syedzayyan/paper_mill_benchmark huggingface dataset:
Measurement of lacunar bone strains and crack formation during tensile loading by digital volume correlation of second harmonic generation images.

The maintenance of healthy bone tissue depends upon the ability of osteocytes to respond to mechanical cues on the cellular level.The combination of digital volume correlation and second harmonic generation microscopy offers the opportunity to investigate the mechanical microenvironment of intact bone on the scale of individual osteocytes.Adult human femurs were imaged under tensile loads of 5 and 15mpa and volumes of approximately 492×429×31μm(3) were analyzed, along with an image of a bone microcrack under the same loading conditions.Principal strains were significantly higher in three-dimensional digital volume correlation when compared to two-dimensional digital image correlation.The average maximum principal strain magnitude was 5.06-fold greater than the applied global strain, with peak strains of up to 23.14-fold over global strains measured at the borders of osteocyte lacunae.Finally, a microcrack that initiated at an osteocyte lacunae had its greatest tensile strain magnitudes at the crack expansion front in the direction of a second lacunae, but strain at the crack border was reduced to background strain magnitudes upon breaching the second lacunae.This serveed to demonstrate the role of lacunae in initiating, mediating and terminating microcrack growth.

Journal: Journal of the mechanical behavior of biomedical materials (2016)
Publication types: Journal Article
Detecting Vehicle Loading Events in Bridge Rotation Data Measured with Multi-Axial Accelerometers.

Structural health monitoring (shm) is critical in the observation and analysis of our national infrastructure of bridges.Due to the ease of measuring bridge rotation, bridge shm using rotation measurements is becoming more popular, as even a single dc accelerometer placed at each end of span can accurately capture bridge deformations.Event detection methods for shm typically entail additional instrumentation, such as strain gauges or continuously recording video cameras, and thus the additional cost limits their utility in resource-constrained environments and for wider deployment.Herein, we present a more cost-effective event detection method which exploits the existing bridge rotation instrumentation (tri-axial mems accelerometers) to also act as a trigger for subsequent stages of the shm system and thus obviates the need for additional vehicle detection equipment.We show how the generalised variance over a short sliding window can be used to robustly discriminate individual vehicle loading events, both in time and magnitude, from raw acceleration data.Numerical simulation results examine the operation of the event detector under varying operating conditions, including vehicle types and sensor locations.The method's application is demonstrated for two case studies involving in-service bridges experiencing live free-flow traffic.An initial implementation on a raspberry pi zero 2 shows that the proposed functionality can be realised in less than 400 arm a32 instructions with a latency of 47 microseconds.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Machine learning prediction of gestational age from metabolic screening markers resistant to ambient temperature transportation: Facilitating use of this technology in low resource settings of South Asia and East Africa.

Knowledge of gestational age is critical for guiding preterm neonatal care.In the last decade, metabolic gestational dating approaches emerged in response to a global health need; because in most of the developing world, accurate antenatal gestational age estimates are not feasible.These methods initially developed in north america have now been externally validated in two studies in developing countries, however, require shipment of samples at sub-zero temperature.Methods a subset of 330 pairs of heel prick dried blood spot samples were shipped on dry ice and in ambient temperature from field sites in tanzania, bangladesh and pakistan to laboratory in iowa (usa).We evaluated impact on recovery of analytes of shipment temperature, developed and evaluated models for predicting gestational age using a limited set of metabolic screening analytes after excluding 17 analytes that were impacted by shipment conditions of a total of 44 analytes.Results with the machine learning model using all the analytes, samples shipped in dry ice yielded a root mean square error (rmse) of 1.19 weeks compared to 1.58 weeks for samples shipped in ambient temperature.Out of the 44 screening analytes, recovery of 17 analytes was significantly different between the two shipment methods and these were excluded from further machine learning model development.The final model, restricted to stable analytes provided a rmse of 1.24 (95% confidence interval (ci) = 1.10-1.37) weeks for samples shipped on dry ice and rmse of 1.28 (95% ci = 1.15-1.39) for samples shipped at ambient temperature.Analysis for discriminating preterm births (gestational age <37 weeks), yielded an area under curve (auc) of 0.76 (95% ci = 0.71-0.81) for samples shipped on dry ice and auc of 0.73 (95% ci = 0.67-0.78) for samples shipped in ambient temperature.Conclusions in this study, we demonstrate that machine learning algorithms developed using a sub-set of newborn screening analytes which are not sensitive to shipment at ambient temperature, can accurately provide estimates of gestational age comparable to those from published regression models from north america using all analytes.If validated in larger samples especially with more newborns <34 weeks, this technology could substantially facilitate implementation in lmics.

