syedzayyan/paper_mill_benchmark huggingface dataset:
Dietary Inclusion of 1,3-Butanediol Increases Dam Circulating Ketones and Increases Progeny Birth Weight.

1,3-butanediol (bd) is a ketogenic substance that can improve piglet growth and survival and potentially increase performance in gilt progeny when provided as a dietary supplement during late gestation.Gilts (n = 77; parity 1) and sows (n = 74; parities 2 and 3) were fed either a standard commercial gestation diet or a diet supplemented with 4% bd from day 90 of gestation until farrowing.Dams fed with diets supplemented with bd had higher plasma beta-hydroxybutyrate (p= 0.01) and lower non-esterified fatty acid concentrations (p< 0.001).The percentage of progeny that were light-for-age (<1.1 kg) at birth was decreased by bd (18.2 vs.13.5%,p< 0.006), particularly in gilts (24.0 vs.18.3%,p< 0.034).Individual birth weights and litter weights birth weights tended to be increased by the bd diet (p= 0.085 and 0.078; respectively) although these effects were not maintained to weaning.Pre-weaning mortality was greater in gilt than in sow progeny and was not altered by dietary bd.Feeding bd in late gestation can improve birth weight, but further work is needed to see if these effects are carried through subsequent stages of growth, particularly in gilt progeny.

Journal: Animals : an open access journal from MDPI (2019)
Publication types: Journal Article
Is Chronic Pain Temporal Pattern Associated with Middle-Aged and Older Adults' Perceptions of their Futures?

A psychological consequence of chronic pain may be an inappropriately limited future time perspective (ftp) for middle-aged and older adults.Ftp is defined as one's perception of time as limited or expansive.Potentially meaningful measures, like pain temporal pattern, are often ignored in the chronic pain literature.The present study uses secondary data to assess the association between pain temporal pattern and ftp, and the moderating effect of pain duration.Among 140 individuals with chronic pain, there was no significant association between pain pattern and ftp.However, both pain-related activity interference and pain duration were associated with ftp where greater interference predicted more limited ftp (b= -0.16,p= .03) and longer pain duration contributed to more expansive ftp (b= 0.001,p= .03).The temporal pattern x pain duration interaction terms were non-significant.We discuss implications, limitations, and future directions of these findings.

Journal: Health psychology bulletin (2021)
Publication types: Journal Article
Effects of a Combined Intradialytic Exercise Training Program and Music on Cardiac Autonomic Nervous System Activity in Hemodialysis Patients.

This study aimed to examine the effect of an intradialytic exercise program in combination with music on heart rate variability (hrv) indices and functional capacity in patients on maintenance hemodialysis (hd).Methods: forty hd patients were randomized to four training groups for six months: the combined music and exercise group (group a), the exercise group (group b), the music group (group c), and the control group (group d).At baseline and after 6 months, all participants underwent both short- (for 30 min) and long- (for 24 h) term measurements of hrv and functional capacity assessment with a 6 min walking test (6mwt).Patients of groups a and c listened to preferred music.Results: long-term hrv analysis showed that standard deviation of all normal-to-normal rr intervals (sdnn) and the square root of the mean squared differences of successive rr intervals (r mssd) were significantly higher at the end of the study in groups a (by 13.2% and 47.3%), b (by 15.1% and 50%), and c (by 9.0% and 30.1%), compared to group d (p < 0.05).Values of r mssd and percentage of rr intervals differing by more than 50 ms from the preceding rr interval (p nn50) were elevated in groups a (by 35.6% and 142.9%), b (by 36.1% and 75%), and c (by 15.2% and 28.6%), compared to baseline measurements (p < 0.05).Also, p nn50 was increased in group a compared to groups b (by 21.4%), c (by 88.9%), and d (by 142.9%) (p < 0.05).Similar results were noted by short-term hrv analysis.Functional capacity was improved at the end of the 6-month study in groups a (by 20.3% and 25.7%) and b (by 15.8% and 21.1%) compared to groups c and d (p < 0.05).Conclusions: intradialytic exercise combined with music-listening can improve the functional capacity and cardiac autonomic nervous system activity in hemodialysis patients.

