syedzayyan/paper_mill_benchmark huggingface dataset:
Microbial transitions from health to disease.

Recent advances in our understanding of the microbial populations that colonize the human mouth, their acquisition, interdependency, and coevolution with the host, bring a different perspective to the mechanisms underpinning the maintenance of periodontal health and the development of disease.In this work we suggest that our knowledge map of the etiology of periodontal health and disease can be viewed as a broad, highly connected, and integrated system that spans the entire spectrum of microbe/host/clinical interactions.The overall concept of present periodontology 2000, that the microbial biofilm can be considered a human tissue of bacteriological origin, is entirely consistent with this integrated system view.The health-associated community structure of microbial biofilms can be considered a system that is normally resilient to perturbation.Equally, there is evidence to suggest that the dysbiotic community structure in disease may share similar resilience properties.In both instances, the resilience may be governed by the precise makeup of the acquired microbiome and by the genetics of the host.Understanding the mechanisms that enable the resistance to change of healthy and dysbiotic microbial populations may be important in the development of approaches to prevent the progression of disease and to restore health in diseased individuals.

Journal: Periodontology 2000 (2021)
Publication types: Journal Article;Review
Mogroside V exerts anti-inflammatory effects on fine particulate matter-induced inflammation in porcine alveolar macrophages.

Mogroside v is the main bioactive component of siraitia grosvenorii (swingle), and has a potential anti-inflammatory function.However, the effect of mogroside v on fine particulate matter (pm2.5)-induced inflammation has not been reported.In the present study, the biological effect of mogroside v on inflammation was investigated in pm2.5- treated porcine alveolar macrophages (3d4/21).The results showed that mogroside v significantly inhibited pm2.5-induced nitric oxide (no) production and rescued the arginase activity inhibited by pm2.5.In the presence of mogroside v, the upregulation of il-18, tnf-α and cox-2 by pm2.5in 3d4/21 cells was inhibited.Mogroside v attenuated pm2.5-induced phosphorylation of nf-κb p65 and the expression of nlrp3.Mogroside v reduced intracellular ros levels induced by pm2.5.In the transcriptomic analysis, inflammation-related genes in 3d4/21 cells were not significantly affected after treatment with mogroside v.These results indicated that mogroside v can alleviate the inflammatory response of porcine alveolar macrophages induced by pm2.5from pig house and that mogroside v may play the role through the antioxidant function of eliminating ros.Mogroside v has a clear anti-inflammatory function in the presence of inflammation.

Journal: Toxicology in vitro : an international journal published in association with BIBRA (2022)
Publication types: Journal Article
Frequency-Resolved Connectome Hubs and Their Test-Retest Reliability in the Resting Human Brain.

Functional hubs with disproportionately extensive connectivities play a crucial role in global information integration in human brain networks.However, most resting-state functional magnetic resonance imaging (r-f mri) studies have identified functional hubs by examining spontaneous fluctuations of the blood oxygen level-dependent signal within a typical low-frequency band (e.g., 0.01-0.08 hz or 0.01-0.1 hz).Little is known about how the spatial distributions of functional hubs depend on frequency bands of interest.Here, we used repeatedly measured r-f mri data from 53 healthy young adults and a degree centrality analysis to identify voxelwise frequency-resolved functional hubs and further examined their test-retest reliability across two sessions.We showed that a wide-range frequency band (0.01-0.24 hz) accessible with a typical sampling rate (fsample= 0.5 hz) could be classified into three frequency bands with distinct patterns, namely, low-frequency (lf, 0.01-0.06 hz), middle-frequency (mf, 0.06-0.16 hz), and high-frequency (hf, 0.16-0.24 hz) bands.The functional hubs were mainly located in the medial and lateral frontal and parietal cortices in the lf band, and in the medial prefrontal cortex, superior temporal gyrus, parahippocampal gyrus, amygdala, and several cerebellar regions in the mf and hf bands.These hub regions exhibited fair to good test-retest reliability, regardless of the frequency band.The presence of the three frequency bands was well replicated using an independent r-f mri dataset from 45 healthy young adults.Our findings demonstrate reliable frequency-resolved functional connectivity hubs in three categories, thus providing insights into the frequency-specific connectome organization in healthy and disordered brains.

