Miracle-dz/UniFAR-FTUs huggingface dataset:
Simple Soil Tests for On-Site Evaluation of Soil Health in Orchards

Standard commercial soil tests typically quantify nitrogen, phosphorus, potassium, pH, and salinity. These factors alone are not sufficient to predict the long-term effects of management on soil health. The goal of this study was to assess the effectiveness and use of simple physical, biological, and chemical soil health indicator tests that can be completed on-site. Analyses were conducted on soil samples collected from three experimental peach orchards located on the Utah State Horticultural Research Farm in Kaysville, Utah. All simple tests were correlated to comparable lab analyses using Pearson’s correlation. The highest positive correlations were found between Solvita® respiration, and microbial biomass (R = 0.88), followed by our modified slake test and microbial biomass (R = 0.83). Both Berlese funnel and pit count methods of estimating soil macro-organism diversity were fairly predictive of soil health. Overall, simple commercially available chemical tests were weak indicators of soil nutrient concentrations compared to laboratory tests. Modified slake tests, Solvita® respiration and soil organism biodiversity counts may be efficient and cost-effective tools for monitoring soil health on-site.
The Macroeconomic Effects of Debt- and Equity-Based Capital Inflows

This paper will consider whether debt- and equity-based capital inflows have different macroeconomic effects. Using external instruments in a structural VAR, we first identify the component of capital inflows that is driven not by domestic economic and financial conditions but by conditions in the rest of the world. We then estimate the response to an exogenous shock to debt or equity-based capital inflows in a structural VAR model that includes domestic variables like GDP, inflation, the exchange rate, stock prices, credit growth, and interest rates. An exogenous increase in debt inflows leads to a significant increase in GDP, inflation, stock prices and credit growth and an appreciation of the exchange rate. An exogenous increase in equity-based capital inflows has almost no effect on the same variables. Thus the macroeconomic effects of exogenous capital inflows are almost entirely due to changes in debt, not equity-based, capital inflows.
Control of turbulent boundary layers

The objective of this paper is to give an overview of recent progress on boundary layer control made by the author’s research group at University of California, Los Angeles. A primary theme is to highlight the importance of a certain linear mechanism and its contribution to skin-friction drag in turbulent boundary layers—and the implication that significant drag reduction can be achieved by altering this linear mechanism. Examples that first led to this realization are presented, followed by applications of linear optimal control theory to boundary-layer control. Results from these applications, in which the linear mechanism in turbulent channel flow was targeted, indirectly confirm the importance of linear mechanisms in turbulent—and hence, nonlinear—flows. Although this new approach has thus far been based solely on numerical experiments which are yet to be verified in the laboratory, they show great promise and represent a fundamentally new approach for flow control. The success and limitations of vari.
Alterations in the proteome of pulmonary alveolar type II cells in the rat after hepatic ischemia-reperfusion

Objective:Hepatic ischemia-reperfusion can be associated with acute lung injury. Alveolar epithelial type II cells (ATII) play an important role in maintaining lung homeostasis in acute lung injury. Design:To study potentially new mechanisms of hepatic ischemia-reperfusion-induced lung injury, we examined how liver ischemia-reperfusion altered the proteome of ATII. Setting:Laboratory investigation. Subjects:Spontaneously breathing male Zucker rats. Interventions:Rats were anesthetized with isoflurane. The vascular supply to the left and medial lobe of the liver was clamped for 75 mins and then reperfused. Sham-operated rats were used as controls. After 8 hrs, rats were killed. Measurements and Main Results:Bronchoalveolar lavage and differential cell counts were performed, and tumor necrosis factor-&agr; and cytokine-induced neutrophil chemotactic factor-1 in plasma were determined by enzyme-linked immunosorbent assay. ATII were isolated, lysed, tryptically digested, and labeled using isobaric tags (iTRAQ). The samples were fractionated by cation exchange chromatography, separated by high-performance liquid-chromatography, and identified using electrospray tandem mass spectrometry. Spectra were interrogated and quantified using ProteinProspector. Quantitative proteomics provided quantitative data for 94 and 97 proteins in the two groups. Significant changes in ATII protein content included 30% to 40% increases in adenosine triphosphate synthases, adenosine triphosphate/adenosine diphosphate translocase, and catalase (all p < .001). Following liver ischemia-reperfusion, there was also a significant increase in the percentage of neutrophils in bronchoalveolar lavage (48% ± 26%) compared with sham-operated controls (5% ± 3%) (p < .01), and plasma tumor necrosis factor-&agr; levels were also significantly increased. Conclusions:The proteins identified by quantitative proteomics indicated significant changes in moderators of cell metabolism and host defense in ATII. These findings provide new insights into possible mechanisms responsible for hepatic ischemia-reperfusion-related acute lung injury and suggest that ATII cells in the lung sense and respond to hepatic injury.
HIF-1 response to hypoxia is functionally separated from the glucocorticoid stress response in the in vitro regenerating human skeletal muscle

