcytidine (ac4C) modification in the RNA viral genome was recently found to promote viral replication; however, the mechanism by which RNA acetylation in the host mRNA regulates viral replication remains unclear. To help elucidate this mechanism, the roles of N-acetyltransferase 10 (NAT10) and ac4C during the infection and replication processes of the alphavirus, Sindbis virus (SINV), were investigated. Cellular NAT10 was upregulated, and ac4C modifications were promoted after alphavirus infection, while the loss of NAT10 or inhibition of its N-acetyltransferase activity reduced alphavirus replication. The NAT10 enhanced alphavirus replication as it helped to maintain the stability of lymphocyte antigen six family member E mRNA, which is a multifunctional interferon-stimulated gene that promotes alphavirus replication. The ac4C modification was thus found to have a non-conventional role in the virus life cycle through regulating host mRNA stability instead of viral mRNA, and its inhibition could be a potential target in the development of new alphavirus antivirals.

IMPORTANCE
The role of N4-acetylcytidine (ac4C) modification in host mRNA and virus replication is not yet fully understood. In this study, the role of ac4C in the regulation of Sindbis virus (SINV), a prototype alphavirus infection, was investigated. SINV infection results in increased levels of N-acetyltransferase 10 (NAT10) and increases the ac4C modification level of cellular RNA. The NAT10 was found to positively regulate SINV infection in an N-acetyltransferase activity-dependent manner. Mechanistically, the NAT10 modifies lymphocyte antigen six family member E (LY6E) mRNA—the ac4C modification site within the 3′-untranslated region (UTR) of LY6E mRNA, which is essential for its translation and stability. The findings of this study demonstrate that NAT10 regulated mRNA stability and translation efficiency not only through the 5′-UTR or coding sequence but also via the 3′-UTR region. The ac4C modification of host mRNA stability instead of viral mRNA impacting the viral life cycle was thus identified, indicating that the inhibition of ac4C could be a potential target when developing alphavirus antivirals.
Automatic patient-level recognition of four
Plasmodium
species on thin blood smear by a real-time detection transformer (RT-DETR) object detection algorithm: a proof-of-concept and evaluation
Authors: Guemas Emilie , Routier Baptiste , Ghelfenstein-Ferreira Théo , Cordier Camille , Hartuis Sophie , Marion Bénédicte , Bertout Sébastien , Varlet-Marie Emmanuelle , Costa Damien , Pasquier Grégoire 
Published: January 2024

ABSTRACT

Malaria remains a global health problem, with 247 million cases and 619,000 deaths in 2021. Diagnosis of
Plasmodium
species is important for administering the appropriate treatment. The gold-standard diagnosis for accurate species identification remains the thin blood smear. Nevertheless, this method is time-consuming and requires highly skilled and trained microscopists. To overcome these issues, new diagnostic tools based on deep learning are emerging. This study aimed to evaluate the performances of a real-time detection transformer (RT-DETR) object detection algorithm to discriminate
Plasmodium
species on thin blood smear images. The algorithm was trained and validated on a data set consisting in 24,720 images from 475 thin blood smears corresponding to 2,002,597 labels. Performances were calculated with a test data set of 4,508 images from 170 smears corresponding to 358,825 labels coming from six French university hospitals. At the patient level, the RT-DETR algorithm exhibited an overall accuracy of 79.4% (135/170) with a recall of 74% (40/54) and 81.9% (95/116) for negative and positive smears, respectively. Among
Plasmodium-
positive smears, the global accuracy was 82.7% (91/110) with a recall of 90% (38/42), 81.8% (18/22), and 76.1% (35/46) for
P. falciparum
,
P. malariae,
and
P. ovale/vivax,
respectively. The RT-DETR model achieved a World Health Organization (WHO) competence level 2 for species identification. Besides, the RT-DETR algorithm may be run in real-time on low-cost devices such as a smartphone and could be suitable for deployment in low-resource setting areas lacking microscopy experts.

IMPORTANCE

Malaria remains a global health problem, with 247 million cases and 619,000 deaths in 2021. Diagnosis of
Plasmodium
species is important for administering the appropriate treatment. The gold-standard diagnosis for accurate species identification remains the thin blood smear. Nevertheless, this method is time-consuming and requires highly skilled and trained microscopists. To overcome these issues, new diagnostic tools based on deep learning are emerging. This study aimed to evaluate the performances of a real-time detection transformer (RT-DETR) object detection algorithm to discriminate
Plasmodium
species on thin blood smear images. Performances were calculated with a test data set of 4,508 images from 170 smears coming from six French university hospitals. The RT-DETR model achieved a World Health Organization (WHO) competence level 2 for species identification. Besides, the RT-DETR algorithm may be run in real-time on low-cost devices and could be suitable for deployment in low-resource setting areas.
Longitudinal genomic surveillance of multidrug-resistant
Escherichia coli
carriage in critical care patients
Authors: El Chaar Mira , Khoury Yaralynn , Douglas Gavin M. , El Kazzi Samir , Jisr Tamima , Soussi Shatha , Merhi Georgi , Moghnieh Rima A. , Shapiro B. Jesse 
Published: January 2024

ABSTRACT

Colonization with multidrug-resistant
Escherichia coli
strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant
E. coli
strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on
E. coli
strains isolated from patients at multiple time points. The
E. coli
isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by
E. coli
sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident
E. coli
strains were tracked over time, five harbored the same
E. coli
strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different
E. coli
strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant
E. coli
strain, is also prevalent among critical care patients and deserves further monitoring.

IMPORTANCE

Understanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track
Escherichia coli
evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging
E. coli
sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.