syedzayyan/paper_mill_benchmark huggingface dataset:
The Trade-Off between Airborne Pandemic Control and Energy Consumption Using Air Ventilation Solutions.

Airborne diseases cause high mortality and adverse socioeconomic consequences.Due to urbanization, more people spend more time indoors.According to recent research, air ventilation reduces long-range airborne transmission in indoor settings.However, air ventilation solutions often incur significant energy costs and ecological footprints.The trade-offs between energy consumption and pandemic control indoors have not yet been thoroughly analyzed.In this work, we use advanced sensors to monitor the energy consumption and pandemic control capabilities of an air-conditioning system, a pedestal fan, and an open window in hospital rooms, classrooms, and conference rooms.A simulation of an indoor airborne pandemic spread of coronavirus (covid-19) is used to analyze the pareto front.For the three examined room types, the pareto front consists of all three air ventilation solutions, with some ventilation configurations demonstrating significant inefficiencies.Specifically, air-conditioning is found to be efficient only at a very high energy cost and fans seem to pose a reasonable alternative.To conclude, a more informed ventilation policy can bring about a more desirable compromise between energy consumption and pandemic spread control.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Clinical Trials of COVID-19 Therapies Should Account for Diabetes and Hyperglycemia.

Complications of coronavirus disease 2019 (covid-19) occur with increased frequency in people admitted to the hospital with diabetes or hyperglycemia.The increased risk for covid-19 infections in the presence of these metabolic conditions is in part due to overlapping pathophysiologic features of covid-19, diabetes, and glucose control.Various antiviral treatments are being tested in covid-19 patients.We believe that in these trials, it will be useful to evaluate treatment effect differences in patients stratified according to whether they have diabetes or hyperglycemia.In this way, it will be possible to better facilitate development of antiviral treatments that are most specifically beneficial for the large subset of covid-19 patients who have diabetes or hyperglycemia.

Journal: Journal of diabetes science and technology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Potential roles of serum ATPase and AMPase in predicting diagnosis of colorectal cancer patients.

Colorectal cancer (crc) is a common gastrointestinal cancer with high incidence and mortality rates.Crc may be associated with regulation of circulating nucleotides.This study aimed to evaluate the serum levels of nucleotide-metabolizing enzymes (atpase and ampase) in patients with crc and to explore the clinical diagnostic value of these enzymes.The gene set variation analysis (gsva) score of the atp-adenosine signature was calculated using tumor samples from the cancer genome atlas (tcga).Atp-adenosine signaling plays a central role in crc progression.A total of 135 subjects, including 87 patients with crc and 48 healthy controls, were included.The serum levels of atpase and ampase in the crc group were significantly higher than those in the control group (p< 0.05).Furthermore, atp and amp hydrolysis levels significantly increased in the advanced crc group (p< 0.05).Atp and amp hydrolysis was decreased by the entpdase inhibitors (pom-1 and arl67156) and cd73 inhibitor (apcp).The sensitivities of atpase and ampase were 95.4% and 75.9%, respectively, which were higher than those of cea (67.8%) and ca19-9 (72.4%).The specificities of atpase and ampase were 69.9% and 73.9%, respectively, which were higher than that of ca19-9 (47.8%).The combination of cea, atpase, and ampase demonstrated high sensitivity (92.0%) and specificity (87.0%).Collectively, atpase and ampase activities are upregulated in crc with considerable diagnostic significance.The combination of cea, atpase, and ampase may provide a novel approach for crc screening.

Journal: Bioengineered (2022)
Publication types: Journal Article
Genomic DNA hydroxymethylation reveals potential role in identification of lung injury in coal-burning arsenicosis populations.

