Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase II/III study of Circulating tumOr DNA as a predictive BiomaRker in Adjuvant chemotherapy in patients with stage II colon cancer: NRG-GI005 (COBRA).

TPS3622 Background: There are currently no validated predictive biomarkers for stage II resected colon cancer (CC) after adjuvant chemotherapy. However, circulating tumor DNA (ctDNA) that is shed into the bloodstream represents a highly specific and sensitive approach for identifying microscopic or residual tumor cells. For patients (pts) with CC, the detection of ctDNA is associated with persistent disease after resection and may outperform traditional clinical and pathological features as a prognostic factor to assess risk for recurrence. We hypothesize that for pts whose stage II colon cancer has been resected and who have no traditional high-risk features, a positive ctDNA status may identify those who will benefit from adjuvant chemotherapy. Methods: In this prospective phase II/III clinical trial, pts (N = 1,408) with resected stage II CC without traditional high-risk features and whom the evaluating oncologist deems suitable for no adjuvant chemotherapy will be randomized 1:1 into 2 arms: standard-of-care/observation (Arm A), or prospective testing for ctDNA (Arm B). Postoperative blood will be analyzed for ctDNA with the GuardantHealth LUNAR panel, covering CC-relevant mutations and CC-specific methylation profiling. Pts in Arm B with ctDNA detected will be treated with 6 months of adjuvant (FOLFOX) chemotherapy. For all pts in Arm A, ctDNA status will be analyzed retrospectively at the time of endpoint analysis. The primary endpoints are clearance of ctDNA with adjuvant chemotherapy (phase II) and recurrence-free survival (RFS) for “ctDNA-detected” pts treated with or without adjuvant chemotherapy (phase III). Secondary endpoints will include time-to-event outcomes (OS, RFS, TTR) by ctDNA marker status and treatment, prevalence of detectable ctDNA in stage II CC, and rates of compliance with assigned intervention. Archived normal and matched tumor and blood samples will be collected for exploratory correlative research. The trial is actively accruing towards the phase II endpoint in North America. NCT#: 04068103. Support: U10-CA-180868, -180822; UG1CA-189867; GuardantHealth. Clinical trial information: NCT04068103.
Solution method for discrete double obstacle problems based on a power penalty approach

We develop a power penalty approach to a finite-dimensional double obstacle problem. This problem is first approximated by a system of nonlinear equations containing two penalty terms. We show that the solution to this penalized equation converges to that of the original obstacle problem at an exponential rate when the coefficient matrices are \begin{document}$ M $\end{document} -matrices. Numerical examples are presented to confirm the theoretical findings and illustrate the efficiency and effectiveness of the new method.
Benthic macroinvertebrates as bioindicators of environmental quality of Pará River estuary, a wetland of Eastern Amazon

The study characterized and evaluated the use of the benthic macroinvertebrate community as an indicator of impacts in different estuarine environments around the Industrial Port Complex (IPC) of Vila do Conde (Pará State, Amazon region). Fauna of beaches and rivers, in sectors of the estuary under different degrees of environmental impact (high, medium, and low), was compared in different seasonal periods. Macrofauna was composed of typically fresh-water and estuarine groups. Beaches presented sediment with a texture ranging from medium to coarse sand, with a less rich macrofauna ( = 4.5 ± SE 0.3 taxa/sample) and dense ( = 1,838.1 ± 164.8 ind./m2) of organisms when compared to rivers ( = 5.9 ± 0.3 taxa/sample, and 3,248.9 ± 77.0 ind./m2), which were environments more muddy. For both environments, sites in the high-impact sector were less rich ( = 4.7 ± 0.3 taxa/sample) and dense ( = 2,812.9 ± 232.7 ind./m2) when compared to those in the low-impact sector ( = 7.6 ± 0.4 taxa/sample, and 3,314.3 ± 230.1 ind./m2). Richness ( = 6.4 ± 0.3 taxa/sample) and density ( = 3,859.4 ± 190.2 ind./m2) were higher in the rainier season when compared to the less rainy season ( = 4.8 ± 0.3 taxa/sample, and 1,933.0 ± 172.1 ind./m2). However, there were no significant seasonal changes in composition. Results indicated that the structure of the benthic macroinvertebrate community surrounding the IPC responds to the loss of environmental quality, with extreme effects of a drop in abundance and diversity. Taxa that are more tolerant (Namalycastis caetensis, Cirolana sp., Pseudosphaeroma sp., Tubificidae, and Chironomidae) and sensitive (Hydropsychidae and Eteone sp.) to impact conditions were identified and evaluated as potential bioindicators.
A Hierarchical Multicast Key Distribution Protocol

