Miracle-dz/UniFAR-FTUs huggingface dataset:
Report from the extended HLA‐DPA1 ~ promoter ~ HLA‐DPB1 haplotype of the 18th international HLA and immunogenetics workshop

The primary goal of the HLA‐DPA1 ~ promoter ~ HLA‐DPB1 haplotype component of the 18th IHIWS was to characterise the extended haplotypes within the HLA‐DP region and survey the extent of genetic diversity in this region across human populations. In this report, we analysed single‐nucleotide polymorphisms (SNPs) in 255 subjects from 6 different cohorts. The results from the HLA‐DP haplotype component have validated findings from the initial pilot study. SNPs in this region were inherited in strong linkage, particularly HLA‐DPA1, SNP‐linked promoter haplotypes and motifs in exon 2 of HLA‐DPB1. We reported 17 SNP‐linked haplotypes in the promoter region. Together with HLA‐DPA1 and HLA‐DPB1 alleles, they formed 74 distinct extended HLA‐DP haplotypes in 438 sequences. We also observed the presence of region‐specific alleles and promoter haplotypes. Our approach involved phasing extended SNPs including promoter SNPs, HLA‐DPA1 and HLA‐DPB1 alleles, in a 22 kb region, GRCh38/hg38 (chr6:33,064,111‐33,086,679), followed by clustering of these SNPs as one extended haplotype. This hierarchical clustering revealed four major clades, suggesting that haplotypes within each clade may have diverged from a common ancestral haplotype and undergone similar evolutionary processes. The correlation between HLA‐DPA1 and the promoter region raises questions about the role of HLA‐DPA1 antigen in the heterodimer. This finding requires validation on a larger sample size specifically designed for anthropological analysis. Nevertheless, the results from this study highlight the clinical potential of selecting better‐matched donors for patients awaiting haematopoietic stem cell transplants from genetically overlapping groups that share common ancestral haplotypes.
Some C ∗ -Algebras with a Single Generator

This paper grew out of the following question: If X is a compact subset of Cn, is C(X) ? Mn (the C*-algebra of n x n matrices with entries from C(X)) singly generated? It is shown that the answer is affirmative; in fact, A 0 Mn is singly generated whenever A is a C*-algebra with identity, generated by a set of n(n + 1)/2 elements of which n(n 1)/2 are selfadjoint. If A is a separable C*-algebra with identity, then A 0 K and A 00 U are shown to be singly generated, where K is the algebra of compact operators in a separable, infinitedimensional Hilbert space, and U is any UHF algebra. In all these cases, the generator is explicitly constructed.
Finite Mixture Distributions

1 General introduction. - 1.1 Introduction. - 1.2 Some applications of finite mixture distributions. - 1.3 Definition. - 1.4 Estimation methods. - 1.4.1 Maximum likelihood. - 1.4.2 Bayesian estimation. - 1.4.3 Inversion and error minimization. - 1.4.4 Other methods. - 1.4.5 Estimating the number of components. - 1.5 Summary. - 2 Mixtures of normal distributions. - 2.1 Introduction. - 2.2 Some descriptive properties of mixtures of normal distributions. - 2.3 Estimating the parameters in normal mixture distributions. - 2.3.1 Method of moments estimation. - 2.3.2 Maximum likelihood estimation. - 2.3.3 Maximum likelihood estimates for grouped data. - 2.3.4 Obtaining initial parameter values for the maximum likelihood estimation algorithms. - 2.3.5 Graphical estimation techniques. - 2.3.6 Other estimation methods. - 2.4 Summary. - 3 Mixtures of exponential and other continuous distributions. - 3.1 Exponential mixtures. - 3.2 Estimating exponential mixture parameters. - 3.2.1 The method of moments and generalizations. - 3.2.2 Maximum likelihood. - 3.3 Properties of exponential mixtures. - 3.4 Other continuous distributions. - 3.4.1 Non-central chi-squared distribution. - 3.4.2 Non-central F distribution. - 3.4.3 Beta distributions. - 3.4.4 Doubly non-central t distribution. - 3.4.5 Planck's distribution. - 3.4.6 Logistic. - 3.4. 7 Laplace. - 3.4. 8 Weibull. - 3.4. 9 Gamma. - 3.5 Mixtures of different component types. - 3.6 Summary. - 4 Mixtures of discrete distributions. - 4.1 Introduction. - 4.2 Mixtures of binomial distributions. - 4.2.1 Moment estimators for binomial mixtures. - 4.2.2 Maximum likelihood estimators for mixtures of binomial distributions. - 4.2.3 Other estimation methods for mixtures of binomial distributions. - 4.3 Mixtures of Poisson distributions. - 4.3.1 Moment estimators for mixtures of Poisson distributions. - 4.3.2 Maximum likelihood estimators for a Poisson mixture. - 4.4 Mixtures of Poisson and binomial distributions. - 4.5 Mixtures of other discrete distributions. - 4.6 Summary. - 5 Miscellaneous topics. - 5.1 Introduction. - 5.2 Determining the number of components in a mixture. - 5.2.1 Informal diagnostic tools for the detection of mixtures. - 5.2.2 Testing hypotheses on the number of components in a mixture. - 5.3 Probability density function estimation. - 5.4 Miscellaneous problems. - 5.5 Summary. - References.
Lipschitz dependence of viscosity solutions of Hamilton-Jacobi equations with respect to the parameter

