syedzayyan/paper_mill_benchmark huggingface dataset:
Retained Localization Wire Fragments in the Breast: Long-term Follow-up.

Historically, wire localization was the most widely utilized procedure for preoperative breast lesion localization.Occasionally a portion of the wire is retained in the breast.When recognized intraoperatively, the fragment can be removed immediately, but some cases are identified during post-surgical mammographic follow-up.There is little research detailing long-term stability of retained wire fragments, associated complications, or management options for cases requiring removal.We aimed to determine how often retained wire fragments remained stable, the frequency with which intervention was required, and methods available for fragment removal.Methods following irb approval, we conducted a retrospective review of patients with a retained wire localization fragment identified by emr search seen at our institution between january 1990 and july 2019.Mammograms, localization images, specimen radiographs, and relevant clinical notes were reviewed.Information collected included breast tissue density, patient age, associated pathology, length of time the fragment was retained, presence and/or absence of fragment migration or other complications, and management of removed fragments.Results eighteen eligible patients were identified with 19 retained wire fragments.Fragments ranged in length from 1 mm -33 mm.Twelve wire fragments had mammograms available to evaluate stability.All twelve fragments were stable mammographically for an average of 96.9 months.Seven wire fragments had no follow-up mammograms available.Eight wire fragments were surgically excised.None were excised due to migration.Conclusion localization wire fragments retained in the breast are at low risk for clinically significant migration and can be safely followed mammographically rather than undergoing immediate surgical excision or imaging-guided percutaneous removal.

Journal: Current problems in diagnostic radiology (2022)
Publication types: Journal Article
Analysis of the chemical composition changes of Gardeniae Fructus before and after processing based on ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry.

Gardeniae fructus, the dry fruit of gardenia jasminoides ellis, has been widely used for the treatment of different diseases.Although four types of processed gardeniae fructus products, characterized by differing effects, are available for clinical use, little is known regarding the respective processing mechanisms.In this study, ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry combined with multivariate statistical analysis was applied to characterize the chemical profiles of the differently processed gardeniae fructus products and to determine differences in their chemical compositions, thereby enabling us to identify those active compounds associated with the observed clinical effects.A total of 125 compounds were accordingly identified, among which, 56 were established as primary contributors to the significant differences (p < 0.01) between crude and processed gardeniae fructus, based on t-test analysis.Furthermore, the potential mechanisms underlying the chemical transformations that occurred during processing were discussed.The findings of this study may not only contribute to the more effective quality control of gardeniae fructus but also provide basic information for elucidating the mechanisms underlying the changes in chemical constituents in response to processing, and provide a basis for further investigations of gardeniae fructus processing mechanisms.

Journal: Journal of separation science (2021)
Publication types: Journal Article
Is there a risk of trace element contamination in herbal preparations? A test study on the lichen Cetraria islandica.

Lichens are a source of unique secondary metabolites, which have been proved to have many biological properties with possible pharmaceutical roles, including e.g.Antioxidant, antimicrobial, antifungal or anti-inflammatory activities and to be worth of consideration for potential human use.However, lichens lack cuticolar tissues and are exposed to several atmospheric contaminants, including trace elements.This work aims at exploring the potential toxicity of herbal preparations derived by the lichen cetraria islandica due to trace element contamination, testing whether different concentrations may be observed, depending on the origin of the raw material.Fourteen samples of c.Islandica, as cut dried thalli occurring on the european market, have been bought from different providers.For each sample, the concentrations of as, cd, co, cu, fe, mn, ni, p, pb, v and zn were measured on comminuted herbal substance and on the corresponding decoction, using atomic emission spectrometry (icp-oes).The elemental concentrations in decoctions were significantly lower than those measured in raw materials, dropping down to levels of negligible health concern.Differences observed in raw materials were not observed anymore in the corresponding decoctions.Also, the elemental transfer rate from dried lichen to decoction was extremely element-specific, ranging from 2% for cu to 95% for zn.

Journal: Chemosphere (2017)
Publication types: Journal Article
Proteomics Uncovers Novel Components of an Interactive Protein Network Supporting RNA Export in Trypanosomes.

