syedzayyan/paper_mill_benchmark huggingface dataset:
Carbodiphosphorane-Stabilized Parent Dioxophosphorane: A Valuable Synthetic HO2P Source.

Introducing a small phosphorus-based fragment into other molecular entities via, for example, phosphorylation/phosphonylation is an important process in synthetic chemistry.One of the approaches to achieve this is by trapping and subsequently releasing extremely reactive phosphorus-based molecules such as dioxophosphoranes.In this work, electron-rich hexaphenylcarbodiphosphorane (cdp) was used to stabilize the least thermodynamically favorable isomer of ho2p to yield monomeric cdp·pho2.The title compound was observed to be a quite versatile phosphonylating agent; that is, it showed a great ability to transfer, for the first time, the hpo2fragment to a number of substrates such as alcohols, amines, carboxylic acids, and water.Several phosphorous-based compounds that were generated using this synthetic approach were also isolated and characterized for the first time.According to the initial computational studies, the addition-elimination pathway was significantly more favorable than the corresponding elimination-addition route for "delivering" the ho2p unit in these reactions.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Young Patients with Hormone Receptor-Positive Breast Cancer Have a Higher Long-Term Risk of Breast Cancer Specific Death.

Although it is widely accepted that hormone receptor (hr) status is associated with later post-diagnostic periods, a debate exists as to whether the association is independent of age.The aim of our study was to confirm the impact of hr status on later period breast cancer-specific death (lp-bcsd) and later period non-breast cancer-specific death (lp-non-bcsd) in different age subgroups.Methods surveillance, epidemiology, and end results databases were utilized to identify 181,108 breast cancer patients with > 5 years survival.The cumulative incidence of lp-bcsd and lp-non-bcsd was calculated using the gray method.The subdistribution hazard ratio (shr) of variables was estimated via the fine and gray proportional hazard regression model.Subgroup analyses for lp-bcsd and lp-non-bcsd were performed according to the hr status.Results the risk of lp-bcsd was exceeded by that of lp-non-bcsd at > 5 years since the diagnosis, particularly in old women.The competing risk regression model indicated that hormone receptor-positive (hr+) was an independent factor for more lp-bcsd (hazard ratio, 1.54; 95% confidence interval, 1.44-1.54;p< 0.001).However, stratified analysis indicated that hr+ was only associated with more lp-bcsd in the young women subgroup.Although hr+ was associated with more lp-non-bcsd, the predictive value of hr+ for lp-non-bcsd was eliminated after adjusting for age.Conclusions hr+ was related to lp-bcsd in the premenopausal population.Lp-bcsd should be an optimal endpoint in future trials designed to evaluate the role of extended adjuvant endocrine therapy.

Journal: Journal of breast cancer (2019)
Publication types: Journal Article
Altered T-Cell Subsets are Associated with Dysregulated Cytokine Secretion of CD4+T Cells During HIV Infection.

Cd4+t cells play a critical role in the regulation of immunopathogenesis in hiv infection.Previous studies have shown contradictory results of the cd4+t-cell responses in people living with hiv (plhiv).Methods a cross-sectional study was performed on 40 healthy controls, 134 art-naïve plhiv, and 34 individuals who experienced 3-year art with low baseline cd4 count from 4 august 2016 to 23 january 2019.We determined the frequencies of cd4+t-cell subsets and described the cytokine secretion pattern of total and subsets of cd4+t cells in these individuals.Results we found that cd4+t cells in plhiv displayed enhanced secretion of pro-inflammation cytokines and polyfunctionality due to hiv disease progression (r= -0.282,p= 0.0035 for ifn-γ;r= -0.412,p= 0.0002 for tnf-α;r= -0.243,p< 0.0001 for gm-csf;r= -0.252,p= 0.0093 for ifn-γ+tnf-α+cells).However, the altered t-cell subsets, as presented by the loss of naïve cells and expansion of memory/effector population in plhiv, were associated with discordant results in total and subsets of cd4+t cells.As major cytokine-producing t subsets, effector/memory cd4 subsets showed impaired cytokine production (p< 0.05).We further demonstrated that 3-year art treatment could improve cd4 counts by increasing the pool of naïve t cells but could not restore cytokine secretion in cd4+t-cell subsets (p< 0.05).Conclusion these data identified the impaired capacity of cytokine secretion in cd4+t-cell subsets due to hiv disease progression, and the altered t-cell subsets were associated with pseudo-elevation of cytokine production in total cd4+t cells.This study collectively suggested the importance of therapies that can preserve and/or enhance the function of cd4+t cells in strategies of hiv remission.

Journal: Journal of inflammation research (2021)
Publication types: Journal Article
Neutrophil extracellular traps: Modulation mechanisms by pathogens.

