syedzayyan/paper_mill_benchmark huggingface dataset:
Comparison of the stability of CYP105A1 and its variants engineered for production of active forms of vitamin D.

Cyp105a1 from streptomyces griseolus converts vitamin d3 to its biologically active form, 1α,25-dihydroxy vitamin d3.R73a/r84a mutation enhanced the 1α- and 25-hydroxylation activity for vitamin d3, while m239a mutation generated the 1α-hydroxylation activity for vitamin d2.In this study, the stability of six cyp105a1 enzymes, including 5 variants (r73a/r84a, m239a, r73a/r84a/m239a (=tri a), tri a/e90a, and tri a/e90d), was examined.Circular dichroism analysis revealed that m239a markedly reduces the enzyme stability.Protein fluorescence analysis disclosed that these mutations, especially m239a, induce large changes in the local conformation around trp residues.Strong stabilizing effect of glycerol was observed.Nondenaturing page analysis showed that cyp105a1 enzymes are prone to self-association.Fluorescence analysis using a hydrophobic probe 8-anilino-1-naphthalenesulfonic acid suggested that m239a mutation enhances self-association and that e90a and e90d mutations, in cooperation with m239a, accelerate self-association with little effect on the stability.

Journal: Bioscience, biotechnology, and biochemistry (2022)
Publication types: Journal Article
Cascade of care of people diagnosed with HIV in New Zealand between 2006 and 2017.

S we estimated the proportion of people reported with hiv in new zealand between 2006 and 2017, and alive in 2017-2019, who were on antiretroviral therapy (art) and had a suppressed viral load (vl), and explored their associated characteristics.Methods data were anonymously linked to information on art and vl within the data collection period (january 2017 to august 2019) using the national health index (nhi), ministry of health and laboratory datasets, as well as information from clinical specialists.Logistic regression was used to test for associations.Sensitivity analyses were undertaken to estimate the range for the key proportions.Results overall, 2355 people were reported with hiv, of whom 116 (5%) had died, 337 (14%) were overseas, and 1701 (72%) were alive in new zealand; for the remaining 201 (9%) the outcome was unknown.Clinical data were available for 1490 people (87.6%): 1408 (94.5%) were on art, 11 (< 1%) were not on art, and for 71 (4.8%) this was unknown.Of those on art, 1156 (82.1%) had a suppressed vl (< 200 copies/m l), 34 (2.4%) were unsuppressed, and for 218 (15.5%) this was unknown.The estimate of the proportion on art ranged from 99% to 78%, and those with a suppressed vl ranged from 98% to 78%.Conclusions among people with hiv in new zealand who are under care, a high proportion were on art and had suppressed vl.Increasing collection of nhis and better linkage with laboratory information will reduce the number with unknown information and provide more complete vl results in the future.

Journal: HIV medicine (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effective lipid extraction from undewatered microalgae liquid using subcritical dimethyl ether.

Recent studies of lipid extraction from microalgae have focused primarily on dewatered or dried samples, and the processes are simple with high lipid yield.Yet, the dewatering with drying step is energy intensive, which makes the energy input during the lipid production more than energy output from obtained lipid.Thus, exploring an extraction technique for just a thickened sample without the dewatering, drying and auxiliary operation (such as cell disruption) is very significant.Whereas lipid extraction from the thickened microalgae is complicated by the high water content involved, and traditional solvent, hence, cannot work well.Dimethyl ether (dme), a green solvent, featuring a high affinity for both water and organic compounds with an ability to penetrate the cell walls has the potential to achieve this goal.Results this study investigated an energy-saving method for lipid extraction using dme as the solvent with an entrainer solution (ethanol and acetone) for flocculation-thickened microalgae.Extraction efficiency was evaluated in terms of extraction time, dme dosage, entrainer dosage, and ethanol:acetone ratio.Optimal extraction occurred after 30 min using 4.2 m l dme per 1 m l microalgae, with an entrainer dosage of 8% at 1:2 ethanol:acetone.Raw lipid yields and its lipid component (represented by fatty acid methyl ester) contents were compared against those of common extraction methods (bligh and dryer, and soxhlet).Thermal gravimetry/differential thermal analysis, fourier-transform infrared spectroscopy, and c/h/n elemental analyses were used to examine differences in lipids extracted using each of the evaluated methods.Considering influence of trace metals on biodiesel utilization, inductively coupled plasma mass spectrometry and inductively coupled plasma atomic emission spectroscopy analyses were used to quantify trace metals in the extracted raw lipids, which revealed relatively high concentrations of mg, na, k, and fe.Conclusions our dme-based method recovered 26.4% of total raw lipids and 54.4% of total fatty acid methyl esters at first extraction with remnants being recovered by a 2nd extraction.In additional, the dme-based approach was more economical than other methods, because it enabled simultaneous dewatering with lipid extraction and no cell disruption was required.The trace metals of raw lipids indicated a purification demand in subsequent refining process.

