syedzayyan/paper_mill_benchmark huggingface dataset:
Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway.

Thioholgamides are ribosomally synthesized and posttranslationally modified peptides (ri pps), with potent activity against cancerous cell lines and an unprecedented structure.Despite being one of the most structurally and chemically complex ri pps, very few biosynthetic steps have been elucidated.Here, we report the completein vitroreconstitution of the biosynthetic pathway.We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing.Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes─tho h/i and tho c/d.Harnessing the power of alpha fold, we deduce that tho d acts as a lyase and also proposes putative catalytic residues.Tho f catalyzes the oxidative decarboxylation of the terminal cys, and the subsequent macrocyclization is facilitated by tho e.This is followed by ser dehydration, which is also carried out by tho c/d.Tho g is responsible for histidine bis-n-methylation, which is a prerequisite for his β-hydroxylation─a modification carried out by tho j.The last step of the pathway is the removal of the leader peptide by tho k to afford mature thioholgamide.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A multimodal fluorescent probe for portable colorimetric detection of pH and it's application in mitochondrial bioimaging.

Mitochondria, as vital energy supplying organelles, play important roles in cellular metabolism, which are closely related with mitochondrial p h (∼8.0).In this work, a novel multimodal fluorescent probe was employed for ratiometric and colorimetric detection of p h.The probe is designed to work by controlling benzothiazole phenol-hemicyanine system as the interaction site and hemicyanine connected by conjugate bonds as the mitochondrial targeting, which also could make the fluorescence of probe red-shifted.This system results in a perfect ratiometric fluorescent response, whose emission changed from red to blue under p h 2.0-10.0, having a broad linear range (p h = 3.0-10.0).And the marked colour change (light yellow to deep purple via naked eye under p h 2.0-11.0) could be used to construct the test strip colorimetry and smartphone app detection method, realizing the fast, portable, and accurate detection of p h in vitro and environment.Besides, the probe owns the characteristics of easy loading, high selectivity and staining ability of mitochondria, and low cytotoxicity, thereby allowing imaging of p h values and real-time monitor the subcellular mitochondria p h changes caused by drugs in living cells.It thus could be used to monitor the organ-specific dynamics related to transitions between pathological and physiological states.

Journal: Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy (2022)
Publication types: Journal Article
Fabrication of Orientation-Tunable Si Nanowires on Silicon Pyramids with Omnidirectional Light Absorption.

In this work, the different orientation of si nws on si pyramids by a two step mace method have been fabricated.By tuning the structure of ag catalyst film and controlling the concentration of h2o2or the etching temperature, the tunability of the orientation of si nws from to on si pyramids was realized.Si structures composed of si pyramids and si nws exhibit better omnidirectional light-trapping ability by multiple reflections.Si structures with structural tunability and enhanced light harvesting performance will find a wide variety of significant applications in solar cells, photodetectors, and optoelectronic devices.

Journal: Langmuir : the ACS journal of surfaces and colloids (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Is vertical transmission the only pathway for Rickettsia felis?

The genus rickettsia encompasses several species grouped into two main clusters, typhus and the transitional groups.The latter group contains rickettsia felis, an endosymbiont of several arthropods with an uncertain human pathogenicity and whose most efficient transmission mechanism described thus far is transovarial.The aim of this study was to evaluate whether this pathway exists using phylogenetic analysis and partial sequences of the 17k da and glt a genes and comparing them with host phylogeny using the cytb region.This is the first study that evaluates the vertical transmission of r.Felis.In general, both phylogenies of r.Felis showed no polytomies, as suspected if this pathway was the only pathway occurring.When phylogenies of the invertebrates and the glt a of r.Felis were compared for strong coevolutionary insight, intricate relationships were observed, suggesting that other transmission pathways must occur, such as horizontal transmission.Further studies are needed to determine which other transmission routes occur in hematophagous arthropods.

Journal: Transboundary and emerging diseases (2022)
Publication types: Journal Article
A case of a primary pulmonary meningioma mimicking a metastasis from a papillary thyroid carcinoma due to a size reduction after radioactive iodine therapy.

Primary pulmonary meningiomas (ppms) are a rare mostly benign disease presenting as a solitary pulmonary nodule and are hardly distinguishable from a metastatic tumor because of a lack of specific radiological features.We described a case of a ppm initially diagnosed as a metastatic lung tumor from thyroid cancer with a size reduction after radioactive iodine therapy.Case presentation a 62-year-old woman who had undergone a total thyroidectomy for a papillary thyroid carcinoma 6 years prior presented with an enlarging pulmonary nodule.The nodule had decreased in size from 7.0 to 5.5 mm after adjuvant radioactive iodine therapy and enlarged to 8.7 mm over the next 5 years.Under a clinical diagnosis of a metastatic lung tumor, she underwent a thoracoscopic pulmonary wedge resection and was pathologically diagnosed with a ppm.Conclusion a surgical resection is required for histological diagnoses of ppms especially in patients with a history of a malignancy.

Journal: Surgical case reports (2020)
Publication types: Journal Article
Mental Imagery to Reduce Alcohol-related harm in patients with alcohol dependence and alcohol-related liver damaGE: the MIRAGE pilot trial protocol.

Introduction in the uk, alcohol use is the main driver of chronic liver disease and each year results in over 1 million unplanned hospital admissions and over 25 000 deaths from alcohol-related liver disease (ar ld).The only effective treatment to prevent progression of liver damage is reducing or ceasing alcohol consumption.Psychological and pharmacological therapies for alcohol misuse are ineffective in patients with ar ld.Functional imagery training (fit) is a novel psychological therapy that builds on motivational interviewing techniques with multisensory imagery.This pilot trial aims to test the feasibility of training alcohol liaison nurses to deliver fit therapy and of recruiting and retaining patients with ar ld and alcohol dependence to a randomised trial of fit and treatment as usual (tau) versus tau alone.Methods and analysis this is a randomised pilot trial of fit and tau versus tau alone in 90 patients with ar ld and alcohol dependence admitted to one of four uk centres.The primary objectives are to estimate rates of screening, recruitment, randomisation, retention, adherence to fit/tau and a preliminary assessment of the fit intervention in the ar ld population.Data from the pilot study will be used to finalise the design of a definitive randomised controlled trial to assess the effectiveness and cost-effectiveness of fit.The proposed primary outcome measure for the definitive trial is self-reported alcohol use assessed using timeline follow-back.Ethics and dissemination research ethics approval was given by the yorkshire and humber-bradford leeds research ethics committee (reference: 21/yh/0044).Eligible patients will be approached and written informed consent obtained prior to participation.Results will be disseminated through peer-reviewed open access journals, international conferences and a lay summary published on the trials unit website and made available to patient groups.Trial registration number isrctn41353774.

Journal: BMJ open (2022)
Publication types: Clinical Trial Protocol;Journal Article;Research Support, Non-U.S. Gov't
Mice alternate between discrete strategies during perceptual decision-making.

Classical models of perceptual decision-making assume that subjects use a single, consistent strategy to form decisions, or that decision-making strategies evolve slowly over time.Here we present new analyses suggesting that this common view is incorrect.We analyzed data from mouse and human decision-making experiments and found that choice behavior relies on an interplay among multiple interleaved strategies.These strategies, characterized by states in a hidden markov model, persist for tens to hundreds of trials before switching, and often switch multiple times within a session.The identified decision-making strategies were highly consistent across mice and comprised a single 'engaged' state, in which decisions relied heavily on the sensory stimulus, and several biased states in which errors frequently occurred.These results provide a powerful alternate explanation for 'lapses' often observed in rodent behavioral experiments, and suggest that standard measures of performance mask the presence of major changes in strategy across trials.

Journal: Nature neuroscience (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
In vitro modeling of endometriosis and endometriotic microenvironment - Challenges and recent advances.

Endometriosis is a chronic condition with high prevalence in reproductive age women, defined as the growth of endometrial tissue outside the uterine cavity, most commonly on the pelvic peritoneum.The ectopic endometrial lesions exist in a unique microenvironment created by the interaction of epithelial, stromal, endothelial, glandular, and immune cell components, dominated by inflammatory, angiogenic, and endocrine signals.Current research is directed at understanding the complex microenvironment of the lesions and its relationship with different endometriosis stages, phenotypes, and disease symptoms and at the development of novel diagnostic and therapeutic concepts that minimalize the undesirable side effects of current medical management.Recreating pathophysiological cellular and molecular mechanisms and identifying clinically relevant metrics to assess drug efficacy is a great challenge for the experimental disease models.This review summarizes the complete range of available in vitro experimental systems used in endometriotic studies, which reflect the multifactorial nature of the endometriotic lesion.The article discusses the simplistic in vitro models such as primary endometrial cells and endometriotic cell lines to heterogeneous 2d co-cultures, and recently more common, 3d systems based on self-organization and controlled assembly, both in microfluidic or bioprinting methodologies.Basic research models allow studying fundamental pathological mechanisms by which menstrual endometrium adheres, invades, and establishes lesions in ectopic sites.The advanced endometriosis experimental models address the critical challenges and unsolved problems and provide an approach to drug screening and medicine discovery by mimicking the complicated behaviors of the endometriotic lesion.

Journal: Cellular signalling (2022)
Publication types: Journal Article;Review
Waning of specific antibodies against Delta and Omicron variants five months after a third dose of BNT162b2 SARS-CoV-2 vaccine in elderly individuals.

The emergence of new sars-co v-2 variants, such as the more transmissible delta and omicron variants, has raised concerns on efficacy of the covid-19 vaccines.Here, we examined the waning of antibody responses against different variants following primary and booster vaccination.We found that antibody responses against variants were low following primary vaccination.The antibody response against omicron was almost non-existent.Efficient boosting of antibody response against all variants, including omicron, was observed following a third dose.The antibody response against the variants tested was significantly higher at one month following booster vaccination, compared with two months following primary vaccination, for all individuals, including the low antibody responders identified at two months following primary vaccination.The antibody response, for all variants tested, was significantly higher at four months post booster than at five months post primary vaccination, and the proportion of low responders remained low (6-11%).However, there was significant waning of antibody response in more than 95% of individuals at four months, compared to one month following booster.We also observed a robust memory b cell response following booster, which remained higher at four months post booster than prior to booster.However, the memory b cell responses were on the decline for 50% of individuals at four months following booster.Similarly, while the t cell response is sustained, at cohort level, at four months post booster, a substantial proportion of individuals (18.8 - 53.8%) exhibited t cell response at four months post booster that has waned to levels below their corresponding levels before booster.The findings show an efficient induction of immune response against sars-co v-2 variants following booster vaccination.However, the induced immunity by the third bnt162b2 vaccine dose was transient.The findings suggest that elderly individuals may require a fourth dose to provide protection against sars-co v-2.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Axial Length Distributions in Patients With Genetically Confirmed Inherited Retinal Diseases.

We investigated axial length (al) distributions in inherited retinal diseases (irds), comparing them with reference cohorts.Methods al measurements from ird natural history study participants were included and compared with reference cohorts (twins uk, raine study gen2-20, and published studies).Comparing with the raine study cohort, formal odds ratios (ors) for al ≥ 26 mm or al ≤ 22 mm were derived for each ird (firth's logistic regression model, adjusted for age and sex).Results measurements were available for 435 patients (median age, 19.5 years).Of 19 diseases, 10 had >10 participants: abca4 retinopathy; cngb3- and cnga3-associated achromatopsia; rpgr-associated disease; rpe65-associated disease; blue cone monochromacy (bcm); bornholm eye disease (bed); tyr- and oca2-associated oculocutaneous albinism; and gpr143-associated ocular albinism.Compared with the twins uk cohort (n = 322; median age, 65.1 years) and raine study cohort (n = 1335; median age, 19.9 years), al distributions were wider in the ird groups.Increased odds for longer als were observed for bcm, bed, rpgr, rpe65, oca2, and tyr; increased odds for short al were observed for rpe65, tyr, and gpr143.In subanalysis of rpgr-associated disease, longer average als occurred in cone-rod dystrophy (n = 5) than rod-cone dystrophy (p = 0.002).Conclusions several diseases showed increased odds for longer al (highest or with bcm); some showed increased odds for shorter al (highest or with gpr143).Patients with rpe65- and tyr-associated disease showed increased odds for longer and for shorter eyes.Albinism genes were associated with different effects on al.These findings add to the phenotype of irds and may yield insights into mechanisms of refractive error development.

Journal: Investigative ophthalmology & visual science (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Childhood Residential Mobility and Mental and Physical Health in Later Life: Findings From the Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study.

The study objective was to investigate the effects of childhood residential mobility on older adult physical and mental health.In reasons for geographic and racial differences in stroke (regards) study, we used linear regression models to investigate if number of moves during childhood predicted mental and physical health (sf-12 mcs, pcs), adjusting for demographic covariates, childhood socioeconomic status (ses), childhood social support, and adverse childhood experiences (aces).We investigated interaction by age, race, childhood ses, and aces.People who moved more during childhood had poorer mcs scores,β= -0.10, se = 0.05,p= 0.03, and poorer pcs scores,β= -0.25, se = 0.06,p< 0.0001.Effects of moves on pcs were worse for black people compared to white people (p= 0.06), those with low childhood ses compared to high childhood ses (p= 0.02), and high aces compared to low aces (p= 0.01).As family instability accompanying residential mobility, family poverty, and adversity disproportionately affect health, black people may be especially disadvantaged.

Journal: Journal of applied gerontology : the official journal of the Southern Gerontological Society (2023)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Lamb Wave-Based Damage Localization and Quantification in Composites Using Probabilistic Imaging Algorithm and Statistical Method.

Quantitatively and accurately monitoring the damage to composites is critical for estimating the remaining life of structures and determining whether maintenance is essential.This paper proposed an active sensing method for damage localization and quantification in composite plates.The probabilistic imaging algorithm and the statistical method were introduced to reduce the impact of composite anisotropy on the accuracy of damage detection.The matching pursuit decomposition (mpd) algorithm was utilized to extract the precise tof for damage detection.The damage localization was realized by comprehensively evaluating the damage probability evaluation results of all sensing paths in the monitoring area.Meanwhile, the scattering source was recognized on the elliptical trajectory obtained through the tof of each sensing path to estimate the damage size.Damage size was characterized by the gaussian kernel probability density distribution of scattering sources.The algorithm was validated by through-thickness hole damages of various locations and sizes in composite plates.The experimental results demonstrated that the localization and quantification absolute error are within 11 mm and 2.2 mm, respectively, with a sensor spacing of 100 mm.The algorithm proposed in this paper can accurately locate and quantify damage in composite plate-like structures.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Standing trans-nasal endoscopic guided CO2laser fenestration of the palatine bone to access the sphenopalatine sinus in a horse.

To describe a novel standing trans-nasal endoscopic guided co2laser fenestration approach to access the sphenopalatine sinus (sps) in the horse.Study design case report.Animals cadaver study and client-owned 20-year-old warmblood gelding.Methods the rostral palatine bone within the nasopharynx was investigated as a possible site for fenestration to access the sps in cadavers.The ability to fenestrate the sps was tested in cadavers using a flexible endoscope and co2laser fiber inserted via biopsy channel.The fenestration procedure was then performed in a clinical case presented for unilateral epistaxis where a soft tissue attenuating mass in the right sps was identified with standing computed tomography (ct).Results the cadaver study demonstrated the appropriate site within the nasopharynx midway between the vomer and dorsal conchal wall.The co2laser successfully ablated the mucosa and palatine bone to enable endoscopic access to the palatine portion of the sps.The endoscopic procedure was performed as a two-step process via standing sedation due to mucosal bleeding obscuring visualization.Access to the sps through fenestration allowed biopsy under direct endoscopic visualization with long-handled bronchoesophageal forceps inserted via the ipsilateral middle meatus.The mass within sps was determined to be an undifferentiated carcinoma.Further treatment was declined and the horse euthanized 6 months following the procedure due to acute onset of neurologic symptoms.Conclusion endoscopically guided fenestration of the rostral palatine bone within the nasopharynx using co2laser in the standing horse provided good access and visualization of the palatine portion of the sps.

Journal: Veterinary surgery : VS (2021)
Publication types: Case Reports;Journal Article
Time-resolved and steady-state irradiation of hydrophilic sulfonated bis-triazinyl-(bi)pyridines - modelling radiolytic degradation.

Efficient separation of the actinides from the lanthanides is a critical challenge in the development of a more sophisticated spent nuclear fuel recycling process.Based upon the slight differences in f-orbital distribution, a new class of soft nitrogen-donor ligands, the sulfonated bis-triazinyl-(bi)pyridines, has been identified and shown to be successful for this separation under anticipated, large-scale treatment conditions.The radiation robustness of these ligands is key to their implementation; however, current stability studies have yielded conflicting results.Here we report on the radiolytic degradation of the sulfonated 2,6-bis(1,2,4-triazin-3-yl)pyridine (btp(s)) and 6,6'-bis(1,2,4-triazin-3-yl)-2,2'-bipyridine (btbp(s)) in aerated, aqueous solutions using a combination of time-resolved pulsed electron techniques to ascertain their reaction kinetics with key aqueous radiolysis products (eaq-, h ̇,  ̇oh, and  ̇no3), and steady state gamma radiolysis in conjunction with liquid chromatography for identification and quantification of both ligands as a function of absorbed dose.These data were used to construct a predictive deterministic model to provide critical insight into the fundamental radiolysis mechanisms responsible for the ligands' radiolytic stability.The first-order decays of btp(s) and btbp(s) are predominantly driven by oxidative processes ( ̇oh and, to a lesser extent, h2o2), for which calculations demonstrate that the rate of degradation is inhibited by the formation of ligand degradation products that undergo secondary reactions with the primary products of water radiolysis.Overall, btp(s) is ∼20% more radiolytically stable than btbp(s), but over 90% of either ligand is consumed within 1 k gy.

Journal: Dalton transactions (Cambridge, England : 2003) (2019)
Publication types: Journal Article