Let $M$ be a closed and smooth manifold and $H_\varepsilon:T^*M\to\mathbf{R}^1$ be a family of Tonelli Hamiltonians for $\varepsilon\geq0$ small. For each $\varphi\in C(M,\mathbf{R}^1)$, $T^\varepsilon_t\varphi(x)$ is the unique viscosity solution of the Cauchy problem \begin{align*} \left\{ \begin{array}{ll} d_tw+H_\varepsilon(x,d_xw)=0, & \ \mathrm{in}\ M\times(0,+\infty),\\ w|_{t=0}=\varphi, & \ \mathrm{on}\ M, \end{array} \right. \end{align*} where $T^\varepsilon_t$ is the Lax-Oleinik operator associated with $H_\varepsilon$. A result of Fathi asserts that the uniform limit, for $t\to+\infty$, of $T^\varepsilon_t\varphi+c_\varepsilon t$ exists and the limit $\bar{\varphi}_\varepsilon$ is a viscosity solution of the stationary Hamilton-Jacobi equation \begin{align*} H_\varepsilon(x,d_xu)=c_\varepsilon, \end{align*} where $c_\varepsilon$ is the unique $k$ for which the equation $H_\varepsilon(x,d_xu)=k$ admits viscosity solutions. In the present paper we discuss the continuous dependence of the viscosity solution $\bar{\varphi}_\varepsilon$ with respect to the parameter $\varepsilon$.
Transcriptomic landscape of endothelial cells: Key tumor microenvironment components indicating variable clinical outcomes in pancreatic ductal adenocarcinoma

Endothelial cells (ECs) present in the tumor microenvironment (TME) exhibit significant diversity that may impact the efficacy of anti‐tumor treatments. Thus, our study sought to elucidate the various clusters of ECs present in pancreatic ductal adenocarcinoma (PDAC) and explore their possible interactions and influence on clinical outcomes. We obtained single‐cell transcriptome data from 24 PDAC tumors and 11 normal pancreases, minimizing any batch effects between samples. Next, we compared the relative abundance of various ECs clusters across distinct sample types. Pseudo‐time analysis was employed to investigate the differentiation origin of ECs. A variety of bioinformatics methods were used to investigate potential communication between ECs and malignant cells, as well as assess metabolic changes, pathway alterations, and immune‐related markers expression within distinct EC clusters. Lastly, we investigated the impact of particular ECs clusters on patient prognosis in bulk transcriptome data. Our study identified seven distinct clusters of ECs, denoted as CA4+ ECs, MMP2+ ECs, SPP1+ ECs, MT1F+ ECs, CCL5+ ECs, RGS5+ ECs, and TYROBP+ ECs. Pseudo‐time analysis suggested that the loss of CA4+ ECs and MT1F+ ECs may promote malignant progression. Cell communication elucidated that MT1F+ ECs exhibited the strongest outgoing interaction strength, whereas RGS5+ ECs displayed the strongest incoming interaction strength. Furthermore, TYROBP+ ECs exhibited greater metabolic activity, and notably, CCL5+ ECs displayed increased expression of immune‐related molecules. Lastly, across cohorts of bulk transcriptome levels, CA4+ ECs, MT1F+ ECs, and RGS5+ ECs consistently demonstrated prognostic indicative effects. PDAC patients exhibit the presence of seven distinct EC clusters, each demonstrating significant metabolic and immunological heterogeneity. Targeted therapeutic approaches directed toward CA4+ ECs and MT1F+ ECs may prove advantageous in addressing challenges associated with PDAC treatment. Additionally, variations in the relative abundance of CA4+ ECs, MT1F+ ECs, and RGS5+ ECs were indicated as predictive of patient prognosis.
Finite-Amplitude Thermal Convection in a Shear Flow with a Curved Vertical Temperature Profile. Part 1. Theory

Cell patterns of the finite-amplitudeBenard-type convection in a shear flow with a curved vertical temperature profile are investigated near the critical state by means of the Landau amplitude equations. The steady solutions are obtained and their stability is discussed in relation to three parameters which represent the deviation of temperature from the linear profile, the magnitude of the shear of the basic flow and the deviation of the Rayleigh number from the critical value for the curved vertical temperature profile, (*R)*. The following results are obtained: (1) The roll solution is unstable only in a narrow range of positive (*R)* when the magnitude of the shear is lesss than a critical value. When its magnitude exceeds the critical value, the solution becomes stable for all positive values of (*R)*. (2) The solution which is reduced to a hexagonal one in the absence of the shear is modified to give a longitudinal one as the magnitude of the shear is increased. The solution becomes unstable when the magnitude of the shear exceeds a critical value.
Robotic assisted radical nephrectomy with Inferior vena cava tumor thrombus

ABSTRACT Purpose: Surgery for renal cell carcinoma (RCC) with an inferior vena cava (IVC) tumor thrombus can be done via a robotic approach. While this approach is thought to minimize blood loss, it may still result in significant losses (1) and current publications indicate that it can require upwards of 3-day hospital stays (1, 2). However, innovative surgical techniques, such as the split and roll, may curtail this. The purpose of this video is to present the case and surgical technique of robotic assisted radical nephrectomy with IVC thrombectomy. Materials and Methods: The patient was a 77-year-old male found to have a right upper pole renal mass on CT urogram. On MRI (Figure 1), a renal mass and level II thrombus was seen. For this case, the Da Vinci Xi Intuitive robotic system was used, with four robotic 8-millimeter (mm) metallic trocars, two 5 mm assistant trocars, and one 12 mm air seal port. The split and roll technique were utilized to access the IVC and lumbar veins. This surgical method uses the adventitia of the IVC as a plane of dissection and safely identifies all branches/tributaries of the IVC to minimize the chance of vascular injury (3). Results: Robotic console time was 150 minutes. The patient had an excellent outcome, with all tumor thrombus removed, less than 50cc of blood loss, and was discharged within 24 hours of the operation. The tumor pathology came back as papillary, high grade, and was stage pT3bN1. Conclusions: The robotic approach with split and roll technique is a great surgical option for urologists to consider in patients with RCC and a level I or II thrombus, which can minimize blood loss and expedite discharge.
Population outcomes, trends and the future of pouch surgery for ulcerative colitis: a 19‐year New South Wales data linkage study

Ileal pouch‐anal anastomosis (IPAA) is considered the gold standard reconstructive option in ulcerative colitis (UC). Recent efforts to improve pouch outcomes have seen a push towards centralisation of surgery. This study aimed to document outcomes following pouch surgery at a population level within New South Wales (NSW), and identify factors associated with, and temporal trends of these outcomes.
Effects of Substance Use and Antisocial Personality on Neuroimaging-Based Machine Learning Prediction of Schizophrenia

Abstract Background and hypothesis Neuroimaging-based machine learning (ML) algorithms have the potential to aid the clinical diagnosis of schizophrenia. However, literature on the effect of prevalent comorbidities such as substance use disorder (SUD) and antisocial personality (ASPD) on these models’ performance has remained unexplored. We investigated whether the presence of SUD or ASPD affects the performance of neuroimaging-based ML models trained to discern patients with schizophrenia (SCH) from controls. Study design We trained an ML model on structural MRI data from public datasets to distinguish between SCH and controls (SCH = 347, controls = 341). We then investigated the model’s performance in two independent samples of individuals undergoing forensic psychiatric examination: sample 1 was used for sensitivity analysis to discern ASPD (N = 52) from SCH (N = 66), and sample 2 was used for specificity analysis to discern ASPD (N = 26) from controls (N = 25). Both samples included individuals with SUD. Study results In sample 1, 94.4% of SCH with comorbid ASPD and SUD were classified as SCH, followed by patients with SCH + SUD (78.8% classified as SCH) and patients with SCH (60.0% classified as SCH). The model failed to discern SCH without comorbidities from ASPD + SUD (AUC = 0.562, 95%CI = 0.400–0.723). In sample 2, the model’s specificity to predict controls was 84.0%. In both samples, about half of the ASPD + SUD were misclassified as SCH. Data-driven functional characterization revealed associations between the classification as SCH and cognition-related brain regions. Conclusion Altogether, ASPD and SUD appear to have effects on ML prediction performance, which potentially results from converging cognition-related brain abnormalities between SCH, ASPD, and SUD.
Sharp threshold for scattering of a generalized Davey-Stewartson system in three dimension