Journal: Life (Basel, Switzerland) (2022)
Publication types: Journal Article
The Impact of Obesity on C1q/TNF-Related Protein-9 Expression and Endothelial Function following Acute High-Intensity Interval Exercise vs. Continuous Moderate-Intensity Exercise.

C1q-tnf-related protein-9 (ctrp9) increases endothelial nitric oxide synthase and reduces vasoconstrictors.There is limited information regarding exercise-mediated ctrp9 in obesity.The purpose of this study was to compare high-intensity interval exercise (hiie) and continuous moderate-intensity exercise (cme) on the ctrp9 response and an indicator of endothelial function (fmd) in obese participants.Sixteen young male participants (9 obese and 7 normal-weight) participated in a counterbalanced and caloric equated experiment: hiie (30 min, 4 intervals of 4 min at 80-90% of vo2max with 3 min rest between intervals) and cme (38 min at 50-60% vo2max).Serum ctrp9 and fmd were measured prior to, immediately following exercise, and 1 h and 2 h into recovery.Ctrp9 was significantly increased immediately following acute hiie and cme in both groups (p= 0.003).There was a greater cme-induced fmd response at 2 h into recovery in obese participants (p= 0.009).A positive correlation between ctrp9 and fmd percent change was observed in response to acute cme when combined with both obese and normal-weight participants (r = 0.589,p= 0.016).The novel results from this study provide a foundation for additional examination of the mechanisms of exercise-mediated ctrp9 on endothelial function in individuals with obesity.

Journal: Biology (2022)
Publication types: Journal Article
Milliwatt three- and four-pulse double electron electron resonance for protein structure determination.

Electron paramagnetic resonance (epr) experiments for protein structure determination using double electron-electron resonance (deer) spectroscopy rely on high-power microwave amplifiers (>300 w) to create the short pulse lengths needed to excite a sizable portion of the spectrum.The recently introduced self-resonant microhelix combines a high b1conversion efficiency with an intrinsically large bandwidth (low q-value) and a high absolute sensitivity.We report dead times in 3-pulse deer experiments as low as 14 ± 2 ns achieved using less than 1 w of power at x-band (nominally 9.5 ghz) for experiments on a molecular ruler and a t4 lysozyme sample for concentrations down to 100 μm.These low-power experiments were performed using an active volume 120 times smaller than that of a standard pulse epr resonator, while only a 11-fold decrease in the signal-to-noise ratio was observed.Small build sizes, as realized with the microhelix, give access to volume-limited samples, while shorter dead times allow the investigation of fast relaxing spin species.With the significantly reduced dead times, the 3-pulse deer experiment can be revisited.Here, we show experimentally that 3-pulse deer offers superior sensitivity over 4-pulse deer.We assert that the microhelix paves the road for low-cost benchtop x-band pulse epr spectrometers by eliminating the need for high-power amplifiers, accelerating the adoption of pulse epr to a broader community.

Journal: Physical chemistry chemical physics : PCCP (2022)
Publication types: Journal Article
Incorporation of information entropy theory, artificial neural network, and soft computing models in the development of integrated industrial water quality index.