In secure group communication, group keys (GK) are used to ensure the confidentiality of communication. The group key distribution (GKD) is responsible for updating and distributing new group keys when the group membership changes. Most well-known GKD protocols are based on a logical key hierarchy (LKH), where only one group controller (GC) is used. These protocols have various issues, including a single point of failure, meaning that the GC often has a huge workload and can be easily overwhelmed. In this paper, we propose a hierarchical multicast key distribution protocol that supports multi-level controllers to manage a group. Each controller just needs to manage the next-level nodes, and if one fails, the superior controller can replace it with minimal work. The proposed protocol effectively balances the work of controllers, greatly improves the reliability of the group key distribution, and also allows group members to build dynamic conferences without controllers. We provide a security proof of the proposed protocol in a symbolic security model and compare it to other protocols in terms of efficiency, functionality, and security.
Orbit codes from forms on vector spaces over a finite field

In this paper we construct different families of orbit codes in the vector spaces of the symmetric bilinear forms, quadratic forms and Hermitian forms on an \begin{document}$ n $\end{document} -dimensional vector space over the finite field \begin{document}$ {\mathbb F_{q}} $\end{document} . All these codes admit the general linear group \begin{document}$ {{{{\rm{GL}}}}}(n,q) $\end{document} as a transitive automorphism group.
Cellular Immune Response (CD8+CD38+) in Relation to Hepatitis B Virus DNA Level and HBsAg Quantification in Hepatitis B Patients

Introduction: Hepatitis B Virus (HBV) infection is a global public health concern. The immune response in HBV represents a key factor in patient outcome. However, the relationship between viral replication and host immune reactivity remains a matter of investigation. Aim: The aim of our study was to investigate whether the cellular immune response of recently diagnosed and treatment naive chronic hepatitis B(CHB) patients may be influenced by the replicative status of HBV. Towards this aim, the correlation between HBV viral load, HBsAg quantification and peripheral T-cell subpopulations CD8+CD38+. Methods: Proportions and absolute counts of CD8 CD38 T cells were determined using three-color flow cytometry in chronic hepatitis B patients (n=50) and healthy controls (n=35). Chronic hepatitis B patients were regularly followed for 48 weeks, during which period the T cell subsets, serum viral load and HBsAg quantitation were measured every 24 months. Results: There was a high level of CD8+CD38+% during the pretreatment stage (Mean 32.4514, standard deviation (SD) 16.8007) compared to the control group (Mean 19.4628, SD 9.75555), p=0.000. Significant decreases in CD8 count were detected 12 months after treatment initiation of HBV therapy (Mean 1359.44, SD 724.362) compared to the control group (Mean 1944.13, SD 948.931), p=0.001. There is a significant correlation between CD8+CD38+ count and serum HBV DNA. A Positive correlation was found between CD8+CD38+ count and HBsAg quantitation. Conclusion: There was a positive correlation between CD8+CD38+ T cells and HBsAg quantitation. The combined use of CD8+CD38+ T cells, HBsAg quantitation and HBV DNA assessment in patients with CHB may guide the clinicians as they guage the likelihood of treatment response.
Effect of Plant Pattern and Density on Yield and Amino Acid Profile of Tepary Bean (Phaseolus acutifolius) in a Semiarid Area

