bluuebunny/crossref_metadata_2025_split huggingface dataset:
First transition dynamics of reaction–diffusion equations with higher order nonlinearity
Authors: Şengül Taylan , Tiryakioglu Burhan , Yıldız Akıl Esmanur 
Published: July 2024

AbstractIn this study, the dynamics of a reaction–diffusion equation on a bounded interval at the first dynamic transition point is investigated. The main difference of this study from the existing ones in the dynamic transition literature is that in this work, no specific form of the nonlinear operator is assumed except that it is an analytic function of and . The linear operator is also assumed to be a general operator with sinusoidal eigenvectors. Moreover, we assume that there is a first transition as a real simple eigenvalue changes sign. With this general framework, we make a rigorous analysis of the dependence of the first transition dynamics on the coefficients of the Taylor expansion of the nonlinear operator. The main tool we use in this study is the center manifold reduction combined with the classification of the dynamic transition theory. This study is a generalization of a recent work where the nonlinear operator contains only low‐order (quadratic and cubic) nonlinearities. The current generalization requires certain technical difficulties such as the validity of the genericity conditions on the Taylor coefficients of the nonlinear operator and a bootstrapping argument using these genericity conditions. The results of this work can be generalized in various directions, which are discussed in the conclusions section.
Assessment of autoantibodies associated with intravenous immunoglobulin replacement therapy in children with primary immunodeficiency
Authors: Özer Murat , Tekeli Seher , Doğan Selçuk , Çetin Sema , Selen Rıdvan , Aytekin Caner 
Published: July 2024

AbstractWhile it is known that immunoglobulin replacement therapy (IgRT) used in the treatment of primary immunodeficiency disorders (PIDs) can lead to the passive transfer of autoantibodies, there is no data indicating that these antibodies can cause clinical symptoms in patients. This study aimed to investigate the presence of autoantibodies and their clinical correlation in patients diagnosed with PIDs receiving IgRT. Paediatric patients who were diagnosed with PIDs, and administered IgRT at our immunology clinic between 1 January 2012 and 31 December 2021, were included in the study. The medical records of these patients were retrospectively analysed, and autoantibodies were screened. Autoantibody screening was conducted at least once in 48 cases. Among these cases, 29 cases (60.4%) demonstrated positivity for at least one of the autoantibodies screened in the study. Among these cases, 23 tested positive for anti‐TPO, 9 for anti‐TG and 2 for both anti‐TPO and anti‐TG. Only two of these patients were confirmed to have Hashimoto's thyroiditis. In 30 cases, autoantibodies related to Celiac disease (CD) were screened, with at least one being positive in five different cases; CD was not confirmed. The results of our study suggest that passive transfer of autoantibodies to patients with IgRT does not cause any significant clinical findings. In addition, in cases of PID, autoantibodies detected in the blood passed to patients with IgRT can lead to misdiagnosis. Screening for autoantibodies in patients with PID undergoing IgRT may not yield accurate results in terms of detecting autoimmune diseases.
Revisiting the charmed circle: A reflexive examination of unanswered questions in the infidelity literature
Authors: Weiser Dana A. , Shrout M. Rosie 
Published: July 2024

AbstractInfidelity is a common experience in romantic relationships, and as such, relationships researchers have amassed a large infidelity literature. In the current manuscript, we provide a brief overview of the infidelity literature, specifically focusing on how infidelity is defined, infidelity attitudes, predictors of infidelity, and infidelity outcomes. Next, we introduce readers to the “Charmed Circle,” a theoretical perspective that conceptualizes monogamous sex as part of society's view of “good, normal, and natural” sex, otherwise known as mononormativity. As scholars, we are equally socialized in a system that endorses and reinforces mononormativity. In this article, we call on scholars to engage in reflexivity and consider how mononormativity has shaped the infidelity literature and their approach to research. We highlight pressing questions within the infidelity literature and argue that by questioning our own biases, assumptions, and methodologies, we will be able to further advance our understanding of infidelity.
Effect of gap size in grass cover on the percentage and rate of dandelion achene germination
Authors: Martinková Zdenka , Honěk Alois 
Published: July 2024

AbstractIn Central Europe, Taraxacum officinale Weber ex Wiggers (dandelion) is an economically important admixture in grasslands. Its spread is supported by its ability to germinate in gaps in grass stands. In a 5‐year experiment, we examined the effect of gap size on the germination rate and percentage of dandelion achenes. Each year, achenes were sown in late spring and mid‐summer in 90 square plots of six sizes, ranging from 2.5 × 2.5 cm to 80 × 80 cm. The plots were placed on a 2 × 6 m experimental area covered with low‐cut lawn. The course of germination varied among individual replicates depending on the weather. In each replicate, however, the rate of germination increased, and the percentage of germinated achenes decreased with increasing gap size. Differences in germination paralleled differences in the microclimate on the soil surface of plots where humidity decreased and temperature increased with plot size. The ultimate cause of this difference was the variance among gaps of different sizes in proportion to which the total area of the gap surface is insolated during the day. The colonization of lawns by dandelion is supported by the formation of small gaps in grass stands.
Antibiotic duration and route for treatment of adults with uncomplicated streptococcal bloodstream infections: a retrospective study in a large healthcare system
Authors: Clutter Dana S. , Samiezade-Yazd Zahra , Champsi Jamila H. , Schapiro Jeffrey , Silverberg Michael J. 
Published: July 2024