In trypanosomatids, transcription is polycistronic and all m rnas are processed by trans-splicing, with export mediated by noncanonical mechanisms.Although m rna export is central to gene regulation and expression, few orthologs of proteins involved in m rna export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components.We previously described conserved m rna export pathway components in trypanosoma cruzi, including orthologs of sub2, a component of the trex complex, and e if4aiii (previously hel45), a core component of the exon junction complex (ejc).Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry.Significant overlap between tc sub2 and tce if4aiii-interacting protein cohorts suggests that both proteins associate with similar machinery.We identified several interactions with conserved core components of the ejc and multiple additional complexes, together with proteins specific to trypanosomatids.Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting rna processing from splicing through to nuclear export and cytoplasmic events.We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of m rna metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome m rna maturation.

Journal: Molecular & cellular proteomics : MCP (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Using low voltage ionization chamber (LVIC) in current mode for energy spectrum reconstruction: Experiments and validation.

Due to the international thermonuclear experimental reactor (iter) radiative environment, in particular during high d-t power phase, classic x-ray detectors, such as semiconductor diodes, might be too fragile and are thus not viable.Instead, robust detectors, such as gas-filled detectors, are nowadays considered.The low voltage ionization chamber (lvic) is one of the most promising candidates for x-ray measurement during the iter nuclear phase.A complete model of the detector, recently developed at irfm (intitute for research on magnetic fusion), now requires experimental validation.Experimental testing at the irfm laboratory of an iter industrial lvic prototype and comparison with modeling are presented.In particular, an original approach to extract information on the x-ray spectrum from current-mode lvic measurement is validated experimentally.

Journal: The Review of scientific instruments (2022)
Publication types: Journal Article
Perspectives of Medicare Advantage Plan Representatives on Addressing Social Determinants of Health in Response to the CHRONIC Care Act.

Importance the passage of the creating high-quality results and outcomes necessary to improve chronic (chronic) care act in 2018 allows medicare advantage (ma) plans, which enroll more than one-third of medicare beneficiaries, greater flexibility to address members' social determinants of health (sdoh) through supplemental benefits.Objective to understand ma plan representatives' perspectives on the importance of addressing members' sdoh and their responses to the passage of the chronic care act.Design, setting, and participants this semistructured qualitative interview study conducted via telephone from july 6, 2018, to november 7, 2018, included participants from 17 ma plans that collectively enrolled more than 13 million ma members (>65% of the total ma market).Data analysis was conducted from september 18, 2018, to december 13, 2018.Main outcomes and measures audio-recorded interviews were transcribed and then analyzed using a modified content analysis approach to identify major themes and subthemes.Results thirty-eight participants representing 17 ma plans varying in region, star rating, and size were interviewed.Analysis of interviews revealed 3 key themes.The first theme was that participants increasingly recognize the value of addressing members' sdoh.The second theme was that participants had different perspectives on whether ma plans should directly address sdoh and how to do so.While some reported that they were taking advantage of the increased flexibility provided by the chronic care act to design new benefits or partner with community-based organizations, others indicated that it was outside of their purview to directly address members' sdoh.The third theme was that participants described complex decision-making around how to provide supplemental benefits, including a need for evidence, return on investment, strong community partnerships, and guidance from the us centers for medicare & medicaid services.Conclusions and relevance these findings suggest that the changes in ma plans' benefit packages in response to the chronic care act and their efforts to address sdoh will vary.Therefore, it is likely that ma enrollees will be differentially affected by the implementation of the chronic care act.

Journal: JAMA network open (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Adolescent intermittent ethanol exposure does not alter responsiveness to ifenprodil or expression of vesicular GABA and glutamate transporters.

Adolescent intermittent ethanol (aie) exposure in the rat results in a retention of adolescent-like responsiveness to ethanol into adulthood characterized by enhanced sensitivity to socially facilitating and decreased sensitivity to socially suppressing and aversive effects.Similar pattern of responsiveness to social and aversive effects of the selective glutamate nmda nr2b receptor antagonist ifenprodil is evident in adolescent rats, suggesting that aie would also retain this pattern of ifenprodil sensitivity into adulthood.Social (experiment 1) and aversive (measured via conditioned taste aversion; experiment 2) effects of ifenprodil were assessed in adult male and female rats following aie exposure.Sensitivity to the social and aversive effects of ifenprodil was not affected by aie exposure.Experiment 3 assessed protein expression of vesicular transporters of gaba (v gat) and glutamate (v glut2) within the prelimbic cortex and nucleus accumbens in adolescents versus adults and in aie adults versus controls.V glut2 expression was higher in adolescents relative to adults within the pr l, but lower in the nac.Aie adults did not retain these adolescent-typical ratios.These findings suggest that aie is not associated with the retention of adolescent-typical sensitivity to nr2b receptor antagonism, along with no aie-induced shift in v glut2 to v gat ratios.

