syedzayyan/paper_mill_benchmark huggingface dataset:
Optimization of the Cetyltrimethylammonium bromide (CTAB) DNA extraction protocol using forest elephant dung samples.

Among non-invasive biological samples, feces offer an important source of dna and can easily be collected.However, working with fecal dna from highly vegetarians species such as elephant is more challenging because plant secondary compounds have an inhibitory effect on pcr reactions.Working with forest elephant dung samples, we tested and adapted a protocol of dna extraction developed on plants based on the cetyltrimethylammonium bromide (ctab) protocol.The protocol is relatively simple and yields a high dna concentration.It is five-time less expensive compared to the methods of benbouza et al.The extracted dna is of good quality and easily amplified by pcr.The high-amplification percentage of mitochondrial genes in fecal dna and subsequent sequencing of pcr products indicate that the proposed optimized method is reliable for molecular analysis of forest elephant dung samples.•our optimized ctab protocol has been adjusted by the addition of sodium dodecyl sulfate (sds) and proteinase k during the lysis phase.The combined effect of these reagents was capable of lysing cell walls and removing proteins efficiently.•moreover, the prolonged time of incubation (overnight incubation at room temperature followed by 3 hours of incubation in a water bath) enhanced the increase of dna yield but make the optimized protocol more time-consuming.

Journal: MethodsX (2022)
Publication types: Journal Article
The role of Gamma Knife radiosurgery in the management of skull base chordoma.

Chordoma is a slow-growing and locally aggressive cancer, which arises from the remnants of the primitive notochord.The first line treatment for the skull base chordoma is neurosurgery.Gamma knife radiosurgery (gks) is often be chosen especially in the setting of residual or recurrent chordomas.The purpose of this study is to evaluate the prognosis of patients with skull base chordoma who underwent gks.Methods the present study was a retrospective analysis of 53 patients with skull base chordomas who underwent gks.Univariate cox and kaplan-meier survival analysis were performed to analyze the relationship between the tumor control time and the clinical characteristics.Results the 1-, 2-, 3-, and 5-year progression free survival (pfs) rates were 87, 71, 51, and 18%, respectively.After performing the univariate analysis, the clinical characteristics were not found to be significantly associated with the time of pfs; however, surgical history, peripheral dose, and tumor volume did have tendencies to predict the prognosis.Conclusion gks provided a safe and relatively effective treatment for residual or recurrent chordomas after surgical resection.A higher tumor control rate depends on two approaches, an appropriate dose of radiation for the tumor and the accurate identification of the tumor margins.

Journal: Frontiers in oncology (2022)
Publication types: Journal Article
IoT snoring sound detector prototype as a model of future participatory healthcare.

Traditional healthcare is centred around providing in-hospital services using hospital owned medical instruments.The covid-19 pandemic has shown that this approach lacks flexibility to insure follow-up and treatment of common medical problems.In an alternative setting adapted to this problem, participatory healthcare can be considered centred around data provided by patients owning and operating medical data collection equipment in their homes.Objective in order to trigger such a shift reliable and price attractive devices need to become available.Snoring, as a human sound production during sleep, can reflect sleeping behaviour and indicate sleep problems as an element of the overall health condition of a person.Methods the use of off-the-shelf hardware from internet of things platforms and standard audio components allows the development of such devices.A prototype of a snoring sound detector with this purpose is developed.Results the device, controlled by the patient and with specific snoring recording and analysing functions is demonstrated as a model for future participatory healthcare.Conclusions design of monitoring devices following this model could allow market introduction of new equipment for participatory healthcare, bringing a care complementary to traditional healthcare to the reach of patients, and could result in benefits from enhanced patient participation.

Journal: Technology and health care : official journal of the European Society for Engineering and Medicine (2022)
Publication types: Journal Article
Functional expression of TRPA1 channel, TRPV1 channel and TMEM100 in human odontoblasts.