Keeping purpose and targeted end-users in perspective, several water quality indices have been developed over the past decades to summarily convey water quality information to decision-makers and the general public.Industrial water quality is often analyzed based on the corrosion and scaling potentials (csps) of water.The commonly used csp index parameters are chloride-sulfate mass ratio, langelier index, larson-skold index, aggressive index, ryznar stability index, and puckorius scaling index.Simultaneous application of these index parameters often classifies a sample into multiple water quality categories, thereby introducing bias in assessment and decision-making.No previous numerical model integrated the csp indices to provide a single, composite index value for a more unbiased interpretation of industrial water quality.Therefore, this paper proposes an integrated industrial water quality index (iiwqi) that integrates the six csp index parameters for direct and concise assessment of industrial water resources.To achieve its aim, this research incorporated information entropy theory and soft computing techniques.The developed iiwqi was applied to water samples from southeastern nigeria.Different classification groups were observed based on the six csp indices.However, the iiwqi summarized the classifications of the water samples into three categories: class 1 (28.57%, slight-medium corrosivity, significant scaling potential); class 2 (46.43%, medium-high corrosivity, no scaling); and class 3 (25.00%, high-very high corrosion, no scaling).Correlation analysis revealed the relationships between the physicochemical variables, csp index parameters, iiwqi, and the entropy-based variability of the iiwqi.The spatiotemporal water quality groups were revealed by q-mode hierarchical dendrograms.Multiple linear regression and two multilayer perceptron neural networks accurately predicted the iiwqi.The findings of this paper could help in better evaluation, interpretation, and management of industrial water quality.

Journal: Environmental monitoring and assessment (2022)
Publication types: Journal Article
Accumulation of RIPK1 into mitochondria is requisite for oxidative stress-mediated necroptosis and proliferation in Rat Schwann cells.

The injury of schwann cells is an important pathological feature of peripheral neuropathy.However, the explicit molecular mechanism and blocking method remains to be explored.In this study, we identified an pivotal executor of necroptosis-ripk1, performed an unique function in response to oxidative stress-induced injury in rat schwann cells.We found that after oxidative stress-simulation by h2o2, ripk1 was activated independent of genetic up-regulation, but through the post-translational modification, including its protein levels, phosphorylation of serine 166 and serine 321 sites and its general ubiquitination levels.Under a confocal microscopy, we found that ripk1 was significantly accumulated into the mitochondria.And the phosphorylation, ubiquitination levels were also elevated in mitochondrial ripk1, as indicated by immunoprecipitation.Through the administration of n-acetyl-l-cysteine (nac), a ros inhibitor, we found that the phosphorylation, ubiquitination and mitochondrial location of ripk1 was significantly suppressed.While administration of necrostatin-1 (nec-1) failed to influence the levels of ros and mitochondrial membrane potential, revealing that ripk1 served as the down-stream regulators of ros.Lastly, pharmacological inhibition of ripk1 by nec-1 attenuated the levels of necroptosis, increased proliferation, as indicated by annexin v/pi evaluation, cck-8 detection, tem scanning and ed u staining.Our results indicate a previous un-recognized post-translational change of ripk1 in response to oxidative stress in schwann cells.

Journal: International journal of medical sciences (2022)
Publication types: Journal Article
piNET-An Automated Proliferation Index Calculator Framework for Ki67 Breast Cancer Images.

In this work, a novel proliferation index (pi) calculator for ki67 images called pi net is proposed.It is successfully tested on four datasets, from three scanners comprised of patches, tissue microarrays (tmas) and whole slide images (wsi), representing a diverse multi-centre dataset for evaluating ki67 quantification.Compared to state-of-the-art methods, pi net consistently performs the best over all datasets with an average pi difference of 5.603%, pi accuracy rate of 86% and correlation coefficient r = 0.927.The success of the system can be attributed to several innovations.Firstly, this tool is built based on deep learning, which can adapt to wide variability of medical images-and it was posed as a detection problem to mimic pathologists' workflow which improves accuracy and efficiency.Secondly, the system is trained purely on tumor cells, which reduces false positives from non-tumor cells without needing the usual pre-requisite tumor segmentation step for ki67 quantification.Thirdly, the concept of learning background regions through weak supervision is introduced, by providing the system with ideal and non-ideal (artifact) patches that further reduces false positives.Lastly, a novel hotspot analysis is proposed to allow automated methods to score patches from wsi that contain "significant" activity.

Journal: Cancers (2020)
Publication types: Journal Article
Gene Expression and Transcriptome Profiling of Changes in a Cancer Cell Line Post-Exposure to Cadmium Telluride Quantum Dots: Possible Implications in Oncogenesis.

