Tag: statistics

IEEE Trans Image Process. 2024 Jan 5;PP. doi: 10.1109/TIP.2023.3348293. Online ahead of print.

ABSTRACT

Recent developments in the field of non-local attention (NLA) have led to a renewed interest in self-similarity-based single image super-resolution (SISR). Researchers usually use the NLA to explore non-local self-similarity (NSS) in SISR and achieve satisfactory reconstruction results. However, a surprising phenomenon that the reconstruction performance of the standard NLA is similar to that of the NLA with randomly selected regions prompted us to revisit NLA. In this paper, we first analyzed the attention map of the standard NLA from different perspectives and discovered that the resulting probability distribution always has full support for every local feature, which implies a statistical waste of assigning values to irrelevant non-local features, especially for SISR which needs to model long-range dependence with a large number of redundant non-local features. Based on these findings, we introduced a concise yet effective soft thresholding operation to obtain high-similarity-pass attention (HSPA), which is beneficial for generating a more compact and interpretable distribution. Furthermore, we derived some key properties of the soft thresholding operation that enable training our HSPA in an end-to-end manner. The HSPA can be integrated into existing deep SISR models as an efficient general building block. In addition, to demonstrate the effectiveness of the HSPA, we constructed a deep high-similarity-pass attention network (HSPAN) by integrating a few HSPAs in a simple backbone. Extensive experimental results demonstrate that HSPAN outperforms state-of-the-art approaches on both quantitative and qualitative evaluations. Our code and a pre-trained model were uploaded to GitHub† for validation.

PMID:38190673 | DOI:10.1109/TIP.2023.3348293

Pediatr Infect Dis J. 2023 Dec 28. doi: 10.1097/INF.0000000000004231. Online ahead of print.

ABSTRACT

BACKGROUND: To determine the epidemiology of rotavirus group A (RVA) infection in symptomatic children, and analyze genotype diversity in association with clinical characteristics, geographical and seasonal changes.

METHODS: The stool samples of symptomatic children 5≥ years old were collected from 5 different hospitals during December 2020 and March 2022. Rotavirus stool antigen test was done and G and P genotypes of the positive samples were determined. Associations of the infection and genotype diversity with demographical and clinical data were assessed by statistical methods.

RESULTS: RVA infection was detected in 32.1% (300/934) of the patients (Ranges between 28.4% and 47.4%). An inverse association with age was detected, where the highest frequency was measured in children ≤12 months of age (175/482, 36.3%). The infection was more frequent during winter (124/284, 43.7%) and spring (64/187, 34.2%). Children who were exclusively fed with breast milk showed a lower rate of infection (72/251, 28.6%). Among the 46 characterized genotypes (17 single- and 29 mixed-genotype infections), G1P[8] and G9P[4] were more frequently detected in children <36 (67/234, 28.63%) and 36-60 (7/24, 29.16%) months of age children, respectively. A seasonal diversity in the circulating genotypes was detected in different cities. Children with G1P[8], G1P[6], and mixed-genotype infection experienced a shorter duration of hospitalization, and a higher frequency of nausea and severe diarrhea, respectively.

CONCLUSIONS: In this study high frequency of RVA infection was detected in symptomatic children in Iran. Moreover, genotype diversity according to geographic area, seasons, age groups, and clinical features of disease was detected.

PMID:38190647 | DOI:10.1097/INF.0000000000004231

Pediatr Infect Dis J. 2023 Dec 28. doi: 10.1097/INF.0000000000004238. Online ahead of print.

ABSTRACT

BACKGROUND: Cytomegalovirus (CMV) infection following allogeneic hematopoietic cell transplantation has considerable morbidity and mortality, and foscarnet is a treatment option that requires renal dose adjustment. Serum creatinine (SCr)-based estimated glomerular filtration rate (eGFR) equations are used to estimate renal function for patients receiving foscarnet, but cystatin C (cysC) has been shown as a possible alternative. Data examining cysC-based eGFR in this population is sparse. Our primary objective was to evaluate outcomes of patients treated with foscarnet dosed utilizing cysC-based eGFR versus SCr-based eGFR.

