Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Analysis of Phosphate Limitation in Geobacteraceae During the Bioremediation 1 of a Uranium-Contaminated Aquifer

Nutrient limitation is an environmental stress that may reduce the effectiveness of 25 bioremediation strategies, especially when the contaminants are organic compounds or when 26 organic compounds are added to promote microbial activities such as metal reduction. Genes 27 indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures 28 of Geobacter sulfureducens . This analysis revealed that genes in the pst-pho operon, which is 29 associated with a high affinity phosphate uptake system in other microorganisms, had 30 significantly higher transcript abundance under phosphate-limiting conditions, with the genes 31 pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript 32 levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes 33 increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU 34 within the subsurface Geobacter species predominating during an in situ uranium bioremediation 35 field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were 36 not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not 37 stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the 38 sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even 39 when experiencing suboptimal phosphate concentrations and that increasing phosphate 40 availability with phosphate additions is difficult to achieve due to the high reactivity of this 41 compound. This transcript-based approach developed for diagnosing phosphate limitation 42 should be applicable to assessing the potential need for additional phosphate in other 43 bioremediation processes. 44
Assessment of a River Reach for Environmental Fluid Dynamics Studies

Turbulence is the fundamental mechanism governing energy transfer in river flows that was conventionally examined in laboratory flumes. Recently, a trend has been observed for constructing larger scale and outdoor facilities that tend to avoid the problems of upscaling of experimental results. This paper presents the results of an experimental study performed on a river reach used as an environmental field laboratory. The study is focused on the understanding of the spatial arrangement of the flow structure and its dependency on the temporal variability of the flow. Detailed measurements were taken using acoustic Doppler velocimeters and their analysis was completed applying the theory of open-channel flows. The obtained results reveal that the flow structure on the river reach resembles characteristics of a typical three-dimensional open-channel flow. Away from the riverbanks, the flow behaves as a quasi-two-dimensional fully developed turbulent open-channel flow thus providing conditions favorable for field experimental studies of shallow mixing layers and flows over patches of submerged aquatic plants. An interesting observation in the seasonal dynamics of turbulent shear stress patterns was that the height of the roughness layer was reduced in the central part of the flow, though the overall roughness coefficient was increased. At the same time, the structure of the secondary flow near the banks was also substantially altered as the secondary circulations observed at low water levels were replaced by flow separation and internal boundary layers at medium water levels.
The application of probiotic fermented milks in cancer and intestinal inflammation

Lactic acid bacteria are present in many foods such as yoghurt and are frequently used as probiotics to improve some biological functions of the host. Many researchers have evaluated the effects of yoghurt and lactic acid bacteria against diseases such as cancer and intestinal inflammation. The preventive effect of probiotics on intestinal carcinogenesis may be associated with changes in the intestinal microbiota, suppressing the growth of bacteria that convert procarcinogens into carcinogens. Other mechanisms could be related to the immune response modulation and have been evaluated using milks fermented with lactic acid bacteria in chemically induced colon cancer and hormone-dependent breast cancer models. We demonstrated, using a murine colon cancer model, that yoghurt consumption inhibited tumour growth by decreasing the inflammatory response by increasing IL-10-secreting cells, cellular apoptosis and diminishing procarcinogenic enzymes. Milk fermented with Lactobacillus helveticus R389 delayed breast tumour growth by decreasing IL-6 and increasing IL-10 in serum and in the mammary glands and tumour-infiltrating immune cells. Previous results obtained with yoghurt administration in a colon cancer model led us to analyse its effect on a trinitrobenzenesulfonic acid-induced intestinal inflammation model in mice. Yoghurt was able to attenuate the symptoms of acute inflammation by reducing inflammatory cytokines, and increasing regulatory cytokine IL-10-producing cells, leading to desirable changes of the intestinal microbiota. It was demonstrated, by using murine models, that the consumption of fermented milks can modulate the immune system and can maintain it in a state of surveillance, which could affront different pathologies such as cancer and intestinal inflammation.
Evolutionary position of breviate amoebae and the primary eukaryote divergence

Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically ‘nomadic’ species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.
The extent of juvenile crust in the Grenville Province: Nd isotope evidence