Neutrophils, as innate effector cells, play an essential role in the containment and elimination of pathogens.Among the main neutrophil mechanisms use for these processes is the release of neutrophil extracellular traps (nets), which consist of decondensed dna decorated with various cytoplasmic proteins.Nets' principal role is the trapping and elimination of infectious agents; therefore, the formation of nets is regulated by bacteria, fungi, parasites, and viruses through different mechanisms: the presence of virulence factors (adhered or secreted), microbial load, size of the microorganism, and even due to other immune cells activation (mainly platelets).This review summarizes the significant aspects that contribute to nets modulation by pathogens and their components, and the effect nets have on these pathogens as a cellular defense mechanism.

Journal: Cellular immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Recruitment of a diverse research cohort in a large metropolitan area for dementia intervention studies.

The human and financial costs of dementia care are growing exponentially.Over five and a half million older americans are estimated to be living with alzheimer's disease and related dementia (adrd).By 2050, this is expected to increase to over 13 million, and persons of color are at the highest risk.Considerable funds have been committed to research to prevent, treat, and care for persons at risk for adrd.However, enrollment of research participants, particularly those coming from diverse backgrounds, is a perennial challenge and has serious implications.This paper quantitatively details the results of a community-based multi-modal outreach effort to recruit a racially diverse sample for non-pharmacological dementia intervention, including referral and participant sources and yield, total recruitment costs and cost per enrolled dyad, and a qualitative description of lessons learned, with particular attention to the recruitment of black participants.The largest number of referrals and referrals converting to study participants, for both black and white persons, were from a maryland department of health mailing to medicaid recipients.There was an important difference in the most effective strategies, proportionally, for white and black participants.The mdh mailing had the highest yield for our black referrals and participants, while professional referrals had the highest yield for white referrals and participants.The total estimated cost of recruitment was $101,058, or $156.19 per enrolled dyad.Ultimately 646 persons with dementia and care partner dyads were enrolled, 323 (50%) of whom were black.

Journal: Contemporary clinical trials (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, P.H.S.
Genomic Analysis of EndophyticBacillus-Related Strains Isolated from the Medicinal PlantOriganum vulgareL. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds.

Multidrug-resistant pathogens represent a serious threat to human health.The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir.The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship.Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant origanum vulgare l.And able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients.The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin a.Endophytes' adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes.The diesel fuel degrading potential was also tested.Strains grew in minimum media supplemented with diesel fuel, but non-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.

Journal: Microorganisms (2022)
Publication types: Journal Article
Whole-lesion Apparent Diffusion Coefficient First- and Second-Order Texture Features for the Characterization of Rectal Cancer Pathological Factors.

The objective of this study was to explore the value of whole-volume apparent diffusion coefficient (adc) features in characterizing pathologic features of rectal cancer.Methods a total of 50 patients who were diagnosed with rectal cancer via biopsy underwent 3-t pretreatment diffusion-weighted imaging.Apparent diffusion coefficient features, including mean, 10th-90th percentile, entropy and entropy(h), derived from whole-lesion volumes were compared between pathologic t1-2 and t3 stages, perineural invasion (pni) present and absent, lymphangiovascular invasion present and absent, and pathological n0 and n+ stage groups.Results entropy and entropy(h) were significantly lower in rectal cancers at t1-2 stages than t3.The 90th percentile of rectal cancers with pni was significantly lower than that of those without pni.All p < 0.05.Conclusions whole-lesion adc entropy and entropy(h) have potential in evaluating different t stages, and 90th percentile can be helpful for determining pni presence of rectal cancers.

Journal: Journal of computer assisted tomography (2018)
Publication types: Journal Article
Beclin 1 functions as a negative modulator of MLKL oligomerisation by integrating into the necrosome complex.

Necroptosis is a form of regulated cell death caused by formation of the necrosome complex.However, the factors modulating this process and the systemic pathophysiological effects of necroptosis are yet to be understood.Here, we identified that beclin 1 functions as an anti-necroptosis factor by being recruited into the necrosome complex upon treatment with tnfα, smac mimetic, and pan-caspase inhibitor and by repressing mlkl oligomerisation, thus preventing the disruption of the plasma membrane.Cells ablated or knocked-out for beclin 1 become sensitised to necroptosis in an autophagy-independent manner without affecting the necrosome formation itself.Interestingly, the recruitment of beclin 1 into the necrosome complex is dependent on the activation and phosphorylation of mlkl.Biochemically, the coiled-coil domain (ccd) of beclin 1 binds to the ccd of mlkl, which restrains the oligomerisation of phosphorylated mlkl.Finally, beclin 1 depletion was found to promote necroptosis in leukaemia cells and enhance regression of xenografted-tumour upon treatment with smac mimetics and caspase inhibitors.These results suggest that beclin 1 functions as a negative regulator in the execution of necroptosis by suppressing mlkl oligomerisation.