Journal: Biotechnology for biofuels (2021)
Publication types: Journal Article
The Third Signal Cytokine Interleukin 12 Rather Than Immune Checkpoint Inhibitors Contributes to the Functional Restoration of Hepatitis D Virus-Specific T Cells.

Hepatitis d virus (hdv) infection affects 15-20 million individuals worldwide and causes severely progressive hepatitis.It is unknown to what extent cellular immune responses contribute to liver disease and control of viral replication in hdv infection.Methods immune cell frequencies and phenotypes were determined in 49 hdv-infected patients, 25 individuals with hepatitis b virus monoinfection and 18 healthy controls.T-cell proliferative and cytokine-producing capacities were analyzed by stimulation with overlapping peptides spanning the large hdv antigen.To restore t-cell responses, blocking antibodies (anti-cytotoxic t-lymphocyte antigen 4, anti-programmed death ligand 1) or proinflammatory cytokines (interleukin [il] 12) were used.Results immune cell frequencies and phenotypes did not vary between the groups.Exclusively, the senescence marker cd57 was significantly up-regulated in cd8+t cells from patients with hepatitis delta.Hdv-specific t-cell proliferation and cytokine production were weak and could only partly be rescued by blockade of the programmed death 1 pathway.However, a more robust and consistent increase in hdv-specific cd4+and cd8+t-cell responses was evident when the third signal cytokine il-12 was added, which also affected cytomegalovirus- and epstein-barr virus-specific t cells.Conclusions this investigation of virus-specific t-cell immunity in patients with hdv infection, the largest to date, revealed premature aging of immune cells and impaired t-cell functionality.This could be restored by blocking inhibitory pathways and, in particular, by supplementing with il-12.

Journal: The Journal of infectious diseases (2017)
Publication types: Journal Article
Benign Effects of Twin Boundaries on Charge Carrier Lifetime in Metal Halide Perovskites by a Time-Domain Study.

Experiments show that two-dimensional twin boundaries (tbs) defects are benign to the excited-state lifetime of metal halide perovskites and solar cells performance.However, the mechanism remains unclear.By performing nonadiabatic (na) molecular dynamics simulations on fapb i3(fa= hc(nh2)2+), we demonstrate that tbs increase the bandgap without introducing midgap states, promote charge separation by localizing electrons and holes that reduce na coupling and accelerate the loss of coherence, slowing nonradiative electron-hole recombination by a factor of 2.3 compared to pristine fapb i3, which occurs within sub-10 ns and agrees well with the experiment.Raising the temperature shortens the coherence time and reduces the na coupling by increasing the charge localization due to the enhanced distortions of inorganic pb-i lattice, making the recombination even slower.Our study rationalizes the positive influence of tbs and temperature on perovskite charge dynamics and emphasizes the roles played by the charge localization and quantum coherence.

Journal: The journal of physical chemistry letters (2021)
Publication types: Journal Article
Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches.