ABSTRACT

Data guiding the duration and route of streptococcal bloodstream infection (BSI) treatment are lacking. We conducted a retrospective cohort study of adults hospitalized with uncomplicated streptococcal BSI in a large integrated healthcare system from 2013 to 2020. The exposures of interest were antibiotic duration (5–10 days vs. 11–15 days) and antibiotic route (oral switch vs. entirely intravenous). The primary outcome was a composite 90-day outcome comprised of all-cause mortality, recurrent streptococcal BSI, or readmission. We performed non-inferiority analyses for each exposure. Separate multivariable Cox proportional hazards regression models were constructed for each exposure. The antibiotic duration analysis included 1,407 patients (5–10 days,
n
= 246; 11–15 days,
n
= 1,161). We found that 5–10-day courses were non-inferior to 11–15-day courses (
P
= 0.047). The antibiotic route analysis included 1,461 patients (oral switch,
n
= 1,112; entirely intravenous,
n
= 349). Oral step-down therapy did not meet the criteria for non-inferiority (
P
= 0.06). In the adjusted models, no significant difference was found in the primary outcome rate by antibiotic duration or antibiotic route at discharge. We found that 5–10-day courses were non-inferior to longer courses, and thus may be a safe and effective treatment option in the treatment of uncomplicated streptococcal bacteremia. Randomized controlled trials are needed to confirm the equivalent outcomes with shorter regimens and to definitively determine the optimal antibiotic route on discharge.
Developing microbiology literacy in biology education college: future teacher candidates
Authors: Fidiastuti Hasminar Rachman , Lestari Sri Rahayu , ‌ Suhadi , Prabaningtyas Sitoresmi 
Published: July 2024

ABSTRACT

Recently, several articles have reflected on the existence of microorganisms in supporting the life and health of living creatures as the beginning of the emergence of microbiology literacy. In the curriculum, understanding the activity of microorganisms has been studied from pre-school, elementary school, and middle school to college. The presence of microorganisms is often associated as a cause of disease. As a result, most students know the negative impact of microorganisms but have not discovered the fundamental role of microorganisms in their lives. Special attention needs to be given as a form of effort to strengthen microbiology literacy. Several studies state that students have an important role in disseminating the concept of sterilization, maintaining a safe distance, and using masks as generally applicable protocols during the pandemic. Therefore, with the aim that microorganisms have an important role, both directly and indirectly and to curb negative perceptions of microorganisms, we propose microbiology competencies among biology education students, who are future teaching candidates. This article identifies the complex challenges of 21st-century microbiology learning and the OECD framework. This approach includes the use of pedagogical interventions with the main objectives: (i) knowledge (to teach fundamental microbiology knowledge, (ii) skills (to increase awareness in recognizing and solving real-life problems), and (iii) attitudes and values (to explain the contribution of microbiology in supporting life).
The cellular Notch1 protein promotes KSHV reactivation in an Rta-dependent manner
Authors: DeCotiis-Mauro Jennifer , Han Sun M. , Mello Helena , Goyeneche Corey , Marchesini-Tovar Giuseppina , Jin Lianhua , Bellofatto Vivian , Lukac David M. 
Published: July 2024

ABSTRACT

The cellular Notch signal transduction pathway is intimately associated with infections by Kaposi’s sarcoma-associated herpesvirus (KSHV) and other gamma-herpesviruses. RBP-Jk, the cellular DNA binding component of the canonical Notch pathway, is the key Notch downstream effector protein in virus-infected and uninfected animal cells. Reactivation of KSHV from latency requires the viral lytic switch protein, Rta, to form complexes with RBP-Jk on numerous sites within the viral DNA. Constitutive Notch activity is essential for KSHV pathophysiology in models of Kaposi’s sarcoma (KS) and Primary Effusion Lymphoma (PEL), and we demonstrate that Notch1 is also constitutively active in infected Vero cells. Although the KSHV genome contains >100 RBP-Jk DNA motifs, we show that none of the four isoforms of activated Notch can productively reactivate the virus from latency in a highly quantitative trans-complementing reporter virus system. Nevertheless, Notch contributed positively to reactivation because broad inhibition of Notch1-4 with gamma-secretase inhibitor (GSI) or expression of dominant negative mastermind-like1 (dnMAML1) coactivators severely reduced production of infectious KSHV from Vero cells. Reduction of KSHV production is associated with gene-specific reduction of viral transcription in both Vero and PEL cells. Specific inhibition of Notch1 by siRNA partially reduces the production of infectious KSHV, and NICD1 forms promoter-specific complexes with viral DNA during reactivation. We conclude that constitutive Notch activity is required for the robust production of infectious KSHV, and our results implicate activated Notch1 as a pro-viral member of a MAML1/RBP-Jk/DNA complex during viral reactivation.