A large Nd isotope data set is presented to generate a crustal formation age map for the southwest Grenville Province, placing it in the context of the province as a whole. Previous studies have shown that most crust in the central and eastern parts of the province is pre-Grenvillian, composed largely of juvenile 1.5, 1.7, 1.9, and 2.7 Ga arc terranes, partly reworked by later ensialic arcs and collision zones. In contrast, new Nd data reported here show that juvenile monocyclic crust is restricted to the SW Grenville Province, in part of the Central Metasedimentary Belt interpreted as a failed backarc rift zone. There is a clear isotopic distinction between this rift zone and the pre-Grenvillian crust on the flanks. On the flanks of the rift zone, there is evidence for two crust-forming events, comprising an earlier (1.5 Ga) juvenile Pinwarian event, and a later 1.4–1.3 Ga continental margin arc (the Elzevirian Orogeny). Based on the geographical distribution of Nd model ages in the SW Grenville Province, a revised tectonic model for the Grenville Orogeny is developed. In this model, backarc spreading created a rift zone behind a (pre-Grenvillian) Elzevirian subduction zone that obliquely straddled the edge of a Mesoproterozoic continental margin. As a result of this geometry, the rift zone died out to the north as it propagated into cold Archean crust. Elzevirian subduction was probably halted by the collision of the continental margin with an offshore arc, and later with a major continental block, giving rise respectively to the Shawinigan and the Ottawan orogenic events. These collisional events can be grouped as parts of the Grenville Orogenic Cycle.
Paleomagnetism of Pleistocene widespread tephra deposits and its implication for tectonic rotation in central Japan

Abstract A single layer of widespread tephra deposits possibly can provide an instantaneous record of the past geomagnetic field and potentially can indicate even a small‐scale tectonic rotation compared to a range of geomagnetic secular variations. We report paleomagnetic data of the Ebisutoge–Fukuda tephra, which is dated at approximately 1.8 Ma and is distributed in central Japan between the Osaka–Kyoto area and the Boso Peninsula. The Fukuda volcanic ash layer and its correlative ash deposits in the Osaka–Kyoto area, near Lake Biwa and in the Mie and Niigata areas yield identical site mean declinations of approximately −170° after tilt correction, whereas moderate inclination shallowing is observed in the upper unit at several localities. Anisotropy measurements both of low‐field magnetic susceptibility and of anhysteretic remanent magnetization suggest that the inclination shallowing results from the biased alignment of magnetic grains, which were deposited in the fluvial environment. The source volcanic unit, Ebisutoge pyroclastic deposits in the Takayama area, yields a mean declination of approximately −155°, showing clockwise deflection from the magnetic directions of the correlative tephra deposits. These results suggest that no significant rotation occurred between the Osaka–Kyoto, Mie and Niigata areas, but that the Takayama area suffered a clockwise rotation in respect to the other areas during the Quaternary. This rotation might have been caused under an east–west stress field associated with the collision of the Okhotsk Plate with the Eurasia Plate.
Quantification of Neonatal Fc Receptor (FcRn) and Beta-2 Microglobulin (ß2M) in Human Liver Tissues by UPLC-MRM-Based Targeted Quantitative Proteomics for Applications in Biotherapeutic PBPK Models

Neonatal Fc receptor (FcRn) and beta-2 microglobulin (ß2M) play an important role in transporting maternal immunoglobulin G (IgG) to fetuses, maintaining the homeostasis of IgG and albumin in human body, and prolonging the half-life of IgG- or albumin-based biotherapeutics. Little is known about the influence of age, gender and race, and interindividual variability of human FcRn and ß2M on the protein level. In this study, an ultra-performance liquid chromatography (UPLC)-multiple reaction monitoring (MRM) mass spectrometry (MS)-based targeted quantitative proteomic method was developed and optimized for the quantification of human FcRn and ß2M. Among the 39 human livers studied (age 13 - 80 years), the mean ({plus minus} S.D.) concentrations of FcRn and ß2M were 147 ({plus minus} 39) and 1250 ({plus minus} 460) pmol/g of liver tissue, respectively. A four-fold interindividual variability (63 - 243 pmol/g of liver tissue) was observed for the hepatic FcRn concentration. A moderate correlation was found between the hepatic ß2M and FcRn expression levels. Influences of age, gender and race on the hepatic expression of FcRn and ß2M were evaluated. The findings from this study may aid the development of physiologically based pharmacokinetic models that incorporate empirical FcRn tissue concentrations and interindividual variabilities, and the development of personalized dosing of biopharmaceuticals. Significance Statement This is the first study to evaluate the influence of age, gender and race on the expression of FcRn and ß2M and their interindividual variability in human livers. This study describes a validated UPLC-MRM-based targeted quantitative proteomic method for quantifying human FcRn and ß2M in biological tissues. Results from this study may aid current development of PBPK models for biotherapeutics, where FcRn plays a significant role in clearance mechanism and its expression level and interindividual variability are largely unknown.
Cold filamentary intensification and oceanic surface convergence lines

