syedzayyan/paper_mill_benchmark huggingface dataset:
Combination of surveillance tools reveals that Yellow Fever virus can remain in the same Atlantic Forest area at least for three transmission seasons.

In brazil, the yellow fever virus (yfv) is endemic in the amazon, from where it eventually expands into epidemic waves.Coastal south-eastern (se) brazil, which has been a yfv-free region for eight decades, has reported a severe sylvatic outbreak since 2016.The virus spread from the north toward the south of the rio de janeiro (rj) state, causing 307 human cases with 105 deaths during the 2016-2017 and 2017-2018 transmission seasons.It is unclear, however, whether the yfv would persist in the coastal atlantic forest of rj during subsequent transmission seasons.Objectives to conduct a real-time surveillance and assess the potential persistence of yfv in the coastal atlantic forest of rj during the 2018-2019 transmission season.Methods we combined epizootic surveillance with fast diagnostic and molecular, phylogenetic, and evolutionary analyses.Findings using this integrative strategy, we detected the first evidence of yfv re-emergence in the third transmission season (2018-2019) in a dying howler monkey from the central region of the rj state.The yfv detected in 2019 has the molecular signature associated with the current se yfv outbreak and exhibited a close phylogenetic relationship with the yfv lineage that circulated in the same atlantic forest fragment during the past seasons.This lineage circulated along the coastal side of the serra do mar mountain chain, and its evolution seems to be mainly driven by genetic drift.The potential bridge vector aedes albopictus was found probing on the recently dead howler monkey in the forest edge, very close to urban areas.Main conclusions collectively, our data revealed that yfv transmission persisted at the same atlantic forest area for at least three consecutive transmission seasons without the need of new introductions.Our real-time surveillance strategy permitted health authorities to take preventive actions within 48 h after the detection of the sick non-human primate.The local virus persistence and the proximity of the epizootic forest to urban areas reinforces the concern with regards to the risk of re-urbanisation and seasonal re-emergence of yfv, stressing the need for continuous effective surveillance and high vaccination coverage in the se region, particularly in rj, an important tourist location.

Journal: Memorias do Instituto Oswaldo Cruz (2019)
Publication types: Journal Article
Quick and efficient quantitative predictions of androgen receptor binding affinity for screening Endocrine Disruptor Chemicals using 2D-QSAR and Chemical Read-Across.

Endocrine disruptor chemicals are synthetic or natural molecules in the environment that promote adverse modifications of endogenous hormone regulation in humans and/or in animals.In the present research, we have applied two-dimensional quantitative structure-activity relationship (2d-qsar) modeling to analyze the structural features of these chemicals responsible for binding to the androgen receptors (log rba) in rats.We have collected the receptor binding data from the edkb database ( and then employed the dtc-qsar tool, available from for dataset division, feature selection, and model development.The final partial least squares model was evaluated using various stringent validation criteria.From the model, we interpreted that hydrophobicity, steroidal nucleus, bulkiness and a hydrogen bond donor at an appropriate position contribute to the receptor binding affinity, while presence of electron rich features like aromaticity and polar groups decrease the receptor binding affinity.Additionally we have also performed chemical read-across predictions using read-across-v3.1 available from and the results for the external validation metrics were found to be better than the qsar-derived predictions.The best quality of external predictions emerged from the q-rasar approach which combines both read-across and qsar.To explore the essential features responsible for the receptor binding, pharmacophore mapping, molecular docking along with molecular dynamics simulation were also performed, and the results are in accordance with the qsar/q-rasar findings.

Journal: Chemosphere (2022)
Publication types: Journal Article
Players with high physical fitness are at greater risk of injury in youth football.

The aim of this study was to investigate physical fitness, football-specific skills, and their association with injury risk in youth football.Altogether 447 male and female players aged 9-14 years (median 12 years) participated in performance tests and prospective follow-up.The physical fitness tests included five-jump test for distance, 30-m sprint, football-specific figure of eight agility, countermovement jump, and yo-yo intermittent endurance test level 1.The football-specific skill tests included dribbling and passing tests.Injuries and exposure were registered during the 20-week follow-up.Our candidate risk factors were low/high level of physical fitness measured with a composite score of physical fitness tests and low/high level of football-specific skills measured with a composite score of dribbling and passing tests.Secondarily, we investigated performance in individual tests and their association with injury risk.During the follow-up, players reported 565 injuries (264 acute and 301 overuse injuries).High level of physical fitness was associated with increased rate of all injuries (age-, sex-, and mean team exposure-adjusted irr: 1.28, 95% ci: 1.04-1.58).The level of football-specific skills had no influence on the overall injury rate.Burden of overuse injuries, but not acute injuries was significantly higher in most fit players compared with the players in the reference group (irr: 2.09, 95% ci: 1.04-4.24).In conclusion, most fit players were at greater risk of sustaining injuries in youth competitive football.