Journal: Neuroscience bulletin (2022)
Publication types: Journal Article
A comparative study of the deviation of the menton on posteroanterior cephalograms and three-dimensional computed tomography.

Facial asymmetry has been measured by the severity of deviation of the menton (me) on posteroanterior (pa) cephalograms and three-dimensional (3d) computed tomography (ct).This study aimed to compare pa cephalograms and 3d ct regarding the severity of me deviation and the direction of the me.Materials and methods pa cephalograms and 3d ct images of 35 patients who underwent orthognathic surgery (19 males and 16 females, with an average age of 22.1±3.3 years) were retrospectively reviewed in this study.By measuring the distance and direction of the me from the midfacial reference line and the midsagittal plane in the cephalograms and 3d ct, respectively, the x-coordinates (x1 and x2) of the me were obtained in each image.The difference between the x-coordinates was calculated and statistical analysis was performed to compare the severity of me deviation and the direction of the me in the two imaging modalities.Results a statistically significant difference in the severity of me deviation was found between the two imaging modalities (δx=2.45±2.03 mm, p<0.05) using the one-sample t-test.Statistically significant agreement was observed in the presence of deviation (k=0.64, p<0.05) and in the severity of me deviation (k=0.27, p<0.05).A difference in the direction of the me was detected in three patients (8.6%).The severity of the me deviation was found to vary according to the imaging modality in 16 patients (45.7%).Conclusion the measurement of me deviation may be different between pa cephalograms and 3d ct in some patients.

Journal: Imaging science in dentistry (2016)
Publication types: Journal Article
Management of type 1 diabetes mellitus during the COVID-19 pandemic.

Patients with type 1 diabetes mellitus (dm) require intensive monitoring, which was adversely affected during coronavirus disease 2019 (covid-19) restrictions.Methods we evaluated the management of type 1 dm and the role of telephonic consultation and follow-up in 46 patients (10 on insulin pump) with type 1 dm at our centre from 1 february 2020 to 31 january 2021.Patients were telephonically counselled fortnightly.Web-based diabetes education sessions for the patients and parents were conducted.Finally, change in hb a1c during the period of the study, frequency of severe hypoglycaemia, hospital admissions for hyperglycaemic emergencies and degree of satisfaction with care rendered by the treating team were assessed by ratings scored by the patients.Results five episodes of severe hypoglycaemia were noted in three patients.Two patients had diabetic ketoacidosis.Patients on insulin pump showed a mean baseline hb a1c of 7.8%.Nine of these patients (90%) showed an improvement in hba1c during the study period compared to 64.3% of patients on conventional regimen.There were no episodes of severe hypoglycaemia or hospitalization with dka noted in these patients.Only two patients had covid-19 disease with mild manifestations.Overall satisfaction levels with therapy were high.Conclusion this study illustrates the role played by teleconsultation and video conferencing during the period of the covid-19 pandemic in ensuring optimal healthcare delivery to patients with type 1 dm.Some of these methods can be used even after the pandemic to improve patient convenience and reduce the out-patient burden on the hospitals.

Journal: Medical journal, Armed Forces India (2021)
Publication types: Journal Article
Access to Care: End-to-End Digital Response for COVID-19 Care Delivery.

The coronavirus disease 2019 pandemic disrupted health care, requiring organizational leaders to act quickly to manage the health-related concerns of individuals and communities.The ability to offer a variety of digitally enabled telehealth services with 24/7 access to nurse practitioners and physician assistants allowed us to care for patients in their homes.It reduced the spread of the virus, protected our employees from further disease spread, and provided early interventions to those in need.The roles of nurse practitioner leaders, the enacted strategies, and patient outcomes demonstrate the impact of an innovative digital care delivery model on care across the continuum.