Trpa1 and trpv1 channels respond to external stimulation as pain mediators and form a complex with a transmembrane protein tmem100 in some tissues.However, their expression and interaction in dental pulp is unclear.To investigate the functional co-expression of trpa1 channel, trpv1 channel and tmem100 in human odontoblasts (hods), immunohistochemistry, immunofluorescence staining and western blot were used to study their co-localization and expression in both native hods and cultured hod-like cells.Calcium imaging was used to detect the functional interaction between trpa1 and trpv1 channels.Immunohistochemistry and multiple immunofluorescence staining of tooth slices showed positive expression of trpa1 channel, trpv1 channel and tmem100 mainly in the cell bodies of hods, and trpa1 channel presented more obvious immunofluorescence in the cell processes than trpv1 channel and tmem100.Halo software analysis showed that trpa1 and trpv1 channels were positively expressed in most tmem100+hods and these three proteins were strongly correlated in hods (p 0.05).Double immunofluorescence staining of cultured hod-like cells visually demonstrated that trpa1 and trpv1 channel were both highly co-localized with tmem100 with similar expressive intensity.Calcium imaging showed that there was a functional interaction between trpa1 and trpv1 channels in hod-like cells, and trpa1 channel might play a greater role in this interaction.Overall, we concluded that trpa1 channel, trpv1 channel and tmem100 could be functionally co-expressed in hods.

Journal: Journal of molecular histology (2021)
Publication types: Journal Article
Efficient in vivo wound healing using noble metal nanoclusters.

The wound healing process involves multiple steps including hemostasis, inflammation, proliferation, and tissue remodeling.Nanomaterials have been employed externally for healing wounds.However, their use as systemic therapeutics has not been extensively explored.We report the use of ultra-small noble metal nanoclusters (ncs) for the treatment of skin wounds.Both in vitro and in vivo studies indicate ncs have comprehensive therapeutic effects for wound healing, promoting cell proliferation and migration while decreasing inflammation.

Journal: Nanoscale (2021)
Publication types: Journal Article;Retracted Publication
Design and Compressive Fatigue Properties of Irregular Porous Scaffolds for Orthopedics Fabricated Using Selective Laser Melting.

An irregular porous structure plays a major role in bone tissue engineering, and it is more suitable for bone tissue growth than a regular porous structure.The response surface method was used to establish a relationship between the average pore size and the design parameters.The technology of selective laser melting was utilized to fabricate the porous ti-6al-4v scaffolds with an irregularity of (0.4) and porosities of (70, 80, and 90%) designed using the voronoi-tessellation method.Compression tests of porous scaffolds showed an elastic modulus range of 0.84-1.97 gpa and an ultimate strength ranging within 21.0-99.1 mpa.The elastic modulus was mainly influenced by the porosity and heat-treatment process.Furthermore, the fatigue test results suggested that the number of cycles (9 × 104to 1.8 × 106) was greatly influenced by the porosity and heat-treatment process.The heat treatment of annealing greatly improved the fatigue performance of porous scaffolds.The irregular porous scaffolds with lower porosity and after full annealing exhibited the best fatigue behavior.

Journal: ACS biomaterials science & engineering (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Impact of thermal processing on the nutrients, phytochemicals, and metal contaminants in edible algae.

Edible algae products have increasingly become a larger component of diets worldwide.Algae can be a source of essential micronutrients and bioactive phytochemicals, although select varieties also often contain elevated concentrations of heavy metal contaminants.Due to the effects thermal processing of foodstuffs can have on levels of nutrients, phytochemicals, and contaminants, it is important to consider the role processing has on the levels of these components in algae food products.Here, we evaluate the literature covering how different types of processing, including commercial thermal application and in-home preparation, affect constituents such as vitamins, minerals, carotenoids, pigment compounds, and metal contaminants.Overall, the literature suggests that there are optimum processing conditions and specific cooking techniques that can be used to increase retention of important nutritional components while also reducing concentrations of metal contaminants.Although further research is needed on how thermal processing affects individual compounds in algae and their ultimate bioavailability, these data should be taken into consideration in order to inform design of product processing to both increase retention of nutritional components and limit metal contaminants.

Journal: Critical reviews in food science and nutrition (2022)
Publication types: Journal Article
Function-Oriented Synthesis of Marine Phidianidine Derivatives as Potential PTP1B Inhibitors with Specific Selectivity.

Phidianidines a and b are two novel marine indole alkaloids bearing an uncommon 1,2,4-oxadiazole ring and exhibiting various biological activities.Our previous research showed that the synthesized phidianidine analogs had the potential to inhibit the activity of protein tyrosine phosphatase 1b (ptp1b), a validated target for type ii diabetes, which indicates that these analogs are worth further structural modification.Therefore, in this paper, a series of phidianidine derivatives were designed and rapidly synthesized with a function-oriented synthesis (fos) strategy.Their inhibitory effects on ptp1b and t-cell protein tyrosine phosphatase (tcptp) were evaluated, and several compounds displayed significant inhibitory potency and specific selectivity over ptp1b.The structure-activity relationship (sar) and molecular docking analyses are also described.

Journal: Marine drugs (2018)
Publication types: Journal Article
Separation of vanadium and tungsten from synthetic and spent catalyst leach solutions using an ion-exchange resin.

Vanadium and tungsten ion adsorption and desorption characteristics and separation conditions were investigated using a simple porous anion-exchange resin.Initially, systematic experimental research was performed using synthetic aqueous vanadium and tungsten solutions.To evaluate the vanadium and tungsten (50-500 mg l-1) isotherm parameters, adsorption was performed at p h 7.0 using 0.5 g of ion-exchange resin at 303 k for 24 h.Well-known adsorption models such as langmuir, freundlich, and temkin were used.Vanadium was desorbed from the resin using hcl and na oh solutions.In contrast, tungsten was not desorbed by the hcl solution, which enabled the separation of the two ions.The desorption reaction reached equilibrium within 30 min of its start, yielding over 90% desorption.We investigated the adsorption mechanism and resin stability with the aid of spectroscopic and microscopic analysis, as well as adsorption results.The applicability and feasibility of the resin was testedviarecovery of both metals from real spent catalysts.The applicability and reusability results indicated that the resin can be used for more than five cycles with an efficacy of over 90%.

Journal: RSC advances (2022)
Publication types: Journal Article
Assessment of changes in genetic transcriptome in nasal epithelial cells exposed to ozone-aged black carbon and pollen allergen by high-throughput transcriptomics.

Air pollution may be associated with increased airway responsiveness to allergens in allergic rhinitis (ar).Ozone-aged environmental black carbon (o3bc) is an important constituent of atmospheric particulate matter (pm), for which the mechanisms underlying its effects have not been fully elucidated in ar.The objective of the present study was to determine the o3bc and pollen-induced alterations in the transcriptome in human nasal epithelial cells (h necs) in vitro.Methods h necs from nasal epithelial mucosal samples of healthy individuals undergoing nasal surgery (turbinoplasty or septoplasty) were established as air-liquid interface (ali) cultures and exposed to o3bc, pollen, or a combination of o3bc+ pollen.Changes in cell viability were analyzed by fluorescence and changes in the transcriptome by high-throughput rna sequencing (rna-seq).Several differentially expressed genes were verified by reverse transcription-quantitative polymerase chain reaction (rt-q pcr).Enrichment analysis, based on gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) database, was performed to determine major biological functions and pathways involved.Results exposure to ≥ 50 μg/ml o3bc or 25 μg/ml o3bc+ 200 μg /ml pollen significantly decreased cell viability of the h necs compared to control (p < 0.05) or 25 μg/ml o3bc alone (p < 0.05); whereas exposure to pollen alone did not alter cell viability at any concentration investigated.High-throughput rna sequencing analysis indicated that there was significant difference in gene expression between pollen or o3bc alone and o3bc+ pollen exposed cells.Exposure to 200 μg/ml o3bc was associated with hypoxia stress response go terms, whereas exposure to 25 μg/ml o3bc+ 200 μg/ml pollen was associated with inflammatory response go terms; including regulation of neutrophil migration and chemotaxis, macrophage differentiation and chemotaxis, mast cell activation, and phagocytosis.Kegg pathway analysis indicated the top 10 upstream regulators to be il1b, csf1, ccl2, tlr2, lpl, igf8, spp1, cxcl8, fcer1g and il1rn; of which expressions of inflammation-related genes il1b, csf1 and fcer1g were significantly increased.Conclusion o3bc and pollen allergen combined exposure may induce innate immune and allergic inflammation in h necs, and therefore potentially exacerbate the symptoms of ar in affected individuals.

Journal: Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology (2021)
Publication types: Journal Article
Efficacy of the Atraumatic Physics Forceps Over Conventional Extraction Forceps in Extraction of Tooth-Does it Offer an Alternative in All Types of Extraction or Only can be Used in Few Selected Types of Extraction: A Comparative Study.

We conducted this study to evaluate the efficacy of physics forceps in dental extractions as compared with conventional forceps and as well as to evaluate its atraumatic point of view.Materials and methods a total of 200 healthy adult patients were included in the study who reported for dental extractions, divided into two groups each containing 100 patients.The patients were randomly allocated into either group by lottery method.Results operating time in the physics forceps group was found to be significantly reduced as well as lesser incidence of dry socket was noted which was statistically significant on the 2ndday postoperatively.However, incidence of root fracture, buccal plate fracture, and gingival lacerations were not found to be statistically significant but their occurrence was less in the physics forceps group as compared with the conventional forceps group.Conclusion to conclude, we can say that extractions done by physics forceps results in significant reduction in unnecessary trauma as well as stress to both the operator and patient.The forceps is an atraumatic extraction system which is a boon for the profession, thereby reducing ridge deformities and preparing the patients for future prosthesis.

Journal: Journal of pharmacy & bioallied sciences (2022)
Publication types: Journal Article
Metasurface-Dressed Two-Dimensional on-Chip Waveguide for Free-Space Light Field Manipulation.

We show that a metasurface-coated two-dimensional (2d) slab waveguide enables the generation of arbitrary complex light fields by combining the extreme versatility and freedom on the wavefront control of optical metasurfaces with the compactness of photonic integrated circuits.We demonstrated off-chip 2d focusing and holographic projection with our metasurface-dressed photonic integrated devices.This technology holds the potential for many other optical applications requiring 2d light field manipulation with full on-chip integration, such as solid-state li dar and near-eye ar/vr displays.

Journal: ACS photonics (2022)
Publication types: Journal Article
Characterization of the Largest Secretory Protein Family, Ricin B Lectin-like Protein, inNosema bombycis: Insights into Microsporidian Adaptation to Host.

Microsporidia are a group of obligate intracellular pathogens infecting nearly all animal phyla.The microsporidian nosema bombycishas been isolated from several lepidopteran species, including the economy-important silkworms as well as several crop pests.Proteins secreted by parasites can be important virulent factors in modulating host pathways.Ricin is a two-chain lectin best known for its extreme vertebrate toxicity.Ricin b lectin-like proteins are widely distributed in microsporidia, especially in n.Bombycis.in this study, we identify 52 ricin b lectin-like proteins (rbls) in n.Bombycis.We show that the n.Bombycis rbls (nb rbls) are classified into four subfamilies.The subfamily 1 was the most conserved, with all members having a ricin b lectin domain and most members containing a signal peptide.The other three subfamilies were less conserved, and even lost the ricin b lectin domain, suggesting that nb rbls might be a multi-functional family.Our study here indicated that the nb rbl family had evolved by producing tandem duplications firstly and then expanded by segmental duplications, resulting in concentrated localizations mainly in three genomic regions.Moreover, based on rna-seq data, we found that several nbrbls were highly expressed during infection.Further, the results show that the nb rbl28 was secreted into host nucleus, where it promotes the expressions of genes involved in cell cycle progression.In summary, the great copy number, high divergence, and concentrated genome distribution of the nb rbls demonstrated that these proteins might be adaptively evolved and played a vital role in the multi-host n.Bombycis.

Journal: Journal of fungi (Basel, Switzerland) (2022)
Publication types: Journal Article
Laser Interstitial Thermal Therapy for Glioblastoma: A Single-Center Experience.

Surgical resection has been shown to prolong survival in patients with glioblastoma multiforme (gbm), although this benefit has not been demonstrated for reoperation following tumor recurrence.Laser interstitial thermal therapy (litt) is a minimally invasive ablation technique that has been shown to effectively reduce tumor burden in some patients with intracranial malignancy.The aim of this study was to describe the safety and efficacy of litt for recurrent and newly diagnosed gbm at a large tertiary referral center.Methods patients with gbm receiving litt were retrospectively analyzed.Overall survival from the time of litt was the primary end point measured.Results there were 69 patients identified for inclusion in this study.The median age of the cohort was 56 years (range, 15-77 years).Median tumor volume was 10.4 cm3(range, 1.0-64.0 cm3).A kaplan-meier estimate of median overall survival for the series from the time of litt was 12 months (95% confidence interval 8-16 months).Median progression-free survival for the cohort from litt was 4 months (95% confidence interval 3-7 months).Adjuvant chemotherapy significantly prolonged progression-free survival and overall survival (p < 0.01 for both) in the cohort.Gross total ablation was not significantly associated with progression-free survival (p = 0.09).Conclusions litt can safely reduce intracranial tumor burden in patients with gbm who have exhausted other adjuvant therapies or are poor candidates for conventional resection techniques.

Journal: World neurosurgery (2021)
Publication types: Journal Article
Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan.

The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total dna.However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions.In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons.When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (mas d) make it possible to separate areas with traditional and gas-hydrate types of deposits.Using cultured methods, we found that representatives of the nocardiaceae family of the phylum actinomycetotawere tied to the areas where gas hydrates were found.The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods.For the first time, this ability was revealed for the genera stenotrophomonas,psychrobacter,micrococcusand peribacillus.The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.

Journal: Biology (2022)
Publication types: Journal Article
Anticancer profile and anti-inflammatory effect of new N-(2-((4-(1,3-diphenyl-1H-pyrazol-4-yl)pyridine sulfonamide derivatives.

A new series of n-(2-((4-(1,3-diphenyl-1h-pyrazol-4-yl)pyridine sulfonamide derivatives 11a-o were designed and synthesized based on our previous works.The new series was tested for its anticancer and anti-inflammatory effects.The anticancer profile of final target compounds was obtained by testing them over 60 cell lines belong to nine types of cancers.Compound 11c showed the highest percent inhibition, so its potency was measured over the most sensitive cell line to determine its ic50over each cell.In addition, compound 11c was tested over kinase panel to get its biological target(s).Compound 11c had strong activity over jnk1, jnk2, p38a and v600ebraf.All final target compounds were tested against the four kinases to build a structure activity relationship.Compound 11c was subjected to cell cycle analysis to check at which phase is affected by 11c.The anti-inflammatory effect of final target compounds was screened by testing their ability to inhibit both nitric oxide release and prostaglandin e2 production on raw 264.7 macrophages in addition to test their cytotoxic effect on the same cells.Compound 11n showed the highest ability to inhibit prostaglandin e2 and all compound showed moderate to low activity regarding inhibition of nitric oxide release.Compound 11n was investigated for its ability to reduce interleukin 6 and tnf-alpha.In addition, compound 11n was tested for its effect on induced nitric oxide synthase (i nos), and cox-2 m rna expression level and its effect on nitric oxide synthase (i nos), cox-1 and cox-2 protein levels where it showed selectivity for cox-2 compared to cox-1 and i nos.

Journal: Bioorganic chemistry (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't