In this paper, we consider the Cauchy problem for the generalized Davey-Stewartson system \begin{eqnarray} &i\partial_t u + \Delta u =-a|u|^{p-1}u+b_1uv_{x_1}, (t,x)\in R \times R^3,\\ &-\Delta v=b_2(|u|^2)_{x_1}, \end{eqnarray} where $a>0,b_1b_2>0$, $\frac{4}{3}+1< p< 5$. We first use a variational approach to give a dichotomy of blow-up and scattering for the solution of mass supercritical equation with the initial data satisfying $J(u_0)<J(R)$, where $J$ stands for the Lagrange functional. The basic strategy is the concentration-compactness arguments from Kenig and Merle [17]. We overcome the main difficulties coming from the lack of scaling invariance and the asymmetrical structure of nonlinearity (in particular, the nonlinearity is non-local). Furthermore, we adapt the standard method from [9] to obtain the blow up criterion.
Changes in cardiac output, rhythm regularity, and symptom severity after electrical cardioversion of atrial fibrillation

Abstract Objectives Symptoms in atrial fibrillation (AF) range from none to disabling. The physiological correlates of AF symptoms are not well characterized. This study investigated the association between physiological parameters and symptom severity before and after electrical cardioversion (EC) of AF. Design We studied 44 patients with persistent AF (age 66.2 ± 7.9 years, 16% females) 4 ± 2 days before and 5 ± 2 days after EC. Physiological parameters included cardiac output (CO; non-invasive inert gas rebreathing), heart rate (HR), RR variability and resting and ambulatory blood pressure (BP). Symptoms and quality of life (QoL) were assessed by the modified European Heart Rhythm Association score (mEHRA), the Atrial Fibrillation Effect on Quality of Life (AFEQT) and the Symptom Checklist for frequency and severity of symptoms (SCL). Results 28 of 44 patients were still in sinus rhythm (SR) at post EC evaluation. Those in SR had a decreased HR (-15.4 ± 13.1 bpm, p < 0.001), and an increased CO (+0.8 ± 0.7 L/min, p < 0.001) as compared to those with recurrent AF. Changes in CO after EC correlated with symptom improvement as scored by AFEQT (r = 0.36; p < 0.05), AFEQT symptoms subscore (r = 0.46; p < 0.01), SCL for frequency (r = 0.62; p < 0.01) and severity (r = 0.33; p < 0.05) of symptoms, and the mEHRA score (r = 0.50; p < 0.01). A decrease in RR variability showed similar correlations with these measures of symptom improvement. Conclusions Improvements in symptoms and quality of life experienced by patients after electrical conversion of atrial fibrillation are correlated with an increase in CO and a decreased RR variability.
Thinking-Spaces for Research- Creation

ion – or at upon least the recognition that more than one kind of abstraction might participate in the facilitation of thinking-space. The first kind of abstraction can be seen in the lines of a square on the floor, the lines of a diagram in a book. The other is the kind of abstraction pertaining to the movement of thought – a non-localisable assemblage of affects,
Biology and management of hemp russet mite (Acari: Eriophyidae)

Hemp is rapidly becoming a crop of global agricultural importance, and one of the more serious pests of this crop is hemp russet mite (HRM) Aculops cannabicola (Acari: Eriophyidae). Significant knowledge gaps presently exist regarding critical aspects of pest biology, quantification of crop damage, and efficacy of pesticides. Here we assessed the role of cannabidiol (CBD) on HRM performance, efficacy of sulfur treatments in field trials, and effect of hot water immersion with and without surfactants in reducing HRM counts on hemp cuttings. We found that HRM fecundity was reduced on a high-CBD cultivar compared with a low-CBD cultivar in detached leaf assays. In contrast, HRM fecundity and survival were not impacted when reared on high-CBD diet in artificial feeding assays. This suggests that cannabinoids other than CBD may aid in reduction of mite populations on the high-CBD cultivar. Sulfur sprays reduced HRM populations by up to 98% with the greatest effects seen in plants receiving dual applications, one during the vegetative period in July and the second at the initiation of flowering in August. Yields of plants treated with sulfur increased by up to 33%, and there was a further increase in cannabinoid production by up to 45% relative to untreated plants. Hot water immersion treatments with and without surfactant solution reduced HRM on infested hemp cuttings, and no phytotoxicity was observed. This study provides novel approaches to mitigating HRM at multiple stages in hemp production.
Alternative Trastuzumab Dosing Schedules Are Associated With Reductions in Health Care Greenhouse Gas Emissions