Cadmium telluride quantum dots (cd te-qds) are acquiring great interest in terms of their applications in biomedical sciences.Despite earlier sporadic studies on possible oncogenic roles and anticancer properties of cd te-qds, there is limited information regarding the oncogenic potential of cd te-qds in cancer progression.Here, we investigated the oncogenic effects of cd te-qds on the gene expression profiles of chang cancer cells.Chang cancer cells were treated with 2 different doses of cd te-qds (10 and 25 μg/ml) at different time intervals (6, 12, and 24 h).Functional annotations helped identify the gene expression profile in terms of its biological process, canonical pathways, and gene interaction networks activated.It was found that the gene expression profiles varied in a time and dose-dependent manner.Validation of transcriptional changes of several genes through quantitative pcr showed that several genes upregulated by cd te-qd exposure were somewhat linked with oncogenesis.Cd te-qd-triggered functional pathways that appear to associate with gene expression, cell proliferation, migration, adhesion, cell-cycle progression, signal transduction, and metabolism.Overall, cd te-qd exposure led to changes in the gene expression profiles of the chang cancer cells, highlighting that this nanoparticle can further drive oncogenesis and cancer progression, a finding that indicates the merit of immediatein vivoinvestigation.

Journal: Dose-response : a publication of International Hormesis Society (2021)
Publication types: Journal Article
Reaction Kinetics of Organic Aerosol Studied by Droplet Assisted Ionization: Enhanced Reactivity in Droplets Relative to Bulk Solution.

Droplet assisted ionization (dai) is a relatively new method for online analysis of aerosol droplets that enables measurement of the rate of an aerosol reaction.Here, we used dai to study the reaction of carbonyl functionalities in secondary organic aerosol (soa) with girard's t (gt) reagent, a reaction that can potentially be used to enhance the detection of soa in online measurements.Soa was produced by α-pinene ozonolysis.Particulate matter was collected on a filter, extracted, and mixed with gt reagent in water.While the reaction hardly proceeded at all in bulk solution, products were readily observed with dai when the solution was atomized to produce micron-size droplets.Varying the droplet transit time between the atomizer and mass spectrometer allowed the reaction rate constant to be determined, which was found to be 4 orders of magnitude faster than what would be expected from bulk solution kinetics.Decreasing the water content of the droplets, either by heating the capillary inlet to the mass spectrometer or by decreasing the relative humidity of the air surrounding the droplets in the transit line from the atomizer to the mass spectrometer, enhanced product formation.The results suggest that reaction enhancement occurs at the droplet surface, which is consistent with previous reports of reaction acceleration during mass spectrometric analysis, where a bulk solution is analyzed with an ionization method that produces aerosol droplets.

Journal: Journal of the American Society for Mass Spectrometry (2021)
Publication types: Journal Article
Influence of milk fat globule membrane and milk protein concentrate treated by ultrasound on the structural and emulsifying stability of mimicking human fat emulsions.

The primary objective of the present study was to investigate the effectiveness of ultrasonic treatment time on the particle size, molecular weight, microstructure and solubility of milk fat globule membrane (rich in phospholipid, mpl) and milk protein concentrate (mpc).The mimicking human fat emulsions were prepared using modified proteins and compound vegetable oil and the structural, emulsifying properties and encapsulation efficiency of emulsions were evaluated.After ultrasonic treatment, the cavitation caused particle size decreased and structure change of both mpl and mpc, resulting in the enhancement of protein solubility.While, there was no significant change in molecular weight.Modified proteins by ultrasonic may cause a reduction in particle size and an improvement in emulsifying stability and encapsulation efficiency of emulsions.The optimal ultrasonic time to improve functional properties of mpl emulsion and mpc emulsion were 3 min and 6 min, respectively.The emulsifying stability of mpl emulsion was superior to mpc emulsion, which indicated that mpl is more suitable as membrane material to simulate human fat.Therefore, the obtained results can provide basis for quality control of infant formula.