Journal: Scandinavian journal of medicine & science in sports (2022)
Publication types: Journal Article
Bones of contention: skeletal patterning across the fin-to-limb transition.

The fin-to-limb transition has long fascinated evolutionary biologists, but a unifying theory as to its developmental origins has remained elusive.New work by hawkins and colleagues demonstrates the surprising potential of teleost fins to exhibit a hox-regulated limb-like skeletal pattern, shedding new light on the evolution of proximo-distal patterning processes.

Journal: Cell (2021)
Publication types: Journal Article;Comment
Core Role of Hydrophobic Core of Polymeric Nanomicelle in Endosomal Escape of siRNA.

Efficient endosomal escape is the most essential but challenging issue for si rna drug development.Herein, a series of quaternary ammonium-based amphiphilic triblock polymers harnessing an elaborately tailored p h-sensitive hydrophobic core were synthesized and screened.Upon incubating in an endosomal p h environment (p h 6.5-6.8), m peg45-p(dpa50-co-dmaema56)-pt53(pddt, the optimized polymer) nanomicelles (pddt-ms) and pddt-ms/si rna polyplexes rapidly disassembled, leading to promoted cytosolic release of internalized si rna and enhanced silencing activity evident from comprehensive analysis of the colocalization and gene silencing using a lysosomotropic agent (chloroquine) and an endosomal trafficking inhibitor (bafilomycin a1).In addition, pddt-ms/si plk1 dramatically repressed tumor growth in both hep g2-xenograft and highly malignant patient-derived xenograft models.Pddt-ms-armed si pd-l1 efficiently blocked the interaction of pd-l1 and pd-1 and restored immunological surveillance in ct-26-xenograft murine model.Pddt-ms/si rna exhibited ideal safety profiles in these assays.This study provides guidelines for rational design and optimization of block polymers for efficient endosomal escape of internalized si rna and cancer therapy.

Journal: Nano letters (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Twin curvilinear vortex beams.

We report on a novel curvilinear optical vortex beam named twin curvilinear vortex beams (tcvbs) with intensity and phase distribution along a pair of two- or three-dimensional curves, both of which share the same shape and the same topological charge.The tcvbs also possess the character of perfect optical vortex, namely having a size independent of topological charge.We theoretically demonstrate that a tcvb rather than a single-curve vortex beam can be created by the fourier transform of a cylindrically polarized beam.The behavior of tcvbs generated through our method is investigated by simulation and experiment, including interference experiments for identifying the vortex property of the tcvbs.The tcvbs may find applications in optical tweezers, such as trapping low refractive index particles in the dark region between two curves and driving them moving along the curvilinear trajectory.

Journal: Optics express (2021)
Publication types: Journal Article
Establishing Occupational Therapy Needs: A Semi-Structured Interview with Hereditary Transthyretin Amyloidosis Patients.

The purpose of this study was to explore the occupational performance and needs of patients with hereditary transthyretin amyloidosis (attrv).A semi-structured interview was conducted by an occupational therapist with 44 patients with val50met-attrv recruited through patient associations.The interview addressed three related dimensions.The first one, the physical dimension, was evaluated using the spanish versions of the barthel index, the lawton and brody scale, and the norfolk questionnaire; the second one, the psychological dimension, was assessed with the warwick-edinburgh mental well-being scale and the sf-36 questionnaire; and the third dimension, the occupational performance, was assessed through unstructured questions on daily occupations, work, roles, and hobbies given the lack of standardized scales.Twenty participants (45.4%) responded that the disease had affected their basic activities of daily living, twenty- four (54.5%) perceived an impact on their instrumental activities of daily living, and all the participants reported that the disease symptoms had affected their ability to perform advanced activities as well as their employment status.Only three patients (6.8%) reported a lack of psychological impairment following disease diagnosis.These findings suggest that a semi-structured interview conducted by an occupational therapist can provide essential information that should be considered for the implementation of occupational therapy programs targeting patients living with a diagnosis of attrv.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Signature of N6-methyladenosine Regulator-Related Genes Predicts Prognoses and Immune Responses for Head and Neck Squamous Cell Carcinoma.