METHODS: We analyzed patients on the transplantation and cellular therapies service at Memorial Sloan Kettering Kids from January 2011 to September 2021 who received allogeneic hematopoietic cell transplantation and ≥14 days of foscarnet for CMV infection. Patients with cysC-based eGFR were compared to a historical cohort of patients who only had SCr-based eGFR. Outcomes included time to CMV clearance, death or change in anti-CMV therapy. Cumulative incidence curves and cause-specific hazards model were used for analysis.

RESULTS: In 61 analyzed patients, no differences were found between the cohorts in cumulative incidence of change in anti-CMV therapy (P = 0.17) or death (P = 0.69). After adjustment for multiple confounders, patients in the SCr cohort seemed to have a higher chance of CMV clearance compared with the cysC cohort, but the difference was not statistically significant (hazard ratio = 2.42, P = 0.089). Patients who received corticosteroids appeared to have lower incidence of CMV clearance (P = 0.056).

CONCLUSIONS: We did not find differences in outcomes when dosing foscarnet using cysC versus SCr for treatment of CMV infection.

PMID:38190640 | DOI:10.1097/INF.0000000000004238

Blood Adv. 2024 Jan 8:bloodadvances.2023012248. doi: 10.1182/bloodadvances.2023012248. Online ahead of print.

NO ABSTRACT

PMID:38190628 | DOI:10.1182/bloodadvances.2023012248

JCO Oncol Pract. 2024 Jan 8:OP2300126. doi: 10.1200/OP.23.00126. Online ahead of print.

ABSTRACT

PURPOSE: National Cancer Institute (NCI) and nonprofit organization (NPO) funding is critical for research and advocacy but may not be equitable across cancers.

METHODS: This study evaluated funding from the NCI and NPOs supporting lung, breast, colorectal, pancreatic, hepatobiliary, prostate, ovarian, cervical and endometrial cancers, leukemia, lymphoma, and melanoma from 2015 to 2018. The primary objectives were to assess for funding disparities across different cancers compared with their incidence and mortality and across racial groups. We also determined if underfunding correlates with fewer clinical trials. Correlations between funding for each cancer and its incidence, mortality, and number of clinical trials were analyzed using descriptive statistics and Pearson correlation coefficients (CCs).

RESULTS: Diseases with the largest combined NCI and NPO funding were breast cancer ($3.75 billion in US dollars [USD]) and leukemia ($1.99 billion USD). Those with the least funding were endometrial ($94 million USD), cervical ($292 million USD), and hepatobiliary cancers ($348 million USD). Disease-specific funding correlated well with incidence but correlated poorly with mortality (Pearson CCs, 0.74; P = .006 and .30, P = .346, respectively). Breast cancer, leukemia, and lymphoma were well-funded while colorectal, lung, hepatobiliary and uterine cancers were underfunded. Higher incidence among Black patients correlated with underfunding. The amount of funding for a particular cancer correlated strongly with the number of clinical trials for that disease (Pearson CC, 0.91; P < .0001).

CONCLUSION: Many cancers with high incidence and mortality rates are underfunded. Cancers that affect Black patients at higher rates are also underfunded. Underfunding strongly correlates with fewer clinical trials, which could impede future advances in underfunded cancers.

PMID:38190584 | DOI:10.1200/OP.23.00126

JCO Precis Oncol. 2024 Jan;8:e2300317. doi: 10.1200/PO.23.00317.