Journal: The journal for nurse practitioners : JNP (2022)
Publication types: Journal Article
Heterogeneous nuclear ribonucleoprotein E1 binds polycytosine DNA and monitors genome integrity.

Heterogeneous nuclear ribonucleoprotein e1 (hn rnp e1) is a tumor suppressor protein that binds site- and structure-specifically to rna sequences to regulate m rna stability, facilitate alternative splicing, and suppress protein translation on several metastasis-associated m rnas.Here, we show that hn rnp e1 binds polycytosine-rich dna tracts present throughout the genome, including those at promoters of several oncogenes and telomeres and monitors genome integrity.It binds dna in a site- and structure-specific manner.Hn rnp e1-knockdown cells displayed increased dna damage signals including γ-h2ax at its binding sites and also showed increased mutations.Uv and hydroxyurea treatment of hn rnp e1-knockdown cells exacerbated the basal dna damage signals with increased cell cycle arrest, activation of checkpoint proteins, and monoubiquitination of proliferating cell nuclear antigen despite no changes in deubiquitinating enzymes.Dna damage caused by genotoxin treatment localized to hn rnp e1 binding sites.Our work suggests that hn rnp e1 facilitates functions of dna integrity proteins at polycytosine tracts and monitors dna integrity at these sites.

Journal: Life science alliance (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Nutrition management of critically ill adult patients requiring non-invasive ventilation: a scoping review protocol.

This scoping review will identify the current available literature and key concepts in the nutrition management of critically ill adult patients requiring non-invasive ventilation.Introduction current international nutrition guidelines include recommendations for the nutrition management of critically ill patients who are receiving invasive mechanical ventilation; however, these guidelines do not address nutrition management of patients receiving non-invasive ventilation.This scoping review aims to explore and describe the existing available literature on the nutrition management of critically ill adults requiring non-invasive ventilation.Inclusion criteria this review will consider original research (qualitative, quantitative, or mixed methods studies) reporting on any nutrition parameter for critically ill adult patients (≥16 years) requiring non-invasive ventilation in the intensive care unit.Concepts of interest based on the general intensive care nutrition literature include route of nutrition, recommendations related to macro- or micro-nutrients, nutrition provision, barriers to nutrition provision, and strategies for nutrition management.Methods this review will be conducted in accordance with jbi methodology for scoping reviews using a three-step search strategy.Medline, embase, scopus, and web of science will be searched to obtain original research available in english and published after 1990.Google scholar will be searched for gray literature.Duplicates will be removed and studies will be selected by two independent reviewers based on the inclusion criteria.The same two reviewers will extract data in duplicate using a data extraction tool.Any disagreements will be resolved via consensus with a third reviewer.Data extraction will be synthesized in tabular and diagrammatic format.

Journal: JBI evidence synthesis (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Young people's perceptions of their parents' expectations and criticism are increasing over time: Implications for perfectionism.

Recent evidence demonstrates rising self-oriented, other-oriented, and socially prescribed perfectionism among young people from the united states, united kingdom, and canada (curran & hill, 2019).One reason why perfectionism is increasing may be that rising competitiveness and individualism are requiring parents to engage in anxious, overly involved, and/or overly controlling forms of parenting.Yet, data to support this claim are limited and contested.In two meta-analyses, we expanded upon and tested this claim by examining whether excessive parental expectations and harsh parental criticism are correlated with perfectionism (study 1) and whether these perceived practices are changing over time among american, canadian, and british college students (study 2).In study 1, meta-analyses found small-to-moderate positive mean weighted effects of parental expectations and parental criticism on self-oriented and other-oriented perfectionism, and large positive mean weighted effects of parental expectations and parental criticism on socially prescribed perfectionism.In study 2, using cross-temporal meta-analysis, we found that mean levels of parental expectations and parental criticism had linearly increased between 1989 and 2019 among college students.With rising competitiveness, individualism, economic inequality, and pressure to excel at school and college as the societal background, increases in parental expectations and parental criticism offer the most plausible explanation for rising perfectionism to date.(psyc info database record (c) 2022 apa, all rights reserved).

