Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Early Physical Therapy on Children of School Age With Hematological Cancer: A Quasi-Randomized Controlled Pilot Study

Purpose: Although physical therapy (PT) positively impacts exercise capacity and health-related quality of life (HRQOL) in children with hematological cancers, the optimal time for intervention is unknown. We compared the effects of PT administered before and after initial cancer treatment on the exercise capacity and HRQOL of children with hematological cancer. Methods: The participants were allocated to early (before initiating treatment) and late PT (after initiating treatment) groups. We evaluated exercise capacity using the 6-min walking distance (6MWD) test and HRQOL using the Pediatric Quality of Life Inventory. Results: Thirteen school children (7-13 years) were included. The early PT cohort had significant improvements in Pediatric Quality of Life Inventory but not 6MWD scores from admission to the completion of initial treatment; however, both scores reduced significantly in the late PT cohort. Conclusions: Early rather than late PT during hospitalization might prevent reduced exercise capacity and improve HRQOL in children with hematological cancers.
B-Spline Modeling of Inertial Measurements for Evaluating Stroke Rehabilitation Effectiveness

Patients who experience upper-limb paralysis after stroke require continual rehabilitation. Rehabilitation must be evaluated for appropriate treatment adjustment; such evaluation can be performed using inertial measurement units (IMUs) instead of standard scales or subjective evaluations. However, IMUs produce large quantities of discretized data, and using these data directly is challenging. In this study, B-splines were used to estimate IMU trajectory data for objective evaluations of hand function and stability by using machine learning classifiers and mathematical indices. IMU trajectory data from a 2018 study on upper-limb rehabilitation were used to validate the proposed method. Features extracted from ${B}$ -spline trajectories could be used to classify individuals in the 2018 study with high accuracy, and the proposed indices revealed differences between these groups. Compared with conventional rehabilitation evaluation methods, the proposed method is more objective and effective.
Decoding movement frequencies and limbs based on steady-state movement-related rhythms from noninvasive EEG

Objective. Decoding different types of movements noninvasively from electroencephalography (EEG) is an essential topic in neural engineering, especially in brain–computer interface. Although the widely used sensorimotor rhythm (SMR) is efficient in limb decoding, it lacks efficacy in decoding movement frequencies. Accumulating evidence supports the notion that the movement frequency is encoded in the steady-state movement-related rhythm (SSMRR). Our study has two primary objectives: firstly, to investigate the spatial–spectral representation of SSMRR in EEG during voluntary movements; secondly, to assess whether movement frequencies and limbs can be effectively decoded based on SSMRR. Approach. To comprehensively examine the representation of SSMRR, we investigated the frequency characteristics and spatial patterns associated with various rhythmic finger movements. Coherence analysis was performed between the sensor or source domain EEG and finger movements recorded by data gloves. A fusion model based on spectral SNR features and filter-bank common spatial pattern features was utilized to decode movement frequencies and limbs. Main results. At the group-level, sensor domain, and source domain coherence maps demonstrated that the accurate movement frequency ( f0 ) and its first harmonic ( f1 ) were encoded in the contralateral motor cortex. For the four-class classification, including two movement frequencies for both hands, the decoding accuracies for externally paced and internally paced movements were 73.14 ± 15.86% and 66.30 ± 17.26% (averaged across ten subjects, chance levels at 31.05% and 30.96%). Notably, the average results of five subjects with the highest decoding accuracies reached 87.21 ± 7.44% and 80.44 ± 7.99%. Significance. Our results verified the EEG representation of SSMRR and proved that the movement frequency and limb could be effectively decoded based on spatial–spectral features extracted from SSMRR. We suggest that SSMRR can serve as a complement to SMR to expand the range of decodable movement types and the approaches of limb decoding.
Surface Shape Perception in Volumetric Stereo Displays

In complex volume visualization applications, understanding the displayed objects and their spatial relationships is challenging for several reasons. One of the most important obstacles is that these objects can be translucent and can overlap spatially, making it difficult to understand their spatial structures. However, in many applications, for example medical visualization, it is crucial to have an accurate understanding of the spatial relationships among objects. The addition of visual cues has the potential to help human perception in these visualization tasks. Descriptive line elements, in particular, have been found to be effective in conveying shape information in surfacebased graphics as they sparsely cover a geometrical surface, consistently following the geometry. We present two approaches to apply such line elements to a volume rendering process and to verify their effectiveness in volume-based graphics. This thesis reviews our progress to date in this area and discusses its effects and limitations. Specifically, it examines the volume renderer implementation that formed the foundation of this research, the design of the pilot study conducted to investigate the effectiveness of this technique, the results obtained. It further discusses improvements designed to address the issues revealed by the statistical analysis. The improved approach is able to handle visualization targets with general shapes, thus making it more appropriate to real visualization applications involving complex objects.
On the role of nucleotides and lipids in the polymerization of the actin homolog MreB from a Gram-positive bacterium