The reflectance images of the oceanic surface are full of surfactant lines created by surface velocity convergences, with typical line spacings of 0.1–10 km, i.e., in the submesoscale range. Here we propose a dynamical explanation by the process of filamentary intensification that shrinks the transverse scale of rectilinear surface temperature extrema at a super‐exponential rate by the action of horizontal deformation flows associated with mesoscale eddies. This process is analogous to deformation‐induced frontogenesis with sharpening temperature gradients accelerated by its ageostrophic secondary circulation. In the particular case of cold filaments, the shrinking rate, surface convergence, and downwelling are especially strong because of the configuration of ageostrophic acceleration. This behavior is demonstrated theoretically with idealized two‐dimensional solutions and illustrated in a realistic regional circulation simulation near Peru.
Importance of pre‐existing oceanic conditions to upper ocean response induced by Super Typhoon Hai‐Tang

This study investigates upper ocean response to Super Typhoon Hai‐Tang, the most intense typhoon in 2005, in the western North Pacific using multi‐satellite microwave data, typhoon data and Argo profiles. Sequential merged microwave sea surface temperature (SST) images show that Hai‐Tang induced four separately cooling responses after its trail in the western North Pacific during 11–18 July. Comparison between upper ocean responses of cooling SST and pre‐typhoon sea surface height suggests that these cooling responses of the upper ocean to Hai‐Tang are closely associated with pre‐existing cyclonic circulation denoted by pre‐existing negative sea surface features. Furthermore, applying Argo profiles, the physical mechanism is confirmed to be associated with pre‐existing cyclonic circulations provide a relatively unstable thermodynamic structure, and therefore cold water would be brought up readily. This paper provides the rather convincing evidence that cyclonic flow and uplifted thermocline are the pre‐existing conditions for intensive cooling following the typhoon passage.
Intratherapeutic Biokinetic Measurements, Dosimetry Parameters Estimate, and Monitoring Treatment Efficacy using Cerenkov Luminescence Imaging in Preclinical Radionuclide Therapy

In recent years, there has been an increasing amount of interest in non-invasive Cerenkov Luminescence Imaging (CLI) of in vivo radionuclide distribution in small animals, a method proven as a high-throughput modality for confirmation of tracer uptake. 11B6 is an IgG 1 monoclonal antibody that is specific for free human kallikrein-related peptidase 2 (hK2) an antigen abundant in malignant prostatic tissue. Free hK2 was targeted in prostate cancer xenografts using 177 Lu-labeled 11B6 in either murine or humanized forms for radionuclide therapy (RNT). In this setting, CLI was investigated as a tool for providing parameters of dosimetric importance during RNT. First, longitudinal imaging of biokinetics using CLI and single-photon emission computed tomography (SPECT) was compared. Second, the CLI signal was correlated to quantitative ex vivo tumor activity measurements. Finally, CLI was used to monitor the radionuclide treatment and it was found that the integrated CLI radiance correlated well with subject-specific tumor volume reduction. Methods: 11B6 was radiolabeled with 177 Lu through the CHX-A ′′ -DTPA chelator. In vivo CLI and SPECT imaging of 177 Lu-DTPA-11B6 uptake was performed in NMRI and Balb/c nude mice with subcutaneous LNCaP xenografts up to 14 d post-injection (p.i.). Tumor size was measured to assess tumor response to radionuclide therapy. Results: CLI correlated well with SPECT imaging and could be employed up to 14 d p.i. of 20 MBq with the specific tracer used. By integrating the CLI radiance as a function of time, a dose metric for the tumors could be formed that correlated exponentially with tumor volume reduction. Conclusions: CLI provided valuable intratherapeutic biokinetic measurements for treatment monitoring and could be used as a tool for subject-specific absorbed dose estimation.
The concept of field capacity revisited: Defining intrinsic static and dynamic criteria for soil internal drainage dynamics

