bluuebunny/crossref_metadata_2025 huggingface dataset:
Mycobacterium tuberculosis: a new hitchhiker in the etiopathogenesis of periodontitis
Authors: MohanaSundaram ArunSundar , Gohil Namra Vinay , Etekochay Maudlyn O. , Patel Premalkumar , Gurajala Swathi , Sathanantham Shanmugarajan Thukani , Nsengiyumva Mugisha , Kumar Santosh , Emran Talha Bin
Published: January 2024

Periodontitis, a chronic inflammatory disease of the gums affects both the ligament and alveolar bone. A severe form of periodontal disease affects a strikingly high number of one billion adults globally. The disease permutes both the soft and hard tissues of the oral cavity leading to localized and systemic diseases. Periodontitis has a deleterious impact on systemic health causing diabetes, cardiovascular diseases (CVD), and other disease. The cause of the enhanced inflammatory process is due to dysbiosis and an unregulated immune response. Innate immune response and T cells trigger uninhibited cytokine release causing an unwarranted inflammatory response. The RANK- RANKL interaction between osteoblasts, immune cells, and progenitor osteoclasts results in the maturation of osteoclasts, which promote bone resorption. It is well established that dysbiosis of the oral cavity has been implicated in periodontitis. But emerging reports suggest that the pulmonary pathogen, Mycobacterium tuberculosis (Mtb), causes extrapulmonary diseases such as periodontitis. Many clinical case reports advocate the involvement of Mtb in periodontitis, which poses a threat with the surge of tuberculosis in HIV and other immunocompromised individuals. Fostering a better understanding of the mechanism, causative agents and control on inflammatory response is imperative in the prevention and treatment of periodontitis.
Protein or branched-chain amino acid intake at breakfast for muscle mass gain in older persons: A protocol for systematic review and meta-analysis
Authors: Ikeda Takashi , Tashiro Naonori , Hasegawa Takeshi , Nishiwaki Hiroki , Ohtsuka Hiroyuki , Matoba Masaaki , Noma Hisashi , Ota Erika
Published: January 2024

Background:

In recent years, prevention of sarcopenia and frailty is a matter of concern for community dwelling older persons. The recommended protein daily intake is not fulfilled by 10% of community-dwelling elderly and 35% of residents in aged-care facilities. Furthermore, the optimum time of protein consumption is unclear because of the varying combinations of intake timing and exercise. Although it is desirable to increase protein intake at breakfast and lunch without reducing intake at supper to maximize muscle protein synthesis, this is not clear for older people. Therefore, before considering whether protein consumption at breakfast is superior to other times of the day, its effectiveness needs to be clarified in older adults.

Methods:

The inclusion criterion will be healthy or frail adults older than 60 years. This protocol of systematic review adhered to the PRISMA 2020 statement. A comprehensive study strategy is designed for PubMed, EMBASE, CENTRAL, and Clinical Trials.gov. Search strategies will be made using Boolean Search Logic by an experienced librarian in systematic review search formula design. Two authors will carry out independent screening of titles, abstracts, and data extraction for randomized controlled trials. Statistical heterogeneity will be assessed by meta-analysis. Assessment of the risk of bias will be conducted using the Risk-of-bias 2 tool. Integrated data will be analyzed using Review Manager software to create summary tables. Findings summary tables for primary and secondary outcomes will be produced in accordance with the procedures in the Cochrane Handbook.

Results:

We believe that the effects of protein or BCAA intake at breakfast in older people analysed in this review will provide evidence that contributes to the establishment of treatment strategies to prevent frailty and sarcopenia.

Conclusion:

The benefits of protein intake at breakfast for the elderly will be clarified. This will encourage hospitals and elderly care facilities to review the content of the diet and encourage the elderly to change their own behavior. This is expected to ultimately reduce healthcare costs.
Targeting bile salt homeostasis in biliary diseases
Authors: Trampert David C. , Kunst Roni F. , van de Graaf Stan F.J.
Published: January 2024

Purpose of review

Advances in the understanding of bile salt synthesis, transport and signalling show the potential of modulating bile salt homeostasis as a therapeutic strategy in cholestatic liver diseases. Here, recent developments in (pre)clinical research in this field is summarized and discussed.

Recent findings

Inhibition of the apical sodium-dependent bile salt transporter (ASBT) and Na+-taurocholate cotransporting polypeptide (NTCP) seems effective against cholestatic liver diseases, as well as Farnesoid X receptor (FXR) agonism or a combination of both. While approved for the treatment of primary biliary cholangitis (PBC) and intrahepatic cholestasis of pregnancy (ICP), ursodeoxycholic acid (UDCA) has retrospectively shown carefully promising results in primary sclerosing cholangitis (PSC). The side chain shortened derivate norUDCA is of further therapeutic interest since its mechanisms of action are independent of the bile salt transport machinery. In the pathogenesis of sclerosing cholangiopathies, a skewed T-cell response with alterations in gut microbiota and bile salt pool compositions are observed. In PSC pathogenesis, the bile salt receptor Takeda G-protein-coupled receptor 5 (TGR5) in cholangiocytes is implicated, whilst in immunoglobulin G4-related cholangitis the autoantigens annexin A11 and laminin 511-E8 are involved in protecting cholangiocytes.