In vivo, bacterial actin MreB assembles into dynamic membrane-associated filamentous structures that exhibit circumferential motion around the cell. Current knowledge of MreB biochemical and polymerization properties in vitro remains limited and is mostly based on MreB proteins from Gram-negative species. In this study, we report the first observation of organized protofilaments by electron microscopy and the first 3D-structure of MreB from a Gram-positive bacterium. We show that Geobacillus stearothermophilus MreB forms straight pairs of protofilaments on lipid surfaces in the presence of ATP or GTP, but not in the presence of ADP, GDP or non-hydrolysable ATP analogs. We demonstrate that membrane anchoring is mediated by two spatially close short hydrophobic sequences while electrostatic interactions also contribute to lipid binding, and show that the population of membrane-bound protofilament doublets is in steady-state. In solution, protofilament doublets were not detected in any condition tested. Instead, MreB formed large sheets regardless of the bound nucleotide, albeit at a higher critical concentration. Altogether, our results indicate that both lipids and ATP are facilitators of MreB polymerization, and are consistent with a dual effect of ATP hydrolysis, in promoting both membrane binding and filaments assembly/disassembly.
Genomic medicine in clinical practice: national genomic medicine program in Japan

Yayoi Ando1, Tatsunori Shimoi2, Tatsuya Suzuki3, Hideki Ueno4, Natsuko Okita1, Kenichi Nakamura5 1Clinical Research Support Office, Research Management Division, National Cancer Center Hospital, Tokyo 104-0045, Japan; 2Department of Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan; 3Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan; 4Clinical Research Support Office, Clinical Research Coordinating Division, National Cancer Center Hospital, Tokyo 104-0045, Japan; 5International Clinical Development, National Cancer Center Hospital, Tokyo 104-0045, Japan
Normoblastemia in COVID-19 patients is associated with more severe disease and adverse outcome.

OBJECTIVES The clinical, pathological, and laboratory correlates of normoblastemia in COVID-19 patients have not been adequately explored. We sought to assess the frequency of normoblastemia in COVID-19, its association with other markers of disease, as well as other clinical outcomes. METHODS All COVID-19 patients seen at our institution with at least one automated complete blood count (aCBC) evaluation from March to May 2020 were included in this retrospective cohort analysis. Results of aCBC and tests for markers of the acute phase response performed within 5 days before the first COVID-19 positive test and 14 days after the last positive test were reviewed. We also evaluated histologic features of the reticuloendothelial system of COVID-19 decedents. RESULTS Among a total of 2501 COVID-19 patients, 715 (28.6%) were found to have normoblastemia. Patients with this abnormality had significantly higher (median, (1st quartile, 3rd quartile) WBC (15.7 (11.2, 23.1) u/L vs. 8.3 (6.2, 11.5) u/L), absolute neutrophil count (7.0 (5.1, 10.1) u/L vs. 5.1 (3.7, 7.3) u/L), immature granulocyte percentage (0.8 (0.5, 1.3)% vs. 0.5 (0.3, 0.8)%), ESR (76.0 (60.5, 100.0) mm/hr vs. 66.0 (45.0, 87.0) mm/hr), ferritin (1404.5 (645.0, 2871.0) ng/mL vs. 672.7 (313.4, 1348.0) ng/mL), INR (1.4 (1.2, 1.7) vs. 1.2 (1.1, 1.3)), D-dimer (8.2 (2.8, 20.0) ug/mL FEU vs. 1.5 (0.8, 3.7) µg/mL FEU), and IL-6 (216.6 (77.7, 315.0) pg/mL vs. 54.3 (23.2, 127.8) pg/mL) levels, and lower hemoglobin (12.5 (10.7, 14.2) g/dL vs. 13.2 (11.8, 14.6) g/dL) and absolute lymphocyte count (1.0 (0.7, 1.3) u/L vs. 1.1 (0.8, 1.5) u/L). The incidence of intubation and ventilation support (61.3% (65/106) vs. 10.5% (31/263)) and mortality rates (37.9%, 271/715 vs. 11.8%, 210/1786), were higher in normoblastemic patients. Multivariable logistic regression revealed normoblastemia to be an independent predictive biomarker of short-term mortality in COVID-19. CONCLUSION Normoblastemia in COVID-19 is associated with markers of severe disease, extramedullary erythropoiesis, and adverse clinical outcome.
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3′-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.
Paleogene biomarker records from the central Arctic Ocean (Integrated Ocean Drilling Program Expedition 302): Organic carbon sources, anoxia, and sea surface temperature