This study aimed to construct a signature of n6-methyladenosine (m6a) regulator-related genes that could be used for the prognosis of head and neck squamous cell carcinoma (hnscc) and to clarify the molecular and immune characteristics and benefits of immune checkpoint inhibitor (ici) therapy using the prognostic signature to define the subgroups of hnscc.This study showed that eighteen m6a regulators were abnormally expressed in the cancer genome atlas (tcga) hnscc tissues compared with those in normal tissues.We constructed a signature of 12 m6a regulator-related genes using the cox risk model, combined with the least absolute shrinkage and selection operator (lasso) variable screening algorithm.Based on the median of the signature risk score, the patients were divided into high- and low-risk groups.The kaplan-meier survival analyses showed that patients with high-risk scores demonstrated poorer overall survival (os) than those with low-risk scores based on tcga-hnscc data (p <0.001).The os of high-risk patients was significantly worse than that of low-risk patients in the gse65858 (p <0.001) and international cancer genome consortium (icgc) oral cancer cohorts (p= 0.0089).Furthermore, immune infiltration analyses showed that 8 types of immune cell infiltration showed highly significant differences between the two risk groups (p <0.001).In the imvigor210core biologies dataset of patients who received icis, the objective response rate (orr) of the low-risk group (32%) was significantly higher than that of the high-risk group (13%).Additionally, patients in the high-risk group presented with a more significant adverse os than that of the low-risk group (p= 0.00032).Gse78220 also showed that the orr of the low-risk group (64%) was higher than that of the high-risk group (43%) and the os of low-risk patients was better than that of high-risk patients (p= 0.0064).The constructed prognostic signature, based on m6a regulator-related genes, could be used to effectively distinguish between prognoses for hnscc patients.The prognostic signature was found to be related to the immune cell infiltration of hnscc; it might help predict the responses and prognoses of icis during treatment.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The Effect of Caspase 8, 9 Gene Polymorphisms on Non-Hodgkin Lymphoma Susceptibility and Clinical/Pathological Features.

Caspases (casps) are the main executors of the apoptotic process.Studies to date have shown the role of caspase-8 (casp8) and caspase-9 (casp9) in carcinogenesis.Therefore, the aim of this study was to investigate the associations between casp9-rs4233532, casp9-rs4646018, and casp8- rs1045485 gene polymorphisms and non-hodgkin lymphoma (nhl) susceptibility in an iranian population-based study.Moreover, it was examined whether such the genotype of these polymorphisms is related with clinicopathological characteristics of nhl.Methods 175 patients with nhl and 175 age- and sex-matched controls were enrolled in this study.We determined the genotypes of single nucleotide polymorphisms (snps) from casp genes with tetra arms-pcr (amplification refractory mutation system) method.Results statistically significant association were observed between casp9-rs4646018 and increased risk of nhl under codominant cc, codominant tc, and dominant tc+cc genetic models.Our results showed that the a allele of casp8-rs1045485 was a protective factor for nhl and gars1045485 genotype significantly reduced risk of nhl.In contrast, casp9- rs4233532 was not linked to nhl susceptibility.No relationship was detected between casp8-rs1045485 and casp9-rs4233532 and nhl clinicopathological characteristics, however genetic variation in casp9-rs4646018 was associated with histology, treatment and radio therapy of nhl.Conclusions our study presented that the casp8- rs1045485 and casp9-rs4646018 polymorphisms could affect the risk of nhl in iranian populations which was the first report to show the significant relationship between rs1045485, rs4646018 polymorphisms and nhl susceptibility.Replication large-scale case-control studies in different ethnicities are warranted to verify these findings.

Journal: Asian Pacific journal of cancer prevention : APJCP (2022)
Publication types: Journal Article
Exploratory Mixed-Methods Study of a Primary Care-Based Intervention Promoting Shared Reading During Infancy.

Parent-child "shared" reading can be a rich source of language exposure.Clinic-based programs, notably reach out and read (ror), are intended to enhance this.However, ror has been traditionally introduced at 6 months and only recently expanded to younger ages.This study explored efficacy of an intervention delivered during pediatric well visits promoting shared reading prior to 6 months old, in terms of home reading attitudes and routines.The intervention group received children's books and anticipatory guidance about benefits of shared reading, whereas the control group received general age-related anticipatory guidance.Surveys were administered at the child's newborn (pre-intervention) and 6-month (post-intervention) well visits.Significant findings at 6 months included more frequent shared reading (p= .03), greater comfort reading at this age (p= .01), and greater importance attributed to shared reading (p= .04) in the intervention group relative to controls.These support the expansion of early literacy interventions such as ror into early infancy.