Journal: Cell death and differentiation (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Characterization of the hierarchical architecture and micromechanical properties of walnut shell (Juglans regia L.).

In the present work a comprehensive characterization of the hierarchical architecture of the walnut shell (juglans regia l.) was carried out using scanning electron microscopy (sem), atomic force microscopy (afm) and confocal laser scanning microscopy (clsm).Furthermore, micromechanical properties (hardness, hitand elastic modulus, eit) of plant tissues were evaluated at cell wall level by applying the instrumented indentation technique (iit).The complex architecture of the material was described in terms of four hierarchical levels (hl): endocarp (h1), plant tissues (h2), plant cells (h3) and cell wall (h4).Our findings revealed that the walnut shell consists of a multilayer structure (sclerenchyma tissue, st; interface tissue, it; porous tissue, pt; and flattened parenchyma tissue, fpt), where differences in the microstructure and composition of plant tissues generate parallel gradients along the cross-section.The indentation tests showed a functional gradient with a sandwich-like configuration, i.e., a lightweight and soft layer (pt, hit= 0.04 gpa) is located between two dense and hard layers (st, hit= 0.33 gpa; fpt, hit= 0.28 gpa); where additionally there is an interface between st and pt (it, hit= 0.16 gpa).This configuration is a successful strategy designed by nature to improve the protection of the kernel by increasing the strength of the shell.Therefore, the walnut shell can be considered as a functionally graded material (fgm), which can be used as bioinspiration for the design of new functional synthetic materials.In addition, we proposed some structure-property-function relationships in the whole walnut shell and in each of the plant tissues.

Journal: Journal of the mechanical behavior of biomedical materials (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Curcumae Radix: a review of its botany, traditional uses, phytochemistry, pharmacology and toxicology.

S curcumae radix, the medicinal part is radix, commonly called as yujin (chinese:), is a widely used traditional chinese medicine for its high medicinal value and health benefits.Curcumae radix has been used to treat conditions such as syndrome of heat disease and unconsciousness, epilepsy and internal stagnation of phlegm, qi stagnation and blood stasis, dysmenorrhoea, jaundice, cholelithiasis caused by dampness heat of liver and gallbladder.This review aims to summarize the botany, traditional usages, processing, phytochemistry, quality control, pharmacology and toxicology of curcumae radix to better understand its therapeutic potential.Key findings so far, a variety of chemical constituents have been isolated and identified from curcumae radix, mainly including volatile oil and diphenylheptanes.Modern research shows that the extracts and compounds from curcumae radix possess wide-ranging pharmacological effects, including anti-tumour, hepatoprotective, anti-inflammatory and analgesic, anti-thrombosis, as well as effects on the nervous system and others.Summary curcumae radix holds an important position in traditional system of medicine.It is cost-effective and an important plant with curative application in contemporary medicine.However, further in-depth studies are also needed to determine the medical uses of this plant and its chemical constituents, pharmacological activity, quality control and toxicology.

Journal: The Journal of pharmacy and pharmacology (2022)
Publication types: Journal Article;Review
Mothers and fathers in the criminal justice system and children's child protective services involvement.

Parental criminal justice system (cjs) involvement is a marker for child protective services (cps) involvement.Objective to document how parental criminal case processing affects children's cps involvement.Participants and setting participants included mothers and fathers with a serious criminal charge (mothers = 78,882; fathers = 165,070) and without any criminal charge (mothers = 962,963; fathers = 743,604) between 2008-2012.Statewide north carolina records on court proceedings, births, cps assessments/investigations, and foster care placements were used.Methods the observational unit was an individual's first charge date of a year.Outcomes were cps assessment/investigation and foster care entry within six months and alternatively three years following the charge.Key explanatory variables were whether the charges resulted in prosecution, conviction following prosecution, and an active sentence conditional on conviction.An instrumental variables approach was used.Results parents charged with a criminal offense had higher rates of having a cps assessment/investigation during the three years preceding the charge than parents who were not charged.Among mothers who were convicted, cps assessment/investigation increased 8.1 percent (95 % ci: 2.2, 13.9) and 9.5 percent (95 % ci: 1.3, 17.6) 6 months and 3 years following the charge.An active sentence increased cps assessment/investigations by 21.6 percent (95 % ci: 6.4, 36.7) within 6 months.For fathers, active sentence increased foster care placement by 1.6 percent (95 % ci: 0.24, 2.9) within 6 months of the criminal charge.Conclusions changing parental incarceration rates would change cps caseloads substantially.The criminal justice and cps systems work with overlapping populations, data and services sharing should be considered a high priority.

