bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the effect of competition on the functional assembly of bryophyte and lichen communities: A process‐based model analysis
Authors: Ma Yunyao , Bader Maaike Y. , Petersen Imke , Porada Philipp 
Published: February 2024

Abstract

Environmental filtering and competition are two fundamental processes that shape plant community assembly in terms of functional composition, that is, the distribution of trait values. Understanding the role of these two processes in the assembly of non‐vascular vegetation, such as bryophytes and lichens, is important since these communities provide essential ecosystem services in many regions around the world, and these depend on functional composition. Responses of non‐vascular communities to environmental selection pressures have been explored in a range of experimental and modelling studies. However, it is still largely unknown to what extent competition affects the distribution of functional traits of non‐vascular communities. Moreover, it remains poorly explored which traits that are associated with competition are key for shaping community functional assembly.

Here, we integrated a field transplantation experiment with a process‐based model to disentangle the effects of environmental filtering and competition on the assembly of non‐vascular communities. Following the validation of environmental selection in the model using field observations, we performed a simulation experiment to understand the impacts of competition on trait distributions in non‐vascular communities growing in two temperate locations that differ in microclimatic conditions (a shaded and an open location).

Our results suggest that the functional composition is likely a result of weak competition or may not depend on competitive exclusion at all while environmental filtering plays an essential role. Plant height seems to be a key trait for competition. However, no single‐trait competition scheme could consistently explain the observed functional composition of the studied non‐vascular communities.

Synthesis. The presented model provides a new trait‐based approach for simulating the functional assembly of non‐vascular communities. Environmental filtering appears to be more essential than competition for predicting trait distributions of non‐vascular communities under temperate climatic conditions and we recommend caution in associating competition to a single trait while analysing community functional assembly.
Cellular iron depletion enhances behavioral rhythm by limiting brain Per1 expression in mice
Authors: Wu Qiong , Ren Qiuyang , Wang Xin , Bai Huiyuan , Tian Dandan , Gao Guofen , Wang Fudi , Yu Peng , Chang Yan‐Zhong 
Published: February 2024

AbstractAimsDisturbances in the circadian rhythm are positively correlated with the processes of aging and related neurodegenerative diseases, which are also associated with brain iron accumulation. However, the role of brain iron in regulating the biological rhythm is poorly understood. In this study, we investigated the impact of brain iron levels on the spontaneous locomotor activity of mice with altered brain iron levels and further explored the potential mechanisms governing these effects in vitro.ResultsOur results revealed that conditional knockout of ferroportin 1 (Fpn1) in cerebral microvascular endothelial cells led to brain iron deficiency, subsequently resulting in enhanced locomotor activity and increased expression of clock genes, including the circadian locomotor output cycles kaput protein (Clock) and brain and muscle ARNT‐like 1 (Bmal1). Concomitantly, the levels of period circadian regulator 1 (PER1), which functions as a transcriptional repressor in regulating biological rhythm, were decreased. Conversely, the elevated brain iron levels in APP/PS1 mice inhibited autonomous rhythmic activity. Additionally, our findings demonstrate a significant decrease in serum melatonin levels in Fpn1cdh5 ‐CKO mice compared with the Fpn1flox/flox group. In contrast, APP/PS1 mice with brain iron deposition exhibited higher serum melatonin levels than the WT group. Furthermore, in the human glioma cell line, U251, we observed reduced PER1 expression upon iron limitation by deferoxamine (DFO; iron chelator) or endogenous overexpression of FPN1. When U251 cells were made iron‐replete by supplementation with ferric ammonium citrate (FAC) or increased iron import through transferrin receptor 1 (TfR1) overexpression, PER1 protein levels were increased. Additionally, we obtained similar results to U251 cells in mouse cerebellar astrocytes (MA‐c), where we collected cells at different time points to investigate the rhythmic expression of core clock genes and the impact of DFO or FAC treatment on PER1 protein levels.ConclusionThese findings collectively suggest that altered iron levels influence the circadian rhythm by regulating PER1 expression and thereby modulating the molecular circadian clock. In conclusion, our study identifies the regulation of brain iron levels as a potential new target for treating age‐related disruptions in the circadian rhythm.
DO STRONGER PATENTS LEAD TO FASTER INNOVATION? THE EFFECT OF CLUSTERED SEARCH
Authors: Das Kaustav , Klein Nicolas 
Published: February 2024

AbstractWe analyze a patent race between two firms choosing between an established and an innovative method. The unique Markov‐perfect equilibrium coincides with the cartel solution if and only if firms have the same ability of leveraging a good innovative method or there is no patent protection. Otherwise, equilibrium efforts are clustered too much in the innovative method, as compared to the cartel benchmark. The expected time to a breakthrough is minimized at an interior patent strength. Thus, a decrease in R&D productivity can go hand‐in‐hand with a concentration of research efforts in riskier areas and stronger patent protections.
Predicting health effects of food compounds via ensemble machine learning
Authors: Mei Suyu 
Published: February 2024

