Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining remote sensing and hydrological models to enhance spatial and temporal variability

The development of water saving measures requires a thorough understanding of the water balance at a high spatial and temporal resolution. Remote sensing is strong in producing information at a high spatial scale, while simulation models are strong in producing water balance estimates at a high temporal resolution. Actual evapotranspiration for an irrigated area in western Turkey was calculated using the SEBAL remote sensing land algorithm using two Landsat images. The hydrological model SWAP was set up to simulate the water balance for the same area, assuming a certain distribution in soil properties, planting dates, and irrigation practices. A comparison between evapotranspiration determined from SEBAL and from SWAP was made, and differences were minimized by adapting the stochastic input in planting date and irrigation practice. The optimized stochastic input data for SWAP was used to simulate all terms of the water balance for the entire irrigation scheme.
Predictors of mTICI 2c/3 over 2b in patients successfully recanalized with mechanical thrombectomy

For patients presenting with acute ischemic stroke (AIS) caused by large vessel occlusions (LVO), mechanical thrombectomy (MT) is the treatment standard of care in eligible patients. Modified Thrombolysis in Cerebral Infarction (mTICI) grades of 2b, 2c, and 3 are all considered successful reperfusion; however, recent studies have shown achieving mTICI 2c/3 leads to better outcomes than mTICI 2b. This study aims to investigate whether any baseline preprocedural or periprocedural parameters are predictive of achieving mTICI 2c/3 in successfully recanalized LVO patients.
Intratumoral perfusion may affect microwave ablation area of hepatocellular carcinoma

Abstract Objectives We aimed to evaluate the effect of intratumoral perfusion on microwave ablation (MWA) area in hepatocellular carcinoma (HCC). Methods Patients who underwent curative MWA for HCC between October 2013 and May 2015 were enrolled. Three days before MWA, contrast-enhanced ultrasound (CEUS) was performed to illustrate the perfusion characteristics of the target lesion. Using the Sonoliver quantification software, time-intensity curves of dynamic CEUS were obtained, and quantitative parameters were extracted. Two microwave antennae were inserted into the center of the tumor and MWA was performed with a continuous power output of 50 W for 5 min. A second CEUS was performed to measure the size of the ablated region. Thereafter, an additional MWA procedure was performed until complete ablation with a 5–10-mm safety margin was achieved. Results A total of 38 patients who underwent curative MWA for 39 HCC nodules were enrolled. The mean age was 57 years (34–80 years), and the median maximum diameter of the HCC was 3.4 cm (interquartile range, 2–6.8 cm). Time-intensity curves were obtained and the area under the curve (AUC) was selected as a parameter for intratumoral perfusion. The AUC was inversely and linearly correlated with the size of the MWA area, including long- and short-axis diameters and ablation volume. A 1,000-dB·s change in the AUC produced an average change of 1.17 ± 0.44 mm, 0.725 ± 0.355 mm, and 2.4995 ± 0.6575 cm³ in the long- and short-axis diameters and ablation volume, respectively. Conclusions The intratumoral perfusion of HCC was inversely correlated with MWA area size.
The threat of increased transmission of non-knowlesi zoonotic malaria in humans: a systematic review

Abstract Abstract Of the 5 human malarial parasites, Plasmodium falciparum and Plasmodium vivax are the most prevalent species globally, while Plasmodium malariae, Plasmodium ovale curtisi and Plasmodium ovale wallikeri are less prevalent and typically occur as mixed-infections. Plasmodium knowlesi, previously considered a non-human primate (NHP) infecting species, is now a cause of human malaria in Malaysia. The other NHP Plasmodium species, Plasmodium cynomolgi, Plasmodium brasilianum, Plasmodium inui, Plasmodium simium, Plasmodium coatneyi and Plasmodium fieldi cause malaria in primates, which are mainly reported in southeast Asia and South America. The non-knowlesi NHP Plasmodium species also emerged and were found to cross-transmit from their natural hosts (NHP) – to human hosts in natural settings. Here we have reviewed and collated data from the literature on the NHPs-to-human-transmitting non-knowlesi Plasmodium species. It was observed that the natural transmission of these NHP parasites to humans had been reported from 2010 onwards. This study shows that: (1) the majority of the non-knowlesi NHP Plasmodium mixed species infecting human cases were from Yala province of Thailand; (2) mono/mixed P. cynomolgi infections with other human-infecting Plasmodium species were prevalent in Malaysia and Thailand and (3) P. brasilianum and P. simium were found in Central and South America.
The eukaryotic translation initiation factor eIF4E unexpectedly acts in splicing thereby coupling mRNA processing with translation

Recent findings position the eukaryotic translation initiation factor eIF4E as a novel modulator of mRNA splicing, a process that impacts the form and function of resultant proteins. eIF4E physically interacts with the spliceosome and with some intron‐containing transcripts implying a direct role in some splicing events. Moreover, eIF4E drives the production of key components of the splicing machinery underpinning larger scale impacts on splicing. These drive eIF4E‐dependent reprogramming of the splicing signature. This work completes a series of studies demonstrating eIF4E acts in all the major mRNA maturation steps whereby eIF4E drives production of the RNA processing machinery and escorts some transcripts through various maturation steps. In this way, eIF4E couples the mRNA processing‐export‐translation axis linking nuclear mRNA processing to cytoplasmic translation. eIF4E elevation is linked to worse outcomes in acute myeloid leukemia patients where these activities are dysregulated. Understanding these effects provides new insight into post‐transcriptional control and eIF4E‐driven cancers.
Relating Air Quality And EnvironmentalPublic Health Tracking Data

Initiated in February 2004, the Public Health Air Surveillance Evaluation (PHASE) Project is a multi-disciplinary collaboration between the Centers for Disease Control and Prevention (CDC), the U.S Environmental Protection Agency (EPA), and three Environmental Public Health Tracking Network (EPHTN) state agencies. The objective of this project is to develop, evaluate, and demonstrate the advantages and limitations of different methods of generating air quality characterization data that could be systematically and routinely available to link with public health surveillance data as part of the Environmental Public Health Tracking Network.
Fluid permeability of deformable fracture networks

We consider the problem of defining the fracture permeability tensor for each grid block in a rock mass from maps of natural fractures. For this purpose we implement a statistical model of cracked rock developed by M. Oda, where the permeability tensor is related to the crack geometry via a volume average of the contribution from each crack in the population. In this model, tectonic stress is implicitly coupled to fluid flow through an assumed relationship between crack aperture and normal stress across the crack. We have included three enhancements to the basic model. (1) A realistic model of crack closure under stress has been added along with the provision to apply tectonic stresses to the fracture system in any orientation. The application of compressive stress results in fracture closure, and consequently, a reduction in permeability. (2) The fracture permeability can be linearly superimposed onto an arbitrary anisotropic matrix permeability. (3) The fracture surfaces are allowed to slide under the application of shear stress, causing fractures to dilate and result in a permeability increase. Through two examples we demonstrate that significant changes in permeability magnitudes and orientations are possible when tectonic stress is applied to fracture systems.
A contemporary analysis of disease upstaging of Gleason 3 + 3 prostate cancer patients after robot‐assisted laparoscopic prostatectomy

Risk of biochemical recurrence (BCR) in localised prostate cancer can be stratified using the 5‐tier Cambridge Prognostic Group (CPG) or 3‐tier European Association of Urology (EAU) model. Active surveillance is the current recommendation if CPG1 or EAU low‐risk criteria are met. We aimed to determine the contemporary rates of upgrading, upstaging and BCR after radical prostatectomy for CPG1 or EAU low‐risk disease.
Rapid Infiltration Measurement of LID Best Management Practices

Infiltration is an essential process of most stormwater low impact development (LID) practices. Measurements of the infiltration capacity applied to a design storm are needed to determine performance, schedule maintenance and meet regulatory requirements. Infiltration rates, however, have great spatial variation and most existing infiltration measurement techniques are relatively slow and require a substantial amount of water. These measurements, therefore, are typically made at only one location. The Modified Philip-Dunne (MPD) infiltrometer is a new technique to measure the saturated hydraulic conductivity (Ksat) of the surface layer of a soil. It is a fast, simple and inexpensive falling head device; suitable for infiltration practices because it can be performed relatively quickly with minimal water to allow one the flexibility to capture the large spatial variability that occurs with infiltration capacities. A user-friendly spreadsheet program and a manual have made the application of the MPD infiltrometer straight-forward so that the infiltration capacity of soil can be obtained quickly. A comparison between the value of Ksat obtained from the MPD, from Double Ring Infiltrometer and from numerical simulations of the three-dimesional axisymmetric Richards equation for homogeneous and non-homogeneous soil will be presented. The MPD infiltrometer has been used in several LID practices, such as rain gardens, infiltration basins and swales. This method, developed for field application, has a simple experimental apparatus, straight-forward mathematical model and requires a small volume of water to perform the test. 4379 World Environmental and Water Resources Congress 2011: Bearing Knowledge for Sustainability © ASCE 2011
Designing a phase‐III time‐to‐event clinical trial using a modified sample size formula and Poisson‐Gamma model for subject accrual that accounts for the lag in site initiation using the PERT distribution