Background: Tepary bean is recognized as a deal crop for cultivation in arid and semi-arid regions. The spatial distribution of plants is an important farming practice. A study was conducted in tepary bean (Phaseolus acutifolius A. Gray) to investigate the effect of planting pattern and plant density on plant yield and amino acid profile.Methods: The experiment was carried out in a split-split plot design with three replications during 2017 and 2018. The main plot comprised planting pattern at two levels, including one-row plantation (PP1) and two-row plantation (PP2) and sub plot comprised plant density at three levels, including high plant density (HPD:50 plant/m2), moderate plant density (MPD:40 plant/m2) and low plant density (LPD: 30 plant/m2). In both years, plants were harvested at the end of pod filling stage at October. Amino acid profiles were determined using a HPLC system. Result: The results showed that in the first year and under PP2, MPD increased the biological yield by 19% and 16% compared to HPD and LPD, respectively. Increased pod yield was observed at MPD compared to HPD and LPD. In the second year under PP1, MPD improved grain yield by 75% and 65% in comparison to HPD and LPD, respectively. Increased protein and amino acid content were observed at MPD and PP2. The greatest amino acid content was Leu followed by Lys, Arg, Phe, Val, Ile, Thr, Tyr, His, Met, Trp and Cys.
Challenges of 'School’s Out, But Class’s On' to School Education: Practical Exploration of Chinese Schools during the COVID-19 Pandemic

“School’s Out, But Class’s On”, i.e. “suspending classes without stopping learning”, specifically refers to China’s education and teaching activities during the postponement period during the COVID-19 pandemic prevention and control period. This was an emergency measure to prevent and control the pandemic in the field of education in China, and it was also a continuation of school education in this special period. During the pandemic period, how school education should operate has become a topic of social concern. I herein discuss the origin and connotation of the concept of “School’s Out, But Class’s On”, analyze the challenges of “School’s Out, But Class’s On” to school education, and then put forward measures for schools to respond to “School’s Out, But Class’s On” and explain the practical significance of “School’s Out, But Class’s On” for school education.
Compréhension du microclimat urbain lyonnais par l’intégration de prédicteurs complémentaires à différentes échelles dans des modèles de régression

Le changement climatique est un phénomène majeur actuel générant de multiples conséquences. En milieu urbain, il exacerbe celui de l’îlot de chaleur urbain. Ces deux manifestations climatiques engendrent des conséquences sur la santé des habitants et sur la sensation d’inconfort thermique ressenti en milieu urbain. Ainsi, il est nécessaire d’estimer au mieux la température de l’air en tout point d’un territoire, notamment face à la rationalisation actuelle du réseau de stations météorologiques fixes de Météo France. La connaissance spatialisée de la température de l’air est de plus en plus demandée pour alimenter des modèles quantitatifs liés à un large éventail de domaines, tels que l’hydrologie, l’écologie ou les études sur les changements climatiques. Cette étude se propose ainsi de modéliser la température de l’air, mesurée durant 4 campagnes mobiles réalisées durant les mois d’été, entre 2016 et 2019, dans Lyon par temps clair, à l’aide de modèle de régressions à partir de 33 variables explicatives issues de données traditionnellement utilisées, de données issues de la télédétection par une acquisition LiDAR (Light Detection And Ranging) ou satellitaire Landsat 8. Trois types de régression statistique ont été expérimentés, la régression partial least square, la régression linéaire multiple et enfin, une méthode de machine learning, la forêt aléatoire de classification et de régression. Par exemple, pour la journée du 30 août 2016, la régression linéaire multiple a expliqué 89% de la variance pour les journées d’étude, avec un RMSE moyen de seulement 0,23°C. Des variables comme la température de surface, le NDVI ou encore le MNDWI impactent fortement le modèle d’estimation.
Ichthyofauna of the Mata de Itamacaoca, an urban protected area from the upper Munim River basin, Northern Brazilian Cerrado

The Munim River basin is one of the main river drainages of the Hydrological unit Maranhão, but there are few published studies which focus on ichthyological surveys and taxonomic work within this basin. The present study aims to provide a fish species inventory of the Mata da Itamacaoca, one of the few urban protected areas from the upper Munim River basin, comparing the ichthyofauna with other lists by conducted at the upper Munim River basin. A total of 42 collection expeditions were conducted, the sampling was conducted at five collecting sites distributed within the boundaries of Mata de Itamacaoca, upper Munim River basin. Diversity indices were calculated and generalised linear models (GLMs) were employed to assess differences in species richness, diversity and evenness depending on season and location in relation to the reservoir dam wall. In order to visualize fish community differences, non-metric multidimensional scaling (nMDS) and a one-way PERMANOVA was used to understand whether factors of site, season and location to the dam wall had an effect on fish community compositions. A total of six orders, 13 families, and 23 fish species were found, and the order with the highest species richness, considering all reaches, was Characiformes followed by Cichliformes. The most abundant species was Nannostomus beckfordi, while Pimelodella parnahybae and Hoplerythrinus unitaeniatus were the rarer species sampled. There were no alien invasive species collected within the study area. Species richness was significantly higher below the dam wall, but there were no other significant differences in diversity indices with regards to season or location. Fish community composition was significantly different above and below the dam wall and was significantly affected by sampling site. Season did not have an effect on fish community. This study corroborates other studies conducted in the Unidade Hidrológica Maranhão sensu Hubbert and Renno (2006), that the ichthyofaunal composition and taxonomy of species within this region face major data deficits, anthropogenic impacts, this study may be a baseline for comparing similar environments throughout the region.
Fine root contribution to the soil carbon stock of an agroforestry system in a Caatinga-Atlantic Forest transition zone