Pirkmajer S, Filipovic D, Mars T, Mis K, Grubic Z. HIF-1 response to hypoxia is functionally separated from the glucocorticoid stress response in the in vitro regenerating human skeletal muscle. Am J Physiol Regul Integr Comp Physiol 299: R1693–R1700, 2010. First published October 13, 2010; doi:10.1152/ajpregu.00133. 2010. —Injury of skeletal muscle is followed by muscle regeneration in which new muscle tissue is formed from the proliferating mononuclear myoblasts, and by systemic response to stress that exposes proliferating myoblasts to increased glucocorticoid (GC) concentration. Because of its various causes, hypoxia is a frequent condition affecting skeletal muscle, and therefore both processes, which importantly determine the outcome of the injury, often proceed under hypoxic conditions. It is therefore important to identify and characterize in proliferating human myoblasts: 1) response to hypoxia which is generally organized by hypoxia-inducible factor-1 (HIF-1 ); 2) response to GCs which is mediated through the isoforms of glucocorticoid receptors (GRs) and 11 -hydroxysteroid dehydrogenases (11 -HSDs), and 3) the response to GCs under the hypoxic conditions and the influence of this combination on the factors controlling myoblast proliferation. Using real-time PCR, Western blotting, and HIF-1 small-interfering RNA silencing, we demonstrated that cultured human myoblasts possess both, the HIF-1 -based response to hypoxia, and the GC response system composed of GR and types 1 and 2 11 -HSDs. However, using combined dexamethasone and hypoxia treatments, we demonstrated that these two systems operate practically without mutual interactions. A seemingly surprising separation of the two systems that both organize response to hypoxic stress can be explained on the evolutionary basis: the phylogenetically older HIF-1 response is a protection at the cellular level, whereas the GC stress response protects the organism as a whole. This necessitates actions, like downregulation of IL-6 secretion and vascular endothelial growth factor, that might not be of direct benefit for the affected myoblasts.
Expression of Cancer-Associated Molecules in Malignant Mesothelioma

Malignant mesothelioma (MM) is a malignant tumor derived from mesothelial cells, native cells of the body cavities. Exposure to asbestos is the most strongly established etiologic factor, predominantly for the most common disease form, pleural mesothelioma. The pathogenesis of MM involves the accumulation of extensive cytogenetic changes, as well as cancer-related phenotypic alterations that facilitate tumor cell survival, invasion and metastasis. This review presents current knowledge regarding the biological characteristics of this disease that are linked to the so-called hallmarks of cancer. In addition, data suggesting that the anatomic site (solid tumor vs. effusion) affects the expression of metastasis-associated and regulatory molecules in MM are presented. Finally, recent work in which high-throughput methodology has been applied to MM research is reviewed. The data obtained in the reviewed research may aid in defining new prognostic markers and therapeutic targets for this aggressive disease in the future.
Smarcd3b and Gata5 promote a cardiac progenitor fate in the zebrafish embryo