A priori estimation of sample size and subject accrual in multi‐site, time‐to‐event clinical trials is often challenging. Such trials are powered based on the number of events needed to detect a clinically significant difference. Sample size based on number of events relates to the expected duration of observation time for each subject. Temporal patterns in site initiation and subject enrollment ultimately affect when subjects can be accrued into the study. Lag times are common as the site start‐up process optimizes, resulting in delays that may curtail observational follow‐up and therefore undermine power. The proposed method introduces a Program Evaluation and Review Technique (PERT) model into the sample size estimation which accounts for the lag in site start‐up. Additionally, a PERT model is introduced into a Poisson‐Gamma subject accrual model to predict the quantity of study sites needed. The introduction of the PERT model provides greater flexibility in both a priori power assessment and planning the number of sites, as it specifically allows for the inclusion of anticipated delays in site start‐up time. This model results in minimal power loss even when PERT distribution inputs are misspecified compared to the traditional assumption of simultaneous start‐up for all sites. Together these updated formulations for sample size and subject accrual models offer an improved method for designing a multi‐site time‐to‐event clinical trial that accounts for a flexible site start‐up process.
Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert

The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40–50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on “returned samples” to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.
Association Between User Interaction and Treatment Response of a Voice-Based Coach for Treating Depression and Anxiety: Secondary Analysis of a Pilot Randomized Controlled Trial

Background The quality of user interaction with therapeutic tools has been positively associated with treatment response; however, no studies have investigated these relationships for voice-based digital tools. Objective This study evaluated the relationships between objective and subjective user interaction measures as well as treatment response on Lumen, a novel voice-based coach, delivering problem-solving treatment to patients with mild to moderate depression or anxiety or both. Methods In a pilot trial, 42 adults with clinically significant depression (Patient Health Questionnaire-9 [PHQ-9]) or anxiety (7-item Generalized Anxiety Disorder Scale [GAD-7]) symptoms or both received Lumen, a voice-based coach delivering 8 problem-solving treatment sessions. Objective (number of conversational breakdowns, ie, instances where a participant’s voice input could not be interpreted by Lumen) and subjective user interaction measures (task-related workload, user experience, and treatment alliance) were obtained for each session. Changes in PHQ-9 and GAD-7 scores at each ensuing session after session 1 measured the treatment response. Results Participants were 38.9 (SD 12.9) years old, 28 (67%) were women, 8 (19%) were Black, 12 (29%) were Latino, 5 (12%) were Asian, and 28 (67%) had a high school or college education. Mean (SD) across sessions showed breakdowns (mean 6.5, SD 4.4 to mean 2.3, SD 1.8) decreasing over sessions, favorable task-related workload (mean 14.5, SD 5.6 to mean 17.6, SD 5.6) decreasing over sessions, neutral-to-positive user experience (mean 0.5, SD 1.4 to mean 1.1, SD 1.3), and high treatment alliance (mean 5.0, SD 1.4 to mean 5.3, SD 0.9). PHQ-9 (Ptrend=.001) and GAD-7 scores (Ptrend=.01) improved significantly over sessions. Treatment alliance correlated with improvements in PHQ-9 (Pearson r=–0.02 to –0.46) and GAD-7 (r=0.03 to –0.57) scores across sessions, whereas breakdowns and task-related workload did not. Mixed models showed that participants with higher individual mean treatment alliance had greater improvements in PHQ-9 (β=–1.13, 95% CI –2.16 to –0.10) and GAD-7 (β=–1.17, 95% CI –2.13 to –0.20) scores. Conclusions The participants had fewer conversational breakdowns and largely favorable user interactions with Lumen across sessions. Conversational breakdowns were not associated with subjective user interaction measures or treatment responses, highlighting how participants adapted and effectively used Lumen. Individuals experiencing higher treatment alliance had greater improvements in depression and anxiety. Understanding treatment alliance can provide insights on improving treatment response for this new delivery modality, which provides accessibility, flexibility, comfort with disclosure, and cost-related advantages compared to conventional psychotherapy. Trial Registration ClinicalTrials.gov NCT04524104; https://clinicaltrials.gov/study/NCT04524104
Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways

Human erythropoiesis is a complex process leading to the production of 2.5 million red blood cells per second. Following commitment of hematopoietic stem cells to the erythroid lineage, this process can be divided into three distinct stages: erythroid progenitor differentiation, terminal erythropoiesis, and reticulocyte maturation. We recently resolved the heterogeneity of erythroid progenitors into four different subpopulations termed EP1–EP4. Here, we characterized the growth factor(s) responsiveness of these four progenitor populations in terms of proliferation and differentiation. Using mass spectrometry‐based proteomics on sorted erythroid progenitors, we quantified the absolute expression of ~5500 proteins from EP1 to EP4. Further functional analyses highlighted dynamic changes in cell cycle in these populations with an acceleration of the cell cycle during erythroid progenitor differentiation. The finding that E2F4 expression was increased from EP1 to EP4 is consistent with the noted changes in cell cycle. Finally, our proteomic data suggest that the protein machinery necessary for both oxidative phosphorylation and glycolysis is present in these progenitor cells. Together, our data provide comprehensive insights into growth factor‐dependence of erythroid progenitor proliferation and the proteome of four distinct populations of human erythroid progenitors which will be a useful framework for the study of erythroid disorders.
The impact of intensity‐modulated radiotherapy in conjunction with chemotherapy on proximal pT3N0 rectal cancer patients after total mesorectum excision

This study aimed to ascertain if the incorporation of intensity‐modulated radiotherapy (IMRT) with chemotherapy (CTx) offered any advantages for patients diagnosed with stage pT3N0 rectal cancer located in the proximal (upper) region following a complete total mesorectum excision (TME).
Effects of Adjuvant Radiation Plus Chemotherapy on Survival Outcomes in Stage III C Endometrial Cancer According to Histology: Analysis of Data from the Surveillance, Epidemiology, and End Results Database

Purpose: To evaluate the survival benefit of radiation plus chemotherapy in adult females with stage IIIC endometrial cancer and to investigate whether the benefit varies according to histology. Methods: Data from adult females with International Federation of Gynecology and Obstetrics (FIGO) stage IIIC endometrial cancer, who underwent at least total hysterectomy between 2010 and 2015, were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Adjuvant treatments were categorized as chemotherapy alone, chemotherapy with external beam radiation therapy (EBRT), chemotherapy with vaginal brachytherapy (VBT), or chemotherapy with EBRT+VBT. Multivariate Cox regression models, Kaplan–Meier curves, and log-rank tests were used to assess the association between treatment modality and overall survival (OS). Results: In total, 2138 cases were identified: stage IIIC1 (n = 1299 [60.8%]) and stage IIIC2 (n = 839 [39.2%]). Median OS for all patients was 48 (interquartile range [IQR] 28-70) months. Regarding adjuvant treatment, 40.5% of patients underwent chemotherapy only, followed by chemotherapy with EBRT (35.5%). Stage IIIC patients treated with chemotherapy plus radiation exhibited a significantly reduced risk for death from endometrial cancer in both univariate and multivariate analyses (P < 0.001). However, when stratified according to histology, OS also differed according to treatment modality when analyzing each histological type; combination therapy was no longer significantly different from chemotherapy alone for any histology (clear cell and carcinosarcoma). Combination therapy was associated with improved OS in patients with IIIC1 and IIIC2 disease. Similar associations were observed in patients with high-grade stage IIIC endometrioids. However, for low-grade tumors, combination therapy was no longer associated with reduced risk for death compared with chemotherapy alone. Conclusion: For patients with stage IIIC endometrial cancer, combined treatment with radiation and chemotherapy was associated with improved OS compared with chemotherapy alone. However, no survival benefit was found, and radiotherapy may be unnecessary in patients with low-grade endometrioids.
Combinatorial activation of the WNT‐dependent fibrogenic program by distinct complement subunits in dystrophic muscle

Fibrosis is associated with compromised muscle functionality in Duchenne muscular dystrophy (DMD). We report observations with tissues from dystrophic patients and mice supporting a model to explain fibrosis in DMD, which relies on the crosstalk between the complement and the WNT signaling pathways and the functional interactions of two cellular types. Fibro‐adipogenic progenitors and macrophages, which populate the inflamed dystrophic muscles, act as a combinatorial source of WNT activity by secreting distinct subunits of the C1 complement complex. The resulting aberrant activation of the WNT signaling in responsive cells, such as fibro‐adipogenic progenitors, contributes to fibrosis. Indeed, pharmacological inhibition of the C1r/s subunits in a murine model of DMD mitigated the activation of the WNT signaling pathway, reduced the fibrogenic characteristics of the fibro‐adipogenic progenitors, and ameliorated the dystrophic phenotype. These studies shed new light on the molecular and cellular mechanisms responsible for fibrosis in muscular dystrophy and open to new therapeutic strategies.