syedzayyan/paper_mill_benchmark huggingface dataset:
Photosynthetic adaptation to polar life: Energy balance, photoprotection and genetic redundancy.

The persistent low temperature that characterize polar habitats combined with the requirement for light for all photoautotrophs creates a conundrum.The absorption of too much light at low temperature can cause an energy imbalance that decreases photosynthetic performance that has a negative impact on growth and can affect long-term survival.The goal of this review is to survey the mechanism(s) by which polar photoautotrophs maintain cellular energy balance, that is, photostasis to overcome the potential for cellular energy imbalance in their low temperature environments.Photopsychrophiles are photosynthetic organisms that are obligately adapted to low temperature (00- 15 °c) but usually die at higher temperatures (≥20 °c).In contrast, photopsychrotolerant species can usually tolerate and survive a broad range of temperatures (50- 40 °c).First, we summarize the basic concepts of excess excitation energy, energy balance, photoprotection and photostasis and their importance to survival in polar habitats.Second, we compare the photoprotective mechanisms that underlie photostasis and survival in aquatic cyanobacteria and green algae as well as terrestrial antarctic and arctic plants.We show that polar photopsychrophilic and photopsychrotolerant organisms attain energy balance at low temperature either through a regulated reduction in the efficiency of light absorption or through enhanced capacity to consume photosynthetic electrons by the induction of o2as an alternative electron acceptor.Finally, we compare the published genomes of three photopsychrophilic and one photopsychrotolerant alga with five mesophilic green algae including the model green alga, chlamydomonas reinhardtii.We relate our genomic analyses to photoprotective mechanisms that contribute to the potential attainment of photostasis.Finally, we discuss how the observed genomic redundancy in photopsychrophilic genomes may confer energy balance, photoprotection and resilience to their harsh polar environment.Primary production in aquatic, antarctic and arctic environments is dependent on diverse algal and cyanobacterial communities.Although mosses and lichens dominate the antarctic terrestrial landscape, only two extant angiosperms exist in the antarctic.The identification of a single 'molecular key' to unravel adaptation of photopsychrophily and photopsychrotolerance remains elusive.Since these photoautotrophs represent excellent biomarkers to assess the impact of global warming on polar ecosystems, increased study of these polar photoautotrophs remains essential.

Journal: Journal of plant physiology (2022)
Publication types: Journal Article;Review
Criteria for Acceptable Dietary Intake Biomarkers.

Dietary intake biomarkers that can be written as actual intake, plus 'error' that is independent of actual intake and confounding factors can substitute for actual intake in disease association analyses.Also, such biomarkers can be used to develop calibration equations using self-reported diet and participant measures, and biomarker-calibrated intakes can be calculated in larger cohorts for use in disease association analyses.Criteria for biomarkers, and for biomarker-calibrated intakes, arise by working back from properties needed for valid disease association analyses.Accordingly, arguments for a potential biomarker are strengthened if error components are small relative to actual intakes, and important sources of reduced sensitivity or specificity are not apparent.Feeding study biomarker development can then involve regression of actual intake on putative biomarkers, with regression r2 values playing a role in biomarker evaluation.In comparison, 'predictive' biomarker status, as argued in this issue by freedman and colleagues for 24-hour urinary sucrose plus fructose as biomarker for total sugars, involves regression of potential biomarker on actual intake and other variables, with parameter stability across populations and limited within-person variability as criteria.The choice of criteria for biomarkers and for biomarker-calibrated intakes, is discussed here, in the context of total sugars intake.See related article by freedman et al., p.1227.

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2022)
Publication types: Editorial;Research Support, N.I.H., Extramural;Comment
Significant Enhancement of the Polarization Holographic Performance of Photopolymeric Materials by Introducing Graphene Oxide.

Relying on various defects and functional oxygen-containing groups on the basal planes, graphene oxide (go) is commonly unitized for intimate mixing with a polymer matrix to fabricate high-performance nanocomposite polymeric materials with the characteristics of graphene.Herein, by introducing go nanosheets in a phenanthraquinone-doped polymethyl methacrylate (pq/pmma) photopolymer, we demonstrate that the polarization holographic diffraction efficiency of nanocomposite materials can be dramatically enhanced up to nearly 10 times and the photosensitivity can also be enhanced by more than 3 times.Experimental observations reveal that the incorporation of go nanosheets serves as a polymerization initiator not only to promote the polymerization of mma monomers and induce the drafting behavior of the pmma polymer on its surface but also to effectively modulate the molecular weight of the pq/pmma photopolymer by adjusting the doping concentration of go nanosheets.The current study, for the first time, demonstrates that the modulation of molecular weight for pq/pmma photopolymers here exerts a significant impact on their holography performance.In addition, due to the strong physisorption of pq photosensitizers onto go nanosheets, the aggregation of pq around go-graft-pmma also facilitates the formation of go-graft-pmma/pq and is beneficial to the enhancement of holographic performance.The emergence of go-graft-pmma/pq nanocomposite materials here is expected to fulfill the requirement of high-performance polarization-sensitive materials in the field of polarization holographic data storage and provide a facile but effective nanocomposite doping strategy to modulate the holographic performance of photopolymers from micro- and mesoscopic levels.

