syedzayyan/paper_mill_benchmark huggingface dataset:
What women want: Women's health in Rural and Regional Australia - Insights from an interprofessional research collaboration between academic researchers, nursing clinicians, and industry professionals.

The aim of this study was to (a) investigate community women's knowledge and experiences of women's health community services in northern rural and regional new south wales, australia; (b) identify any existing gaps in community women's health programs in this region and (c) to contribute to service provision, strategic planning, and industry professional development of community nurse researchers in collaboration with industry.The research took place in northern new south wales local health district (nnswlhd) australia, which is comprised of tweed/byron, richmond and clarence health service groups, during may to september 2019.Participants comprised 13 women's health service clients over the age of 18 years and less than 74 years, attending health services clinics within nnswlhd.The research was undertaken as a partnership between three senior healthcare professionals (clinical nurse consultants), one from each health service group, and academic researchers, who provided the key senior healthcare professionals with research training and guidance.Key themes related to primary healthcare experiences and needs of women living in nnswlhd, and the quality of women's primary healthcare services in that region.Thematic analysis revealed four key themes and several sub-themes.These were (1) knowledge and awareness of services, (2) barriers to access, (3) personal issues and (4) a need for women-centred care.The major issues women experienced were deficits in services, lengthy wait times and poor access.Additional funding is necessary to uphold community women's health nurse positions in rural health to improve women's health outcomes in these locations.

Journal: Health & social care in the community (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.

Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity.Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in rna sequencing of the cells.The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements.Follicular lymphoma, a malignancy of mature b cells that continuously acquire mutations in parallel in the exome and in b cell receptor loci, presents a unique opportunity to join exome-derived mutations with b cell receptor sequences as independent sources of evidence for clonal evolution.Methods here, we propose cactus, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell rna sequencing data to map single cells to given imperfect genotypes of tumor clones.Results we apply cactus to two follicular lymphoma patient samples, integrating three measurements: whole exome, single-cell rna, and b cell receptor sequencing.Cactus outperforms a predecessor model by confidently assigning cells and b cell receptor-based clusters to the tumor clones.Conclusions the integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors.Cactus opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies.Cactus is written in r and source code, along with all supporting files, are available on git hub ( ).

Journal: Genome medicine (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Solvent-Dependent Asymmetric Synthesis of Alkynyl and Monofluoroalkenyl Isoindolinones by CpRhIII-Catalyzed C-H Activation.

The asymmetric synthesis of alkynyl and monofluoroalkenyl isoindolinones from n-methoxy benzamides and α,α-difluoromethylene alkynes is enabled by c-h activation with a chiral cp rh iiicatalyst.Remarkably, product formation is solvent-dependent; alkynyl isoindolinones are afforded in me oh (up to 86 % yield, 99.6 % ee) whereas monofluoroalkenyl isoindolinones are generated ini pr cn (up to 98:2 z/e, 93 % yield, 86 % ee).Mechanistic studies revealed chiral allene and e-configured alkenyl rhodium species as reaction intermediates.The latter is transformed into the corresponding z-configured monofluoroalkene upon protonation in thei pr cn system and into an alkyne by an unusual anti β-f elimination in the me oh system.Notably, kinetic resolution processes occur in this reaction.Despite the moderate enantiocontrol for the formation of the chiral allene, the z-monofluoroalkenyl isoindolinones and alkynyl isoindolinones were obtained in good enantiopurities by one or two sequential kinetic resolution processes.

Journal: Angewandte Chemie (International ed. in English) (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Lower Bladder Toxicity of SalvageVersusAdjuvant Modern Radiotherapy for Prostate Cancer Patients.