ABSTRACT

Advances in genomics have enabled anticancer therapies to be tailored to target specific genomic alterations. Single-arm trials (SATs), including those incorporated within umbrella, basket, and platform trials, are widely adopted when it is not feasible to conduct randomized controlled trials in rare biomarker-defined subpopulations. External controls (ECs), defined as control arm data derived outside the clinical trial, have gained renewed interest as a strategy to supplement evidence generated from SATs to allow comparative analysis. There are increasing examples demonstrating the application of EC in precision oncology trials. The prospective application of EC in conducting comparative studies is associated with distinct methodological challenges, the specific considerations for EC use in biomarker-defined subpopulations have not been adequately discussed, and a formal framework is yet to be established. In this review, we present a framework for conducting a prospective comparative analysis using EC. Key steps are (1) defining the purpose of using EC to address the study question, (2) determining if the external data are fit for purpose, (3) developing a transparent study protocol and a statistical analysis plan, and (iv) interpreting results and drawing conclusions on the basis of a prespecified hypothesis. We specify the considerations required for the biomarker-defined subpopulations, which include (1) specifying the comparator and biomarker status of the comparator group, (2) defining lines of treatment, (3) assessment of the biomarker testing panels used, and (4) assessment of cohort stratification in tumor-agnostic studies. We further discuss novel clinical trial designs and statistical techniques leveraging EC to propose future directions to advance evidence generation and facilitate drug development in precision oncology.

PMID:38190581 | DOI:10.1200/PO.23.00317

J Refract Surg. 2024 Jan;40(1):e20-e29. doi: 10.3928/1081597X-20231212-02. Epub 2024 Jan 1.

ABSTRACT

PURPOSE: To evaluate the efficacy of paired opposite clear corneal incisions (OCCIs) in Implantable Collamer Lens (ICL; STAAR Surgical) implantation surgery for correcting preexisting low-to-moderate astigmatism and observe their influence on corneal aberration.

METHODS: This prospective controlled randomized study included 123 eyes: 73 eyes in the ICL surgery group (control group) and 50 eyes in the ICL combined with OCCI group (OCCI group). All patients had corneal astigmatism between 0.50 and 3.00 D. Parameters considered included uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), refraction, keratometry, slit-lamp biomicroscopy, indirect ophthalmoscopy, corneal topography, and higher order aberrations (HOAs). The Alpins method was used to analyze the correction of astigmatism. The follow-up period lasted for 12 months.

RESULTS: Both groups showed a statistically significant improvement in mean UDVA and CDVA after surgery. At 1 and 12 months, the OCCI group had statistically better UDVA than the control group (P = .021 and .01). The OCCI group showed a significant reduction in mean refractive astigmatism from -0.835 ± 0.274 to -0.535 ± 0.353 and -0.450 ± 0.346 D postoperatively (P < .05) after 1 and 12 months. No significant change was observed in the control group (P > .05). The average magnitude of surgically induced astigmatism (SIA) was 0.911 ± 0.442 and 0.811 ± 0.397 D at 1 and 12 months postoperatively, respectively, in the OCCI group, which was slightly lower than the target induced astigmatism. The difference in SIA between the OCCI and control groups was significant by the end of 1 and 12 months postoperatively (P < .0001). The mean correction index was below 1, suggesting an undercorrection effect caused by clear corneal incisions in the opposite direction. HOAs increased in both the control and OCCI groups after surgery (t = 5.668, P < .0001, t = 3.773, P = .0003, respectively), with oblique trefoil only significantly increasing in the OCCI group.

CONCLUSIONS: This study demonstrated that OCCIs represent a secure, efficient, reliable, and long-term technique for reducing preexisting low-to-moderate corneal astigmatism during ICL surgery. However, OCCIs did not show any advantageous impact in terms of wavefront aberrations when compared to the traditional single-incision method. The presence of oblique trefoil may be the main contributor to the alteration of HOAs during OCCI surgery. [J Refract Surg. 2024;40(1):e20-e29.].

PMID:38190562 | DOI:10.3928/1081597X-20231212-02

J Refract Surg. 2024 Jan;40(1):e1-e9. doi: 10.3928/1081597X-20231204-02. Epub 2024 Jan 1.

ABSTRACT

PURPOSE: To determine the visual outcomes and safety 12 months after implantation of the Presbia Flexivue Microlens refractive corneal inlay.