Journal: Clinical pediatrics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Are contralateral submental artery perforator flaps feasible for the reconstruction of postoperative defects of oral cancer?

We evaluated the clinical applications of the reconstruction of postoperative defects of the oral cavity using contralateral submental artery flaps.Methods a retrospective study of 18 patients with postoperative intraoral cancer defects reconstructed with contralateral submental artery perforator flaps between october 2018 and october 2019 in our department was conducted.The defect area, flap size, and complications were evaluated.Results all patients were diagnosed based on pathological examinations: 2 with adenoid cystic carcinoma and 16 with squamous cell carcinoma.The submental artery perforator flap used for simultaneous repair was 8 to 15 cm in length and 4 to 6.5 cm in width.The survival rate of flap reconstruction was 100% with no donor site complications.Conclusions contralateral submental artery flap reconstruction is a suitable alternative for moderate to large intraoral defects, postoperative mouth floor defects, and oral cavity composite defects of oral malignant tumors without contralateral lymph node metastases.

Journal: Head & neck (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A note on estimating safety performance functions with a flexible specification of traffic volume.

In this note, a flexible approach to allow for variation in the impact of traffic volume in the estimation of safety performance functions (spfs) is proposed.The approach generalizes a recently proposed approach by gayah and donnell (2021) (gd) titled "estimating safety performance functions for two-lane rural roads using an alternative functional form for traffic volume".Gd approach proposes a multiple regime structure for aadt impact while explicitly constraining the impact at the regime threshold to be the same.While the gd approach provides a flexible structure, the framework as proposed calls for careful judgement for threshold selection and additional model estimation complexity for the aadt constraint.The current note establishes the equivalence of the proposed approach with the gd approach and subsequently presents a more flexible model structure that improves on the gd approach.Subsequently, we document the advantages of our proposed approach in terms of model estimation, parameter significance testing, flexibility to consider multiple traffic volume ranges and ease of accommodating random parameters for analysis.Finally, we present potential directions for future research.

Journal: Accident; analysis and prevention (2022)
Publication types: Journal Article
The role of neural flexibility in cognitive aging.

Studies assessing relationships between neural and cognitive changes in healthy aging have shown that a variety of aspects of brain structure and function explain a significant portion of the variability in cognitive outcomes throughout adulthood.Many studies assessing relationships between brain function and cognition have utilized time-averaged, or static functional connectivity methods to explore ways in which brain network organization may contribute to aspects of cognitive aging.However, recent studies in this field have suggested that time-varying, or dynamic measures of functional connectivity, which assess changes in functional connectivity over the course of a scan session, may play a stronger role in explaining cognitive outcomes in healthy young adults.Further, both static and dynamic functional connectivity studies suggest that there may be differences in patterns of brain-cognition relationships as a function of whether or not the participant is performing a task during the scan.Thus, the goals of the present study were threefold: (1) assess whether neural flexibility during both resting as well as task-based scans is related to participant age and cognitive performance in a lifespan aging sample, (2) determine whether neural flexibility moderates relationships between age and cognitive performance, and (3) explore differences in neural flexibility between rest and task.Participants in the study were 386 healthy adults between the ages of 20-80 who provided resting state and/or task-based (matrix reasoning) functional magnetic resonance imaging (f mri) scan data as part of their participation in two ongoing studies of cognitive aging.Neural flexibility measures from both resting and task-based scans reflected the number of times each node changed network assignment, and were averaged both across the whole brain (global neural flexibility) as well as within ten somatosensory/cognitive networks.Results showed that neural flexibility was not related to participant age, and that task-based global neural flexibility, as well as task-based neural flexibility in several networks, tended to be negatively related to reaction times during the matrix reasoning task, however these effects did not survive strict multiple comparisons correction.Resting state neural flexibility was not significantly related to either participant age or cognitive performance.Additionally, no neural flexibility measures significantly moderated relationships between participant age and cognitive outcomes.Further, neural flexibility differed as a function of scan type, with resting state neural flexibility being significantly greater than task-based neural flexibility.Thus, neural flexibility measures computed during a cognitive task may be more meaningfully related to cognitive performance across the adult lifespan then resting state measures of neural flexibility.

Journal: NeuroImage (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural