syedzayyan/paper_mill_benchmark huggingface dataset:
Outcomes of patients with small and node-negative HER2-positive early breast cancer treated with adjuvant chemotherapy and anti-HER2 therapy-a sub-analysis of the ALTTO study.

Patients with small node-negative her2-positive breast cancer are commonly treated with paclitaxel and 1 year of adjuvant trastuzumab.We performed a sub-analysis of the altto trial to explore the long-term outcomes of patients with small node-negative tumours.Methods the altto trial randomised 8381 patients with early her2-positive bc treated with adjuvant chemotherapy (anthracycline/taxane- or taxane/carboplatin-based), to trastuzumab (t), lapatinib (l), their sequence (t → l) or their combination (l + t).Patients with tumours ≤3 cm and node-negative were included in this sub-analysis.Results a total of 2821 patients were analysed (median follow-up of 7 years).The median age was 52 years, and most patients had tumours ≤2 cm (64.3%).The 7-year disease-free survival (dfs) was 88.1% (95% ci: 86.7-89.3%).Dfs was similar for arms t, t + l and t⟶l and significantly lower for arm l (stratified log-rank p = 0.031).The 7-year overall survival rate was 95.9% (95% ci: [95.0-96.6%) and the 7-year time-to-distant recurrence was 93.4% (95% ci: 92.3-94.4%).Conclusion with most patients treated with anthracycline-based regimens, altto shows that patients with small tumours treated with trastuzumab and concomitant chemotherapy have excellent long-term outcomes, similar to those of the apt trial.Trial registration clinicaltrials.gov identifier nct00490139.

Journal: British journal of cancer (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Synergistically segmenting choroidal layer and vessel using deep learning for choroid structure analysis.

The choroid is the most vascularized structure in the human eye, whose layer structure and vessel distribution are both critical for the physiology of the retina, and disease pathogenesis of the eye.Although some works have used graph-based methods or convolutional neural networks to separate the choroid layer from the outer-choroid structure, few works focused on further distinguishing the inner-choroid structure, such as the choroid vessel and choroid stroma.approach.inspired by the multi-task learning strategy, in this paper, we propose a segmentation pipeline for choroid analysis which can separate the choroid layer from other structures and segment the choroid vessel synergistically.The key component of this pipeline is the proposed choroidal u-shape network (cunet), which catches both correlation features and specific features between the choroid layer and the choroid vessel.Then pixel-wise classification is generated based on these two types of features to obtain choroid layer segmentation and vessel segmentation.Besides, the training process of cunet is supervised by a proposed adaptive multi-task segmentation loss which adds a regularization term that is used to balance the performance of the two tasks.main results.experiments show the high performance (4% higher dice score) and less computational complexity (18.85 m lower size) of our proposed strategy.significance.the high performance and generalization on both choroid layer and vessel segmentation indicate the clinical potential of our proposed pipeline.

Journal: Physics in medicine and biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Material Hardship in Families With Low Income: Positive Effects of Coparenting on Fathers' and Mothers' Parenting and Children's Prosocial Behaviors.

Families with low income experience high levels of economic insecurity, but less is known about how mothers and fathers in such families successfully navigate coparenting and parenting in the context of material hardship.The current study utilized a risk and resilience framework to investigate the underlying family processes linking material hardship and children's prosocial behaviors in a sample of socioeconomically disadvantaged mother-father families with preschoolers from the building strong families project (n= 452).Coparenting alliance and mothers' and fathers' responsive parenting were examined as mediators.Results of structural equation modeling showed that coparenting alliance was associated with higher levels of both mothers' and fathers' responsive parenting.Subsequently, both parents' responsive parenting were associated with higher levels of children's prosocial behaviors.Material hardship was not associated with coparenting alliance and either parent's responsive parenting.Tests of indirect effects confirmed that the effects of coparenting alliance on children's prosocial behaviors were mediated through both mothers' and fathers' responsive parenting.Overall, these results suggest that when mothers and fathers have a strong coparenting alliance, they are likely to withstand the negative effects of material hardship and thus engage in positive parenting behaviors that benefit their children's prosocial development.Family strengthening interventions, including responsible fatherhood programs, would do well to integrate a strong focus on enhancing a positive coparenting alliance between mothers and fathers.

Journal: Frontiers in psychology (2021)
Publication types: Journal Article
Preliminary Clinical Trial of Biomarkers to Predict Response to Sublingual Immunotherapy for Japanese Cedar Pollinosis.