Journal: Journal of global health (2022)
Publication types: Journal Article
Effects of Anharmonicity, Recrossing, Tunneling, and Pressure on the H-Abstractions from Dimethylamine by Triplets O and O2.

Rate constants of the h-abstraction reactions from dimethylamine (dma) by triplets o and o2are theoretically determined with the canonical variational transition-state theory (cvt).By comparing the barrier heights and reaction energies obtained from different density-functional theory methods to those computed from the gold-standard method ccsd(t)/cbs(t-q), we identify the m08-hx/ma-tzvp method as the best with a mean unsigned deviation of 1.0 kcal mol-1.On the basis of the optimized geometries and frequencies with the selected method, the rate constants are calculated using the cvt method combined with the multistructural torsional anharmonicity and small-curvature tunnelling (ms-cvt/sct) options in the temperature range 200-2000 k.The calculations show that oh and ho2are mainly produced from the direct abstraction from the c-h bond.The multistructural torsional anharmonicity has a large contribution to the rate constants, and the effects of recrossing and tunneling at the n-site are more important than those at c-site.Additionally, given the formation of reactant complex between dma and triplet o, the h-abstraction channel is not favored at high pressure.Our calculations with both the polyrate and mess codes agree with the reported data within the uncertainty.

Journal: The journal of physical chemistry. A (2022)
Publication types: Journal Article
Pd-catalyzed allylative dearomatisation using Grignard reagents.

Pd-catalyzed allylative dearomatisation of naphthyl halides is shown to be feasible by employing grignard reagents.The high reactivity of the nucleophile allows for fast reactions and low catalyst loading, while a plethora of successfully substituted compounds illustrate the broad scope.Five membered heteroaromatic compounds are also demonstrated to be reactive under similar conditions.

Journal: Chemical communications (Cambridge, England) (2021)
Publication types: Journal Article
Inhibition of O-GlcNAcylation Decreases the Cytotoxic Function of Natural Killer Cells.

Natural killer (nk) cells mediate killing of malignant and virus-infected cells, a property that is explored as a cell therapy approach in the clinic.Various cell intrinsic and extrinsic factors affect nk cell cytotoxic function, and an improved understanding of the mechanism regulating nk cell function is necessary to accomplish better success with nk cell therapeutics.Here, we explored the role of o-glc nacylation, a previously unexplored molecular mechanism regulating nk cell function.O-glc nacylation is a post-translational modification mediated by o-glc nac transferase (ogt) that adds the monosaccharide n-acetylglucosamine to serine and threonine residues on intracellular proteins and o-glc nacase (oga) that removes the sugar.We found that stimulation of nk cells with the cytokines interleukin-2 (il-2) and il-15 results in enhanced o-glc nacylation of several cellular proteins.Chemical inhibition of o-glc nacylation using osmi-1 was associated with a decreased expression of nk cell receptors (nkg2d, nkg2a, nkp44), cytokines [tumor necrosis factor (tnf)-α, interferon (ifn-γ)], granulysin, soluble fas ligand, perforin, and granzyme b in nk cells.Importantly, inhibition of o-glc nacylation inhibited nk cell cytotoxicity against cancer cells.However, increases in o-glc nacylation following oga inhibition using an oga inhibitor or sh rna-mediated suppression did not alter nk cell cytotoxicity.Finally, we found that nk cells pretreated with osmi-1 to inhibit o-glc nacylation showed compromised cytotoxic activity against tumor cellsin vivoin a lymphoma xenograft mouse model.Overall, this study provides the seminal insight into the role of o-glc nacylation in regulating nk cell cytotoxic function.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Confirmation of the Factor Structure and Reliability of the 'Adult Eating Behavior Questionnaire' in an Adolescent Sample.

