syedzayyan/paper_mill_benchmark huggingface dataset:
Effect ofPiriformospora indica-Induced Systemic Resistance and Basal Immunity AgainstRhizoctonia cerealisandFusarium graminearumin Wheat.

Wheat is among the top 10 and most widely grown crops in the world.However, wheat is often infected with many soil-borne diseases, including sharp eyespot, mainly caused by the necrotrophic fungus rhizoctonia cerealis, and fusarium head blight (fhb), caused by fusarium graminearum, resulting in reduced production.piriformospora indicais a root endophytic fungus with a wide range of host plants, which increases their growth and tolerance to biotic and abiotic stresses.In this study, the capability of p.Indicato protect wheat seedlings against r.Cerealisand f.Graminearumwas investigated at the physiological, biochemical, and molecular levels.Our results showed that p.Indicasignificantly reduced the disease progress on wheat caused by f.Graminearumand r.Cerealis in vivo, but not showed any antagonistic effect on f.Graminearumand r.Cerealis in vitro.Additionally,p.Indicacan induce systemic resistance by elevating h2o2content, antioxidase activity, relative water content (rwc), and membrane stability index (msi) compared to the plants only inoculated with f.Graminearumor r.Cerealisand control.Rna-seq suggested that transcriptome changes caused by f.Graminearumwere more severe than those caused by r.Cerealis.the number of differentially expressed genes (degs) in the transcriptome can be reduced by the addition of p.Indica:for f.Graminearumreduced by 18% and for r.Cerealisreduced 58%.The degs related to disease resistance, such as wrky and mapk, were upregulated by p.Indicacolonization.The data further revealed that the transcriptional resistance to f.Graminearumand r.Cerealismediated by p.Indicais quite different.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
The oak gall wasps of Israel (Hymenoptera, Cynipidae, Cynipini)-diversity, distribution and life history.

Oak-galling wasps (hymenoptera: cynipidae, cynipini) have been studied in israel only superficially so far, despite interest in the israeli fauna given its location at the southern edge of distribution range of the wasps and their oak hosts.We provide the first comprehensive review of the israeli fauna of oak cynipids based on an extensive survey of the five naturally occurring oak species in israel.We report 53 cynipid species, 37 of which are reported from israel for the first time, 10 are currently known only from this country, and 9 are undescribed.With 27 species, andricus is by far the biggest genus in israel, followed by cerroneuroterus, neuroterus plagiotrochus, and pseudoneuroterus with 4 species each.Andricus megalucidus is synonymized under a.Cecconii and cerroneuroterus cerrifloralis is synonymized under c.Lanuginosus.The sexual generations of andricus cecconii, a.Coriariformis, a.Coriarius, a.Miriami, cerroneuroterus lanuginosus and pseudoneuroterus macropterus are reported here for the first time.We recorded 65 gall types, with bud galls being the most common and conspicuous, followed by leaf and catkin galls.We provide illustrated keys for all israeli species based on their galls, as well as information on host associations, life history, phenology and distribution patterns where available.21 cynipid species are associated with quercus ithaburensis and 27 species are associated with q.Boissieri, whereas q.Libani, q.Calliprinos and q.Cerris host much fewer species.Most species are currently known from either their sexual or asexual generation while only 24% of them are known from both.Mount hermon was found to be an important hotspot, hosting about half of the israeli cynipid fauna, and species richness generally declines from the golan heights southwards to the judean mountains.Cynipid species that are associated with oaks of sections cerris and quercus in europe are mostly associated with the same sections in israel.

Journal: Zootaxa (2018)
Publication types: Journal Article
CeO2-Azacrown Conjugate as a Nanoplatform for Combined Radiopharmaceuticals.

This study is one of the first attempts to assess ce o2nanoparticles as a nanoplatform for radiopharmaceuticals with radionuclides.The process of functionalization using a bifunctional azacrown ligand is described, and the resulting conjugates are characterized by ir and raman spectroscopy.Their complexes with207bi show a high stability in medically relevant media, thus encouraging the further study of these conjugates in vivo as potential combined radiopharmaceuticals.