Modulating bile salt homeostasis has proven a promising treatment strategy in models of cholestasis and are continuously being further developed. Confirmatory clinical studies are needed in order to assess the proposed treatment strategies in patients allowing for a broader therapeutic arsenal in the future.
Effectiveness of rivaroxaban in preventing cerebral venous thromboembolism: a systematic review and meta-analysis
Authors: Netha Aadarsh , Mazhar Saad , Azhar Aima , Moeez Abdul , Choradia Aakash , Mohtashim Ali , Anees Usama , Ejaz Umer , Tariq Muhammad Uzair , Jawad Sayed
Published: January 2024

Background:

Cerebral venous thromboembolism (CVT) poses a significant risk of venous infarction and haemorrhage, which can lead to neurological deficits and, in severe cases, even death. The optimal treatment regimen for patients with CVT remains unclear.

Methods:

MEDLINE, Embase, Google Scholar, Web of Science (WoS), and Cochrane Central databases were searched for randomized controlled trials (RCTs) and observational studies assessing the efficacy and safety of rivaroxaban in patients with CVT. All-site venous thromboembolism (VTE), risk of clinically relevant non-major bleeding, incidence of partial recanalization, complete recanalization and major haemorrhage were among outcomes of interest. Mantel–Haenszel weighted random-effects model was used to calculate relative risks (RRs) with 95% CIs.

Results:

The analysis included 1 RCT and 3 observational studies containing 211 patients. Compared to vitamin K antagonists (VKAs), rivaroxaban did not significantly decrease the all-site VTE [RR 0.31 (95% CI 0.01, 8.43); P=0.49, I2=0%]. Compared with VKAs, patients on rivaroxaban did not show a significantly reduced risk of recurrent cerebral venous thrombosis. In terms of incidence of partial recanalization, there was no discernible difference between rivaroxaban and VKAs [RR 0.90 (95% CI 0.66, 1.22); P=0.49, I2=0%]. There was no discernible difference in incidence of complete recanalization [RR 0.98 (95% CI 0.32, 3.03); P=0.97, I2=28%] and incidence of major haemorrhage [RR 0.19 (95% CI 0.01, 4.54); P=0.30].

Conclusion:

Rivaroxaban was found to have similar efficacy to VKAs. Due to its lower risk of severe bleeding and no need for INR monitoring, rivaroxaban may be a preferable treatment option for CVT.
A Moderation Model for Bolstering Resilience to Suicidal Psychopathology
Authors: Garg Sunny , Kharb Aakanksha
Published: January 2024

Positive sociopsychological constructs and coping flexibility may be helpful for alleviating suicidal psychopathology, although relatively little research has examined this possibility among medical students. This survey aimed to investigate whether positive sociopsychological constructs and coping flexibility could buffer the negative impact of daily life stress and bolster the resilience to suicidal ideations and attempts among medical students. This cross-sectional model was based on a study of 787 Indian medical students (725 women and 62 men; mean age, 21.08 years; SD = 2.78; range, 19–37 years) who were asked to complete a battery of self-administered questionnaires. For the purpose of determining the independent and interaction impacts of potential variables of influence, hierarchical multiple linear regression models were used. The moderation analysis investigated that the association between daily life stress and suicidal ideation was buffered among the students having higher levels of positive mental health and coping flexibility, whereas this association was no longer significant at the highest level of positive mental health. Furthermore, the relationship between daily life stress and suicidal attempts continued to be buffered by above-average levels of coping flexibility, emotional stability (ES), and optimism. These findings represent that promoting positive mental health, coping flexibility, ES, and optimism may be a promising approach to mitigate suicidal thoughts and attempts in interventions for medical students at high risk. These modifiable moderating factors can be enhanced by empirically supported treatment and prevention efforts to bolster suicidal resilience.
A Transdiagnostic Model for Depression, Anxiety, and Obsessive-Compulsive Disorder
Authors: Oktay Fatma , Dağ İhsan
Published: January 2024

Depression, obsessive-compulsive disorder (OCD), and anxiety disorders (ADs) can seriously impair functionality. Studies have shown that there are common mechanisms in the emergence of these disorders. This study discussed unpredictability beliefs, family unpredictability, locus of control, intolerance of uncertainty, emotional regulation difficulties, and coping styles. In this study, a model created with these transdiagnostic variables that play a role in the emergence of depression, OCD, and ADs was tested. The sample of the study consisted of 795 people. The model explained a significant part of the variance in psychological symptoms. In addition to various limitations, it is thought that this study has important contributions to the field by examining the relationships between unpredictability beliefs and various variables for the first time, and bringing together many transdiagnostic factors related to psychological symptoms. In addition, it provides valuable information for clinicians as it provides a basis for intervention programs targeting many transdiagnostic mechanisms.
Effect of a Virtual Reality Simulation Modality on Registered Nurse Knowledge and Behavior Related to Clostridioides difficile Prevention
Authors: Phillips Jessica M. , Harper Mary G. , Brecht Mary-Lynn , DeVon Holli A.
Published: January 2024

Virtual reality simulation (VRS) has emerged as an educational methodology in nursing professional development. A cluster randomized controlled trial was conducted with a sample of clinical registered nurses to compare effectiveness of VRS and traditional education on knowledge and behavior related to Clostridioides difficile prevention. No significant differences were found in the effectiveness of the two modalities, suggesting the usefulness of VRS as a teaching methodology.
Quality Improvement Project to Standardize a Nurse Extern Program Across A Multistate Health System
Authors: Walter Mandy
Published: January 2024

A multistate health system updated the nurse extern policy and skills list. Because of a knowledge gap and inconsistent practices, there was a need for a standardized program. A literature review, Internet search, and focus group informed the creation of the nurse extern program. The program, which includes a toolkit and role-specific pathways, aligns training practices across the health system.
Reconstruction of an Early-Stage Scapholunate Advanced Collapse Wrist with the 3-Ligament Tenodesis Procedure: A Controversial Reappraisal
Authors: Dullemans Kasper N. , van der Oest Mark J. W. , Hakkesteegt Stefanie N. , Vermeulen Guus M. , Zuidam J. Michiel , Duraku Liron S. ,   Hand-Wrist Study Group, Feitz Reinier
Published: January 2024

Background:

The authors hypothesized that the 3-ligament tenodesis (3-LT) procedure is still sufficient—even in scapholunate advanced collapse (SLAC) cases—to reduce pain and improve wrist function. The authors compared patient-reported outcomes of scapholunate interosseus ligament (SLIL) injury patients with SLAC, to SLIL injury patients treated with 3-LT, and then to patients who underwent proximal row carpectomy (PRC), as a control group.

Methods:

The authors included all patients with a traumatic SLIL injury and associated SLAC components treated with 3-LT and completed patient-rated wrist evaluation (PRWE) questionnaires preoperatively and at 12-month follow-up. First, the authors compared matched patients with SLIL injury and SLIL injury with SLAC, stage 1 to 3, who received 3-LT. Second, the authors compared patients who received 3-LT with patients who underwent PRC, while having SLAC stage 2 or 3.

Results:

The authors compared 51 patients with SLAC to 95 patients with SLIL injury who had a 3-LT procedure, and 10 3-LT patients were compared with 18 patients undergoing PRC, given SLAC stage 2 or 3. In both analyses, the PRWE scores had significantly improved in all groups; however, no significant differences in PRWE were found between 3-LT in SLIL injury and SLIL injury with SLAC (6.9 points; 95% CI, −14.92 to 1.22; P = 0.096) and between 3-LT and PRC, given SLAC stage 2 or 3, 15.1 points (not enough power).

Conclusions:

There is no difference in PRWE between matched SLIL injury patients with or without degenerative changes treated with a 3-LT. Therefore, the 3-LT procedure seems to be a viable treatment option for patients with early-stage SLAC wrist.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Patient Decision Aids for Breast Cancer Reconstruction: A Systematic Review and Network Meta-Analysis of Randomized Controlled Trials
Authors: Su Yunjhen , Sun Chin-Yu , Chiu Wen-Kuan , Kang Yi-No , Chen Chiehfeng
Published: January 2024

Background:

Breast cancer has surpassed lung cancer to become the most frequently diagnosed cancer in women. There has been a dramatic increase in the use of breast reconstruction after mastectomy. However, struggle in making decisions regarding breast reconstruction has existed. Thus, a study of decision aids (DAs) needs to be conducted, and further studies are needed to promote better DAs. This review discusses how DAs can be used to help women make decisions about breast reconstruction after mastectomy. In addition, the review was the first to compare different DA formats to determine which one is most effective.

Methods:

The authors searched for relevant studies published before October of 2022 in PubMed and Embase using the medical subject headings “breast reconstruction” and “decision aid.” Demographic data and decision, outcomes, and instruments used for assessment were also collected. Risk of bias was measured by the Cochrane Risk of Bias 2 tool.

Results:

A network meta-analysis of 14 RCTs with a total of 1401 patients were included. A total of 90.9% participants presented usable results for evaluation of decisional conflict, and web-based DA (−0.3; 95% CI, −0.56 to −0.05) showed significant improvement; 50.3% of participants provided results of decisional regret, and no subgroups showed significant reduction; 60.3% of participants contributed to results for knowledge, and web-based DA (0.61; 95% CI, 0.01 to 1.21) showed the most positive effect. A total of 44.5% of participants were included for evaluation of satisfaction, and web-based DA (0.44; 95% CI, 0.15 to 0.72) revealed significant increase.

Conclusion:

The review concluded that web-based DAs are the favorable format of DA.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, II.
Extracranial Vascular Malformations Increase Cardiovascular Disease Risk: A Nationwide Population-Based Cohort Study
Authors: Ryu Jeong Yeop , Chang Yong June , Lee Joon Seok , Choi Kang Young , Yang Jung Dug , Lee Seok-Jong , Lee Jongmin , Huh Seung , Kim Ji Yoon , Chung Ho Yun
Published: January 2024

Background:

Extracranial vascular malformations affect vessel inflammation, clotting, and ischemia. However, the relationship between extracranial vascular malformations and myocardial infarction (MI) or stroke has not been fully elucidated. Limited studies have investigated the association between extracranial vascular malformations and cardiovascular diseases.

Methods:

A total of 48,701 patients with extracranial vascular malformations and a control cohort of 487,010 age- and sex-matched participants from the Korean National Health Insurance database were included. The incidence and risk of MI, ischemic stroke (IS), and hemorrhagic stroke (HS) between participants with extracranial vascular malformations and the control cohort was compared.

Results:

After adjusting for other cardiovascular disease risk factors, the adjusted hazard ratios (aHRs) for venous malformations, capillary malformations (CMs), arteriovenous malformations (AVMs), and lymphatic malformations in patients with acute MI were 1.25 (CI, 1.04 to 1.50), 1.41 (CI, 1.24 to 1.61), 1.68 (CI, 1.18 to 2.37), and 1.40 (CI, 1.31 to 1.48), respectively. For IS, the aHRs were 1.55 (CI, 1.35 to 1.77), 1.92 (CI, 1.74 to 2.11), 1.13 (CI, 0.78 to 1.64), and 1.51 (CI, 1.44 to 1.58), respectively. For HS, the aHRs were 1.51 (CI, 1.12 to 2.05), 5.63 (CI, 4.97 to 6.38), 2.93 (CI, 1.82 to 4.72), and 1.34 (CI, 1.20 to 1.50), respectively.

Conclusions:

Independent of cardiovascular risk factors, extracranial vascular malformations were associated with an increased risk of MI, IS, and HS. For patients with CMs and AVMs, intracerebral hemorrhage risk was particularly high, accounting for 563% and 293%, respectively. Therefore, even in patients with extracranial CMs or AVMs, performing diagnostic evaluations for cerebral AVMs and using measures to prevent intracerebral hemorrhage are crucial.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, II.
Evaluating Independent Double Checks in the Pediatric Intensive Care Unit: A Human Factors Engineering Approach
Authors: Konwinski Leah , Steenland Caryn , Miller Kayla , Boville Brian , Fitzgerald Robert , Connors Robert , Sterling Elizabeth , Stowe Alicia , Rajasekaran Surender
Published: January 2024

Objectives

The goal of this human factors engineering-led improvement initiative was to examine whether the independent double check (IDC) during administration of high alert medications afforded improved patient safety when compared with a single check process.

Methods

The initiative was completed at a 24-bed pediatric intensive care unit and included all patients who were on the unit and received a medication historically requiring an IDC. The total review examined 37,968 high-risk medications administrations to 4417 pediatric intensive care unit patients over a 40-month period. The following 5 measures were reviewed: (1) rates of reported medication administration events involving IDC medications; (2) hospital length of stay; (3) patient mortality; (4) nurses’ favorability toward single checking; and (5) nursing time spent on administration of IDC medications.

Results

The rate of reported medication administration events involving IDC medications was not significantly different across the groups (95% confidence interval, 0.02%–0.08%; P = 0.4939). The intervention also did not significantly alter mortality (P = 0.8784) or length of stay (P = 0.4763) even after controlling for the patient demographic variables. Nursing favorability for single checking increased from 59% of nurses in favor during the double check phase, to 94% by the end of the single check phase. Each double check took an average of 9.7 minutes, and a single check took an average of 1.94 minutes.

Conclusions

Our results suggest that performing independent double checks on high-risk medications administered in a pediatric ICU setting afforded no impact on reported medication events compared with single checking.
Artificial intelligence-enabled ophthalmoscopy for papilledema: a systematic review protocol
Authors: Rambabu Lekaashree , Smith Brandon G. , Tumpa Stasa , Kohler Katharina , Kolias Angelos G. , Hutchinson Peter J. , Bashford Tom ,   on behalf of the EyeVu Consortium
Published: January 2024

Papilledema is a pathology delineated by the swelling of the optic disc secondary to raised intracranial pressure (ICP). Diagnosis by ophthalmoscopy can be useful in the timely stratification of further investigations, such as magnetic resonance imaging or computed tomography to rule out pathologies associated with raised ICP. In resource-limited settings, in particular, access to trained specialists or radiological imaging may not always be readily available, and accurate fundoscopy-based identification of papilledema could be a useful tool for triage and escalation to tertiary care centres. Artificial intelligence (AI) has seen a rise in neuro-ophthalmology research in recent years, but there are many barriers to the translation of AI to clinical practice. The objective of this systematic review is to garner and present a comprehensive overview of the existing evidence on the application of AI in ophthalmoscopy for papilledema, and to provide a valuable perspective on this emerging field that sits at the intersection of clinical medicine and computer science, highlighting possible avenues for future research in this domain.
Noise constrains heterospecific eavesdropping more than conspecific reception of alarm calls
Authors: Zhou You , Radford Andrew N. , Magrath Robert D.
Published: January 2024

Many vertebrates eavesdrop on alarm calls of other species, as well as responding to their own species' calls, but eavesdropping on heterospecific alarm calls might be harder than conspecific reception when environmental conditions make perception or recognition of calls difficult. This could occur because individuals lack hearing specializations for heterospecific calls, have less familiarity with them, or require more details of call structure to identify calls they have learned to recognize. We used a field playback experiment to provide a direct test of whether noise, as an environmental perceptual challenge, reduces response to heterospecific compared to conspecific alarm calls. We broadcast superb fairy-wren (
Malurus cyaneus
) and white-browed scrubwren (
Sericornis frontalis
) flee alarm calls to each species with or without simultaneous broadcast of ambient noise. Using two species allows isolation of the challenge of heterospecific eavesdropping independently of any effect of call structure on acoustic masking. As predicted, birds were less likely to flee to heterospecific than conspecific alarm calls during noise. We conclude that eavesdropping was harder in noise, which means that noise could disrupt information on danger in natural eavesdropping webs and so compromise survival. This is particularly significant in a world with increasing anthropogenic noise.
Ecological structure of diversity-dependent diversification in Phanerozoic marine bivalves
Authors: Foote Michael , Edie Stewart M. , Jablonski David
Published: January 2024

Rigorous analysis of diversity-dependence—the hypothesis that the rate of proliferation of new species is inversely related to standing diversity—requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment–water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.
Sir William Stanley Peart. 31 March 1922—14 March 2019
Authors: Gordon David
Published: January 2024

Sir Stanley Peart began his academic career with two fine original pieces of work: elucidating the neurotransmitter discharged from sympathetic nerves to the viscera; and characterizing the amino-acid sequence of angiotensin, the peptide released by the action of the enzyme renin. The influence of both these lines of work has been profound. First, on the understanding of neurotransmission in the autonomic nervous system, the peripheral nervous system that regulates involuntary processes in the viscera. Second, on the control of the vascular system; on hypertension and the design of antihypertensive drugs; on creation of analogues and antagonists of angiotensin; and on the therapeutic potential of inhibitors of angiotensin-converting enzyme. These achievements required intense application, originality of ideas and technique and good scientific taste in the choice of collaborators. However, he chose not to remain in the laboratory, but explicitly to be a clinician scientist, with his research growing from and illuminated by clinical practice. He created a fruitful and durable school of research in hypertension and the related subjects, inspiring and influencing a generation of clinician scientists. Among his strengths were the ability to analyse and constructively criticize research, and to recognize the aptitudes and abilities of all who had the pleasure of working with him. His academic career began as a medical student at St Mary's Hospital Medical School in London, and he spent almost all of his career at St Mary's, including 31 years as professor of medicine.
Heat conduction in live tissue during radiofrequency electrosurgery
Authors: Ran Junren , El-Kebir Hamza , Lee Yongseok , Chamorro Leonardo P. , Berlin Richard , Aguiluz Cornejo Gabriela M. , Benedetti Enrico , Giulianotti Pier C. , Bhargava Rohit , Bentsman Joseph , Ostoja-Starzewski Martin
Published: January 2024

In this paper, we propose a method to model radiofrequency electrosurgery to capture the phenomena at higher temperatures and present the methods for parameter estimation. Experimental data taken from our surgical trials performed on
in vivo
porcine liver show that a non-Fourier Maxwell–Cattaneo-type model can be suitable for this application when used in combination with an Arrhenius-type model that approximates the energy dissipation in physical and chemical reactions. The resulting model structure has the advantage of higher accuracy than existing ones, while reducing the computation time required.
A spatio-temporal model of multi-marker antimalarial resistance
Authors: Foo Yong See , Flegg Jennifer A.
Published: January 2024

The emergence and spread of drug-resistantPlasmodium falciparumparasites have hindered efforts to eliminate malaria. Monitoring the spread of drug resistance is vital, as drug resistance can lead to widespread treatment failure. We develop a Bayesian model to produce spatio-temporal maps that depict the spread of drug resistance, and apply our methods for the antimalarial sulfadoxine-pyrimethamine. We infer from genetic count data the prevalences over space and time of various malaria parasite haplotypes associated with drug resistance. Previous work has focused on inferring the prevalence of individual molecular markers. In reality, combinations of mutations at multiple markers confer varying degrees of drug resistance to the parasite, indicating that multiple markers should be modelled together. However, the reporting of genetic count data is often inconsistent as some studies report haplotype counts, whereas some studies report mutation counts of individual markers separately. In response, we introduce a latent multinomial Gaussian process model to handle partially reported spatio-temporal count data. As drug-resistant mutations are often used as a proxy for treatment efficacy, point estimates from our spatio-temporal maps can help inform antimalarial drug policies, whereas the uncertainties from our maps can help with optimizing sampling strategies for future monitoring of drug resistance.
From intestine to beyond:
Salmonella
entry factors display distinct transcription pattern upon infection in murine models
Authors: Koczerka Michaël , Lantier Isabelle , Morillon Marie , Deperne Justine , Clamagirand Camille D. , Virlogeux-Payant Isabelle , Grépinet Olivier
Published: January 2024

The infectious process of bacteria of the genus
Salmonella
requires the finely regulated use of various virulence factors. Among them, the type 3 secretion system-1 (T3SS-1) and the Rck and PagN invasins are involved in the internalization of the pathogen within eukaryotic cells, but their precise role in the host and in the pathogenic process is still poorly understood. In this study, we aimed to determine the kinetics of expression of these entry factors in a typhoid fever-like and a gastroenteritis model in mice by
in vivo
imaging using bioluminescent
Salmonella
Typhimurium reporter strains carrying chromosomal transcriptional fusions. Only
pagN
and T3SS-1 transcription has been clearly identified. Independently of the pathological model, the caecum was identified as the main transcription site of both
pagN
and the T3SS-1-encoding gene both at early and late stages of the infection. An intense transcription of
pagN
was also observed in deep organs in the typhoid fever-like model, while that of T3SS-1 remained quite sporadic in these organs, and mainly focused on the intestine all along the infection. This work will help to understand the respective role of these entry factors at the cellular level in the pathogenesis of
Salmonella in vivo
.
Features and networks of the mandible on computed tomography
Authors: Pham Tuan D. , Holmes Simon B. , Patel Mangala , Coulthard Paul
Published: January 2024

The mandible or lower jaw is the largest and hardest bone in the human facial skeleton. Fractures of the mandible are reported to be a common facial trauma in emergency medicine and gaining insights into mandibular morphology in different facial types can be helpful for trauma treatment. Furthermore, features of the mandible play an important role in forensics and anthropology for identifying gender and individuals. Thus, discovering hidden information of the mandible can benefit interdisciplinary research. Here, for the first time, a method of artificial intelligence-based nonlinear dynamics and network analysis are used for discovering dissimilar and similar radiographic features of mandibles between male and female subjects. Using a public dataset of 10 computed tomography scans of mandibles, the results suggest a difference in the distribution of spatial autocorrelation between genders, uniqueness in network topologies among individuals and shared values in recurrence quantification.
Genetic and behavioural factors affecting interpopulation colour pattern variation in two congeneric chameleon species
Authors: Keren-Rotem Tammy , Main Devon C. , Barocas Adi , Donaire-Barroso David , Haddas-Sasson Michal , Vila Carles , Shaharabany Tal , Wolf Lior , Tolley Krystal A. , Geffen Eli
Published: January 2024

We conducted a study on interpopulation variation of colour patterns in two congeneric chameleon species, which have an analogous life history. Both species are able to rapidly change colour pattern, and their context-dependent colour patterns often vary across a wide geographical range. Specifically, we tested four hypotheses that can explain the observed interpopulation variation of colour patterns by a series of behavioural field trials where the colour patterns of individuals were recorded and later analysed by a deep neural network algorithm. We used redundancy analysis to relate genetic, spectral and behavioural predictors to interpopulation colour pattern distance. Our results showed that both isolation by distance (IBD) and alternative mating tactics were significant predictors for interpopulation colour pattern variation in
Chamaeleo chamaeleon
males. By contrast, in
Chamaeleo dilepis
, the interpopulation colour pattern variation was largely explained by IBD, and evidence for alternative mating tactics was absent. In both chameleon species, the environmental colours showed no evidence of influencing chameleon interpopulation colour pattern variation, regardless of sex or behavioural context. This contrasting finding suggests that interpopulation context-dependent colour pattern variations in each species are maintained under a different set of selective pressures or circumstances.
General efficiency relation for dissipative molecular machines
Authors: Lin Milo M.
Published: January 2024

Living systems use chemical fuel to process information, assemble structures and maintain fluxes. Many of these processes are dissipative: energy is consumed purely to maintain non-equilibrium steady-state outputs. How efficiently the input energy is transduced toward the output dissipation as opposed to being lost during intermediate steps, and whether the efficiency is constrained by general principles or specific fine-tuning, are open questions. Here, applying a recent mapping from non-equilibrium systems to battery-resistor circuits, an analytic expression for the efficiency of any dissipative molecular machine driven by a chemical potential difference is derived. This expression disentangles the chemical potential from the machine’s details, whose effect on the efficiency is fully specified by a constant called the load resistance. The efficiency passes through an inflection point separating totally inefficient machines from efficient machines if the balance between chemical potential difference and load resistance exceeds thermal noise. This explains all-or-none dynein stepping with increasing ATP concentration observed in single-molecule experiments. These results indicate that energy transduction in living systems is efficient not because of idiosyncratic optimization of biomolecules, but rather because the concentration of chemical fuel is kept above a threshold level.
Cranes soar on thermal updrafts behind cold fronts as they migrate across the sea
Authors: Pekarsky Sasha , Shohami David , Horvitz Nir , Bowie Rauri C. K. , Kamath Pauline L. , Markin Yuri , Getz Wayne M. , Nathan Ran
Published: January 2024