Introduction appetitive traits, including food responsiveness, enjoyment of food, satiety responsiveness, emotional over- and under-eating, food fussiness and slowness in eating, have been captured across childhood using the children's eating behavior questionnaire (cebq).The adult eating behavior questionnaire (aebq) has explored these traits in adults, but not adolescents.This study aimed to test the factor structure and reliability of the aebq in a sample of uk adolescents, and explore demographic differences.Materials and methods confirmatory factor analysis (cfa) tested an 8-factor and a 7-factor aebq, based on valid, completed aebq responses (n= 913) from adolescents aged 11-18 recruited from four london secondary schools.Test-retest reliability was analyzed in a subsample (n= 106) 2-weeks later, and 492 participants completed the dutch eating behavior questionnaire (debq) to assess convergent validity.Demographic differences were explored using a multiple indicator multiple cause (mimic) model.Results the cfa revealed an adequate model fit for a 7-factor structure without hunger [rmsea = 0.038 (90% ci:0.035,0.041); cfi = 0.926, tli = 0.916; and χ2(df = 595) = 8502.69,p 0.70).The icc for the test-retest was above 0.70.Comparisons with the debq supported the convergent validity of the aebq.Older age was associated with greater food responsiveness and enjoyment of food (allp-values < 0.005).Females reported higher levels of emotional over-eating, satiety responsiveness, and slowness in eating than males (allp-values ≤ 0.003).Conclusion this study supports the use of the 7-factor aebq as a reliable measure of appetitive traits in adolescents.

Journal: Frontiers in psychology (2019)
Publication types: Journal Article
Biglycan neo-epitope (BGN262), a novel biomarker for screening early changes in equine osteoarthritic subchondral bone.

Native biglycan (bgn), which can undergo proteolytic cleavage in pathological conditions, is well known to be involved in bone formation and mineralization.This study aimed to delineate the specific cleavage fragment, a neo-epitope for bgn (bgn262), in synovial fluid (sf) from young racehorses in training, osteoarthritic (oa) joints with subchondral bone sclerosis (scbs), and chip fracture joints.Design a custom-made inhibition elisa was developed to quantify bgn262in sf.Cohort 1: a longitudinal study comprising 10 racehorses undergoing long-term training.Cohort 2: a cross-sectional study comprising joints from horses (n = 69) with different stages of oa and radiographically classified scbs.Cohort 3: a cross-sectional study comprising horses (n = 9) with chip fractures.Receiver operating characteristic (roc) curve analysis was performed (healthy joints vs chip joints) to evaluate bgn262robustness.Results cohort 1: sf bgn262levels from racehorses showed a statistical increase during the first 6 months of the training period.Cohort 2: bgn262levels were significantly higher in the sf from severe scbs joints.Cohort 3: sf bgn262levels in chip fracture joints showed a significant increase compared to normal joints.The roc analysis showed an auc of 0.957 (95% c.i 0.868-1.046), indicating good separation between the groups.Conclusions the data presented show that bgn262levels increase in sf in correlation with the initiation of training, severity of scbs, and presence of chip fractures.This suggests that bgn262is a potential predictor and a novel biomarker for early changes in subchondral bone (scb), aiming to prevent catastrophic injuries in racehorses.

Journal: Osteoarthritis and cartilage (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Infant lung function: criteria for selecting tidal flow-volume loops.

Tidal flow-volume (tfv) loops are commonly recorded in infants during sleep, due to the more regular breathing patterns compared to the awake state.Standardised deselection of loops outside pre-specified ranges are based on periods of regular breathing, while criteria and available software for visual evaluation of tfv loops are lacking.We aimed to determine the reliability of standardised criteria for manual selection of infant tfv loops.Methods using a pre-defined set of criteria, three independent raters manually evaluated tfv loops among 57 randomly selected awake healthy 3-month-old infants with available tfv measurements in the scandinavian preventing atopic dermatitis and allergies in children (prevent adall) study.The tfv loops were sampled using the eco medics exhalyzer d.Criteria for selecting tfv loops included reproducible shape and volume with only one peak in tidal expiratory flow (ptef), excluding loops with no clear or uneven flow towards ptef.By intraclass coefficient (icc), the reliability of agreement between raters was determined for the time to ptef (t ptef) to expiratory time (t e) and other tfv loop parameters.Results five infants had unsuccessful tests.Among the remaining 52 infants, the raters selected a median of 25, 26 and 15 loops per test.The iccs (95% ci) were 0.97 (0.92-0.98) fort ptef/t e, 0.99 (0.99-1.00) for respiratory rate, 0.98 (0.97-0.99) for tidal volume per kg and 0.98 (0.97-0.99) for expiratory volume, reflecting excellent agreement in all categories.Conclusion manual tfv loop selection using standardised criteria provides a reliable alternative for lung function measures in awake infants with interrupted breathing cycles in a real-life setting.