/aim in prostate cancer, postoperative radiotherapy timing is debated to avoid overtreatments and toxicities.This study compared acute and late rectal and bladder toxicities in the adjuvant and salvage setting.Patients and methods in total, 129 patients were analyzed in two groups: adjuvant radiotherapy (a rt) and salvage radiotherapy (s rt).Results in a rt and s rt, grade 1 (g1) acute bladder toxicities were detected in 40 and 30 patients, and grade 2 (g2) in 1 and 6; g1 late bladder toxicities were described in 30 and 20, and g2 in 6 and 2, respectively.In a rt and s rt, acute g1 rectal toxicities were reported in 18 and 27 patients, and g2 in 5 and 4, respectively.Late rectal g1 toxicities were observed in 10 patients, g2 in 6 and g3 in 1 in the a rt.In s rt, 8 patients and 1 developed g1 and g2 toxicities, respectively.Regarding bladder toxicity, a higher incidence occurred in a rt; late toxicity was lower in s rt.Conclusion adjuvant and salvage rt in prostate cancer treatment resulted in acceptable toxicities.

Journal: In vivo (Athens, Greece) (2022)
Publication types: Journal Article
Cancer as a death sentence: developing an initial program theory for an IVR intervention.

To address current trends in poor health-seeking behaviour and late cancer diagnosis in many low- and middle-income countries, like uganda, it is important to explore innovative awareness building interventions.One possible intervention is a common digital format, an interactive voice response (ivr) system, which is suitable for individuals with low technological and reading literacy.It is increasingly acknowledged that developing digital interventions requires co-creation with relevant stakeholders and explication of program developers' assumptions, to make them effective, sustainable, and scalable.To this end, we sought to develop an initial program theory for a co-created ivr system for cancer awareness in uganda.Utilising principles of the realist approach, a qualitative exploratory study was conducted through seven focus group discussions (fgds) with people living with cancer (plwc), health workers, and policy makers.Thematic analysis of the transcripts resulted in the emergence of four major themes.Through all themes the most consistent finding was that myths, misconceptions, and misinformation about cancer were related to every aspect of the cancer journey and influenced the experiences and lives of plwc and their caregivers.Participants were positive about the potential of an ivr system but also had reservations about the design and reach of the system.The resulting initial program theory proposes that a context-specific ivr system has the potential to improve awareness on cancer, provided attention is given to aspects such as language, message framing, and accuracy.

Journal: Health promotion international (2022)
Publication types: Journal Article
lncRNA DLEU1 Modulates Proliferation, Inflammation, and Extracellular Matrix Degradation of Chondrocytes through Regulating miR-671-5p.

Long noncoding rnas (lnc rnas) have been shown to be involved in the development of osteoarthritis.However, the expression, function, and mechanism of dleu1 in oa development remain largely unclear.The present reference demonstrates that dleu1 is overexpressed in oa specimens compared to control cartilages.Inflammatory cytokines il-1β, tnf-α, and il-6 induce dleu1 expression in chondrocytes.Ectopic expression of dleu1 induces chondrocyte proliferation, degradation of ecm, and inflammation mediators such as il-6, il-8, and tnf-αsecretion.Moreover, we demonstrated that dleu1 targets mi r-671-5p expression in chondrocytes.Overexpression of dleu1 suppresses mi r-671-5p expression in chondrocytes.The expression of mi r-671-5p is decreased in oa specimens compared to control cartilages.There is a negative correlation between the expression of mi r-671-5p and dleu1 in oa specimens.Inflammatory mediators il-1β, tnf-α, and il-6 suppress mi r-671-5p expression in oa specimens.Elevated expression of mi r-671-5p suppresses chondrocyte proliferation, degradation of ecm, and secretion of inflammation mediators.Dleu1 overexpression promotes chondrocytes proliferation, degradation of ecm, and secretion of inflammation mediators via regulating mi r-671-5p.These results suggested that dleu1 acts as one destructive role in oa development via regulating mi r-671-5p.

Journal: Journal of immunology research (2022)
Publication types: Journal Article
On the Origin of Zero Interface Resistance in the Li6.25Al0.25La3Zr2O12|Li0System: An Atomistic Investigation.