Journal: Nanomaterials (Basel, Switzerland) (2022)
Publication types: Journal Article
A Mouse Model of Latent Tuberculosis Infection to Study Intervention Strategies to Prevent Reactivation.

Infection with mycobacterium tuberculosis (mtb) is the leading cause of death in human immunodeficiency virus (hiv)+ individuals, particularly in sub-saharan africa.Management of this deadly co-infection is a significant global health challenge that is exacerbated by the lack of efficient vaccines against both mtb and hiv, as well as the lack of reliable and robust animal models for mtb/hiv co-infection.Here we describe a tractable and reproducible mouse model to study the reactivation dynamics of latent mtb infection following the loss of cd4+ t cells as it occurs in hiv-co-infected individuals.Whereas intradermally (i.d.) infected c57bl/6 mice contained mtb within the local draining lymph nodes, depletion of cd4+ cells led to progressive systemic spread of the bacteria and induction of lung pathology.To interrogate whether reactivation of mtb after cd4+ t cell depletion can be reversed, we employed interleukin (il)-2/anti-il-2 complex-mediated cell boost approaches.Although populations of non-cd4 lymphocytes, such as cd8+ memory t cells, natural killer (nk) cells and double-negative (dn) t cells significantly expanded after il-2/anti-il-2 complex treatment, progressive development of bacteremia and pathologic lung alterations could not be prevented.These data suggest that the failure to reverse mtb reactivation is likely not due to anergy of the expanded cell subsets and rather indicates a limited potential for il-2-complex-based therapies in the management of mtb/hiv co-infection.

Journal: PloS one (2016)
Publication types: Journal Article
Methodology for assessing the vulnerability of built cultural heritage.

The conservation of constructions, and especially of built heritage, requires complex studies concerning their global vulnerability.These studies have to consider the current state of the building, i.e.The degradation degree, and the factors that mostly affect the building and, therefore, generate alterations.These factors are not limited to the structure of the building, location and environmental factors are also involved.Hence, the assessment of built heritage vulnerability should consider the building itself and also be extended to the site and the environment.This work presents a systematic and reproducible methodology for the quantification of the global vulnerability in different typologies of constructions and environments.The proposed methodology establishes a relationship between the existing alterations (a) and the main factors (f) that affect vulnerability (v) by means of an afv (alteration/factor/vulnerability) diagram.Based on these results alteration and vulnerability indices are calculated.The obtained afv diagram allows the comparison between different constructions or separate areas within the same construction.This methodology was validated in two early twentieth-century constructions that form part of the reinforced concrete architectural heritage of the basque country: the punta begoña galleries (getxo, spain) and the aqueduct of the araxes paper mill (tolosa, spain).

Journal: The Science of the total environment (2022)
Publication types: Journal Article
Sex-Specific Causal Relations between Steroid Hormones and Obesity-A Mendelian Randomization Study.

Steroid hormones act as important regulators of physiological processes including gene expression.They provide possible mechanistic explanations of observed sex-dimorphisms in obesity and coronary artery disease (cad).Here, we aim to unravel causal relationships between steroid hormones, obesity, and cad in a sex-specific manner.In genome-wide meta-analyses of four steroid hormone levels and one hormone ratio, we identified 17 genome-wide significant loci of which 11 were novel.Among loci, seven were female-specific, four male-specific, and one was sex-related (stronger effects in females).As one of the loci was the human leukocyte antigen (hla) region, we analyzed hla allele counts and found four hla subtypes linked to 17-oh-progesterone (17-ohp), including hla-b*14*02.Using mendelian randomization approaches with four additional hormones as exposure, we detected causal effects of dehydroepiandrosterone sulfate (dhea-s) and 17-ohp on body mass index (bmi) and waist-to-hip ratio (whr).The dhea-s effect was stronger in males.Additionally, we observed the causal effects of testosterone, estradiol, and their ratio on whr.By mediation analysis, we found a direct sex-unspecific effect of 17-ohp on cad while the other four hormone effects on cad were mediated by bmi or whr.In conclusion, we identified the sex-specific causal networks of steroid hormones, obesity-related traits, and cad.