Arsenic (as) is a toxic metalloid element that causes lung cancer and multiple non-malignant respiratory diseases.The toxicity of arsenic is mediated in part by epigenetic mechanisms, such as alterations in dna methylation.While increasing studies have highlighted the potential importance of arsenic exposure to dna methylation patterns and the subsequent risks for arsenic toxicity, there has been little focus on dna hydroxymethylation-a negative regulation mechanism of dna methylation.Therefore, this study aimed to investigate the relationship between genomic dna methylation/hydroxymethylation and lung injury in arsenicosis populations.First, an increased risk of lung injury and exacerbation of lung function impairment in the arsenicosis population was confirmed.Levels of 5-methylcytosine/deoxycytidine (5 m c/d c), 5-hydroxymethylcytosine/deoxycytidine (5 hm c/d c) and 5 hm c/5 m c in genomic dna of peripheral blood were decreased in the arsenicosis population compared to in the control.Additionally, multivariate logistic regression models showed an increased risk of chest digital radiography (dr) abnormalities when 5 hm c/d c and 5 hm c/5 m c levels were lower (or = 3.12 and 3.96, all p < 0.001).For 3 years follow-up, regression analysis showed that a decline in 5 hm c/d c was significantly associated with the decline of lung function parameters [forced vital capacity (fvc), forced expiratory volume in 1 s (fev1) and maximal mid-expiratory flow (mmef); β = 0.167, 0.122 and 0.073, respectively; all p < 0.05].Using the receiver operating characteristic (roc) curve, a combination of 5 hm c/5 d c and 5 hm c/5 m c obtained the highest value for distinguishing lung injury in all subjects (auc = 0.82, p < 0.01).In contrast, in arsenicosis subjects, 5 hm c/d c was better at distinguishing lung injury (auc = 0.84, p < 0.01).Together, the results revealed that a decrease in genomic dna hydroxymethylation markers was associated with lung injury in coal-burning arsenicosis populations.Genomic dna hydroxymethylation could be a novel biomarker for identifying the risk of lung injury caused by coal-burning arsenicosis.

Journal: Environmental research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Information transmission in mPFC-BLA network during exploratory behavior in the open field.

Exploratory behavior plays a fundamental role in motivation, learning, and well-being of organisms.The open field test (oft) is a classic method to investigate the exploratory behavior in rodents, also a widely adopted and pharmacologically validated procedure for evaluating anxiety and depression.Several lines of evidence have shown that medial prefrontal cortex (m pfc) and basolateral amygdala (bla) play crucial roles in anxiety-like or depression-like exploratory behavior.However, the dynamic characterization of the m pfc-bla network in exploratory behavior is less well understood.Therefore, this study aimed to investigate the information transmission mechanism in the m pfc-bla network during exploratory behavior.Local field potentials (lfps) from m pfc and bla were simultaneously recorded while the rats performed the oft.Directed transfer function (dtf), which was derived from granger causal connectivity analysis, was applied to measure the functional connectivity among lfps.Information flow (if) was calculated to explore the dynamics of information transmission in the m pfc-bla network.Our results revealed that, for both m pfc and bla, the theta-band functional connectivity in periphery was significantly higher than that in center of the open field.The if from bla to m pfc in the open field task was significantly higher than that from m pfc to bla.These results suggest that the functional connectivity and if in the m pfc-bla network are related to the exploratory behavior, and information transmission from bla to m pfc could be predominant for exploratory behavior.

Journal: Behavioural brain research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Molecular dynamics simulation for mechanism revelation of the safety and nutrition of lipids and derivatives in food: State of the art.

Molecular dynamics (md) simulation has proved to be a powerful tool in the study of proteins, nucleic acids, lipids, and carbohydrates et al.In fields of health, nutrition, and food science.In particular, md simulation has been employed in the investigation of various lipid systems such as triglycerides, phospholipid membranes, etc.Due to the continuous updating of computing resources and the development of new md simulation methods and force field parameters, the simulation's time and size scale of lipids system has increased by several orders of magnitude.However, md simulation cannot be used for systems invovle chemical reactions.These greatly limit its further application in the field of lipid research.This paper reviews the progress and development of md simulation, especially for the application of md simulation in different lipid systems.In this paper, md simulation and its general workflow was briefly introduced firstly.Subsequently, the application of md simulation in various lipid systems was reviewed in-depth.Finally, the limitation and future prospects of md simulation in lipid research were also discussed.This review provided new insights into the investigation of md simulation, and a novel thought for lipid study.We believe that md simulation will exhibit more and more great advantages in the investigation of lipids in the future due to the development of novlel methods.