Across many soil types and conditions, post wetting soil internal drainage exhibits predictable dynamics that lead to a stable and repeatable hydration state termed “field capacity” (FC). Soil regulation of internal drainage toward FC has long been recognized as producing a useful hydrologic benchmark for modeling and for estimation of plant available soil water. To overcome ambiguities and inconsistencies in various ad hoc definitions of FC, we propose using a soil intrinsic characteristic length (a matric potential value derived from drainable soil pore size distribution) to characterize the loss of hydraulic continuity associated with the attainment of FC. The resulting static criterion for FC was extended to formulate a self‐consistent dynamic criterion based on soil internal drainage dynamics. A systematic evaluation of the proposed definitions of FC using numerical simulations and experimental data reveals remarkable consistency and predictability across a wide range of soil types. The new metrics add definitiveness and robustness of this widely used concept with potential expansion to additional agronomic, hydrologic, ecological, and climatic applications.
A Mini-Surge on the Ryder Glacier, Greenland, Observed by Satellite Radar Interferometry

Satellite radar interferometry reveals that the speed of the Ryder Glacier increased roughly threefold and then returned to normal (100 to 500 meters/year) over a 7-week period near the end of the 1995 melt season. The accelerated flow represents a substantial, though short-lived, change in ice discharge. During the period of rapid motion, meltwater-filled supraglacial lakes may have drained, which could have increased basal water pressure and caused the mini-surge. There are too few velocity measurements on other large outlet glaciers to determine whether this type of event is a widespread phenomenon in Greenland, but because most other outlet glaciers are at lower latitudes, they should experience more extensive melting, making them more susceptible to meltwater-induced surges.
Use of Interactive Voice Response Technology by Poison Centers during the H1N1 Outbreak

Web publication: 20 September 2010 Abstract Introduction: Interactive voice response (IVR) technology may facilitate poison centers to handle increased call volumes that may occur during public health emergencies. On 28 April 2009, the Texas Poison Center Network (TPCN) added a HlNl message in English and Spanish to its IVR system. This study tested whether IVR technology could be used to assist Texas poison centers during the HlNl outbreak. Methods: The distribution of callers who accessed the HlNl message during 29 April-31 May 2009 was determined with respect to message language, subsequent caller action, and date of the call. Results: The HlNl message was accessed by 1,142 callers, of whom, 92.9% listened to the message in English, and 7.1% listened to the message in Spanish. After listening to the message, 33.3% hung up while 66.7% spoke to a poison center agent. The number of callers who accessed the message was highest on 29 April 2009 and then declined. Conclusions: Interactive voice response technology can be used to assist poison centers to provide information and handle calls from the public during a 'public health emergency.
Effects of Hepatitis B Surface Antigen on Virus-specific and Global T Cells in Patients With Chronic HBV infection.

BACKGROUND & AIMS Chronic hepatitis B virus (HBV) infection is characterized by the presence of defective viral envelope proteins (hepatitis B surface antigen, HBsAg) and the duration of infection-most patients acquire the infection at birth or during the first years of life. We investigated the effects of these factors on patients' lymphocyte and HBV-specific T-cell populations. METHODS We collected blood samples and clinical data from 243 patients with HBV infection (3-75 years old) in the United Kingdom and China. We measured levels of HBV DNA, HBsAg, HBeAg, and alanine aminotransferase; analyzed HBV genotypes; and isolated peripheral blood mononuclear cells (PBMC). In PBMC from 48 patients with varying levels of serum HBsAg, we measured 40 markers on nature killer (NK) and T cells by mass cytometry. PBMC from 189 patients with chronic infection and 38 patients with resolved infections were incubated with HBV peptide libraries, and HBV-specific T cells were identified by interferon gamma ELISpot assays or flow cytometry. We used multivariate linear regression and performed variable selection using Akaike's information criterion to identify covariates associated with HBV-specific responses of T cells. RESULTS Although T and NK cell phenotypes and functions did not change with level of serum HBsAg, numbers of HBs-specific T cells correlated with serum levels of HBsAg (r=0.3367; P<.00001). After we performed the variable selection, the multivariate linear regression model identified patient age as the only factor significantly associated with numbers of HBs-specific T cells (P=.000115). In patients younger than 30 years, HBs-specific T cells constituted 28.26% of the total HBV-specific T cells; this value decrease to 7.14% in patients older than 30 years. CONCLUSIONS In an analysis of immune cells from patients with chronic HBV infection, we found the duration of HBsAg exposure, rather than quantity of HBsAg, associates with the level of anti-HBV immune response. Although the presence of HBs-specific T cells might not be required for clearance of HBV infection in all patients, strategies to restore anti-HBV immune responses should consider patients younger than 30 years.