O objetivo deste trabalho foi avaliar a distribuicao de raizes finas e sua influencia no estoque de carbono orgânico total do solo, em 20 cm de profundidade, em um sistema agroflorestal de Grevillea robusta e Coffea arabica. O estudo foi realizado em um sistema agroflorestal estabelecido ha 15 anos em uma area de transicao dos biomas Caatinga e Mata Atlântica no Brasil. Arvores de Grevillea robusta mais representativas da classe de diâmetro de maior frequencia foram selecionadas e definidas tres distâncias de coleta destas arvores (0, 0,75 e 1,50 m) e duas profundidades do solo (0–10 e 10–20 cm). As raizes presentes nas amostras foram digitalizadas e quantificadas com auxilio de um software. Na menor distância da camada superficial houve predominio de raizes com diâmetro de 0,6 mm, enquanto, em todas as distâncias da camada 10–20 cm, houve dominância de raizes com diâmetro de 0,4 mm. Na distância de 0,75 m, o estoque de carbono das raizes foi superior na profundidade de 0–10 cm (0,60 Mg ha-1). O estoque de carbono orgânico do solo tambem apresentou maior resultado na camada 0-10 cm em relacao a camada 10–20 cm, embora com variacao significativa apenas na distância de 1,5 m. Na camada superficial, ocorreu maior concentracao de raizes finas, provavelmente influenciada por uma maior disponibilidade de agua e nutrientes provenientes dos residuos vegetais. O estoque de carbono do solo nao esta intimamente relacionado com a densidade de raizes e estoque de carbono das raizes. Os dados apresentados neste estudo nao fornecem uma conclusao definitiva.
A Comparative Study of the Power of Parametric and Permutation Tests for a Multidimensional Two-sample Location Problem

Objective: A comparison of multidimensional populations is a very interesting and common statistical problem. It most often involves verifying a hypothesis about the equality of mean vectors in two populations. The classical test for verification of this hypothesis is the Hotelling’s T 2 test. Another solution is to use simulation and randomization methods to test the significance of differences between the studied populations. Permutation tests are to enable statistical inference in situations where it is not possible to use classical parametric tests. These tests are supposed to provide comparable power to parametric tests with a simultaneous reduction of assumptions, e.g. regarding the sample size taken or the distribution of the tested variable in the population. The purpose of this study is a comparative analysis of the parametric test, the (usual) permutation test, and the nonparametric permutation procedure using two-stage ASL determination. Research Design & Methods: The study considered the analysis of multivariate data. The paper presents theoretical considerations and refers to the Monte Carlo simulation. Findings: The article presents a permutational, complex procedure for assessing the overall ASL (achieved significance level) value. The applied nonparametric statistical inference procedure uses combining functions. A simulation study was carried out to determine the size and power of the test under normality. A Monte Carlo simulation made it possible to compare the empirical power of this test with that of Hotelling’s T 2 test. The most powerful test was the permutation test based on a two-stage ASL determination method using the Fisher combining function. Implications/Recommendations: The advantage of the proposed method is that it can be used even when samples are taken from any type of continuous distributions in a population. Contribution: The proposed test can be used in the analysis of multidimensional economic phenomena.
Extreme capillary heterogeneities and in situ fluid compartmentalization due to clusters of deformation bands in sandstones