Journal: ERJ open research (2022)
Publication types: Journal Article
Resilience and Mental Health Among Regularly and Intermittently Active Older Adults: Results From a Four-Year Longitudinal Study.

This study aims to investigate whether regularly active individuals have different levels of mental health and resilience compared to intermittently active individuals.Methods in this 4-year longitudinal study, 180 older people were included.General linear models were used to assess the level of physical activity, psychological resilience, and mental health among regularly and intermittently active older adults.Results those who maintained regular physical activity were more resilient than those who did not.However, no differences were observed for mental health outcomes.Although those with higher levels of resilience had fewer mental health problems, there were no significant differences between the groups based on their level of physical activity.Conclusion differences in resilience levels favoring regularly active individuals were found.In both groups, resilience was inversely associated with mental health problems.These findings may help elucidate the underlying mechanisms in the relationship between physical activity and health outcomes.

Journal: Journal of applied gerontology : the official journal of the Southern Gerontological Society (2022)
Publication types: Journal Article
Visual outcomes and complications of manual small-incision cataract surgery in patients with pseudoexfoliation.

Pseudoexfoliation is an age-related fibrillopathy characterized by the deposition of fibrillar material in the eye with an increased risk of complications during cataract surgery.Aim was to study visual outcomes and complications in patients with pseudoexfoliation undergoing manual small-incision cataract surgery (msics).Methods prospective observational study was performed on 152 patients with pseudoexfoliation above 50 years undergoing msics in a tertiary hospital from december 2016 to november 2017.Intraoperative and postoperative complications were documented with follow-up on postoperative day 1, 1stweek, 1stmonth, and 3rdmonth.Results preoperative small pupil was noted in 49 eyes (32.2%), and 19 (12.5%) required intraoperative measures.Intraocular complications noted were zonular dialysis in five (3.3%), posterior capsular rupture in one (0.7%), and iridodialysis in one (0.7%).On postoperative day 1, the most common complication was corneal edema in 134 patients but clinically significant in only 23 (15.1%).Postoperative complications at 3 months were irregular pupil in 17 cases and decentered iol in three cases.Intraocular pressure decreased with each visit [preoperative mean: 14.39 (±3.4) and 13.37 (±2.0) 12.53 (±1.4) mm hg at 1 and 3 months, respectively].There was a significant improvement in vision from the first day mean pinhole vision of 0.26 (±0.24) to mean best corrected visual acuity (bcva) of 0.09 (±0.22) and 0.07 (±0.22) at 1 and 3 months, respectively.Mean endothelial cell loss was 193.16 (7.79%) and 266.01 (10.68%) at 1 and 3 months, respectively.Conclusion pseudoexfoliation has an increased risk of complications during cataract surgery.Msics gives good outcomes in terms of visual recovery and postoperative outcomes.

Journal: Indian journal of ophthalmology (2022)
Publication types: Observational Study;Journal Article
Spiro-Twisted Benzoxazine Derivatives Bearing Nitrile Group for All-Solid-State Polymer Electrolytes in Lithium Batteries.