Understanding the nature of ion transfer at the interface between li metal and solid electrolytes (se) is essential for further optimization of all-solid-state li-ion batteries.Thus, the li transfer across the se|li metal interface is investigated by means of ab initio calculations based on density functional theory in this work.The aluminum-doped garnet li6.25al0.25la3zr2o12(llzo) is considered as a model se due to its practical stability against li metal.A low-energy interface model in bicrystal geometry is constructed and investigated by nudged elastic band calculations as well as ab initio molecular dynamics (aimd) simulations.In order to distinguish between interface and bulk transport in the aimd simulations, a post-processing protocol is developed.We find that the activation energies and diffusivities of li are comparable in bulk llzo and across the interface, substantiating that the interface kinetics are not rate-limiting.Moreover, electronic structure analysis indicates that charge transfer occurs gradually.Finally, al3+loss of llzo at the interface rationalizes the experimentally observed phase transition from cubic to tetragonal observed close to li metal contacts.

Journal: ACS applied materials & interfaces (2021)
Publication types: Journal Article
Accurately Measuring Molecular Rotational Spectra in Excited Vibrational Modes.

Although gas phase rotational spectroscopy is a mature field for which millions of rotational spectral lines have been measured in hundreds of molecules with sub-mhz accuracy, it remains a challenge to measure these rotational spectra in excited vibrational modes with the same accuracy.Recently, it was demonstrated that virtually any rotational transition in excited vibrational modes of most molecules may be made to lase when pumped by a continuously tunable quantum cascade laser (qcl).Here, we demonstrate how an infrared qcl may be used to enhance absorption strength or induce lasing of terahertz rotational transitions in highly excited vibrational modes in order to measure their frequencies more accurately.To illustrate the concepts, we used a tunable qcl to excite v3r-branch transitions in n2o and either enhanced absorption or induced lasing on 20 v3rotational transitions, whose frequencies between 299 and 772 ghz were then measured using either heterodyne or modulation spectroscopy.The spectra were fitted to obtain the rotational constants b3and d3, which reproduce the measured spectra to within the experimental uncertainty of ± 5 k hz.We then show how this technique may be generalized by estimating the threshold power to make any rotational transition lase in any n2o vibrational mode.

Journal: Applied spectroscopy (2022)
Publication types: Journal Article
Elevated Intracranial Pressure in Patients with Craniosynostosis by Optical Coherence Tomography.

Craniosynostosis may lead to elevated intracranial pressure, which may be implicated with impaired neurocognitive development.However, accurately measuring intracranial pressure is challenging, and patterns in craniosynostosis patients are poorly characterized.Spectral-domain optical coherence tomography may enable noninvasive assessment of intracranial pressure in pediatric patients with craniosynostosis.Methods pediatric patients with craniosynostosis undergoing surgical intervention between 2014 and 2019 prospectively underwent optical coherence tomographic evaluation.Intracranial pressure was directly measured intraoperatively in a subset of cases.Optical coherence tomographic parameters were compared to directly measured intracranial pressure and used for pattern assessment.Results optical coherence tomography was performed in 158 subjects, among which 42 underwent direct intracranial pressure measurement during an initial cranial procedure.Maximal retinal nerve fiber layer thickness, maximal retinal thickness, and maximal anterior projection optical coherence tomographic parameters were positively correlated with intracranial pressure (p ≤ 0.001), with all parameters showing significantly higher values in patients with intracranial pressure thresholds of 15 mm hg (p < 0.001) and 20 mm hg (p ≤ 0.007).Patients with maximal retinal nerve fiber layer thickness and maximal anterior projection exceeding set thresholds in optical coherence tomography of either eye demonstrated 77.3 percent sensitivity and 95.0 percent specificity for detecting intracranial pressure above 15 mm hg, and 90.0 percent sensitivity and 81.3 percent specificity for detecting intracranial pressure above 20 mm hg.Patients with associated syndromes or multiple suture involvement and patients aged 9 months or older were significantly more likely to have elevated intracranial pressure above 15 mm hg (p ≤ 0.030) and above 20 mm hg (p ≤ 0.035).Conclusions spectral-domain optical coherence tomography can noninvasively detect elevated intracranial pressure in patients with craniosynostosis with reliable sensitivity and specificity.This technology may help guide decisions about the appropriate type and timing of surgical treatment.Clinical question/level of evidence diagnostic, i.