Journal: Psychological bulletin (2022)
Publication types: Journal Article;Meta-Analysis
Mechanism of LSD1 in oxygen-glucose deprivation/reoxygenation-induced pyroptosis of retinal ganglion cells via the miR-21-5p/NLRP12 axis.

Retinal ganglion cells (rgcs) are important retinal neurons that connect visual receptors to the brain, and lysine-specific demethylase 1 (lsd1) is implicated in the development of rgcs.This study expounded the mechanism of lsd1 in oxygen-glucose deprivation/reoxygenation (ogd/r)-induced pyroptosis of rgcs.Methods mouse rgcs underwent ogd/r exposure, and then rgc viability was examined using the cell counting kit-8 method.The m rna levels of caspase 1, the protein levels of nod-like receptor family pyrin domain-containing 3 (nlrp3), n-terminal fragment of gasdermin d (gsdmd-n), and cleaved-caspase1, and the concentrations of interleukin (il)-1β and il-18 were respectively examined.Subsequently, lsd1 expression was intervened to explore the underlying effect of lsd1 on ogd/r-induced pyroptosis of rgcs.Afterwards, the enrichments of lsd1 and histone h3 lysine 4 methylation (h3k4me) 1/2 on the micro rna (mi r)-21-5p promoter were determined using chromatin-immunoprecipitation assay.And the binding interaction between mi r-21-5p and nlrp12 was detected using dual-luciferase and rna pull-down assays.Finally, the effects of mi r-21-5p/nlrp12 on lsd1-mediated pyroptosis of rgcs were verified through functional rescue experiments.Results ogd/r treatment increased pyroptosis of rgcs and lsd1 expression.Silencing lsd1 declined levels of caspase 1 m rna, nlrp3, gsdmd-n, cleaved-caspase1, il-1β, and il-18 and limited pyroptosis of ogd/r-treated rgcs.Mechanically, lsd1 suppressed mi r-21-5p expression via demethylation of h3k4me2 on the mi r-21-5p promoter to hamper the binding of mi r-21-5p to nlrp12, and thereby increased nlrp12 expression.Silencing mi r-21-5p or overexpressing nlrp12 facilitated ogd/r-induced pyroptosis of rgcs.Conclusion lsd1-mediated demethylation of h3k4me2 decreased mi r-21-5p expression to increase nlrp12 expression, promoting pyroptosis of ogd/r-treated rgcs.

Journal: BMC neuroscience (2022)
Publication types: Journal Article
The Impact of Contact Structure and Mixing on Control Measures and Disease-Induced Herd Immunity in Epidemic Models: A Mean-Field Model Perspective.

The contact structure of a population plays an important role in transmission of infection.Many 'structured models' capture aspects of the contact pattern through an underlying network or a mixing matrix.An important observation in unstructured models of a disease that confers immunity is that once a fraction [formula: see text] has been infected, the residual susceptible population can no longer sustain an epidemic.A recent observation of some structured models is that this threshold can be crossed with a smaller fraction of infected individuals, because the disease acts like a targeted vaccine, preferentially immunising higher-risk individuals who play a greater role in transmission.Therefore, a limited 'first wave' may leave behind a residual population that cannot support a second wave once interventions are lifted.In this paper, we set out to investigate this more systematically.While networks offer a flexible framework to model contact patterns explicitly, they suffer from several shortcomings: (i) high-fidelity network models require a large amount of data which can be difficult to harvest, and (ii) very few, if any, theoretical contact network models offer the flexibility to tune different contact network properties within the same framework.Therefore, we opt to systematically analyse a number of well-known mean-field models.These are computationally efficient and provide good flexibility in varying contact network properties such as heterogeneity in the number contacts, clustering and household structure or differentiating between local and global contacts.In particular, we consider the question of herd immunity under several scenarios.When modelling interventions as changes in transmission rates, we confirm that in networks with significant degree heterogeneity, the first wave of the epidemic confers herd immunity with significantly fewer infections than equivalent models with less or no degree heterogeneity.However, if modelling the intervention as a change in the contact network, then this effect may become much more subtle.Indeed, modifying the structure disproportionately can shield highly connected nodes from becoming infected during the first wave and therefore make the second wave more substantial.We strengthen this finding by using an age-structured compartmental model parameterised with real data and comparing lockdown periods implemented either as a global scaling of the mixing matrix or age-specific structural changes.Overall, we find that results regarding (disease-induced) herd immunity levels are strongly dependent on the model, the duration of the lockdown and how the lockdown is implemented in the model.