Journal: Food research international (Ottawa, Ont.) (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Prognostic alternative splicing regulatory network of RBM25 in hepatocellular carcinoma.

Rna-binding motif protein 25 (rbm25) is a poorly characterized rna-binding protein that is involved in several biological processes and regulates the proliferation and metastasis of tumor cells.The regulatory role of rbm25 in hepatocellular carcinoma (hcc) is unknown.Here, rbm25 expression and outcomes in hcc patients were evaluated using the cancer genome atlas database.Rbm25 was overexpressed in hcc patients compared with the healthy group.The high expression of rbm25 in tumor tissues was significantly related to poor overall survival (p<0.001).Overexpression of rbm25 significantly contributed to poorer survival in male patients and n0 stage patients (p<0.001).Spearman analysis and weighted gene co-expression network analysis identified 694 rbm25-related genes.Protein-protein interaction network analysis revealed the cluster with the highest score, which positively correlated with rbm25.Cdca5 and incenp were identified as the core functional genes related to rbm25.The overexpression of cdca5 and incenp in hcc patients was examined using the human protein atlas database.The findings collectively indicated that rbm25 may interact with cdca5 and incenp to regulate hcc.Our detailed characterization of rbm25 protein interactions and related core functional genes provides a basis for further studies aimed at identifying molecular regulatory pathways or splicing events.

Journal: Bioengineered (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Modeling Methamphetamine Use Disorder and Relapse in Animals: Short- and Long-term Epigenetic, Transcriptional., and Biochemical Consequences in the Rat Brain.

Methamphetamine use disorder (mud) is a neuropsychiatric disorder characterized by binge drug taking episodes, intervals of abstinence, and relapses to drug use even during treatment.Mud has been modeled in rodents and investigators are attempting to identify its molecular bases.Preclinical experiments have shown that different schedules of methamphetamine self-administration can cause diverse transcriptional changes in the dorsal striatum of sprague-dawley rats.In the present review, we present data on differentially expressed genes (degs) identified in the rat striatum following methamphetamine intake.These include genes involved in transcription regulation, potassium channel function, and neuroinflammation.We then use the striatal data to discuss the potential significance of the molecular changes induced by methamphetamine by reviewing concordant or discordant data from the literature.This review identified potential molecular targets for pharmacological interventions.Nevertheless, there is a need for more research on methamphetamine-induced transcriptional consequences in various brain regions.These data should provide a more detailed neuroanatomical map of methamphetamine-induced changes and should better inform therapeutic interventions against mud.

Journal: Neuroscience and biobehavioral reviews (2023)
Publication types: Journal Article;Review
Characterization of a novel thermophilic beta-glucosidase fromThermotogasp. and its application in the transformation of notoginsenoside R1.

A novel β-glucosidase (thglu3) was identified from thermotogasp.Which had biotransformation activity for notoginsenoside r1 (nr-r1).Sequence analysis of thglu3 revealed that it could be classified into glycoside hydrolase family 3 (gh3).The gene encoding a 719-amino acid protein was cloned and expressed in escherichia coli.the recombinant enzyme was purified, and its molecular weight was approximately 81 k da.The recombinant thglu3 exhibited an optimal activity at 75 °c and p h 6.4.The β-glucosidase had high selectivity for cleaving the outer glucose moiety at the c20 position of nr-r1, which produced the more pharmacologically active notoginsenoside r2 (nr-r2).Under the optimal reaction conditions for gram-scale production, 30 g nr-r1 was transformed to nr-r2 using 20 g crude enzyme at p h 6.4 and 75 °c within 1 h with a molar yield of 93%.This study was the first report of the highly efficient and selective gram-scale transformation of nr-r2 from nr-r1 by a thermophilic β-glucosidase.

Journal: 3 Biotech (2022)
Publication types: Journal Article
Comparative Genome Analysis ofStreptococcus suisSerotype 9 Isolates from China, The Netherland, and the U.K.

Streptococcus suis(s.Suis) is an important swine pathogen and an emerging zoonotic agent worldwide.Serotype 9 is the most prevalent serotype in several european countries but it is relatively rare in china.In this study, through the investigation of the serotypes of 279s.Suisstrains isolated from china from 2015 to 2017, it was found that serotype 9 is the second most prevalent serotype (43 out of 279), behind serotype 2 (83 out of 279).Next, the 43 serotype 9 isolates were sequenced and compared with those from the netherland (28) and the u.k.(eight).For the purpose of comparison, the strain d12 (gca_000231905), which has completed genome sequences, was also incorporated.Phylogenetic tree analysis showed that the strains from china and the u.k.Were heterogeneous.In contrast, all but one from the netherland belonged to the same clade.The dominant clades of chinese strains (33) and strains from the netherland (27) were very similar.Both of them may have originated from the same strain about 70 years ago.Then, the distributions of virulence-associated genes and antibiotic resistance genes among different clades and sources were analyzed.By comparison, strains from the netherland carried more virulence-associated genes and those from the u.k.Had more antibiotic resistance genes.Additionally, some virulence-associated genes (sal kandsal r) and antibiotic resistance genes (lincomycin and spectinomycin) existed only in several chinese strains.In conclusion, our data displayed the population characteristics and differences of s.Suisserotype 9 between china and europe, suggesting that they have taken different evolutionary paths.

Journal: Life (Basel, Switzerland) (2021)
Publication types: Journal Article
PARACENTRAL ACUTE MIDDLE MACULOPATHY IN GIANT CELL ARTERITIS.

To report the occurrence of paracentral acute middle maculopathy (pamm) in giant cell arteritis (gca), describe its features and outcomes, and identify risk factors associated with pamm in patients with gca.Methods review of medical records of patients with gca who were examined in the rothschild foundation hospital.Patients were divided into three groups: gca with pamm (group 1), gca with ophthalmic involvement but without pamm (group 2), and gca without ophthalmic involvement (group 3).We analyzed the data for age, sex, medical history, laboratory testing, visual acuity, and posterior segment vascular involvement.Results among the 96 patients who met the inclusion criteria, 52 had ophthalmic involvement, and 16 patients were included in group 1 (gca with pamm).In this subgroup, the mean age was 81.6 years and was found to be older than other groups.The visual prognosis was similar between groups 1 and 2.Of the 20 eyes with pamm, 35% were also associated with homolateral anterior ischemic optic neuropathy.No statistical difference was found in initial symptoms, signs, and laboratory testing.Conclusion paracentral acute middle maculopathy is frequently observed lesions in ocular gca.Patients can present with isolated findings of pamm as the only indication of gca.Optical coherence tomography of the macula should be routinely performed in patients with suspected gca, specifically if they complain of visual changes, to look for signs of ischemia in the middle layers of the retina.Isolated pamm should raise suspicion for gca in patients at risk.

Journal: Retina (Philadelphia, Pa.) (2022)
Publication types: Journal Article
Imatinib Mesylate Induces Necroptotic Cell Death and Impairs Autophagic Flux in Human Cardiac Progenitor Cells.

The receptor tyrosine kinase inhibitor imatinib improves patient cancer survival but is linked to cardiotoxicity.This study investigated imatinib's effects on cell viability, apoptosis, autophagy, and necroptosis in human cardiac progenitor cells in vitro.Imatinib reduced cell viability (75.9 ± 2.7% vs.100.0 ± 0.0%) at concentrations comparable to peak plasma levels (10 μm).Imatinib reduced cells' tmrm fluorescence (74.6 ± 6.5% vs.100.0 ± 0.0%), consistent with mitochondrial depolarisation.Imatinib increased lysosome and autophagosome content as indicated by lamp2 expression (2.4 ± 0.3-fold) and acridine orange fluorescence (46.0 ± 5.4% vs.9.0 ± 3.0), respectively.Although imatinib increased expression of autophagy-associated proteins and also impaired autophagic flux, shown by proximity ligation assay staining for lamp2 and lc3ii (autophagosome marker): 48 h of imatinib treatment reduced visible puncta to 2.7 ± 0.7/cell from 11.3 ± 2.1 puncta/cell in the control.Cell viability was partially recovered by autophagosome inhibition by wortmannin, with the viability increasing 91.8 ± 8.2% after imatinib-wortmannin co-treatment (84 ± 1.5% after imatinib).Imatinib-induced necroptosis was associated with an 8.5 ± 2.5-fold increase in mixed lineage kinase domain-like pseudokinase activation.Imatinib-induced toxicity was rescued by rip1 inhibition: 88.6 ± 3.0% vs.100.0 ± 0.0% in the control.Imatinib applied to human cardiac progenitor cells depolarises mitochondria and induces cell death through necroptosis, recoverable by rip1 inhibition, with a partial role for autophagy.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Staphylococcal Complement Evasion Protein Sbi Stabilises C3d Dimers by Inducing an N-Terminal Helix Swap.

Staphylococcus aureusis an opportunistic pathogen that is able to thwart an effective host immune response by producing a range of immune evasion molecules, including s.Aureusbinder of ig g (sbi) which interacts directly with the central complement component c3, its fragments and associated regulators.Recently we reported the first structure of a disulfide-linked human c3d17cdimer and highlighted its potential role in modulating b-cell activation.Here we present an x-ray crystal structure of a disulfide-linked human c3d17cdimer, which undergoes a structurally stabilising n-terminal 3d domain swap when in complex with sbi.These structural studies, in combination with circular dichroism and fluorescence spectroscopic analyses, reveal the mechanism underpinning this unique helix swap event and could explain the origins of a previously discovered n-terminally truncated c3dg dimer isolated from rat serum.Overall, our study unveils a novel staphylococcal complement evasion mechanism which enables the pathogen to harness the ability of dimeric c3d to modulate b-cell activation.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Anti-biofilm Fe3O4@C18-[1,3,4]thiadiazolo[3,2-a]pyrimidin-4-ium-2-thiolate Derivative Core-shell Nanocoatings.

The derivatives 5,7-dimethyl[1,3,4]thiadiazolo[3,2-a]pyrimidin-4-ium-2-thiolate (1) and 7-methyl-5-phenyl[1,3,4]thiadiazolo[3,2-a]pyrimidin-4-ium-2-thiolate (2) were fully characterized by single-crystal x-ray diffraction.Their supramolecular structure is built through both π-π stacking and c=s-π interactions for both compounds.The embedment of the tested compounds into fe3o4@c18core-shell nanocoatings increased the protection degree against candida albicansbiofilms on the catheter surface, suggesting that these bioactive nanocoatings could be further developed as non-cytotoxic strategies for fighting biofilm-associated fungal infections.

Journal: Materials (Basel, Switzerland) (2020)
Publication types: Journal Article
Ginkgolide B Suppresses TLR4-Mediated Inflammatory Response by Inhibiting the Phosphorylation of JAK2/STAT3 and p38 MAPK in High Glucose-Treated HUVECs.

Ginkgolide b is a ginkgo bilobaleaf extract that has been identified as a natural platelet-activating factor receptor (pafr) antagonist.We investigated the effect of ginkgolide b on high glucose-induced tlr4 activation in human umbilical vein endothelial cells (huvecs).Methods protein expression was analyzed by immunoblotting.Small-interfering rna (si rna) was used to knock down pafr and tlr4 expression.Results ginkgolide b suppressed the expression of tlr4 and my d88 that was induced by high glucose.Ginkgolide b also reduced the levels of platelet endothelial cell adhesion molecule-1, interleukin-6, and monocyte chemotactic protein 1.Further, we examined the association between pafr and tlr4 by coimmunoprecipitation.The result showed that high glucose treatment caused the binding of pafr and tlr4, whereas ginkgolide b abolished this binding.The functional analysis indicated that pafr si rna treatment reduced tlr4 expression, and tlr4 si rna treatment decreased pafr expression in high glucose-treated huvecs, further supporting the coimmunoprecipitation data.Ginkgolide b inhibited the phosphorylation of janus kinase 2 (jak2)/signal transducer and activator of transcription 3 (stat3) and p38 mitogen-activated protein kinase (mapk).Conclusion ginkgolide b exerted protective effects by inhibiting the tlr4-mediated inflammatory response in high glucose-treated endothelial cells.The mechanism of action of ginkgolide b might be associated with inhibition of the jak2/stat3 and p38 mapk phosphorylation.

Journal: Oxidative medicine and cellular longevity (2017)
Publication types: Journal Article