Journal: Metabolites (2021)
Publication types: Journal Article
A haptoglobin (HP) structural variant alters the effect of APOE alleles on Alzheimer's disease.

Haptoglobin (hp) is an antioxidant of apolipoprotein e (apoe), and previous reports have shown hp binds with apoe and amyloid beta (aβ) to aid its clearance.A common structural variant of the hp gene distinguishes it into two alleles: hp1 and hp2.Methods hp genotypes were imputed in 29 cohorts from the alzheimer's disease genetics consortium (n = 20,512).Associations between the hp polymorphism and alzheimer's disease (ad) risk and age of onset through apoe interactions were investigated using regression models.Results the hp polymorphism significantly impacts ad risk in european-descent individuals (and in meta-analysis with african-descent individuals) by modifying both the protective effect of apoe ε2 and the detrimental effect of apoe ε4.The effect is particularly significant among apoe ε4 carriers.Discussion the effect modification of apoe by hp suggests adjustment and/or stratification by hp genotype is warranted when apoe risk is considered.Our findings also provided directions for further investigations on potential mechanisms behind this association.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association (2023)
Publication types: Meta-Analysis;Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Adsorption and catalytic degradation of organic contaminants by biochar: Overlooked role of biochar's particle size.

Biochar (bc) is considered as a promising adsorbent and/or catalyst for the removal of organic contaminants.However, the relationship between the particle size of bc and its adsorption/catalysis performance is largely unclear.We therefore investigated the influence of particle size on the performance of bc pyrolyzed at 300-900 °c in trichloroethylene (tce) adsorption and persulfate (ps) activation for sulfamethazine (smt) degradation.The results showed that high-temperature pyrolyzed bc (bc900) presented superior adsorption capacity for tce and excellent catalytic activity for ps activation to degrade smt.Compared to 150-250 μm, 75-150 μm and pristine bc900, 0-75 μm bc900 showed the highest tce adsorption efficiency, which increased by 19.5-62.3%.Similarly, smt removal by bc900/ps systems also increased from 24.2% to 98.3% with decreasing bc particle size.However, the catalytic activity of bc after grinding was not significantly improved as expected, indicating the properties of biochar was not only controlled by size effect.Characterization measurements proved that small-sized bc tended to have larger specific surface area, more micropores, higher conductivity, rich graphitic domains and surface redox-active functional groups, thus resulting in an enhanced adsorption and catalytic ability of bc.

Journal: Journal of hazardous materials (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The mSteps pilot study: Analysis of the distance walked using a novel smartphone application in multiple sclerosis.

Clinical studies in multiple sclerosis (ms) often require accurate measurement of walking distance.Utilisation of electronic devices could theoretically improve this.Mobile devices have the potential to continuously monitor health by collecting movement data.Popular fitness trackers record steps taken and distance travelled, typically using a fixed-stride length.However, applications using fixed-stride length may be less accurate in those with altered gait patterns.While useful for everyday purposes, medical monitoring requires greater accuracy.Objective our aim was to determine the agreement and reliability of using a smartphone application to measure distance walked.Method a phone application (m steps) was developed and tested in a pilot study and then a validation study, looking at an indoor and outdoor setting with people with multiple sclerosis (pw ms) and a control cohort.Results in the pilot study, the 95% limits of agreement (loa) for outdoor tracking in control cohort lay within the a priori defined limit; however, the indoor tracking in both cohorts did not meet the defined limit.The app was then successfully validated outdoors in pw ms.Conclusion m steps could be used to accurately measure distance outdoors in pw ms.There is still a need for solutions to accurately and reliably measure distance walked indoors.

Journal: Multiple sclerosis (Houndmills, Basingstoke, England) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Brief Report: Sibling Feelings Toward their Brother or Sister With or Without Autism or Intellectual Disability.

The present study examined 97 adolescent siblings of individuals with autism spectrum disorder (asd), intellectual and developmental disabilities (idd), or no disabilities.Siblings reported on their feelings toward their brother or sister (anxiety, hostility, and positive affect), and parents reported on general optimism, child behavior problems, and perceptions of how the child impacts the family, including the sibling.There were no differences between siblings of individuals with asd and siblings of individuals with idd on any sibling self-reported feelings toward their brother or sister, though parents of individuals with asd reported significantly less optimism and more negative perception of the child's impact on the family than did parents of children with idd or no disability.

Journal: Journal of autism and developmental disorders (2019)
Publication types: Journal Article
Three critical factors affecting automated image species recognition performance for camera traps.

Ecological camera traps are increasingly used by wildlife biologists to unobtrusively monitor an ecosystems animal population.However, manual inspection of the images produced is expensive, laborious, and time-consuming.The success of deep learning systems using camera trap images has been previously explored in preliminary stages.These studies, however, are lacking in their practicality.They are primarily focused on extremely large datasets, often millions of images, and there is little to no focus on performance when tasked with species identification in new locations not seen during training.Our goal was to test the capabilities of deep learning systems trained on camera trap images using modestly sized training data, compare performance when considering unseen background locations, and quantify the gradient of lower bound performance to provide a guideline of data requirements in correspondence to performance expectations.We use a dataset provided by parks canada containing 47,279 images collected from 36 unique geographic locations across multiple environments.Images represent 55 animal species and human activity with high-class imbalance.We trained, tested, and compared the capabilities of six deep learning computer vision networks using transfer learning and image augmentation: dense net201, inception-res net-v3, inception v3, nasnet mobile, mobile net v2, and xception.We compare overall performance on "trained" locations where dense net201 performed best with 95.6% top-1 accuracy showing promise for deep learning methods for smaller scale research efforts.Using trained locations, classifications with <500 images had low and highly variable recall of 0.750 ± 0.329, while classifications with over 1,000 images had a high and stable recall of 0.971 ± 0.0137.Models tasked with classifying species from untrained locations were less accurate, with dense net201 performing best with 68.7% top-1 accuracy.Finally, we provide an open repository where ecologists can insert their image data to train and test custom species detection models for their desired ecological domain.

Journal: Ecology and evolution (2020)
Publication types: Journal Article
Maximizing Property Tuning of Phosphorus Corrole Photocatalysts through a Trifluoromethylation Approach.

An eight-member series of cf3-substituted difluorophosphorus corroles was prepared for establishing a structure-activity profile of these high-potential photosensitizers.It consisted of preparing all four possible isomers of the monosubstituted corrole and complexes with 2-, 3-, 4-, and 5-cf3groups on the macrocycle's periphery.The synthetic pathway to these cf3-substituted derivatives, beginning with (tpfc)pf2, involves two different initial routes: (i) direct electrophilic cf3incorporation using fso2cf2co2me and copper iodide, or (ii) bromination to achieve the 2,3,8,17,18-pentabrominated compound using excess bromine in methanol.Crystallographic investigations revealed that distortion of the original planar macrocycle is evident even in the monosubstituted case and that it becomes truly severe for the penta-cf3-substituted derivative 5.There is a shift in redox potentials of about 193 m v per -cf3group, which decreases to only 120 m v for the fifth one in 5.Differences in the electronic spectra suggest that the gouterman four orbital model decreases in relevance upon gradual -cf3substitution, a conclusion that was corroborated by dft calculations.The very significant energy lowering of the frontier orbitals suggested that photoexcitation should lead to a highly oxidizing photocatalyst.This hypothesis was proven true by finding that the most synthetically accessible cf3-substituted derivative is an excellent catalyst for the photoinduced conversion of bromide to bromine (phenol, toluene, and benzene assay).

Journal: Inorganic chemistry (2019)
Publication types: Journal Article
Urinary CXCL10 Measurement in Late Renal Allograft Biopsies Predicts Outcome Even in Histologically Quiescent Patients.