Journal: Bulletin of mathematical biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Induction of AmpC-Mediated β-Lactam Resistance Requires a Single Lytic Transglycosylase in Agrobacterium tumefaciens.

The remarkable ability of agrobacterium tumefaciens to transfer dna to plant cells has allowed the generation of important transgenic crops.One challenge of a.Tumefaciens-mediated transformation is eliminating the bacteria after plant transformation to prevent detrimental effects to plants and the release of engineered bacteria to the environment.Here, we use a reverse-genetics approach to identify genes involved in ampicillin resistance, with the goal of utilizing these antibiotic-sensitive strains for plant transformations.We show that treating a.Tumefaciens c58 with ampicillin led to increased β-lactamase production, a response dependent on the broad-spectrum β-lactamase amp c and its transcription factor, amp r.Loss of the putativeamp dorthologueatu2113led to constitutive production of amp c-dependent β-lactamase activity and ampicillin resistance.Finally, one cell wall remodeling enzyme, mlt b3, was necessary for the amp c-dependent β-lactamase activity, and its loss elicited ampicillin and carbenicillin sensitivity in the a.Tumefaciens c58 and gv3101 strains.Furthermore, gv3101 δmlt b3transforms plants with efficiency comparable to that of the wild type but can be cleared with sublethal concentrations of ampicillin.The functional characterization of the genes involved in the inducible ampicillin resistance pathway of a.Tumefaciens constitutes a major step forward in efforts to reduce the intrinsic antibiotic resistance of this bacterium.importanceagrobacterium tumefaciens, a significant biotechnological tool for production of transgenic plant lines, is highly resistant to a wide variety of antibiotics, posing challenges for various applications.One challenge is the efficient elimination of a.Tumefaciens from transformed plant tissue without using levels of antibiotics that are toxic to the plants.Here, we present the functional characterization of genes involved in β-lactam resistance in a.Tumefaciens.Knowledge about proteins that promote or inhibit β-lactam resistance will enable the development of strains to improve the efficiency of agrobacterium-mediated plant genetic transformations.Effective removal of agrobacteriumfrom transformed plant tissue has the potential to maximize crop yield and food production, improving the outlook for global food security.

Journal: Applied and environmental microbiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Deep brain stimulation enhances movement complexity during gait in individuals with Parkinson's disease.

Deep brain stimulation (dbs) is associated with substantial improvements in motor symptoms of pd.Emerging evidence has suggested that nonlinear measures of complexity may provide greater insight into the efficacy of anti-pd treatments.This study investigated sample entropy and complexity index values in individuals with pd when dbs was off compared to on.Five individuals with pd using dbs performed a four-minute treadmill walking task while 3d kinematics were collected over two periods of 30 s.Participants were tested in the dbs-on and dbs-off conditions.Sample entropy (se) and complexity index (ci) values were calculated for ankle, knee and hip joint angles.Paired samples t-tests were used to compare mean se and ci values between the dbs-off and dbs-on conditions, respectively.No differences in se or ci were observed between the dbs-on and dbs-off conditions at the ankle.At the knee, the dbs-on was associated with greater se and ci values than the dbs-off condition.At the hip, dbs-on was associated with greater se and ci values than the dbs-off condition.Dbs enhances complexity of movement at the hip and knee joints while complexity at the ankle joint is not significantly altered.Greater complexity of knee and hip joint motion may represent increased adaptability and a greater number of available strategies to complete the gait task.

Journal: Neuroscience letters (2020)
Publication types: Journal Article