Journal: Ultrasonics sonochemistry (2022)
Publication types: Journal Article
From ARDS to pulmonary fibrosis: the next phase of the COVID-19 pandemic?

While the coronavirus disease 19 (covid-19) pandemic has transformed the medical and scientific communites since it was first reported in late 2019, we are only beginning to understand the chronic health burdens associated with this disease.Although covid-19 is a multi-systemic disease, the lungs are the primary source of infection and injury, resulting in pneumonia and, in severe cases, acute respiratory distress syndrome (ards).Given that pulmonary fibrosis is a well-recognized sequela of ards, many have questioned whether covid-19 survivors will face long-term pulmonary consequences.This review is aimed at integrating our understanding of the pathophysiologic mechanisms underlying fibroproliferative ards with our current knowledge of the pulmonary consequences of covid-19 disease.

Journal: Translational research : the journal of laboratory and clinical medicine (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.;Review
Dynamic Regional Brain Atrophy Rates in the First Year After Ischemic Stroke.

And purpose brain atrophy can be regarded as an end-organ effect of cumulative cardiovascular risk factors.Accelerated brain atrophy is described following ischemic stroke, but it is not known whether atrophy rates vary over the poststroke period.Examining rates of brain atrophy allows the identification of potential therapeutic windows for interventions to prevent poststroke brain atrophy.Methods we charted total and regional brain volume and cortical thickness trajectories, comparing atrophy rates over 2 time periods in the first year after ischemic stroke: within 3 months (early period) and between 3 and 12 months (later period).Patients with first-ever or recurrent ischemic stroke were recruited from 3 melbourne hospitals at 1 of 2 poststroke time points: within 6 weeks (baseline) or 3 months.Whole-brain 3t magnetic resonance imaging was performed at 3 time points: baseline, 3 months, and 12 months.Eighty-six stroke participants completed testing at baseline; 125 at 3 months (76 baseline follow-up plus 49 delayed recruitment); and 113 participants at 12 months.Their data were compared with 40 healthy control participants with identical testing.We examined 5 brain measures: hippocampal volume, thalamic volume, total brain and hemispheric brain volume, and cortical thickness.We tested whether brain atrophy rates differed between time points and groups.A linear mixed-effect model was used to compare brain structural changes, including age, sex, years of education, a composite cerebrovascular risk factor score, and total intracranial volume as covariates.Results atrophy rates were greater in stroke than control participants.Ipsilesional hemispheric, hippocampal, and thalamic atrophy rates were 2 to 4 times greater in the early versus later period.Conclusions regional atrophy rates vary over the first year after stroke.Rapid brain volume loss in the first 3 months after stroke may represent a potential window for intervention.Registration: url: unique identifier: nct02205424.

Journal: Stroke (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Wettability patterning in microfluidic devices using thermally-enhanced hydrophobic recovery of PDMS.

Spatial control of wettability is key to many applications of microfluidic devices, ranging from double emulsion generation to localized cell adhesion.A number of techniques, often based on masking, have been developed to produce spatially-resolved wettability patterns at the surface of poly(dimethylsiloxane) (pdms) elastomers.A major impediment they face is the natural hydrophobic recovery of pdms: hydrophilized pdms surfaces tend to return to hydrophobicity with time, mainly because of diffusion of low molecular weight silicone species to the surface.Instead of trying to avoid this phenomenon, we propose in this work to take advantage of hydrophobic recovery to modulate spatially the surface wettability of pdms.Because temperature speeds up the rate of hydrophobic recovery, we show that space-resolved hydrophobic patterns can be produced by locally heating a plasma-hydrophilized pdms surface with microresistors.Importantly, local wettability is quantified in microchannels using a fluorescent probe.This "thermo-patterning" technique provides a simple route to in situ wettability patterning in closed pdms chips, without requiring further surface chemistry.

Journal: Soft matter (2019)
Publication types: Journal Article