In response to the massive use of biocides for controlling listeria monocytogenes (hereafter lm) contaminations along the food chain, strains showing biocide tolerance emerged.Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 lm strains from different lineages, ecological, geographical and temporal origins.Mobile elements, including prophage-related loci, the tn6188_qac h transposon and p lmst6_emr c plasmid, were widespread across lineage i and ii food strains and associated with tolerance to benzalkonium-chloride (bc), a quaternary ammonium compound (qac) widely used in food processing.The p lmst6_emr c was also associated with tolerance to another qac, the didecyldimethylammonium-chloride, displaying a pleiotropic effect.While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with bc or polymeric biguanide tolerance.The latter was restricted to lineage i strains from animal and the environment.In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the lm adaptation to biocide, especially in food strains but also from animal and the environment.These markers could aid to monitor and predict the spread of biocide tolerant lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.

Journal: Food microbiology (2022)
Publication types: Journal Article
Interviews with patients aged 6-17 years provide valuable insights for physicians who need to deliver an epilepsy diagnosis.

Meeting children's needs when communicating an epilepsy diagnosis can have a large impact on their treatment.We investigated children's experiences and wishes concerning their first conversation about epilepsy.Methods this prospective study was performed in the neuropaediatric departments of two german university hospitals from 2 october 2018 to 12 april 2019.The semi-structured interview contained open questions, and multiple answers were allowed.Results we interviewed 101 patients (57 male) aged 6-17 (median 11) years and asked them to put themselves in the place of a physician delivering an epilepsy diagnosis.They said they would be careful and friendly and consider the children's feelings (29%), give them detailed information about their condition (29%) and reduce their fears and offer hope (26%).They would tell them the importance of always taking their medication and explain why (25%), make sure that the conversation took place in a comfortable setting (21%), explain any safety precautions (19%), keep the conversation straightforward and provide examples (16%).Conclusion children with epilepsy provided concrete recommendations for physicians delivering an epilepsy diagnosis, with regard to the ideal setting, important topics and optimal communication.The recommendations could help physicians meet children's needs.

Journal: Acta paediatrica (Oslo, Norway : 1992) (2021)
Publication types: Journal Article
Mechanochemical ring-opening metathesis polymerization: development, scope, and mechano-exclusive polymer synthesis.

Ruthenium-alkylidene initiated ring-opening metathesis polymerization has been realized under solid-state conditions by employing a mechanochemical ball milling method.This method promotes greenness and broadens the scope to include mechano-exclusive products.The carbene- and pyridine-based grubbs 3rd-generation complex outperformed other catalysts and maintained similar mechanistic features of solution-phase reactions.High-speed ball milling provides sufficient mixing and energy to the solid reaction mixture, which is composed of an initiator and monomers, to minimize or eliminate the use of solvents.Therefore, the solubility and miscibility of monomers and ru-initiators are not limiting factors in solid-state ball milling.A wide variety of solid monomers, including ionomers, fluorous monomers, and macromonomers, were successfully polymerized under ball milling conditions.Importantly, direct copolymerization of immiscible (ionic/hydrophobic) monomers exemplifies the synthesis of mechano-exclusive polymers that are difficult to make using traditional solution procedures.Finally, the addition of a small amount of a liquid additive (i.e., liquid-assisted grinding) minimized chain-degradation, enabling high-molecular-weight polymer synthesis.

Journal: Chemical science (2022)
Publication types: Journal Article
Self assembled arjunolic acid acts as a smart weapon against cancer through TNF- α mediated ROS generation.

Arjunolic acid (aa) a plant derived pentacyclic triterpenoid which showed effective anticancer activity against mcf-7 and he la cells as well as no significant toxic effect was observed against normal lymphocytes.In the current study the self assemble property of arjunolic acid gives an extra emphasis on anticancer activity which was proved by several fluorescence studies like ros generation, et br/ao and dapi staining.At a selected dose of 50μg/ml aa disrupt the redox balance inside the cancer cells by producing reactive oxygen species.The apoptotic event was mediated by two key regulator proteins tnf-α and nf-κß which was proved here.The increment of the pro-inflammatory cytokines indicates the ros mediated pathway of cancer cell apoptosis.