Development of the heart requires recruitment of cardiovascular progenitor cells (CPCs) to the future heart-forming region. CPCs are the building blocks of the heart, and have the potential to form all the major cardiac lineages. However, little is known regarding what regulates CPC fate and behavior. Activity of GATA4, SMARCD3 and TBX5 – the `cardiac BAF' (cBAF) complex, can promote myocardial differentiation in embryonic mouse mesoderm. Here, we exploit the advantages of the zebrafish embryo to gain mechanistic understanding of cBAF activity. Overexpression of smarcd3b and gata5 in zebrafish results in an enlarged heart, whereas combinatorial loss of cBAF components inhibits cardiac differentiation. In transplantation experiments, cBAF acts cell autonomously to promote cardiac fate. Remarkably, cells overexpressing cBAF migrate to the developing heart and differentiate as cardiomyocytes, endocardium and smooth muscle. This is observed even in host embryos that lack endoderm or cardiac mesoderm. Our results reveal an evolutionarily conserved role for cBAF activity in cardiac differentiation. Importantly, they demonstrate that Smarcd3b and Gata5 can induce a primitive, CPC-like state.
PRECLINICAL EVALUATION AND INTRAOPERATIVE HUMAN RETINAL IMAGING WITH A HIGH-RESOLUTION MICROSCOPE-INTEGRATED SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY DEVICE

Purpose: The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Methods: Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board–approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Results: Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole and vitreomacular traction, and demonstrated postsurgical changes in retinal morphology. Two cohorts of five patients were imaged. In the second cohort, the predefined end points were exceeded with ≥80% correlation between microscope-mounted OCT and HHOCT imaging in 100% of the patients. Conclusion: This report describes high-resolution MIOCT imaging using the prototype device in human eyes during vitreoretinal surgery, with successful achievement of predefined end points for imaging. Further refinements and investigations will be directed toward fully integrating MIOCT with vitreoretinal and other ocular surgery to image surgical maneuvers in real time.
Performance Changes of Elite Paralympic Judo Athletes During a Paralympic Games Cycle: A Case Study with the Brazilian National Team

Abstract The aim of this study was to describe the variations in power performance of elite Paralympic judo athletes across three consecutive training cycles of preparation for the ParaPan American Games, the World Championship and the Paralympic Games. Eleven Paralympic judokas from the Brazilian National team participated in this study. They were repeatedly assessed using squat and countermovement jumps, mean propulsive power (MPP) in the jump-squat (JS), the bench press and prone bench pull at several moments of the preparation. Training supervision based on the optimum power zone (range of loads where power production is maximized) was provided in the final cycle, prior to the Paralympic Games. Magnitude-based inference was used to compare the repeated measurements of power performance. Lower and upper limb muscle power gradually increased throughout the cycles; however, the best results in all exercises were observed prior to the Paralympic Games, during which the team won four silver medals. As an illustration, prior to participation in the Paralympic Games the MPP in the JS was likely to very likely higher than prior to the World Championship (effect size [ES] = 0.77) and ParaPan American Games (ES = 0.53), and in January and March 2016 (ES = 0.98 and 0.92, respectively; months preceding the Paralympic Games). Power performance assessments can provide information about the evolution of Paralympic judokas, and training at the optimum power zone seems to constitute an effective method to improve lower and upper limb power in these athletes.
To Clone or Not To Clone: Method Analysis for Retrieving Consensus Sequences In Ancient DNA Samples

The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from “modern” DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be “gold standards” in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones. To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
SPred: Large-scale Harvesting of Semantic Predicates

We present SPred, a novel method for the creation of large repositories of semantic predicates. We start from existing collocations to form lexical predicates (e.g., break ) and learn the semantic classes that best fit the argument. To do this, we extract all the occurrences in Wikipedia which match the predicate and abstract its arguments to general semantic classes (e.g., break BODY PART, break AGREEMENT, etc.). Our experiments show that we are able to create a large collection of semantic predicates from the Oxford Advanced Learner’s Dictionary with high precision and recall, and perform well against the most similar approach.
Association between gene and miRNA expression profiles and stereotyped subset #4 B-cell receptor in chronic lymphocytic leukemia

In this study we investigated specific biological and clinical features associated with chronic lymphocytic leukemia (CLL) patients carrying stereotyped BCR subset #4 (IGHV4–34) among a prospective cohort of 462 CLL/MBL patients in early stage (Binet A). All subset #4 patients (n = 16) were characterized by the IGHV mutated gene configuration, and absence of unfavorable cytogenetic lesions, NOTCH1 or SF3B1 mutations. Gene and miRNA expression profiling evidenced that the leukemic cells of subset #4 cases showed significant downregulation of WDFY4, MF2A and upregulation of PDGFA, FGFR1 and TFEC gene transcripts, as well as the upregulation of miR-497 and miR-29c. The transfection of miR-497 mimic in primary leukemic CLL cells induced a downregulation of BCL2, a known validated target of this miRNA. Our data identify biological characteristics associated with subset #4 patients, providing further evidence for the putative role of BCR in shaping the features of the tumor cells in CLL.
Performance of downlink massive MIMO in ricean fading channels with ZF precoder