As part of the planning for a future multicenter study, this preliminary clinical trial used serum samples from patients to identify biomarkers for predicting the therapeutic effects of sublingual immunotherapy (slit) for japanese cedar pollinosis (jcp).Methods this prospective study included patients undergoing slit for jcp at our hospital.All enrolled patients (n = 17) started slit between june and november of 2015.With informed consent from the patients, blood samples were obtained in january, march, and june of 2016, and patients completed the japan rhino-conjunctivitis quality of life questionnaire (jrqlq).On the basis of the jrqlq results, the 6 patients with the best outcomes were included in the high-response group (hrg), and the 5 patients with the worst outcomes were included in the poor-response group (prg).We then compared serum data between the two groups, to identify useful biomarkers.Results il-12p70 and vegf levels tended to be higher in the hrg than in the prg in january, march, and june (0.10 > p > 0.05).In addition, the june il-17 level was significantly higher (p < 0.05) in the hrg than in the prg.Conclusions il-12p70 and vegf may be useful biomarkers for predicting the effects of slit.In addition, although il-17 does not appear to be useful as a biomarker for evaluating treatment response at the start of slit, it may be useful as a biomarker after the beginning phase of slit.

Journal: Journal of Nippon Medical School = Nippon Ika Daigaku zasshi (2020)
Publication types: Journal Article
New Th17-specific therapeutic strategies for HIV remission.

Of review this review highlights current knowledge on the dichotomous role played by t helper 17 cells (th17)-polarized cd4 t cells in maintaining mucosal immunity homeostasis versus fueling hiv/simian immunodeficiency virus (siv) replication/persistence during antiretroviral therapy (art), with a focus on molecular mechanisms underlying these processes.Recent finding th17 cells bridge innate and adaptive immunity against pathogens at mucosal barrier surfaces.Th17 cells are located at portal sites of hiv/siv entry, express a unique transcriptional/metabolic status compatible with viral replication, and represent the first targets of infection.The paucity of th17 cells during hiv/siv infection is caused by infection itself, but also by an altered th17 differentiation, survival, and trafficking into mucosal sites.This causes major alterations of mucosal barrier integrity, microbial translocation, and disease progression.Unless initiated during the early acute infection phases, art fails to restore the frequency/functionality of mucosal th17 cells.A fraction of th17 cells is long-lived and carry hiv reservoir during art.Recent studies identified th17-specific host factors controlling hiv transcription, a step untargeted by current art.Summary the identification of molecular mechanisms contributing to hiv replication/persistence in mucosal th17 cells paves the way toward the design of new th17-specific therapeutic strategies aimed at improving mucosal immunity in hiv-infected individuals.

Journal: Current opinion in HIV and AIDS (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
A Germanium Catalyst Accelerates the Photoredox α-C(sp3)-H Alkylation of Primary Amines.

Site-selective c(sp3)-h functionalizations using photoredox catalysis (pc) and hydrogen atom transfer (hat) catalysis have received increasing attention.Here, we report a ph2ge cl2cocatalyst that greatly improves the yield of α-c(sp3)-h alkylation of primary amines catalyzed by a pc-hat hybrid system.The α-position of the amino group selectively reacted even when weaker c-h bonds existed in the substrates.This finding may help the design of a novel site-selective hybrid catalysis.

Journal: Organic letters (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Detecting Bacterial-Human Lateral Gene Transfer in Chronic Lymphocytic Leukemia.

Chronic lymphocytic leukemia (cll) is a very common and mostly incurable b-cell malignancy.Recent studies revealed high interpatient mutational heterogeneity and worsened therapy response and survival of patients with complex genomic aberrations.In line with this, a better understanding of the underlying mechanisms of specific genetic aberrations would reveal new prognostic factors and possible therapeutic targets.It is known that chromosomal rearrangements including dna insertions often play a role during carcinogenesis.Recently it was reported that bacteria (microbiome)-human lateral gene transfer occurs in somatic cells and is enriched in cancer samples.To further investigate this mechanism in cll, we analyzed paired-end rna sequencing data of 45 cll patients and 9 healthy donors, in which we particularly searched for bacterial dna integrations into the human somatic genome.Applying the burrows-wheeler aligner (bwa) first on a human genome and then on bacterial genome references, we differentiated between sequencing reads mapping to the human genome, to the microbiome or to bacterial integrations into the human genome.Our results indicate that cll samples featured bacterial dna integrations more frequently (approx.Two-fold) compared to normal samples, which corroborates the latest findings in other cancer entities.Moreover, we determined common integration sites and recurrent integrated bacterial transcripts.Finally, we investigated the contribution of bacterial integrations to oncogenesis and disease progression.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Hepatosplenic Candidiasis in Patients With Hematological Malignancies: A 13-Year Retrospective Cohort Study.