Journal: Plastic and reconstructive surgery (2022)
Publication types: Journal Article
Morphometry Difference of the Hippocampal Formation Between Blind and Sighted Individuals.

The detailed morphometry alterations of the human hippocampal formation (hf) for blind individuals are still understudied.50 subjects were recruited from yantai affiliated hospital of binzhou medical university, including 16 congenital blindness, 14 late blindness, and 20 sighted controls.Volume and shape analysis were conducted between the blind (congenital or late) and sighted groups to observe the (sub)regional alterations of the hf.No significant difference of the hippocampal volume was observed between the blind and sighted subjects.Rightward asymmetry of the hippocampal volume was found for both congenital and late blind individuals, while no significant hemispheric difference was observed for the sighted controls.Shape analysis showed that the superior and inferior parts of both the hippocampal head and tail expanded, while the medial and lateral parts constrained for the blind individuals as compared to the sighted controls.The morphometry alterations for the congenital blind and late blind individuals are nearly the same.Significant expansion of the superior part of the hippocampal tail for both congenital and late blind groups were observed for the left hippocampi after fdr correction.Current results suggest that the cross-model plastic may occur in both hemispheres of the hf to improve the navigation ability without the stimuli of visual cues, and the alteration is more prominent for the left hemisphere.

Journal: Frontiers in neuroscience (2021)
Publication types: Journal Article
Simple fabrication of inner chitosan-coated alginate hollow microfiber with higher stability.

Sodium alginate (na a) has been widely used as microfiber-based scaffold material.However, ca-alginate microfiber might disintegrate in the physiological environment due to the loss of calcium ions, which will limit its long-term application in tissue engineering.In this work, to enhance the stability of ca-alginate microfiber in the physiological environment, an inner chitosan coating was introduced to ca-alginate hollow microfiber by one step via a microfluidic device.A more stable composite microfiber with double cross-linking layers was generated.The stability of the microfiber was studied in the pbs solution (p h 7.4) to identify the coating effect on the hollow structure.The results revealed that chitosan component bonded an na a layer to form a stable polyelectrolyte complex membrane in the inner wall of the microfiber, which stabilized the hollow region even though the ca-alginate shell was disintegrated by pbs solution.In addition, the introduction of chitosan coating improved the inner environment of the low affinity of alginate to cell surfaces and facilitated the cell adhesion and culture in the microfiber.Hep g2 cells in the microfibers displayed favorable cell viability and proliferation ability.We believe that this work will lead to the development of innovative methodologies and materials for both cell culture and tissue engineering application.© 2019 wiley periodicals, inc.J biomed mater res part b: appl biomater 107b:2527-2536, 2019.

Journal: Journal of biomedical materials research. Part B, Applied biomaterials (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Learning from the density to correct total energy and forces in first principle simulations.

We propose a new molecular simulation framework that combines the transferability, robustness, and chemical flexibility of an ab initio method with the accuracy and efficiency of a machine learning model.The key to achieve this mix is to use a standard density functional theory (dft) simulation as a preprocessor for the atomic and molecular information, obtaining a good quality electronic density.General, symmetry preserving, atom-centered electronic descriptors are then built from this density to train a neural network to correct the baseline dft energies and forces.These electronic descriptors encode much more information than local atomic environments, allowing a simple neural network to reach the accuracy required for the problem of study at a negligible additional cost.The balance between accuracy and efficiency is determined by the baseline simulation.This is shown in results where high level quantum chemical accuracy is obtained for simulations of liquid water at standard dft cost or where high level dft-accuracy is achieved in simulations with a low-level baseline dft calculation at a significantly reduced cost.