Cxcl10 is a promising early noninvasive diagnostic marker for allograft rejection and predictive for long-term outcomes.However, its value when measured later in the posttransplant course has not yet been accurately analyzed.Methods we investigated urinary cxcl10 in 141 patients from a prospective, observational renal transplant cohort with 182 clinically indicated allograft biopsies performed >12 months posttransplant and corresponding urines.Urinary cxcl10 was retrospectively quantified on stored urines using the msd v-plex chemokine panel 1 sandwich immunoassay (meso scale discovery).The primary outcome was a composite of allograft loss/renal function decline (>30% estimated glomerular filtration rate [e gfr]-decrease between index biopsy and last follow-up).Results seventy-two patients (51%) reached the primary outcome, and their urinary cxcl10 levels were significantly higher at the time of their biopsy compared with patients with stable allograft function (median 9.3 ng/mmol vs 3.3 ng/mmol, p 7.0 ng/mmol; p = .0001).Even in histologically quiescent patients, high urinary cxcl10 was associated with inferior endpoint-free graft survival (p = .003), and it was an independent predictor of the primary outcome (p = .03).Conclusions this study demonstrates that urinary cxcl10 has a promising diagnostic performance for detection of late allograft rejection and is an independent predictor of long-term renal allograft outcomes, even in histologically quiescent patients.

Journal: Transplantation proceedings (2021)
Publication types: Journal Article;Observational Study
PACKMAN-Molecule: Python toolbox for structural bioinformatics.

Packman-molecule is a structural bioinformatics toolbox in the form of an application programming interface that contains several utilities that can be used for structural bioinformatics applications.It has already been used in several applications, and its added features and unique object hierarchy make it readily extensible, feature-rich and user-friendly.The tutorial for it is available at: availability and implementation packman-molecule is freely available with an mit license on git hub at

Journal: Bioinformatics advances (2022)
Publication types: Journal Article
Cotton Cord Coated with Cyclodextrin Polymers for Paraquat Removal from Water.

The contamination of hazardous agrochemical substances in water caused essential trouble for humans and the environment.The functional textile was used as an effective adsorbent for paraquat removal from an aqueous solution.The coating of anionic cyclodextrin polymer, issued from the cross-linking between 1,2,3,4-butanetetracarboxylic acid and β-cyclodextrin in the presence of poly (vinyl alcohol), on the cotton cord, was firstly investigated.Their physicochemical characteristics were also characterized by gravimetry, acid-base titration, atr-ftir,13c nmr, tga, and stereo-microscopy.The bdp5 system revealed 107.3% coating yield, 1.13 mmol/g cooh groups, and 95.1% paraquat removal for 25 mg/l of initial concentration.The pseudo-second-order model was appropriate for kinetics using 6 h of contact time.Langmuir isotherm was suitable with the maximum adsorption of 30.3 mg/g for paraquat adsorption.The weight loss was 10.7% and 7.8%, respectively, for water and 5%v/vof hci in ethanol after 120 h of contact time.Finally, the reusability efficiency stayed at 88.9% after five regeneration.

Journal: Polymers (2022)
Publication types: Journal Article
Wetting Characteristics of Nanosilica-Poly (acrylic acid) Transparent Anti-Fog Coatings.

The effect of particle loading on the wetting properties of coatings was investigated by modifying a coating formulation based on hydrophilic silica nanoparticles and poly (acrylic acid) (paa).Water contact angle (wca) measurements were conducted for all coatings to characterize the surface wetting properties.Wettability was improved with an increase in particle loading.The resulting coatings showed superhydrophilic (sh) behavior when the particle loading was above 53 vol.%.No new peaks were detected by attenuated total reflection (atr-ftir).The surface topography of the coatings was studied by atomic force microscopy (afm) and scanning electron microscopy (sem).The presence of hydrophilic functional groups and nano-scale roughness were found to be responsible for superhydrophilic behavior.The surface chemistry was found to be a primary factor determining the wetting properties of the coatings.Adhesion of the coatings to the substrate was tested by tape test and found to be durable.The antifogging properties of the coatings were evaluated by exposing the films under different environmental conditions.The sh coatings showed anti-fogging behavior.The transparency of the coatings was significantly improved with the increase in particle loading.The coatings showed good transparency (>85% transmission) when the particle loading was above 84 vol.%.

Journal: Polymers (2022)
Publication types: Journal Article