[1] During Integrated Ocean Drilling Program Expedition 302 (Arctic Coring Expedition (ACEX)) a more than 200 m thick sequence of Paleogene organic carbon (OC)-rich (black shale type) sediments was drilled. Here we present new biomarker data determined in ACEX sediment samples to decipher processes controlling OC accumulation and their paleoenvironmental significance during periods of Paleogene global warmth and proposed increased freshwater discharge in the early Cenozoic. Specific source-related biomarkers including n-alkanes, fatty acids, isoprenoids, carotenoids, hopanes/hopenes, hopanoic acids, aromatic terpenoids, and long-chain alkenones show a high variability of components, derived from marine and terrestrial origin. The distribution of hopanoic acid isomers is dominated by compounds with the biological 17β(H), 21β(H) configuration indicating a low level of maturity. On the basis of the biomarker data the terrestrial OC supply was significantly enriched during the late Paleocene and part of the earliest Eocene, whereas increased aquatic contributions and euxinic conditions of variable intensity were determined for the Paleocene-Eocene thermal maximum and Eocene thermal maximum 2 events as well as the middle Eocene time interval. Furthermore, samples from the middle Eocene are characterized by the occurrence of long-chain alkenones, high proportions of lycopane, and high ratios (>0.6) of (n-C35 + lycopane)/n-C31. The occurrence of C37-alkenenones, which were first determined toward the end of the Azolla freshwater event, indicates that the OC becomes more marine in origin during the middle Eocene. Preliminary U37K′-based sea surface temperature (SST) values display a long-term temperature decrease of about 15°C during the time interval 49–44.5 Ma (25° to 10°C), coinciding with the global benthic δ18O cooling trend after the early Eocene climatic optimum. At about 46 Ma, parallel with onset of ice-rafted debris, SST (interpreted as summer temperatures) decreased to values <15°C. For the late early Miocene a SST of 11°–15°C was determined. Most of the middle Eocene ACEX sediments are characterized by a smooth short-chain n-alkane distribution, which may point to natural oil-type hydrocarbons from leakage of petroleum reservoirs or erosion of related source rocks and redeposition.
Separating Well Log Data to Train Support Vector Machines for Lithology Prediction in a Heterogeneous Carbonate Reservoir

The prediction of lithology is necessary in all areas of petroleum engineering. This means that to design a project in any branch of petroleum engineering, the lithology must be well known. Support vector machines (SVM’s) use an analytical approach to classification based on statistical learning theory, the principles of structural risk minimization, and empirical risk minimization. In this research, SVM classification method is used for lithology prediction from petrophysical well logs based on petrographic studies of core lithology in a heterogeneous carbonate reservoir in southwestern Iran. Data preparation including normalization and attribute selection was performed on the data. Well by well data separation technique was used for data partitioning so that the instances of each well were predicted against training the SVM with the other wells. The effect of different kernel functions on the SVM performance was deliberated. The results showed that the SVM performance in the lithology prediction of wells by applying well by well data partitioning technique is good, and that in two data separation cases, radial basis function (RBF) kernel gives a higher lithology misclassification rate compared with polynomial and normalized polynomial kernels. Moreover, the lithology misclassification rate associated with RBF kernel increases with an increasing training set size.
Titan zonal wind corroboration via the huygens DISR solar zenith angle measurement

The in situ measurement of the vertical profile of Titan’s zonal wind is a major objective of the Huygens probe mission, as specifically addressed by the Doppler Wind Experiment (DWE). It now appears likely that an independent, if somewhat less accurate corroboration of the zonal wind retrieval will be afforded by the measured variation of the solar zenith angle Z from the Huygens Descent Imager/Spectral Radiometer (DISR) throughout the course of the probe’s atmospheric descent. The analyzed synergism of the DWE and DISR solar-Z measurements should provide an enhanced evaluation of the Titan atmospheric circulation.
Characterizing Spatial Pattern in Ecosystem Service Values when Distance Decay Doesn’t Apply: Choice Experiments and Local Indicators of Spatial Association