Journal: The Journal of chemical physics (2019)
Publication types: Journal Article
Facilitators and barriers to seeking and engaging with antenatal care in high-income countries: A meta-synthesis of qualitative research.

Inadequate attendance to antenatal care has been associated with negative maternal and fetal outcomes, including stillbirth.This study aimed to identify facilitators and barriers to antenatal care attendance.A systematic search was conducted in march 2019 and updated in january 2021.Qualitative studies involving pregnant or post-partum women up to 12 months from high-income countries that provided data about facilitators and barriers to antenatal care attendance were sought.Meta-ethnography was used to inform this meta-synthesis.Fifteen studies were included in the analysis.Findings indicate that inadequate antenatal care attendance is influenced at different levels.Aspects like sociodemographic factors, difficulties navigating the health system, administrative delays, lack of flexibility and tailored care, constant change of carer and communication issues also act as barriers.These issues affect women's access to knowledge and the formation of women's beliefs and feelings towards seeking care.On the contrary, having a positive attitude towards the pregnancy, encountering empathetic healthcare professionals and availing of social support acted as facilitators.The reasons why women seek or delay attending antenatal care are multifactorial and can be explained using the social determinants of health framework.Any response needs to be taken across all levels of influence and not just focused on the individual.A better understanding of the barriers and facilitators to antenatal care might contribute to informing intervention or policy development addressing this issue.

Journal: Health & social care in the community (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Non-canonical inflammasome activation analysis in a mouse model of Citrobacter rodentium infection.

Infection of mice with citrobacter rodentium is a useful model for studying the pathogenicity of enteropathogenic and enterohemorrhagic escherichia coli, pathogens that have a close association with humans.Here, we provide a protocol detailing the approaches for non-canonical inflammasome analysis in a mouse model of c.Rodentium infection, including preparation of bacteria, oral administration of bacteria to mice, counting colony-forming units to quantify bacterial colonization, and analysis of expression and activation of inflammasome-related factors.For complete details on the use and execution of this protocol, please refer to tsutsuki et al.(2022).

Journal: STAR protocols (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Mercury in fish from streams and rivers in New York State: Spatial patterns, temporal changes, and environmental drivers.

Mercury (hg) concentrations in freshwater fish across the state of new york frequently exceed guidelines considered harmful to humans and wildlife, but statewide distribution and temporal changes are not well known for the state's streams and rivers.We analyzed existing data to describe recent spatial patterns, identify key environmental drivers, and assess temporal changes.Size classes within sportfishes and prey fishes formed 'functional taxa' (ft), and standardized scores were generated from 2007-2016 data for 218 sites.Muscle hg in ≥1 sportfish ft exceeded human-health guidelines of 50 ng/g (sensitive populations) and 300 ng/g (general population, gp) at 93 and 56% of sites, respectively, but exceeded 1000 ng/g (a state threshold) at only 10% of sites.Whole-body hg in ≥1 prey fish ft exceeded wildlife thresholds of 40 ng/g and 100 ng/g at 91 and 51% of sites, respectively.Environmental drivers of recent spatial patterns include extent of forest cover and storage, the latter an indicator of wetlands.Standardized hg scores increased with increasing atmospheric hg deposition and storage across rural 'upland' regions of new york.However, scores were not related to atmospheric deposition in more-developed 'lowland' regions due to the limited methylation potential of urban landscapes.Comparisons of 2010-2015 sportfish hg concentrations with those of 1998 and 2000-2005 showed inconsistent temporal changes both among and within eight sites examined.Some recent stream and river fish hg spatial patterns differed from those of lake-based studies, highlighting the importance of new york's flowing waters to future hg monitoring and risk assessment.

Journal: Ecotoxicology (London, England) (2020)
Publication types: Journal Article