Thermal soaring conditions above the sea have long been assumed absent or too weak for terrestrial migrating birds, forcing obligate soarers to take long detours and avoid sea-crossing, and facultative soarers to cross exclusively by costly flapping flight. Thus, while atmospheric convection does develop at sea and is used by some seabirds, it has been largely ignored in avian migration research. Here, we provide direct evidence for routine thermal soaring over open sea in the common crane, the heaviest facultative soarer known among terrestrial migrating birds. Using high-resolution biologging from 44 cranes tracked across their transcontinental migration over 4 years, we show that soaring performance was no different over sea than over land in mid-latitudes. Sea-soaring occurred predominantly in autumn when large water-air temperature difference followed mid-latitude cyclones. Our findings challenge a fundamental migration research paradigm and suggest that obligate soarers avoid sea-crossing not due to the absence or weakness of thermals but due to their low frequency, for which they cannot compensate with prolonged flapping. Conversely, facultative soarers other than cranes should also be able to use thermals over the sea. Marine cold air outbreaks, imperative to global energy budget and climate, may also be important for bird migration.
Who innovates? Abundance of novel and familiar food changes which animals are most persistent
Authors: Kikuchi David W.
Published: January 2024

Novel behaviours are the raw material of cultural evolution, yet we do not have a clear picture of when they are likely to arise. I use a state-dependent model to examine how individual age and energy reserves interact with the abundance of known and novel prey to promote dietary innovation (incorporating a new food item into the diet). I measure innovativeness as persistence in attempting to capture novel prey. I find a trend towards greater persistence among younger individuals. Decreased abundance of known prey and increased abundance of novel prey also favour persistence. However, many exceptions to these trends occur. These exceptions are critical because they may explain inconsistencies among studies of animal innovation. Care must be taken in experiments to control for multiple factors relevant to an animal's energy budget and foraging opportunities. We may learn more about innovation in experimental contexts by (i) manipulating the abundance of novel and familiar food resources, (ii) directly measuring animal age and condition, and—where possible—(iii) fitting nonlinear models to innovative behaviour. Results indicate that selection for persistence may also favour neophilia.
Anisotropic interaction and motion states of locusts in a hopper band
Authors: Weinburd Jasper , Landsberg Jacob , Kravtsova Anna , Lam Shanni , Sharma Tarush , Simpson Stephen J. , Sword Gregory A. , Buhl Camille
Published: January 2024

Swarming locusts present a quintessential example of animal collective motion. Juvenile locusts march and hop across the ground in coordinated groups called hopper bands. Composed of up to millions of insects, hopper bands exhibit aligned motion and various collective structures. These groups are well-documented in the field, but the individual insects themselves are typically studied in much smaller groups in laboratory experiments. We present, to our knowledge, the first trajectory data that detail the movement of individual locusts within a hopper band in a natural setting. Using automated video tracking, we derive our data from footage of four distinct hopper bands of the Australian plague locust,Chortoicetes terminifera. We reconstruct nearly 200 000 individual trajectories composed of over 3.3 million locust positions. We classify these data into three motion states: stationary, walking and hopping. Distributions of relative neighbour positions reveal anisotropies that depend on motion state. Stationary locusts have high-density areas distributed around them apparently at random. Walking locusts have a low-density area in front of them. Hopping locusts have low-density areas in front and behind them. Our results suggest novel insect interactions, namely that locusts change their motion to avoid colliding with neighbours in front of them.
Exploring how the fast-slow pace of life continuum and reproductive strategies structure microorganism life history variation
Authors: Romeijn Josje , Smallegange Isabel
Published: January 2024

Studying life history strategies in microorganisms can help predict their performance when complex microbial communities can be categorised into groups of organisms with similar strategies. Microorganisms are typically classified as copiotroph or oligotroph, but it has been proven difficult to generalise their life history strategies to broad lineages. Here we tested if the fast-slow continuum and reproductive strategy framework of macro-organismal life histories can be applied to microorganisms. We used demographic and energy budget data from 13 microorganisms (bacteria, fungi, a protist and a plant) to examine how generation time, survivorship, growth form, age at maturity, recruitment success, and net reproductive rate structure microbial life histories. We found that 79% of microorganism life-history variation fell along two uncorrelated axes. Like macro-organisms, we found a fast–slow pace of life continuum, including shorter-lived microorganisms at one end, and longer-lived microorganisms that mature later in life at the other. Also, like macro-organisms, we found a second, reproductive strategy axis, with microorganisms with greater lifetime reproductive success and decreased mortality at older age at one end, and microorganisms with the opposite characteristics at the other end. Microorganismal life history strategies did not covary proportionally to their shared evolutionary history. Thus, whereas this work suggests that the macro-organismal fast-slow continuum and reproductive strategy framework could be realistically applied to microorganisms, their life history processes cannot be inferred from patterns in taxonomic composition.
Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken
Authors: Rios-Galicia Bibiana , Sáenz Johan S. , Yergaliyev Timur , Roth Christoph , Camarinha-Silva Amélia , Seifert Jana
Published: January 2024

Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870T=LMG 32876T), Limosilactobacillus galli sp. nov. (DSM 113833T=LMG 32623T), Limosilactobacillus avium sp. nov. (DSM 113849T=LMG 32671T), Limosilactobacillus pulli sp. nov. (DSM 115077T=LMG 32877T), Limosilactobacillus viscerum sp. nov. (DSM 113835T=LMG 32625T), Limosilactobacillus difficilis sp. nov. (DSM 114195T=LMG 32875T) and Clostridium butanoliproducens (DSM 115076T=LMG 32878T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Faecalispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860T=LMG 32675T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species

Clostridium jeddahense

and

Clostridium sporosphaeroides

to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.
Changes in quality characteristics of makjang
depending on fermentation location and complex starters
Authors: Park Jieon , Han Myeong-Hui , Jeong Woosoo , Yeo Soo-Hwan , Kim So-Young
Published: January 2024

This study aimed to investigate the quality and microbial population changes for
90 days under two fermentation conditions, outdoors and indoors (35°C),
with starters (single or mixed) in soybean paste. Bacillus
velezensis NY12-2 (S1), Debaryomyces hansenii
D5-P5 (S2), Enterococcus faecium N78-11 (S3), and their
mixtures (M) were used for the makjang fermentation. The
content of amino-type nitrogen among the makjang samples was
highly shown in the indoors, followed by M, S3, and S2. The glutamic and
aspartic acid contents in the M sample fermented in the indoors showed the
highest values of 867.42±77.27 and 243.20±15.79 mg/g,
respectively. By the electronic tongue analysis, the M sample fermented in the
indoors exhibited lower saltiness and higher umami than the others.
Consequently, we expect that using mixed strains, such as Bacillus,
Debaryomyces, and Enterococcus, under constant
conditions showed potential to the quality improvement of soy products.
Comparison of in vitro antioxidant capacities of Phragmites communis Trin. and Phragmites japonica Steud.
Authors: Yun Kyeong Won , Seo Kyoung Sun
Published: January 2024

The rhizome of Phragmites communis Trin. is used for vomiting and belching by clearing stomach and the sprout is used as tea. Phragmites japonica is similar with P. communis except the color of sheath is purple. This study is aimed to compare the in vitro antioxidant activity, total polyphenol and flavonoids contents of P. communis and P. japonica. The antioxidant activities of fractions from the two Phragmites plants were evaluated by 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2’-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging assay. The antioxidant activity varied with plant parts and extract solvents. The fractions of leaf extract from the two Phragmites plants (4.06± 1.32-16.47±1.28%) showed higher antioxidant activity by DPPH assay compared with rhizome fractions of two Phragmites plants (0.00±0.00-14.15±0.07%), these are lower compared with ascorbic acid and butylhydroxyanisole (BHA). The highest ABTS radical scavenging activity was found for rhizome ether fraction, namely 74.95±0.56% and 73.04±1.85% for P. communis and P. japonica, these are higher than BHA. The total polyphenol and flavonoids contents were different with plant parts and extract solvents, likewise antioxidant activity. A significant correlation was shown between DPPH and ABTS radical scavenging activity. Considering the results of this study, the leaves and stems of P. communis and P. japonica are expected to be used as natural antioxidants.
Physiological activities of Pyrus pyrifolia Nakai,
malt, Ziziphus jujuba Mill., Leonurus
japonicus Houtt., Scutellaria baicalensis, and
their mixtures
Authors: Lee SooJung , Kim HyunJun , Chung Mi Ja
Published: January 2024

This study investigated the anti-inflammatory, trypsin activity, and antioxidant
effects of 11 kinds of plant extracts to discover materials for developing
optimal mixtures that improve inflammation and help digestion. Ziziphus
jujuba Mill. (ZJ), Leonurus japonicus Houtt. (LJ),
Scutellaria baicalensis (SB), Platycodon
grandiflorum, and Aster scaber extracts had
excellent anti-inflammatory effects by reducing excessive nitric oxide (NO) and
tumor necrosis factor-α content in lipopolysaccharide (LPS)-stimulated
RAW264.7 macrophages. The malt (MA), Pyrus pyrifolia Nakai
(PP), Raphanus sativus L., Platycodon
grandiflorum extracts among the 11 kinds of plant extracts had high
trypsin activity. The antioxidant activity of the plant extracts was examined by
the DPPH radical scavenging activity, and the SB, PE, JU, and MA extracts had
high antioxidant activity. Therefore, PP, MA, ZJ, LJ, and SB were selected to
develop optimal mixtures that improve inflammation and help digestion. The
extract of plant mixture containing PP, MA, ZJ, LJ, and SB in the ratio
1:1:2:1:2 (w/w) significantly inhibited NO production than the extract of PP,
MA, ZJ, LJ, and SB, respectively, in LPS-stimulated RAW 264.7 macrophages. The
DPPH radical scavenging activity of the mixture extract was significantly higher
than the extract of PP, MA, ZJ, and LJ, respectively.