Journal: ACS applied materials & interfaces (2021)
Publication types: Journal Article
Abnormal dynamic functional network connectivity in first-episode, drug-naïve patients with major depressive disorder.

Dynamic functional network connectivity (d fnc) could capture temporal features of spontaneous brain activity during mri scanning, and it might be a powerful tool to examine functional brain network alters in major depressive disorder (mdd).Therefore, this study investigated the changes in temporal properties of d fnc of first-episode, drug-naïve patients with mdd.A total of 48 first-episode, drug-naïve mdd patients and 46 age- and gender-matched healthy controls were recruited in this study.Sliding windows were implied to construct d fnc.We assessed the relationships between altered d fnc temporal properties and depressive symptoms.Receiver operating characteristic (roc) curve analyses were used to examine the diagnostic performance of these altered temporal properties.The results showed that patients with mdd have more occurrences and spent more time in a weak connection state, but with fewer occurrences and shorter dwell time in a strong connection state.Importantly, the fractional time and mean dwell time of state 2 was negatively correlated with hamilton depression rating scale (hdrs) scores.Roc curve analysis demonstrated that these temporal properties have great identified power including the fractional time and mean dwell time in state 2, and the auc is 0.872, 0.837, respectively.The auc of the combination of fractional time and mean dwell time in state 2 with age, gender is 0.881.Our results indicated the temporal properties of d fnc are altered in first-episode, drug-naïve patients with mdd, and these changes' properties could serve as a potential biomarker in mdd.

Journal: Journal of affective disorders (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Benefit and Harm of Active Surveillance for Biopsy-proven Renal Oncocytoma: A Systematic Review and Pooled Analysis.

Context active surveillance (as) of biopsy-proven renal oncocytomas may reduce overtreatment.However, on biopsy, the risk of misdiagnosis owing principally to entities with peculiar hybrids and overlap morphology, and phenotypes argues for early intervention.Objective to assess the benefit and harm of as in biopsy-proven renal oncocytoma.Evidence acquisition a systematic review was conducted according to the preferred reporting items for systematic reviews and meta-analyses (prisma).We systematically searched pub med, scopus, and web of science databases from september 26 up to october 2021, for studies that analyzed the outcomes of as in patients with biopsy-proven renal oncocytoma.Evidence synthesis a total of ten studies with 633 patients met our inclusion criteria and were included for analysis.After a median follow-up of 34.5 mo (95% confidence interval [ci] 30.6-38.4), the overall definitive treatment rate from as to definitive treatment was 17.3% (n= 75/433, six studies).The pooled pathological agreement between the initial renal mass biopsy and the surgical pathology report was 91.1%.The main indications for surgery during follow-up were rapid tumor growth and patient request.The pooled median growth rate was 1.55 mm/yr (95% ci 0.9-2.2).No metastasis or death related to renal oncocytoma was reported.Conclusions annual tumor growth of biopsy-proven renal oncocytoma is low.As is oncologically safe, with favorable compliance of patients.Crossover to definitive treatment revealed a strong concordance between biopsy and final pathology.Further studies on the long-term outcomes of as are needed.Patient summary in this study, we examined the benefit and harm of active surveillance (as) in biopsy-proven oncocytoma.Based on the available data, as appears oncologically safe and may represent a promising alternative to immediate treatment.Patients should be included in as decision discussions.

Journal: European urology open science (2022)
Publication types: Journal Article;Review
Resistin forms a network with inflammatory cytokines and is associated with prognosis in major burns.

In current intensive care treatment, some patients with severe burns cannot be saved due to progressive organ failure.Further investigation of the pathogenesis of severe burns is needed to improve the mortality rate.In burns, inflammatory cytokines form a network that leads to an inflammatory response.Adipocytes secrete physiologically active substances (adipokines).The roles of adipokines have not been completely clarified in burn patients.This study aimed to determine the relation between serial changes of adipokines and clinical course in severely burned patients.Methods this was a single-center, retrospective, observational study.Patients' blood samples were collected on the day of injury and around 1 week later.Adipokines (adiponectin, angiotensinogen, chemerin, cxcl-12/sdf-1, leptin, resistin, vaspin, visfatin), various inflammatory cytokines, syndecan-1 and c1 esterase inhibitor were measured.Results thirty-eight patients were included.Resistin levels were significantly higher in the non-survivors versus survivors on day 1 after burn injury.Hierarchical clustering analysis showed common clusters on day 1 and at 1 week after burn injury (resistin, il-6, il-8, il10 and mcp-1).The correlation coefficient of resistin to sofa score at 1 week was significant.Logistic regression analysis showed a significant relation of resistin levels on day 1 with prognosis; the area under the roc curve for resistin was 0.801.Conclusions in the acute phase of burns, resistin was associated with other pro-inflammatory cytokines and was related to the severity and prognosis of major burns.

Journal: Burns : journal of the International Society for Burn Injuries (2022)
Publication types: Observational Study;Journal Article
Harnessing electrical-to-biochemical conversion for microbial synthesis.

Electrical-to-biochemical conversion (e2bc) drives cell metabolism for biosynthesis and has become a promising way to realize green biomanufacturing.This review discusses the following aspects: 1.The natural e2bc processes and their underlying e2bc mechanism; 2.Development of artificial e2bc for tunable microbial electrosynthesis; 3.Design of electrobiochemical systems using self-powered, light-assisted, and nano-biohybrid approaches; 4.Synthetic biology methods for efficient microbial electrosynthesis.This review also compares e2bc with electrocatalysis-biochemical conversion (ec2bc), as both strategies may lead to future carbon negative green biomanufacturing.

Journal: Current opinion in biotechnology (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Microstructural modifications induced in Si+-implanted yttria-stabilised zirconia: a combined RBS-C, XRD and Raman investigation.

The structural differences in (100)-, (110)- and (111)-oriented cubic yttria-stabilised zirconia (ysz) single crystals after implantation with 2 me v si+ions at the fluences of 5 × 1015, 1 × 1016and 5 × 1016cm-2were studied using rutherford backscattering spectrometry in the channelling mode (rbs-c), x-ray diffraction (xrd) and raman spectroscopy.The rbs-c results show that the damage accumulation in the 〈110〉 direction exhibits a lower level of disorder (<0.3) than the other orientations (<0.6) and it seems that the (110) crystallographic orientation is the most resistant to radiation damage.The experimental results from the rbs measurement were compared with the results from the xrd measurements.The xrd data were analysed using the standard two-beam dynamical x-ray diffraction theory and the pure isotropic strain was deduced from the fit for the fluence of 5 × 1015cm-2.It was shown that the maximum value of the isotropic strain does not depend on the surface orientation.The increase in signal intensity at ∼689 cm-1is probably related to an increase in implantation defects such as oxygen vacancies.

Journal: Physical chemistry chemical physics : PCCP (2022)
Publication types: Journal Article
Therapeutic outcomes of embolotherapy of extremity bone intraosseous arteriovenous malformation with ethanol, coils, and n-butyl cyanoacrylate.

We evaluated the therapeutic outcomes of embolotherapy for bone arteriovenous malformations (avms) affecting the extremities using ethanol, coils, and n-butyl cyanoacrylate (nbca).Methods we reviewed the data from 36 patients (18 males, 18 females; mean age 25 years; age range, 1-64 years) with bone avms affecting their extremities who had undergone embolotherapy using ethanol, coils, and nbca from december 1996 to july 2019.Of the 36 patients, 19 had had pure bone avms and 17 mixed bone and soft tissue (mbs) avms.Embolotherapy was performed using direct puncture or a transvenous or an intra-arterial approach (range, 1-18 procedures; mean, 5 procedures).During the 178 embolotherapy procedures, ethanol was used in all 36 patients, except for 1.Coils were used in 14 patients, and nbca and a lipiodol mixture in 9 patients.The therapeutic outcomes were evaluated by the clinical symptom response and the degree of devascularization on follow-up angiography or computed tomography.The major and minor complications were also evaluated.Results the clinical success (cure or markedly improvement) rate of embolotherapy for pure bone avms was significantly better than that for the mbs avms (88% vs 18%; p < .001).The complete devascularization rate of the bone avm component of the mbs avms was 71%; however, the cure rate of the mbs avms was 0% owing to the remaining soft tissue avms.Of the 36 patients, 12 experienced complications, including 11 minor (2 skin bullae formation and 10 transient peripheral nerve injury) and 1 major (longstanding nerve palsy).Conclusions embolotherapy for bone avms affecting the extremities using ethanol, coils, and an nbca mixture is effective and safe for the resolution or improvement of symptoms, especially in those with pure bone avms.

Journal: Journal of vascular surgery (2021)
Publication types: Comparative Study;Journal Article
Full-state time-varying asymmetric constraint control for non-strict feedback nonlinear systems based on dynamic surface method.

We investigate the tracking control problem for a non-strict feedback nonlinear system with external disturbance and time-varying asymmetric full state constraints.Firstly, the unknown nonlinear term with external disturbance in the system are estimated by fuzzy logic system.The backstepping method is applied to the design of adaptive fuzzy controller.However, to prevent that the constraints are overstepped by introducing an improved log-type time-varying asymmetric barrier lyapunov function (tablf) in each step of backstepping design.Secondly, the dynamic surface control (dsc) is introduced in the designed algorithm to solve the computational explosion problem of controller caused by the derivative of control law.The proposed control scheme can speed up the tracking speed of the system.Compared with the previous work, it is verified that the combination of dsc and tablf can obtain good performance within the constraint range, and can ensure fast and stable tracking convergence under external disturbance.Finally, two simulation examples verify the performance of the adaptive controller.

Journal: Scientific reports (2022)
Publication types: Journal Article
A theory-based meta-regression of factors influencing clinical decision support adoption and implementation.

The purpose of the study was to explore the theoretical underpinnings of effective clinical decision support (cds) factors using the comparative effectiveness results.Materials and methods we leveraged search results from a previous systematic literature review and updated the search to screen articles published from january 2017 to january 2020.We included randomized controlled trials and cluster randomized controlled trials that compared a cds intervention with and without specific factors.We used random effects meta-regression procedures to analyze clinician behavior for the aggregate effects.The theoretical model was the unified theory of acceptance and use of technology (utaut) model with motivational control.Results thirty-four studies were included.The meta-regression models identified the importance of effort expectancy (estimated coefficient = -0.162; p = .0003); facilitating conditions (estimated coefficient = 0.094; p = .013); and performance expectancy with motivational control (estimated coefficient = 1.029; p = .022).Each of these factors created a significant impact on clinician behavior.The meta-regression model with the multivariate analysis explained a large amount of the heterogeneity across studies (r2 = 88.32%).Discussion three positive factors were identified: low effort to use, low controllability, and providing more infrastructure and implementation strategies to support the cds.The multivariate analysis suggests that passive cds could be effective if users believe the cds is useful and/or social expectations to use the cds intervention exist.Conclusions overall, a modified utaut model that includes motivational control is an appropriate model to understand psychological factors associated with cds effectiveness and to guide cds design, implementation, and optimization.

Journal: Journal of the American Medical Informatics Association : JAMIA (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Systematic Review
Pharmacological management of abnormal tone and movement in cerebral palsy.

The evidence base to guide the pharmacological management of tone and abnormal movements in cerebral palsy (cp) is limited, as is an understanding of routine clinical practice in the uk.We aimed to establish details of motor phenotype and current pharmacological management of a representative cohort across a network of uk tertiary centres.Methods prospective multicentre review of specialist motor disorder clinics at nine uk centres, collecting data on clinical features and pharmacological management of children and young people (cyp) with cp over a single calendar month.Results data were collected from 275 cyp with cp reviewed over the calendar month of october 2017.Isolated dystonia or spasticity was infrequently seen, with a mixed picture of dystonia and spasticity ± choreoathetosis identified in 194/275 (70.5%) of cyp.A comorbid diagnosis of epilepsy was present in 103/275 (37.4%).The most commonly used medications for abnormal tone/movement were baclofen, trihexyphenidyl, gabapentin, diazepam and clonidine.Medication use appeared to be influenced separately by the presence of dystonia or spasticity.Botulinum toxin use was common (62.2%).A smaller proportion of children (12.4%) had undergone a previous neurosurgical procedure for tone/movement management.Conclusions cyp with cp frequently present with a complex movement phenotype and comorbid epilepsy.They have multiple therapy, medical and surgical management regimens.Future trials of therapeutic, pharmacological or surgical interventions in this population must adequately encompass this complexity in order to be translatable to clinical practice.

Journal: Archives of disease in childhood (2019)
Publication types: Journal Article
Rational Engineering of Homoserine O-Succinyltransferase fromEscherichia colifor Reduced Feedback Inhibition by Methionine.

Methionine is an essential amino acid in all living organisms and has been used in various industrial applications such as food and feed additives.However, inhibition of enzymes involved in methionine biosynthesis is considered to be a crucial bottleneck for an efficient bio-based methionine production process.Homoserine o-succinyltransferase from escherichia coli(ec hst) has been reported to be feedback inhibited by the final product methionine.To understand the regulation mechanism of the enzyme and generate a feedback-resistant mutant, we determined the crystal structure of ec hst and elucidated the binding site of homoserine and succinyl-co a.The enzyme kinetic experiments of ec hst revealed that the enzyme is noncompetitively inhibited by methionine with a kivalue of 2.44 m m, and we also identified a putative inhibitor binding site located in the vicinity of the substrate binding site.We then generated the ec hstt242avariant with reduced feedback inhibition with a kivalue of 17.40 m m.

Journal: Journal of agricultural and food chemistry (2022)
Publication types: Journal Article