IMPORTANCE
Kaposi's sarcoma-associated herpesvirus (KSHV) manipulates the host cell oncogenic Notch signaling pathway for viral reactivation from latency and cell pathogenesis. KSHV reactivation requires that the viral protein Rta functionally interacts with RBP-Jk, the DNA-binding component of the Notch pathway, and with promoter DNA to drive transcription of productive cycle genes. We show that the Notch pathway is constitutively active during KSHV reactivation and is essential for robust production of infectious virus progeny. Inhibiting Notch during reactivation reduces the expression of specific viral genes yet does not affect the growth of the host cells. Although Notch cannot reactivate KSHV alone, the requisite expression of Rta reveals a previously unappreciated role for Notch in reactivation. We propose that activated Notch cooperates with Rta in a promoter-specific manner that is partially programmed by Rta’s ability to redistribute RBP-Jk DNA binding to the virus during reactivation.
Metabolic changes in
Toxoplasma gondii
-infected host cells measured by autofluorescence imaging
Authors: Gallego-López Gina M. , Contreras Guzman Emmanuel , Desa Danielle E. , Knoll Laura J. , Skala Melissa C. 
Published: July 2024

ABSTRACT

Toxoplasma gondii,
the causative agent of toxoplasmosis, is an obligate intracellular parasite that infects warm-blooded vertebrates across the world. In humans, seropositivity rates of
T. gondii
range from 10% to 90% across communities. Despite its prevalence, few studies address how
T. gondii
infection changes the metabolism of host cells. In this study, we investigate how
T. gondii
manipulates the host cell metabolic environment by monitoring the metabolic response over time using noninvasive autofluorescence lifetime imaging of single cells, metabolite analysis, extracellular flux analysis, and reactive oxygen species (ROS) production. Autofluorescence lifetime imaging indicates that infected host cells become more oxidized and have an increased proportion of bound NAD(P)H compared to uninfected controls. Over time, infected cells also show decreases in levels of intracellular glucose and lactate, increases in oxygen consumption, and variability in ROS production. We further examined changes associated with the pre-invasion “kiss and spit” process using autofluorescence lifetime imaging, which also showed a more oxidized host cell with an increased proportion of bound NAD(P)H over 48 hours compared to uninfected controls, suggesting that metabolic changes in host cells are induced by
T. gondii
kiss and spit even without invasion.

IMPORTANCE

This study sheds light on previously unexplored changes in host cell metabolism induced by
T. gondii
infection using noninvasive, label-free autofluorescence imaging. In this study, we use optical metabolic imaging (OMI) to measure the optical redox ratio (ORR) in conjunction with fluorescence lifetime imaging microscopy (FLIM) to noninvasively monitor single host cell response to
T. gondii
infection over 48 hours. Collectively, our results affirm the value of using autofluorescence lifetime imaging to noninvasively monitor metabolic changes in host cells over the time course of a microbial infection. Understanding this metabolic relationship between the host cell and the parasite could uncover new treatment and prevention options for
T. gondii
infections worldwide.
De novo genome assembly of endophytic fungus
Nemania diffusa
strain YAFEF818, isolated from
Artemisia argyi
Authors: Yu Jiaojun , Yuan Xiaolong , Kui Yan , Li Yunqin , Bi Wei , Wang Yi 
Published: July 2024

ABSTRACT

Here, we report a draft genome sequence of endophytic fungus
Nemania diffusa
YAFEF818, isolated from
Artemisia argyi
. Oxford Nanopore Technologies PromethION and Illumina NovaSeq sequence reads were assembled using NECAT and polished using pilon to yield a 55.63 Mb genome.
Complete genome sequence of
Enterococcus faecalis
B05
Authors: Li Jiahao , Wu Xiuyun , Meng Jing 
Published: July 2024

ABSTRACT

Enterococcus faecalis
, a gram-positive bacterium, is the main intestinal bacteria in humans and animals. We report here the complete genome sequence of
E. faecalis
B05, whose genome length is 2,745,741 bp, containing 2,503 protein-coding genes, with a GC content of 37.64%.
Impact of diet change on the gut microbiome of common marmosets (
Callithrix jacchus
)
Authors: Tang-Wing Cassandra , Mohanty Ipsita , Bryant MacKenzie , Makowski Katherine , Melendez Daira , Dorrestein Pieter C. , Knight Rob , Caraballo-Rodríguez Andrés Mauricio , Allaband Celeste , Jenné Keith 
Published: July 2024

ABSTRACT

Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (
Callithrix jacchus
), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in
Escherichia coli
and
Prevotella
species and an increase in
Bifidobacterium
species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that
Bifidobacterium
species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change.