SummaryIdentifying natural or synthetic compounds in foods and assaying their bioactivities have significantly contributed to promoting human health. In this work, we propose a machine learning framework to predict 101 classes of health effects of food compounds at a large scale. In this framework, random undersampling boosting (RUSBoost) is used as base learners to tackle the problem of skewed class distributions and MACCSKeys similarity spectra are proposed as a feature engineering strategy to represent chemical molecules including food compounds, natural products and drugs. Computational results show that RUSBoost learners encouragingly reduce model biases, and that the knowledge learnt from food compounds is well transferable to natural products (0.8406–0.9040 recall rates for antibacterial, antivirals, pesticide and anticancer effects) and drugs (0.789–0.9690 recall rates for antibacterial, antiviral, antineoplastic and analgesic effects). and. Dozens of novel effects have been validated in recent literature. These pieces of evidence show that the proposed framework could help us to find lead compounds from food as potential pharmaceuticals and repurpose drugs for anticancer, antiviral or antibacterial therapies. Finally, we use the proposed framework to predict beneficial and risky health effects of food flavour compounds as case studies for recipe composing.
Efficacy and safety of bipolar fractional radiofrequency vs. 2940‐nm Er:YAG ablative fractional laser in striae distensae treatment: A split abdomen study
Authors: Shen Jie , Jin Jing‐Jing , Huang Jian‐Hua , Wang Hong‐Wei , Shi Lei 
Published: February 2024

AbstractBackgroundStriae distensae (SD) is a challenging cosmetic condition. Ablative fractional laser (AFL) is an effective method for treating SD. Recently, fractional radiofrequency (FRF) has been shown to be a promising treatment for SD; however, few studies have shown the differences between FRF and AFL in the treatment of SD.AimsThis study aimed to evaluate and compare the clinical efficacy and safety of bipolar FRF with 2940‐nm erbium yttrium aluminum garnet (Er:YAG) AFL in the treatment of SD.Patients/MethodsTwenty volunteers with abdominal SD were enrolled in this study. One half of the abdomen was treated with 2940‐nm Er:YAG AFL, whereas the other half was treated with bipolar FRF, with three sessions at 4‐week intervals. Photographic evaluations of clinical improvement were conducted by two independent investigators before and after treatment, and the patients provided self‐assessments. Two participants underwent three punch biopsies, one before treatment and two obtained from bilateral representative skin lesions on the abdomen 3 months following the final treatment.ResultsClinical improvements were observed in SD on both sides of the abdomen after the two treatments. Post‐treatment skin biopsies revealed increased thickness in the epidermis and dermis, and higher collagen and elastin density compared to those at the baseline. No statistically significant differences were observed in the clinical outcomes between the two treatment approaches.ConclusionsThe efficacy and safety of bipolar FRF treatment are comparable to those of 2940‐nm Er:YAG AFL treatment, providing an alternative and effective treatment for SD.
Complete genome sequence of
Afipia carboxidovorans
strain SH125, a non-denitrifying nitrous oxide-reducing bacterium isolated from anammox biomass
Authors: Oba Kohei , Yasuda Shohei , Terada Akihiko 
Published: February 2024

ABSTRACT

Here, we report a genome sequence of
Afipia carboxidovorans
strain SH125 isolated from an anammox reactor. This facultative anaerobic strain possesses the clade I-type nitrous oxide (N
2
O) reductase gene, devoid of nitrite- and nitric oxide reductase genes. Deciphering the genome will help explore N
2
O reducers instrumental in N
2
O mitigation.
Mapping niche-specific two-component system requirements in uropathogenic
Escherichia coli
Authors: Brannon John R. , Reasoner Seth A. , Bermudez Tomas A. , Comer Sarah L. , Wiebe Michelle A. , Dunigan Taryn L. , Beebout Connor J. , Ross Tamia , Bamidele Adebisi , Hadjifrangiskou Maria 
Published: February 2024

ABSTRACT

Sensory systems allow pathogens to differentiate between different niches and respond to stimuli within them. A major mechanism through which bacteria sense and respond to stimuli in their surroundings is two-component systems (TCSs). TCSs allow for the detection of multiple stimuli to lead to a highly controlled and rapid change in gene expression. Here, we provide a comprehensive list of TCSs important for the pathogenesis of uropathogenic
Escherichia coli
(UPEC). UPEC accounts for >75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggers
E. coli
invasion of bladder cells and an intracellular pathogenic cascade. Intracellular
E. coli
are safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellular
E. coli
. To survive in these intimately connected, yet physiologically diverse niches
E. coli
must rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify—for the first time—a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct.