Abstract Previous work has shown that individual deformation bands act like capillary barriers and influence fluid saturation. More common in nature, however, are clusters of deformation bands that form complex three dimensional geometries. The aim of this study is to analyze the extent and mechanisms of fluid compartmentalization due to clustered bands. Drainage multiphase fluid flow experiments were performed on a Navajo sandstone core sample characterized by diversely oriented clusters of deformation bands, that sub-divide the host rock into several compartments. Medical X-ray CT images were acquired while nitrogen was injected at progressively higher flow rates into a water-saturated core during transient and steady-state conditions. Spatial and temporal analyses of the non-wetting phase plume migration suggest that deformation bands act like capillary barriers and contribute to the development of an extremely tortuous saturation front. Differential pressure behavior across the core is linked to the breakthrough of N2 into the individual compartments, resulting in highly variable N2 saturation throughout the experiment. Migration into downstream compartments occurs via the exceedance of capillary entry pressure in portions of the bands. Simulation models of simplified systems demonstrate that capillary end effects and discontinuities in the deformation bands impact fluid saturation. The experiments and models presented here show that clusters of deformation bands have the potential to strongly compartmentalize a sandstone reservoir. Hence, prior analysis of the geometry of deformation band structures in a reservoir could significantly reduce the risk of overestimating reservoir capacity, and improve predictions of fluid mobility.
Simulation of Highly Nonlinear Electrokinetics Using a Weak

We present a numerical model for simulating highly nonlinear electrokinetic phenomena which happen at high zeta potentials. In this model, the electric double layer is realized by solving a partial differential equation (PDE) on the double-layer-inducing surface. This surface PDE is derived by conserving ionic charge in the double layer. A normal ohmic current and a tangential surface conduction current are both considered in the charge conservation. We also allow for a nonlinear surface capacitance, which relates the surface charge density to the zeta potential of the surface. This model is more advanced than the linear models based on Debye Huckel approximation. The linear model ignores the presence of surface conduction completely and uses a linearized surface capacitance. These simplifications are not valid for situations in which the zeta potential is much higher than the thermal voltage. With our model, we have quantified the impact of surface conduction on the magnitude of induced-charge-electroosmotic slip velocity. We predict that surface conduction significantly reduces the slip velocity and thus needs to be accounted for in all high-voltage electroosmotic simulations.
A univariable and multivariable analysis of time-to-event data based on restricted mean survival time: A combination with traditional survival methods.

Background Hazard ratio is considered as an appropriate effect measure of time-to-event data. However, hazard ratio is only valid when proportional hazards (PH) assumption is met. The use of the restricted mean survival time (RMST) is proposed and recommended without limitation of PH assumption. Method 4405 osteosarcomas were captured from Surveillance, Epidemiology and End Results Program Database. Traditional survival analyses and RMST-based analyses were integrated into a flowchart and applied for univariable and multivariable analyses, using hazard ratio (HR) and difference in RMST (survival time lost or gain, STL or STG) as effect measures. The relationship between difference in RMST and HR were explored when PH assumption was and was not met, respectively. Results In univariable analyses, using difference in RMST calculated by Kaplan-Meier methods as reference, pseudo-value regressions (R2=0.99) and inverse probability of censoring probability (IPCW) regressions with group-specific weights (R2=1.00) provided more consistent estimation on difference in RMST than IPCW with individual weights (R2=0.09). In multivariable analysis, age (HR:1.03, STL: 3.86 months), diagnosis in 1970~1980s (HR:1.39 STL:27.49 months), metastasis (HR:4.47, STL: 202 months), surgery (HR:0.58, SLG:35.55 months) and radiation (HR:1.46, SLT:44.65 months), met PH assumption and were main independent factors for overall survival. In both univariable and multivariable variables, a robust negative logarithmic linear relationship between HRs estimated by Cox regression and differences in RMST by pseudo-value regressions was only observed when PH assumption was hold (Difference in RMST = -109.3✕ln (HR) - 0.83, R² = 0.97, and Difference = -127.7✕ln (HR) – 9.49, R² = 0.93, respectively. ) Conclusion The flowchart will be intuitive and helpful to instruct appropriate use of RMST based and traditional methods. RMST-based methods provided an absolute effect measure to inspect effects of covariates on survival time and promote evidence communication with HR. Difference in RMST should be reported with hazard ratio routinely.