IMPORTANCE

Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in
Bifidobacterium
species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing
Bifidobacterium
species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
Evaluation of concordance of new QuantiFERON-TB Gold Plus platforms for
Mycobacterium tuberculosis
infection diagnosis in a prospective cohort of household contacts
Authors: Ruiz-Tagle Cinthya , García Patricia , Hernández Mariluz , Balcells María Elvira 
Published: July 2024

ABSTRACT

Interferon-gamma (IFN-γ) release assays play a pivotal role in tuberculosis infection (TBI) diagnosis, with QuantiFERON-TB Gold Plus—an enzyme-linked immunosorbent assay (ELISA)—among the most widely utilized. Newer QuantiFERON-TB platforms with shorter turnaround times were recently released. We aimed to evaluate these platforms’ agreement in the diagnosis of TBI. Blood samples from a prospective cohort of tuberculosis household contacts were collected at baseline and after 12 weeks of follow-up, and tested with LIAISON, an automated chemiluminescence immunoassay (CLIA) system, QIAreach, a lateral flow (QFT-LF) semi-automated immunoassay, and the ELISA QuantiFERON-TB Gold Plus platform. Test concordances were analyzed. ELISA vs CLIA overall agreement was 83.3% for all tested samples (120/144) [Cohen’s kappa coefficient (κ): 0.66 (95% CI: 0.54–0.77)]. Samples positive with CLIA provided consistently higher IFN-γ levels than with ELISA (
P
< 0.001). Twenty-four (16.7%) discordant pairs were obtained, all CLIA-positive/ELISA-negative: 15 (62.5%) had CLIA IFN-γ levels within borderline values (0.35–0.99 IU/mL) and 9 (37.5%) >0.99 IU/mL. QFT-LF showed only 76.4% (68/89) overall agreement with ELISA [κ: 0.53 (95% CI: 0.37–0.68)] with 21 (23.6%) discordant results obtained, all QFT-LF-positive/ELISA-negative. Overall concordance between ELISA and CLIA platforms was substantial, and only moderate between ELISA and QFT-LF. The CLIA platform yielded higher IFN-γ levels than ELISA, leading to an almost 17% higher positivity rate. The techniques do not seem interchangeable, and validation against other gold standards, such as microbiologically-confirmed tuberculosis disease, is required to determine whether these cases represent true new infections or whether CLIA necessitates a higher cutoff.

IMPORTANCE

Tuberculosis is an airborne infectious disease caused by
Mycobacterium tuberculosis
that affects over 10 million people annually, with over 2 billion people carrying an asymptomatic tuberculosis infection (TBI) worldwide. Currently, TBI diagnosis includes tuberculin skin test and the blood-based interferon-gamma (IFN-γ) release assays, with Qiagen QuantiFERON-TB Gold Plus (QFT) being among those most widely utilized. We evaluated Qiagen's newer QFT platforms commercially available in a prospective cohort of tuberculosis contacts. A substantial agreement was obtained between the current QFT-enzyme-linked immunosorbent assay (ELISA) and the new QFT-chemiluminescence immunoassay (CLIA) platform, although QFT-CLIA provided higher concentrations of IFN-γ, leading to a 16.6% higher positivity rate. We highlight that both platforms may not be directly interchangeable and that further validation is required.
New and emerging treatments for major depressive disorder
Authors: Njenga Cecilia , Ramanuj Parashar Pravin , de Magalhães Frederico Jose Coelho , Pincus Harold Alan 
Published: July 2024

Abstract
Major depressive disorder (MDD) affects a substantial portion of the population; however, much is still unknown about the pathophysiology of this disorder. Treatment resistance highlights the heterogeneous nature of MDD and the need for treatments to target more than monoamine neurotransmission. This review summarizes research into the new and emerging targets of MDD. These include drugs such as psychedelics, antibiotics, opioid modulators, neuropeptides, and onabotulinumtoxin. Neuromodulatory treatments such as light based therapies and neuromodulation involving either magnetic or electrical stimulation are also discussed. Almost all interventions, pharmacological and neuromodulation, were trialed as adjunctive treatments to an antidepressant. Most research has been conducted on psychedelics, with trials suggesting rapid antidepressant and anti-suicidal effects. Trial findings, tolerability, study design limitations and quality of research have been considered throughout this review. There remains challenges in forming recommendations with the current research at present. With there being considerable interest into the research of new and emerging treatments—in particular, psychedelics—there may be scope in the future to form more robust recommendations.