In this study, two nitrile-functionalized spiro-twisted benzoxazine monomers, namely 2,2'-((6,6,6',6'-tetramethyl-6,6',7,7'-tetrahydro-2h,2'h-8,8'-spirobi[indeno[5,6-e][1,3]oxazin]-3,3'(4h,4'h)-diyl)bis(4,1-phenylene))diacetonitrile (tsbzbc) and 4,4'-(6,6,6',6'-tetramethyl-6,6',7,7'-tetrahydro-2h,2'h-8,8'-spirobi[indeno[5,6-e][1,3]oxazin]-3,3'(4h,4'h)-diyl)dibenzonitrile (tsbzbn) were successfully developed as cross-linkable precursors.In addition, the incorporation of the nitrile group by covalent bonding onto the crosslinked spiro-twisted molecular chains improve the miscibility of spe membranes with lithium salts while maintaining good mechanical properties.Owing to the presence of a high fractional free volume of spiro-twisted matrix, the -cn groups would have more space for rotation and vibration to assist lithium migration, especially for the benzyl cyanide-containing spe.When combined with poly (ethylene oxide) (peo) electrolytes, a new type of cn-containing semi-interpenetrating polymer networks for solid polymer electrolytes (spes) were prepared.The peo-tsbzbc and peo-tsbzbn composite spes (with 20 wt% crosslinked structure in the polymer) are denoted as the bc20 and bn20, respectively.The bc20 sample exhibited an ionic conductivity (σ) of 3.23 × 10-4s cm-1at 80 °c and a li+ion transference number of 0.187.The li fe po4(lfp)|bc20|li sample exhibited a satisfactory charge-discharge capacity of 163.6 m ah g-1at 0.1 c (with approximately 100% coulombic efficiency).Furthermore, the li|bc20|li cell was more stable during the li plating/stripping process than the li|bn20|li and li|peo|li samples.The li|bc20|li symmetric cell could be cycled continuously for more than 2700 h without short-circuiting.In addition, the specific capacity of the lfp|bc20|li cell retained 87% of the original value after 50 cycles.

Journal: Polymers (2022)
Publication types: Journal Article
Modelling the concentration of anti-SARS-CoV-2 immunoglobulin G in intravenous immunoglobulin product batches.

Plasma-derived intravenous immunoglobulin (ivig) products contain a dynamic spectrum of immunoglobulin (ig) g reactivities reflective of the donor population from which they are derived.We sought to model the concentration of anti-severe acute respiratory syndrome coronavirus 2 (sars-co v-2) ig g which could be expected in future plasma pool and final-product batches of csl behring's immunoglobulin product privigen.Study design and methods data was extracted from accessible databases, including the incidence of coronavirus disease 2019 and sars-co v-2 vaccination status, antibody titre in convalescent and vaccinated groups and antibody half-life.Together, these parameters were used to create an integrated mathematical model that could be used to predict anti-sars-co v-2 antibody levels in future ivig preparations.Results we predict that anti-sars-co v-2 ig g concentration will peak in batches produced in mid-october 2021, containing levels in the vicinity of 190-fold that of the mean convalescent (unvaccinated) plasma concentration.An elevated concentration (approximately 35-fold convalescent plasma) is anticipated to be retained in batches produced well into 2022.Measurement of several privigen batches using the phadiatm eli atm sars-co v-2-sp1 ig g binding assay confirmed the early phase of this model.Conclusion the work presented in this paper may have important implications for physicians and patients who use privigen for indicated diseases.

Journal: PloS one (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Halomonas tibetensis sp. nov., isolated from saline lakes on Tibetan Plateau.

Strains pyc13tand zgt13 were isolated from lake pengyan and lake zigetang on tibetan plateau, respectively.Both strains were gram-negative, catalase- and oxidase-positive, aerobic, rod-shaped, nonmotile, and nonflagellated bacteria.Phylogenetic analysis based on 16s r rna gene sequences showed that strains pyc13tand zgt13 belong to the genus halomonas, with halomonas alkalicola 56-l4-10a en tas their closest neighbor, showing 97.4% 16s r rna gene sequence similarity.The predominant respiratory quinone of both strains was q-9, with q-8 as a minor component.The major fatty acids of both strains were c18:1ω6c/c18:1ω7c, c16:1ω6c/c16:1ω7c, c16:0, and c12:03oh.The polar lipids of both strains consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid, phospholipids of unknown structure containing glucosamine, and unidentified phospholipids.The dna g + c content of pyc13tand zgt13 were 62.6 and 63.4 mol%, respectively.The dna-dna hybridization values of strain pyc13twere 34, 41, 61, 35, and 35% with the reference strains h.Alkalicola 56-l4-10a en t, h.Sediminicola cps11t, h.Mongoliensis z-7009t, h.Ventosae al12t, and h.Fontilapidosi 5crt, respectively.Phenotypic, biochemical, genotypic, and dna-dna hybridization data showed that strains pyc13tand zgt13 represent a new species within the genus halomonas, for which the name h.Tibetensis sp.Nov.Is proposed.The type strain is pyc13t(= cgmcc 1.15949t= kctc 52660t).

Journal: Journal of microbiology (Seoul, Korea) (2018)
Publication types: Journal Article