METHODS: In this prospective, non-randomized trial, 22 patients with a mean age of 52.54 ± 2.86 years were implanted with the Flexivue Microlens refractive corneal inlay in the non-dominant eye at the Department of Ophthalmology, Goethe University, Frankfurt, Germany. Corrected near, intermediate, and distance (CNVA, CIVA, and CDVA) visual acuity and uncorrected near, intermediate, and distance (UNVA, UIVA, and UDVA) visual acuity, manifest refraction, subjective quality of vision, endothelial cell count, and contrast sensitivity were measured 1 day, 1 week, and 1, 3, 6, and 12 months postoperatively.

RESULTS: For binocular CDVA, no patient lost two or more lines and 30% lost only one line at the 12-month visit. In the eye that had surgery, 85% of the patients lost two or more lines of UDVA, which was statistically significant. Sixty-five percent of the patients gained one or more lines in binocular UIVA, and 80% achieved 20/40 or better in DCIVA. UNVA showed a statistically significant improvement, with 90% of the patients achieving 20/40 or better 12 months after implantation. A total of 85% gained two or more lines in binocular UNVA.

CONCLUSIONS: This refractive corneal inlay showed an improvement in binocular UNVA, UIVA, CNVA, and CIVA, whereas binocular CDVA and UDVA were not statistically affected. [J Refract Surg. 2024;40(1):e1-e9.].

PMID:38190559 | DOI:10.3928/1081597X-20231204-02

Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2309825120. doi: 10.1073/pnas.2309825120. Epub 2024 Jan 8.

ABSTRACT

The impact of sexual selection on the evolution of birds has been widely acknowledged. Although sexual selection has been hypothesized as a driving force in the occurrences of numerous morphological features across theropod evolution, this hypothesis has yet to be comprehensively tested due to challenges in identifying the sex of fossils and by the limited sample size. Confuciusornis sanctus is arguably the best-known early avialan and is represented by thousands of well-preserved specimens from the Early Cretaceous Jehol lagerstätte, which provides us with a chance to decipher the strength of sexual selection on extinct vertebrates. Herein, we present a morphometric study of C. sanctus based on the largest sample size of this taxon collected up to now. Our results indicate that the characteristic elongated paired rectrices is a sexually dimorphic trait and statistically robust inferences of the sexual dimorphism in size, shape, and allometry that have been established, providing the earliest known sexual dimorphism in avian evolution. Our findings suggest that sexual selection, in conjunction with natural selection, does act upon body size and limb length ratio in early birds, thereby promoting a deeper understanding of the role of sexual selection in large-scale phylogenetic evolution.

PMID:38190528 | DOI:10.1073/pnas.2309825120

Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2315857121. doi: 10.1073/pnas.2315857121. Epub 2024 Jan 8.

ABSTRACT

Epstein-Barr virus (EBV) infection has long been associated with multiple sclerosis (MS), but the role of EBV in the pathogenesis of MS is not clear. Our hypothesis is that a major fraction of the expanded clones of T lymphocytes in the cerebrospinal fluid (CSF) are specific for autologous EBV-infected B cells. We obtained blood and CSF samples from eight relapsing-remitting patients in the process of diagnosis. We stimulated cells from the blood with autologous EBV-infected lymphoblastoid cell lines (LCL), EBV, varicella zoster virus, influenza, and candida and sorted the responding cells with flow cytometry after 6 d. We sequenced the RNA for T cell receptors (TCR) from CSF, unselected blood cells, and the antigen-specific cells. We used the TCR Vβ CDR3 sequences from the antigen-specific cells to assign antigen specificity to the sequences from the CSF and blood. LCL-specific cells comprised 13.0 ± 4.3% (mean ± SD) of the total reads present in CSF and 13.3 ± 7.5% of the reads present in blood. The next most abundant antigen specificity was flu, which was 4.7 ± 1.7% of the reads in the CSF and 9.3 ± 6.6% in the blood. The prominence of LCL-specific reads was even more marked in the top 1% most abundant CSF clones with statistically significant 47% mean overlap with LCL. We conclude that LCL-specific sequences form a major portion of the TCR repertoire in both CSF and blood and that expanded clones specific for LCL are present in MS CSF. This has important implications for the pathogenesis of MS.

PMID:38190525 | DOI:10.1073/pnas.2315857121