IMPORTANCE

While two-component system (TCS) signaling has been investigated at depth in model strains of
Escherichia coli
, there have been no studies to elucidate—at a systems level—which TCSs are important during infection by pathogenic
Escherichia coli
. Here, we report the generation of a markerless TCS deletion library in a uropathogenic
E. coli
(UPEC) isolate that can be leveraged for dissecting the role of TCS signaling in different aspects of pathogenesis. We use this library to demonstrate, for the first time in UPEC, that niche-specific colonization is guided by distinct TCS groups.
Advancing
Toxoplasma gondii
multiplex serology
Authors: Jeske Rima , Becker Nico , Kroeller Lea , Mentzer Alexander J. , Brenner Nicole , Guy Edward , Waterboer Tim , Butt Julia 
Published: February 2024

ABSTRACT

Toxoplasma gondii
is a highly prevalent pathogen causing zoonotic infections with significant public health implications. Yet, our understanding of long-term consequences, associated risk factors, and the potential role of co-infections is still limited. Seroepidemiological studies are a valuable approach to address open questions and enhance our insights into
T. gondii
across human populations. Here, we present substantial advancements to our previously developed
T. gondii
multiplex serology assay, which is based on the immunodominant antigens SAG1 and P22. While our previous bead-based assay quantified antibody levels against multiple targets in a high-throughput fashion requiring only a small sample volume, impaired assay characteristics emerged in sample dilutions beyond 1:100 and when being transferred to magnetic beads. Both are now critical for inclusion in large-scale seroprevalence studies. Using the truncated versions, SAG1D1 and P22trunc, significantly enhanced signal-to-noise ratios were achieved with almost perfect concordance with the gold-standard Sabin–Feldman dye test. In sample dilutions of 1:100, the diagnostic accuracy of SAG1D1 and P22trunc reached sensitivities (true positive rates) of 98% and 94% and specificities (true negative rates) of 93% and 95%, respectively. Importantly, performance metrics were reproducible in a 1:1,000 sample dilution, using both magnetic and nonmagnetic beads. Thresholds for seropositivity were derived from finite mixture models and performed equally well as thresholds by receiver operating characteristic analysis. Our improved multiplex serology assay is therefore able to generate robust and reproducible performance metrics under various assay conditions. Inclusion of
T. gondii
antibody measurements with other pathogens, in multiplex serology panels will allow for large-scale seroepidemiological research.

IMPORTANCE

Toxoplasma gondii
is a pathogen of significant public health concern due to its widespread prevalence and zoonotic potential. However, our understanding of key aspects, such as risk factors for infection and disease, potential outcomes, and their trends, remains limited. Seroepidemiological studies in large cohorts are invaluable for addressing these questions but remain scarce. Our revised multiplex serology assay equips researchers with a powerful tool capable of delivering
T. gondii
serum antibody measurements with high sensitivity and specificity under diverse assay conditions. This advancement paves the way for the integration of
T. gondii
antibody measurements into multi-pathogen multiplex serology panels, promising valuable insights into public health and pathogen interactions.
Effect of smoking cessation interventions on abstinence and tuberculosis treatment outcomes among newly diagnosed patients: a randomized controlled trial
Authors: Khan Muhammad Tahir , Zaheer Sidra , Amar Washdev , Shafique Kashif 
Published: February 2024

ABSTRACT

The study evaluates the effectiveness of smoking cessation interventions [Behavioral Change Communication (BCC) and Behavioral Change Communication plus bupropion (BCC+)] compared to conventional Directly Observed Therapy Short Course (DOT) treatment in improving pulmonary tuberculosis treatment outcomes and abstinence among newly diagnosed pulmonary tuberculosis (PTB) patients, highlighting the scarcity of robust experimental studies. The current randomized controlled trial, conducted at Ojha Institute of Chest Diseases between October 2017 and June 2019, randomized 292 patients who were current smokers with newly diagnosed pulmonary tuberculosis into three arms: control (
n
= 97), BCC (
n
= 97), and BCC+ (
n
= 98) arms. The outcomes of the interventions were compared in terms of favorable treatment outcomes and abstinence achieved at the end of 6 months. Baseline characteristics were compared between groups. Cox regression quantified the effect size of interventions for both outcome variables and reported as (crude and adjusted) hazard ratios with 95% confidence intervals (CI). No statistically significant difference was observed in baseline characteristics in each arm. Both BCC+ and BCC showed a statistically significant effect in achieving favorable PTB outcomes at 6 months (aHR 2.37, 95% CI 1.52–3.70 and aHR 2.34, 95% CI 1.51–3.60), as well as for abstinence from smoking at 6 months (BCC+: aHR 4.03, 95% CI 2.18–7.44 and BCC: aHR 3.87, 95% CI 2.12–7.05) compared to the control arm. Both BCC and BCC+ aided by pharmacologic agents such as bupropion when incorporated with conventional DOTs were found to be significantly effective in attaining favorable tuberculosis treatment outcomes as well as in attaining smoking abstinence at the end of the 6-month treatment.