Hepatosplenic candidiasis (hsc) used to be reported in patients with acute myeloid leukemia (aml) without antifungal prophylaxis.The aim was to describe the clinical features and outcomes of hsc over the last 13 years in a single french hematology center.Methods all patients diagnosed with hsc between 2008 and 2020 were included in a single-center retrospective cohort study.Data were collected from patient charts, and hsc was classified according to the 2020 european organisation for research and treatment of cancer/mycoses study group definitions.Results sixty patients were included, with 18.3% proven, 3.3% probable, and 78.3% possible hsc according to the 2020 european organization for research and treatment of cancer mycoses study group classification.Among them, 19 patients were treated for acute myeloid leukemia (aml), 21 for lymphomas, and 14 for acute lymphoblastic leukemia.Hsc occurred in 13 patients after autologous stem cell transplantation for lymphoma.At hsc diagnosis, 13 patients were receiving antifungal prophylaxis.candidacolonization was present in 84.2%, with prior candidemia in 36.7% of cases.Β-d-glucans was positive in 55.8%, and 45.8% of tissue biopsies were contributive.First-line antifungal therapy was azoles in 61.7%, and steroids were associated in 45% of cases.At 3 months of follow-up, partial response to antifungal therapy was 94.2%.At last follow-up (mean, 22.6 months), 41 patients (68.3%) presented a complete hematological remission and 22 patients were deceased, none because of hsc.Conclusions the epidemiology of hsc has changed in the last decade, with fewer cases occurring in the aml setting.A better identification of patients at risk could lead to specific prophylaxis and improved diagnosis.

Journal: Open forum infectious diseases (2022)
Publication types: Journal Article
"Doulas shouldn't be considered visitors, we should be considered a part of [the] team": doula care in Georgia, USA during the COVID-19 pandemic.

Doula support improves maternal-child health outcomes.However, during the covid-19 pandemic, hospitals restricted the number of support people allowed during childbirth.An academic-community research team conducted 17 in-depth interviews and structured surveys with doulas in metro-atlanta, georgia, usa from november 2020 to january 2021.Surveys were analysed for descriptive statistics in stata v.14, and interviews were analysed in dedoose using a codebook and memo-ing for thematic analysis.All 17 doulas reported covid-19 changed their practices: most were unable to accompany clients to delivery (14), started using personal protective equipment (13), used virtual services (12), and had to limit the number of in-person prenatal/postpartum visits (11).Several attended more home births (6) because birthing people were afraid to have their babies in the hospital.Some stopped seeing clients altogether due to safety concerns (2).Many lost clientele who could no longer afford doula services, and some offeredpro bonoservices.Most doulas pointed to restrictive hospital policies that excluded doulas and disallowed virtual support as they felt doulas should be considered a part of the team and clients should not be forced to decide between having their doula or their partner in the room.Covid-19 has severely impacted access to and provision of doula care, mostly due to economic hardship for clients and restrictive hospital policies.At the same time, doulas and their clients have been resourceful - using virtual technology, innovative payment models, and home births.

Journal: Sexual and reproductive health matters (2022)
Publication types: Journal Article
Comparison of the prognosis of primary vs. progressive muscle invasive bladder cancer after radical cystectomy: Results from a large multicenter study.

To assess whether progressive and primary muscle invasive bladder cancer (mibc) have different prognosis after radical cystectomy or not.To date only a few data are available on this topic with conflicting results.Further studies on large cohort are needed to clarify these outcomes that may influence bladder cancer management for these patients.Material and methods a multicentre retrospective study was conducted on patient treated for mibc at 5 centres between 2005 and 2015 by radical cystectomy.Patients' outcomes were compared between patients with primary mibc vs.Progressive mibc subsequent to a history of non-muscle invasive bladder cancer (nmibc).Results a total of 1197 patients were included.Median (iq) age was 65 (58-72) years and median follow-up was 65 months.Baseline characteristics were similar between the groups as well as the tumour p t stage, n status and positive surgical margins.Patients with progressive mibc had worse overall survival (os) (hazard ratio [hr] 1.36, [95%ci 1.10-1.76]; p = 0.004), cancer specific survival (css) (hr 1.41 [1.13-1.78]; p = 0.002), and recurrence-free survival (rfs) (hr 1.21 [1.01-1.49]; p = 0.05).Pathological stage ≥p t3, positive surgical margins, and positive lymph nodes status (p n+) were also found as predictors of os, css, and rfs.Conclusions our results suggest that patient having a progressive bc have a worse prognosis in terms of os, pfs, and css than patient with primary disease.These 2 groups may require different management and patients with high risk nmibc should be assessed properly to avoid progression and be offered early cystectomy.

Journal: Urologic oncology (2021)
Publication types: Comparative Study;Journal Article;Multicenter Study
Relationship between hypertension and non-obstructive coronary artery disease in chronic coronary syndrome (the NORIC registry).