Journal: Developmental psychobiology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Incorporating economic constraints for optimal control of immunizing infections.

It is well-known that the interruption of transmission of a disease can be achieved, provided the vaccinated population reaches a threshold depending on, among others, the efficacy of vaccines.The purpose of this paper is to address the optimal vaccination strategy by imposing the economic constraints.In particular, an s--(i,v)--s model used to describe the spreading of the disease in a well-mixed population and a cost function consisting of vaccination and infection costs are proposed.The well-definedness of the above-described modeling is provided.We were then able to provide an optimal strategy to minimize the cost for all parameters.In particular, the optimal vaccination level to minimize the cost can be completely characterized for all parameters.For instance, the optimal vaccination level can be classified by the magnitude of the failure rate of the vaccine with other parameters being given.Under these circumstances, the optimal strategy to minimize the cost is roughly to eliminate the disease locally (respectively, choose an economic optimum resulting in not to wipe out the disease completely or take no vaccination for anyone) provided the vaccine failure rate is relatively small (respectively, intermediate or large).Numerical simulations to illustrate our main results are also provided.Moreover, the data collected at the height of the covid-19 pandemic in taiwan are also numerically simulated to provide the corresponding optimal vaccination strategy.

Journal: Chaos (Woodbury, N.Y.) (2022)
Publication types: Journal Article
Expectancy modulates pupil size both during endogenous orienting and during re-orienting of spatial attention: A study with isoluminant stimuli.

We have recently demonstrated that when endogenous orienting of spatial attention is guided by central directional cues that reliably predict the position of lateral targets.Pupil dilation (pdil) is higher as compared with directional cues that do not predict target position.These findings were interpreted as reflecting different levels of locus coeruleus-noradrenergic activity during endogenous orienting.In contrast to this, we were not able to highlight reliable differences between pdil responses to infrequent invalid targets that are associated with predictive cues and frequent invalid targets that are associated with non-predictive ones.These null findings might have been due to the spurious influence of transitory changes in luminance at the moment of target presentation or to the short time window used for the analysis of target-related changes in pdil.Here, we re-explored cue- and target-related changes in pdil using cue and target stimuli that were kept isoluminant to their background and long lasting cue and target periods for data recording and analysis.We fully replicate our previous cue-related results and, in addition, we demonstrate that infrequent invalid targets in the predictive experimental condition evoke larger pdil as compared with frequent ones.Analyses with linear mixed models highlighted that both during the cue and target period, higher levels of pdil were associated with slower reaction times.These findings confirm that pdil is a reliable marker of the expectancy components of endogenous cue-related and exogenous target-related orienting of spatial attention.

Journal: The European journal of neuroscience (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of fishing rope strength on the severity of large whale entanglements.

Entanglement in fixed fishing gear affects whales worldwide.In the united states, deaths of north atlantic right (eubalaena glacialis) and humpback whales (megaptera novaeangliae) have exceeded management limits for decades.We examined live and dead whales entangled in fishing gear along the u.s.East coast and the canadian maritimes from 1994 to 2010.We recorded whale species, age, and injury severity and determined rope polymer type, breaking strength, and diameter of the fishing gear.For the 132 retrieved ropes from 70 cases, tested breaking strength range was 0.80-39.63 k n (kilo newtons) and the mean was 11.64 k n (sd 8.29), which is 26% lower than strength at manufacture (range 2.89-53.38 k n, mean = 15.70 k n [9.89]).Median rope diameter was 9.5 mm.Right and humpback whales were found in ropes with significantly stronger breaking strengths at time of manufacture than minke whales (balaenoptera acuturostrata) (19.30, 17.13, and 10.47 mean k n, respectively).Adult right whales were found in stronger ropes (mean 34.09 k n) than juvenile right whales (mean 15.33 k n) and than all humpback whale age classes (mean 17.37 k n).For right whales, severity of injuries increased since the mid 1980s, possibly due to changes in rope manufacturing in the mid 1990s that resulted in production of stronger ropes at the same diameter.Our results suggest that broad adoption of ropes with breaking strengths of ≤ 7.56 k n (≤ 1700 lbsf) could reduce the number of life-threatening entanglements for large whales by at least 72%, and yet could provide sufficient strength to withstand the routine forces involved in many fishing operations.A reduction of this magnitude would achieve nearly all the mitigation legally required for u.s.Stocks of north atlantic right and humpback whales.Ropes with reduced breaking strength should be developed and tested to determine the feasibility of their use in a variety of fisheries.