Journal: Child abuse & neglect (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Using next generation sequencing for molecular detection and differentiation of Anaplasma phagocytophilum variants from host seeking Ixodes scapularis ticks in the United States.

Anaplasmosis is increasingly common in the united states, with cases being reported over an expanding geographic area.To monitor for changes in risk of human infection, the u.s.Centers for disease control and prevention monitors the distribution and abundance of host-seeking vector ticks (ixodes scapularis and ixodes pacificus) and their infection with anaplasma phagocytophilum.While several variants of a.Phagocytophilum circulate in i.Scapularis, only the human-active variant (ap-ha) appears to be pathogenic in humans.Failure to differentiate between human and non-human variants may artificially inflate estimates of the risk of human infection.Efforts to differentiate the ap-ha variant from the deer variant (ap-v1) in ticks typically rely on traditional pcr assays coupled with sequencing of pcr products.However, laboratories are increasingly turning to next generation sequencing (ngs) to increase testing efficiency, retain high sensitivity, and increase specificity compared with traditional pcr assays.We describe a new ngs assay with novel targets that accurately segregate the ap-ha variant from other non-human variants and further identify unique clades within the human and non-human variants.Recognizing that not all investigators have access to ngs technology, we also developed a pcr assay based on one of the novel targets so that variants can be visualized using agarose gel electrophoresis without the need for subsequent sequencing.Such an assay may be used to improve estimates of human risk of developing anaplasmosis in north america.

Journal: Ticks and tick-borne diseases (2022)
Publication types: Journal Article
Synthesis of Indolizines from Pyridinium Salts and Ethyl Bromodifluoroacetate.

Here we present a novel annulation of pyridinium salts with br cf2co2et to access the indolizine derivatives with high efficiency.The α substitution of pyridine plays a key role in determining the reaction pathways.Various types of indolizines can be conveniently accessed from easily available pyridinium salts under mild and simple reaction conditions.

Journal: Organic letters (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Editorial Commentary: Causes of Failure After Arthroscopic Rotator Cuff Repair.

Causes of failure after arthroscopic rotator cuff repair include patient factors, tear factors, and surgical factors.Failure may occur at the suture-tendon interface, the bone-tendon interface, or the bone-anchor interface.Low bone mineral density (bmd) in the greater tuberosity has been reported as a prognostic factor for recurrent tears following rotator cuff repair, and although most studies suggest the tendon-to-suture interface as the "weakest link," patients with low bmd may have lower suture anchor pull-out strength.A potential alternative cause of failure is the suture cutting through the greater tuberosity bone in patients with low bmd.Knotless suture bridge constructs or single-row constructs may be more susceptible to a suture cutting through the bone.The knotted suture bridge technique, wherein the medial mattress sutures are tied, may to some extent "shield" against complete cut-through.When bone quality appears poor, a common response is to change the type of anchor, size of anchor, or the location of the anchor.Other factors, such as bone preparation, suture type, suture tensioning, and anchor type (e.g., internal vs external locking), may all potentially affect suture cutting through weak bone.

Journal: Arthroscopy : the journal of arthroscopic & related surgery : official publication of the Arthroscopy Association of North America and the International Arthroscopy Association (2021)
Publication types: Editorial;Comment
Elimination of HIV transmission in Japanese MSM with combination interventions.

Japan has a concentrated hiv epidemic, with the majority of transmission among men who have sex with men (msm).This study aimed to explore the effect of behavioral and biomedical interventions on the hiv epidemic and forecast the time required to eliminate hiv transmission among japanese msm.Methods a deterministic compartmental model was built to estimate and forecast the hiv epidemic among japanese msm from 2010 to 2050.Elimination of hiv transmission among msm was defined as incidence less than 1/1000 person-years.The time required for eliminating hiv transmission under different scenarios was calculated.Findings under the current policies, hiv transmission cannot be eliminated by 2050.Both behavioral and biomedical interventions can achieve elimination of hiv among msm by 2050 with annual number of sexual partners among high-risk msm less than 9, or with condom use rate above 65%, or with testing and treatment rate above 80%, or with more than 10% pr ep coverage rate.Under comprehensive interventions, hiv elimination will be achieved in 2032, 2025 and 2024 using weak, moderate and strong intervention combinations, respectively.Interpretation both behavioural and biomedical interventions can achieve elimination of hiv among msm by 2050, but comprehensive interventions can accelerate the realization of this goal with higher feasibility.Funding this study was funded by a health and labor sciences research grant (research on hiv/aids) from the ministry of health labour and welfare (21hb0701) and national natural science foundation of china (no.81773543 and 81973150), and the kc wong education foundation.

Journal: The Lancet regional health. Western Pacific (2022)
Publication types: Journal Article