The burden of non-obstructive coronary artery disease (cad) in the society is high, and there is currently limited evidence-based recommendation for risk stratification and treatment.Previous studies have demonstrated an association between increasing extent of non-obstructive cad and cardiovascular events.Whether hypertension, a modifiable cardiovascular risk factor, is associated with extensive non-obstructive cad in patients with symptomatic chronic coronary syndrome (ccs) remains unclear.Methods we included 1138 patients (mean age 62±11 years, 48% women) with symptomatic ccs and non-obstructive cad (1-49% lumen diameter reduction) by coronary computed tomography angiography (ccta) from the norwegian registry for invasive cardiology (noric).The extent of non-obstructive cad was assessed as coronary artery segment involvement score (sis), and extensive non-obstructive cad was adjudicated when sis >4.Hypertension was defined as known hypertension or use of antihypertensive medication.Results hypertension was found in 45% of patients.Hypertensive patients were older, with a higher sis, calcium score, and prevalence of comorbidities and statin therapy compared to the normotensive (all p<0.05).There was no difference in the prevalence of hypertension between sexes.Univariable analysis revealed a significant association between hypertension and non-obstructive cad.In multivariable analysis, hypertension remained associated with extensive non-obstructive cad, independent of sex, age, smoking, diabetes, statin treatment, obesity and calcium score (or 1.85, 95% ci [1.22-2.80], p = 0.004).Conclusion in symptomatic ccs, hypertension was associated with extensive non-obstructive cad by ccta.Whether hypertension may be a new treatment target in symptomatic non-obstructive cad needs to be explored in future studies.Clinical trial registration clinical trials.gov: identifier nct04009421.

Journal: PloS one (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses toCandida albicans.

Tetraspanins are a family of proteins possessing four transmembrane domains that help in lateral organization of plasma membrane proteins.These proteins interact with each other as well as other receptors and signaling proteins, resulting in functional complexes called "tetraspanin microdomains." tetraspanins, including cd82, play an essential role in the pathogenesis of fungal infections.Dectin-1, a receptor for the fungal cell wall carbohydrate β-1,3-glucan, is vital to host defense against fungal infections.The current study identifies a novel association between tetraspanin cd82 and dectin-1 on the plasma membrane of candida albicans-containing phagosomes independent of phagocytic ability.Deletion of cd82 in mice resulted in diminished fungicidal activity, increased c.Albicansviability within macrophages, and decreased cytokine production (tnf-α, il-1β) at both m rna and protein level in macrophages.Additionally, cd82 organized dectin-1 clustering in the phagocytic cup.Deletion of cd82 modulates dectin-1 signaling, resulting in a reduction of src and syk phosphorylation and reactive oxygen species production.Cd82 knockout mice were more susceptible to c.Albicansas compared with wild-type mice.Furthermore, patient c.Albicans-induced cytokine production was influenced by two human cd82 single nucleotide polymorphisms, whereas an additional cd82 single nucleotide polymorphism increased the risk for candidemia independent of cytokine production.Together, these data demonstrate that cd82 organizes the proper assembly of dectin-1 signaling machinery in response to c.Albicans.

Journal: Journal of immunology (Baltimore, Md. : 1950) (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Monitoring healthy and disturbed sleep through smartphone applications: a review of experimental evidence.

Smartphone applications are considered as the prime candidate for the purposes of large-scale, low-cost and long-term sleep monitoring.How reliable and scientifically grounded is smartphone-based assessment of healthy and disturbed sleep remains a key issue in this direction.Here we offer a review of validation studies of sleep applications to the aim of providing some guidance in terms of their reliability to assess sleep in healthy and clinical populations, and stimulating further examination of their potential for clinical use and improved sleep hygiene.Electronic literature review was conducted on pubmed.Eleven validation studies published since 2012 were identified, evaluating smartphone applications' performance compared to standard methods of sleep assessment in healthy and clinical samples.Studies with healthy populations show that most sleep applications meet or exceed accuracy levels of wrist-based actigraphy in sleep-wake cycle discrimination, whereas performance levels drop in individuals with low sleep efficiency (se) and in clinical populations, mirroring actigraphy results.Poor correlation with polysomnography (psg) sleep sub-stages is reported by most accelerometer-based apps.However, multiple parameter-based applications (i.e., early sense, sleep ap) showed good capability in detection of sleep-wake stages and sleep-related breathing disorders (srbd) like obstructive sleep apnea (osa) respectively with values similar to psg.While the reviewed evidence suggests a potential role of smartphone sleep applications in pre-screening of srbd, more experimental studies are warranted to assess their reliability in sleep-wake detection particularly.Apps' utility in post treatment follow-up at home or as an adjunct to the sleep diary in clinical setting is also stressed.

Journal: Sleep & breathing = Schlaf & Atmung (2019)
Publication types: Journal Article;Review