Journal: Conservation biology : the journal of the Society for Conservation Biology (2016)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Tools to Measure Autophagy Using High Content Imaging and Analysis.

Macroautophagy, hereafter referred to as autophagy, is a predominately pro-survival catabolic process responsible for the degradation of long-lived or aggregated proteins, invading microorganisms and damaged or redundant intracellular organelles.Removal of these entities is achieved through encompassment of the target by the autophagosome and subsequent delivery to the lysosome.The use of fluorescence microscopy is a common method to investigate autophagy through monitoring the spatial and temporal recruitment both of autophagosomal markers and cargo to the autophagosome.In this section, we will discuss the use of high content imaging (hci) and analysis in the study of autophagy with reference to commonly used markers of autophagosomal formation.

Journal: Methods in molecular biology (Clifton, N.J.) (2018)
Publication types: Journal Article
Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network.

Chronic levodopa therapy, the gold-standard treatment for parkinson's disease (pd), leads to the emergence of involuntary movements, called levodopa-induced dyskinesia (lid).Cerebellar stimulation has been shown to decrease lid severity in pd patients.Here, in order to determine how cerebellar stimulation induces lid alleviation, we performed daily short trains of optogenetic stimulations of purkinje cells (pc) in freely moving lid mice.We demonstrated that these stimulations are sufficient to suppress lid or even prevent their development.This symptomatic relief is accompanied by the normalization of aberrant neuronal discharge in the cerebellar nuclei, the motor cortex and the parafascicular thalamus.Inhibition of the cerebello-parafascicular pathway counteracted the beneficial effects of cerebellar stimulation.Moreover, cerebellar stimulation reversed plasticity in d1 striatal neurons and normalized the overexpression of fos b, a transcription factor causally linked to lid.These findings demonstrate lid alleviation and prevention by daily pc stimulations, which restore the function of a wide motor network, and may be valuable for lid treatment.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Improved analysis of ground vibrations produced by man-made sources.

Man-made sources of ground vibration must be carefully monitored in urban areas in order to ensure that structural damage and discomfort to residents is prevented or minimised.The research presented in this paper provides a comparative evaluation of various methods used to analyse a series of tri-axial ground vibration measurements generated by rail, road, and explosive blasting.The first part of the study is focused on comparing various techniques to estimate the dominant frequency, including time-frequency analysis.The comparative evaluation of the various methods to estimate the dominant frequency revealed that, depending on the method used, there can be significant variation in the estimates obtained.A new and improved analysis approach using the continuous wavelet transform was also presented, using the time-frequency distribution to estimate the localised dominant frequency and peak particle velocity.The technique can be used to accurately identify the level and frequency content of a ground vibration signal as it varies with time, and identify the number of times the threshold limits of damage are exceeded.

Journal: The Science of the total environment (2018)
Publication types: Journal Article
Spatiotemporal dynamics of suspended particulate matter in the Bohai Sea, China over the past decade from the space perspective.

Suspended particulate matter (spm) concentration is an important biogeochemical parameter for water quality assessment and morphodynamic studies.In this study, the four recent spm retrieval models developed for bohai sea were evaluated using in situ datasets, and the best performing model was selected to investigate the spatiotemporal dynamics of spm in bohai sea from 2011 to 2021 based on 1164 satellite imageries.The results indicated that the satellite-derived spm concentrations had a high accuracy (r2= 0.86, relative percentage difference = 33.71 %).The spm concentrations in the bohai sea demonstrated a significant decadal decreasing trend (0.503 mg/l/yr), and the distribution area with low spm ( 500 × 104t/m) controlled 74.8 % of monthly spm variations within 3-km area off the estuary, 45 % of that within 5-km area, and 28.4 % of that within 10-km area.

Journal: The Science of the total environment (2022)
Publication types: Journal Article