Journal: Heliyon (2020)
Publication types: Journal Article
Evaluation of Genotoxicity of SU-Eohyeol Pharmacopuncture Using an In Vitro Chromosome Aberration Test in Chinese Hamster Lung Cell.

S this study was conducted to evaluate the safety of su-eohyeol pharmacopuncture (suep) by assessing its potential to cause chromosomal abnormalities in chinese hamster lung cells (chl/ic).Methods a dose-curve was conducted to determine the highest dose of suep.Doses of 10, 5, 2.5, 1.25, 0.625, and 0.313% were used, and no cytotoxicity or suep precipitation was observed.Suep doses of 10, 5, and 2.5%, with positive and negative controls, were used in a chromosome aberration test.Results in this study, the frequency of abnormal chromosomal cells in the suep group did not show a statistically significant difference from that of the negative control group in short-term treatments with and without metabolic activation and the continuous treatment without metabolic activation.Compared with the negative control group, the positive control group had a significantly higher frequency of cells with structural chromosomal abnormalities.This test's results satisfied all conditions for determining the results.Conclusion suep did not induce chromosomal aberrations under the conditions of this study.Other toxicity evaluations, safety studies in humans, and various clinical trials are required to evaluate the safety and efficacy of suep.

Journal: Journal of pharmacopuncture (2022)
Publication types: Journal Article
Rapid Uptake of Testing for Chlamydia, Gonorrhea, and HIV From an Online Platform, April-October 2020.

The baltimore city health department (baltimore, md) promoted iwant the kit for chlamydia, gonorrhea, and hiv testing to city residents and clinic patients when covid-19 restricted in-person clinic services.From april to october 2020, monthly online iwant the kit orders increased by 645%.A high prevalence of chlamydia and gonorrhea was detected, and 96% of users who tested positive for chlamydia and gonorrhea were successfully contacted for treatment.Uptake by baltimore city health department priority populations and excellent treatment linkage demonstrated how a public health-academic partnership successfully addressed a service gap during the pandemic.(am j public health.2022;112(7):985-989.

Journal: American journal of public health (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, P.H.S.
Two-dimensional finite quantum Hall clusters of electrons with anisotropic features.

Low-dimensional nano and two-dimensional materials are of great interest to many disciplines and may have a lot of applications in fields such as electronics, optoelectronics, and photonics.One can create quantum hall phases by applying a strong magnetic field perpendicular to a two-dimensional electron system.One characterizes the nature of the system by looking at magneto-transport data.There have been a few quantum phases seen in past experiments on ga as/al ga as heterostructures that manifest anisotropic magnetoresistance, typically, in high landau levels.In this work, we model the source of anisotropy as originating from an internal anisotropic interaction between electrons.We use this framework to study the possible anisotropic behavior of finite clusters of electrons at filling factor 1/6 of the lowest landau level.

Journal: Scientific reports (2022)
Publication types: Journal Article
Study on Quality Control of CompoundAnoectochilus roxburghii(Wall.) Lindl. by Liquid Chromatography-Tandem Mass Spectrometry.

Compound anoectochilus roxburghii (wall.) lindl.(a.Roxburghii) oral liquid (carol) is a hospital preparation of a.Roxburghii and ganoderma lucidum (g.Lucidum), which have hepatoprotective effects.Eight active components (five nucleosides/nucleobases and three triterpenoid acids) in carol, a.Roxburghii, and g.Lucidum were simultaneously detected by high-performance liquid chromatography−tandem mass spectrometry (lc−ms/ms).The multiple reaction monitoring (mrm) mode was applied for the detection of analytes.These eight compounds were separated well within 12 min and quantified using the internal standard working curve method.The method showed good linearity (r2 > 0.9935) and high sensitivity (limit of detection = 0.29 ng/m l).The analyte recovery ranged from 85.07% to 97.50% (relative standard deviation < 3.31%).The content of the target analytes in four batches of carol, and the raw materials of g.Lucidum and a.Roxburghii from the five regions was determined using this method.The contents of guanosine and ganoderic acid a in four batches of oral liquid were high and stabilized and could be recommended as quality markers (q-marker) for carol.Simultaneous qualitative and quantitative analysis of nucleosides and triterpenoid acids in carol, a.Roxburghii, and g.Lucidum by lc−ms/ms based on the mrm model was reported for the first time.The proposed method provides a sensitive, rapid, and reliable approach for the quality control of chinese medicinal products.

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
Atypical Lemierre's Syndrome. A Case Report and Review of Literature.

Lemierre's syndrome (ls) is a rare disease entity, which can be catastrophic if organism-directed treatment is not initiated early.Lemierre's syndrome is frequently caused by fusobacterium infection which is frequently susceptible to clindamycin.Evidence suggests there is an increase in the incidence of cases of drug resistant fusobacterium species.Through this case we present a unique case of a 45-year-old caucasian female with lemierre's syndrome due to polymicrobial organisms that were resistant to clindamycin thus developing recurrent infections despite being on antibiotics.

Journal: Journal of community hospital internal medicine perspectives (2022)
Publication types: Case Reports;Journal Article
Quantification of cyanobacterial cyclic di-guanosine monophosphate (c-di-GMP) by liquid chromatography electrospray ionization tandem mass spectrometry.

Cyclic di-guanosine monophosphate (c-di-gmp) is a second messenger found ubiquitously in bacteria.This signaling molecule regulates a variety of physiological activities such as phototaxis and flocculation in cyanobacteria and is critical for their environmental adaptation.Although genes encoding the enzymes for synthesis and/or degradation of c-di-gmp are found in the genomes of both multicellular and unicellular cyanobacteria, little is known about the biological functions of these enzymes in cyanobacterial cells.Here we have established a robust and highly sensitive liquid chromatography tandem mass spectrometry (lc-ms/ms)-based method for c-di-gmp quantification using a cost-effective solvent, methanol.Quantification methods were validated by measuring c-di-gmp in the cyanobacterium synechococcus elongatus pcc 7942 through spiking and recovery assays after which the method was applied to examine short-term changes in cellular levels of c-di-gmp in response to a transition from light to dark or from dark to light in s.Elongatus.Results showed that a transient increase in c-di-gmp upon transitioning from light to dark was occurring which resembled responses involving cyclic adenosine monophosphate and other second messengers in cyanobacteria.These findings demonstrated that our method enabled relatively specific and sensitive quantification of c-di-gmp in cyanobacteria at lower cost.

Journal: Journal of microbiological methods (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Protein Complex Identification and quantitative complexome by CN-PAGE.

The majority of cellular processes are carried out by protein complexes.Various size fractionation methods have previously been combined with mass spectrometry to identify protein complexes.However, most of these approaches lack the quantitative information which is required to understand how changes of protein complex abundance and composition affect metabolic fluxes.In this paper we present a proof of concept approach to quantitatively study the complexome in the model plant arabidopsis thaliana at the end of the day (ed) and the end of the night (en).We show that size-fractionation of native protein complexes by clear-native-page (cn-page), coupled with mass spectrometry can be used to establish abundance profiles along the molecular weight gradient.Furthermore, by deconvoluting complex protein abundance profiles, we were able to drastically improve the clustering of protein profiles.To identify putative interaction partners, and ultimately protein complexes, our approach calculates the euclidian distance between protein profile pairs.Acceptable threshold values are based on a cut-off that is optimized by a receiver-operator characteristic (roc) curve analysis.Our approach shows low technical variation and can easily be adapted to study in the complexome in any biological system.

Journal: Scientific reports (2019)
Publication types: Journal Article