Stated preference analyses commonly impose strong and unrealistic assumptions in response to spatial welfare heterogeneity. These include spatial homogeneity or continuous distance decay. Despite their ubiquity in the valuation literature, global assumptions such as these have been increasingly abandoned by non-economics disciplines in favor of approaches that allow for spatial patchiness. This paper develops parallel methods to evaluate local patchiness and hot spots in stated preference welfare estimates, characterizing relevant patterns overlooked by traditional approaches. The analysis draws from a choice experiment addressing river restoration. Results demonstrate shortcomings in standard treatments of spatial heterogeneity and insights available through alternative methods.
Plant species identity and plant-induced changes in soil physicochemistry—but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome

Abstract The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.
Organic orchard floor management in peach: effects on arthropods and associated fruit injury in the Intermountain West

Understanding orchard floor management is critical to organic tree-fruit production systems given its impact on weeds, soil fertility, tree health, and crop yield. Several viable options are available to producers for weed management and promotion of organic fertility, including use of turf and broadleaf alleyway covers and living and nonliving tree-row mulches. While these measures can be effective, little is known about how these strategies influence arthropod pests, which cause fruit injury. Here, we assessed 6 organic orchard floor management strategies for their impact on arthropod abundance and diversity in an organic peach production system in northern Utah from 2010 to 2014, using sweep netting and pitfall collections along with observed peach fruit damage. Generally, we found that alleyway and tree-row treatments had no impact on total arthropod diversity, species richness, or community diversity. However, earwig (Forficula auricularia) abundance was significantly impacted by alleyway and tree-row treatments that resulted in increased fruit injury. Trefoil alleyway treatments consistently increased earwig abundance across life-history stages, while mulch or Alyssum (straw) tree-row treatments harbored more earwigs and, as a result, increased earwig fruit injury. Since earwigs are especially prone to damaging young, developing fruits, it is imperative that more work is done to assess earwig abundances and life-history traits. Our results demonstrate that detrimental arthropods are sensitive to orchard floor management and can further inform integrated pest management approaches that complement sustainability goals.
Parenting a child with cancer and maintaining a healthy couple relationship: Findings from the Family Talk Intervention

Despite the challenges that caring for a child with cancer brings for parents, little knowledge is available concerning the effects on the parents’ couple relationship. Furthermore, few interventions have been designed to support parents in their couple relationship. The aim of this paper was, therefore, to explore parents’ experiences of their couple relationship while having a dependent child with cancer and the support they received from a family‐based intervention, the Family Talk Intervention (FTI).
Risk Factors for Bleeding in Cancer Patients Treated with Conventional Dose Followed by Low-Dose Apixaban for Venous Thromboembolism

BACKGROUND Incidence of and risk factors for bleeding in cancer patients with venous thromboembolism (VTE) treated with apixaban are poorly described. METHODS We analyzed data from the prospective CAP study where 298 cancer patients with any type of VTE received 5 mg apixaban twice daily for 6 months, and then 2.5 mg apixaban twice daily for 30 months. For most analyses major bleedings and clinically relevant non-major bleedings were merged to "clinically relevant bleedings". Risk factors were estimated by odds ratios (OR) and 95% confidence intervals (CI). RESULTS The incidence of clinically relevant bleedings was 38% per person year during the first 6 months of treatment, 21% per person year from 7 to 12 months, and between 4% and 8% per person year from 13 to 36 months. Clinically relevant bleedings were associated with age above 74 years (OR 2.0, 95% CI 1.0-4.1), BMI below 21.7 (OR 2.3, 95% CI 1.1-4.8), and hemoglobin at baseline below 10.5 for females (OR 2.8, 95% CI 1.1-7.3) and 11.1 for males (OR 3.3, 95% CI 1.3-8.4) during the first 6 months. Gastrointestinal (GI) or urogenital cancer were not associated with clinically relevant bleedings compared with other cancers. Among patients with luminal GI-cancer, non-resected cancer had increased risk of bleeding (OR 3.4, 95% CI 1.0-11.6) compared with resected GI-cancer. CONCLUSION It was very few bleedings while patients were on low-dose apixaban. Factors associated with bleeding in patients treated with full-dose apixaban were high age, low BMI, and low hemoglobin, and probably non-resected luminal GI-cancer.