IMPORTANCE

This study shows that adding smoking cessation programs (with or without extra drugs like bupropion) to standard Directly Observed Treatment Short Course (DOTs) treatment for people who have recently been diagnosed with pulmonary tuberculosis has a great positive impact on how well the overall antituberculosis treatment works. Our trial shows very promising results for such a combined therapy (DOTs and smoking cessation) in a country where the burden of both tuberculosis and smoking is very high.
Orthopaedic trauma patients’ experiences with emergency department care and follow-up through Virtual Fracture Care review: a qualitative study
Authors: Willinge Gijs JA , Spierings Jelle F , Mathijssen Elke M , Goslings J Carel , Twigt Bas T , van Veen Ruben N 
Published: February 2024

ObjectivesThis study aimed to identify factors influencing orthopaedic trauma patients’ experiences and satisfaction with emergency department (ED) care and follow-up through Virtual Fracture Care (VFC) review workflow.DesignThis study employed an explorative, descriptive, qualitative design using individual, semistructured interviews.SettingAn urban level 2 trauma centre and teaching hospital in Amsterdam, the Netherlands.ParticipantsEligible patients were Dutch-speaking or English-speaking orthopaedic trauma patients, aged 18 years or above, who visited the hospital’s ED between June and September 2022, and were treated through VFC review workflow. Exclusion criteria were: reason for follow-up other than injury, eye/motor/verbal score <15 at ED admission, follow-up treatment in another hospital, treatment initiated in another hospital, acute hospital admission (<24 hours). Twenty-three patients were invited for participation, of whom 15 participated and were interviewed.ResultsSeveral influential factors contributed to seven generic themes: (1) waiting times, (2) information provision, (3) healthcare professional communication, (4) care expectations, (5) care coordination, (6) care environment and (7) patient condition. Overall, participants were satisfied with received care. Interpersonal skills of healthcare professionals, and timing and content of provided information were specifically valued. Additionally, patients stated that their needs in the ED differed from those after ED discharge, and appreciated the way the VFC review workflow addressed this. Points of improvement included more active involvement of patients in the care process and prevention of inconsistent instructions by different healthcare professionals.ConclusionsPatient experiences with ED care and VFC review follow-up are influenced by factors categorised into seven themes. The VFC review workflow effectively addresses these factors, leading to positive feedback. Recommendations for healthcare professionals include anticipating evolving post-ED information needs, engaging patients early to provide clarity about the care process, involving them in treatment decisions and expanding information provision across the entire care pathway.
Sight-threatening diabetic retinopathy and its predictors among patients with diabetes visiting Adare General Hospital in Southern Ethiopia: a hospital-based cross-sectional study
Authors: Alemayehu Henok Biruk , Tilahun Mikias Mered , Abebe Marshet Gete , Tegegn Melkamu Temeselew 
Published: February 2024

ObjectiveThe study aimed to determine the prevalence of sight-threatening diabetic retinopathy and its predictors among patients with diabetes attending Adare General Hospital in Southern Ethiopia.DesignA hospital-based cross-sectional study was conducted using a systematic random sampling method.SettingThe study was conducted at the diabetic clinic of Adare General Hospital in Sidama region, Southern Ethiopia.ParticipantsThe study included 391 patients with diabetes aged ≥18 years who had attended the diabetic clinic of Adare General Hospital in Southern Ethiopia.Main outcome measuresData were collected using questionnaires completed by an interviewer, a review of medical records and eye examinations.ResultThe study included 391 patients with diabetes with a median age of 49 years. The prevalence of sight-threatening diabetic retinopathy was 10.7% (95% CI: 7.7% to 14%). Rural dwellers (adjusted OR (AOR)=2.17, 95% CI: 1.05 to 4.46), duration of diabetes ≥6 years (AOR=2.43, 95% CI: 1.06 to 5.57), poor glycaemic control (AOR=2.80, 95% CI: 1.03 to 7.64), low physical activity (AOR=2.85, 95% CI: 1.01 to 8.05), hypertension (AOR=3.25, 95% CI: 1.48 to 7.15) and diabetic peripheral neuropathy (AOR=3.32, 95% CI: 1.18 to 9.33) were significantly associated with sight-threatening diabetic retinopathy.ConclusionThis study showed a high prevalence of sight-threatening diabetic retinopathy. Sight-threatening diabetic retinopathy was significantly associated with modified factors such as glycaemic control, hypertension, physical activity and diabetic peripheral neuropathy. Therefore, all patients with diabetes were recommended to maintain normal blood glucose, avoid hypertension, exercise regularly and have regular eye examinations.