PURPOSE Cancer care–related greenhouse gas (GHG) emissions harm human health. Many cancer drugs are administered at greater-than-necessary doses, frequencies, and durations. Alternative dosing strategies may enable reductions in cancer care GHG emissions without compromising patient outcomes. MATERIALS AND METHODS We used streamlined life-cycle analysis in a case-control simulation to estimate the relative reductions in GHG emissions that would be expected to result from using each of three alternative dosing strategies of trastuzumab (6-month adjuvant treatment duration, once every 4-week dosing, and both) in human epidermal growth factor receptor 2 (HER2)+ breast cancer. Using primary data and conversion factors from the environmental science literature, we estimated per-patient relative reduction in GHG emissions and, using SEER data, health impacts (in terms of disability-adjusted life-years [DALYs] and excess mortality per kg CO2) on bystanders for each alternative dosing strategy. RESULTS Compared with the trastuzumab dosing strategy commonly used at baseline (12-month duration of adjuvant therapy and once every 3-week dosing in all settings), adoption of both 6-month adjuvant trastuzumab and once every 4-week trastuzumab dosing would reduce GHG emissions by 4.5%, 18.7%, and 14.6% in the neoadjuvant, adjuvant, and metastatic settings, respectively. We estimate that US-based adoption of alternative trastuzumab dosing would reduce annual DALYs and excess lives lost due to environmental impact of US-based trastuzumab therapy for HER2+ breast cancer by 1.5 and 0.9, respectively. CONCLUSION Alternative dosing strategies may materially reduce the population health impacts of cancer care by reducing environmental impact. Regulatory decision making and health technology assessments should consider a treatment's environmental and population health impacts. Clinical trials of alternative dosing strategies are justified on the basis of environmental and population health impacts.
Long-term care facilities' response to the COVID-19 pandemic: An international, cross-sectional survey.

AIMS To (i) assess the adherence of long-term care (LTC) facilities to the COVID-19 prevention and control recommendations, (ii) identify predictors of this adherence and (iii) examine the association between the adherence level and the impact of the pandemic on selected unfavourable conditions. DESIGN Cross-sectional survey. METHODS Managers (n = 212) and staff (n = 2143) of LTC facilities (n = 223) in 13 countries/regions (Brazil, Egypt, England, Hong Kong, Indonesia, Japan, Norway, Portugal, Saudi Arabia, South Korea, Spain, Thailand and Turkey) evaluated the adherence of LTC facilities to COVID-19 prevention and control recommendations and the impact of the pandemic on unfavourable conditions related to staff, residents and residents' families. The characteristics of participants and LTC facilities were also gathered. Data were collected from April to October 2021. The study was reported following the STROBE guidelines. RESULTS The adherence was significantly higher among facilities with more pre-pandemic in-service education on infection control and easier access to information early in the pandemic. Residents' feelings of loneliness and feeling down were the most affected conditions by the pandemic. More psychological support to residents was associated with fewer residents' aggressive behaviours, and more psychological support to staff was associated with less work-life imbalance. CONCLUSIONS Pre-pandemic preparedness significantly shaped LTC facilities' response to the pandemic. Adequate psychological support to residents and staff might help mitigate the negative impacts of infection outbreaks. IMPACT This is the first study to comprehensively examine the adherence of LTC facilities to COVID-19 prevention and control recommendations. The results demonstrated that the adherence level was significantly related to pre-pandemic preparedness and that adequate psychological support to staff and residents was significantly associated with less negative impacts of the pandemic on LTC facilities' staff and residents. The results would help LTC facilities prepare for and respond to future infection outbreaks. PATIENT OR PUBLIC CONTRIBUTION No Patient or Public Contribution.
Applications of CRISPR technology in cellular immunotherapy

CRISPR technology has transformed multiple fields, including cancer and immunology. CRISPR‐based gene editing and screening empowers direct genomic manipulation of immune cells, opening doors to unbiased functional genetic screens. These screens aid in the discovery of novel factors that regulate and reprogram immune responses, offering novel drug targets. The engineering of immune cells using CRISPR has sparked a transformation in the cellular immunotherapy field, resulting in a multitude of ongoing clinical trials. In this review, we discuss the development and applications of CRISPR and related gene editing technologies in immune cells, focusing on functional genomics screening, gene editing‐based cell therapies, as well as future directions in this rapidly advancing field.