We investigate the achievable sum rate and energy efficiency of zero-forcing precoded downlink massive multiple-input multiple-output systems in Ricean fading channels. A simple and accurate approximation of the average sum rate is presented, which is valid for a system with arbitrary rank channel means. Based on this expression, the optimal power allocation strategy maximizing the average sum rate is derived. Moreover, considering a general power consumption model, the energy efficiency of the system with rank-1 channel means is characterized. Specifically, the impact of key system parameters, such as the number of users N, the number of BS antennas M, Ricean factor K and the signal-to-noise ratio (SNR) ρ are studied, and closed-form expressions for the optimal ρ and M maximizing the energy efficiency are derived. Our findings show that the optimal power allocation scheme follows the water filling principle, and it can substantially enhance the average sum rate in the presence of strong line-of-sight effect in the low SNR regime. In addition, we demonstrate that the Ricean factor K has significant impact on the optimal values of M, N and ρ.
Polarisation provoquée : expérimentation, modélisation et applications géophysiques

Les mecanismes produisant les signaux observes par la methode de Polarisation Provoquee (PP) sur une large gamme de frequences (entre 1 mHz et 20 kHz) ne sont pas encore completement identifies. Deux sujets particuliers ont ete abordes dans cette these. L'origine du signal observe a haute frequence (>1 kHz) a ete analyse en effectuant des mesures de la resistivite complexe sur de l'eau a differentes salinites. Les resultats montrent des ecarts sur la phase par rapport a la reponse attendue a haute frequence. Ils dependent du type d'electrode de mesures et de la conductivite du milieu. Un modele base sur un circuit electrique equivalent a ete propose pour modeliser ces effets. Nous avons aussi explore le mecanisme responsable de la polarisation en presence de grains semi-conducteurs en analysant la dependance de temps de relaxation. La reponse spectrale d'un milieu sableux sature a ete etudiee en variant la concentration et le type de l'electrolyte, la taille, le type et la quantite de grains semi-conducteurs inseres. En utilisant la methode des elements finis, nous avons entrepris une simulation numerique 2D basee sur la solution des equations de Poisson-Nernst-Planck dans le domaine temporel et spectral. Les resultats experimentaux sont conformes a ceux issus de la simulation numerique et montrent une decroissance comparable du temps de relaxation avec l'augmentation de la concentration de l'electrolyte. Finalement, une campagne geophysique de terrain sur un site paleo-miniers contenant des grains semi-conducteurs complete l'approche de laboratoire. Des mesures de PP temporelles permettent de delimiter les zones de scories sur le site et d'en estimer le volume.
Role of CD200 in differential diagnosis of mature B‐cell neoplasm

CD 200 is a type I immunoglobulin super family membrane glycoprotein, which is expressed in various mature B‐cell neoplasm (MBN). This study aimed at analyzing the expression pattern of CD200 by flow cytometry immunophenotyping (FCI) and to evaluate its utility in narrowing down the differential diagnosis of MBN, particularly in low‐grade lymphomas.
Joint Scheduling and Resource Allocation in CDMA Systems

In this paper, the scheduling and resource allocation problem for the downlink in a code-division multiple access (CDMA)-based wireless network is considered. The problem is to select a subset of the users for transmission and for each of the users selected, to choose the modulation and coding scheme, transmission power, and number of codes used. We refer to this combination as the physical layer operating point (PLOP). Each PLOP consumes different amounts of code and power resources. The resource allocation task is to pick the ¿optimal¿ PLOP taking into account both system-wide and individual user resource constraints that can arise in a practical system. This problem is tackled as part of a utility maximization problem framed in earlier papers that includes both scheduling and resource allocation. In this setting, the problem reduces to maximizing the weighted throughput over the state-dependent downlink capacity region while taking into account the system-wide and individual user constraints. This problem is studied for the downlink of a Gaussian broadcast channel with orthogonal CDMA transmissions. This results in a tractable convex optimization problem. A dual formulation is used to obtain several key structural properties. By exploiting this structure, algorithms are developed to find the optimal solution with geometric convergence.