Miracle-dz/UniFAR-FTUs huggingface dataset:
Uptake of C14-atrazine by prairie grasses in a phytoremediation setting

ABSTRACT Agrochemicals significantly contribute to environmental pollution. In the USA, atrazine is a widely used pesticide and commonly found in rivers, water systems, and rural wells. Phytoremediation can be a cost-effective means of removing pesticides from soil. The objective of this project was to investigate the ability of prairie grasses to remove atrazine. 14C-labeled atrazine was added to sterilized sand and water/nutrient cultures, and the analysis was performed after 21 days. Switchgrass and big bluestem were promising species for phytoremediation, taking up about 40% of the applied [14C] in liquid hydroponic cultures, and between 20% and 33% in sand cultures. Yellow Indiangrass showed low resistance to atrazine toxicity and low uptake of [14C] atrazine in liquid hydroponic cultures. Atrazine degradation increased progressively from sand to roots and leaves. Most atrazine taken up by prairie grasses from sand culture was degraded to metabolites, which accounted for 60–80% of [14C] detected in leaves. Deisopropylatrazine (DIA) was the main metabolite detected in sand and roots, whereas in leaves further metabolism took place, forming increased amounts of didealkylatrazine (DDA) and an unidentified metabolite. In conclusion, prairie grasses achieved high atrazine removal and degradation, showing a high potential for phytoremediation.
Bacteriophage therapy for membrane biofouling in membrane bioreactors and antibiotic‐resistant bacterial biofilms

To demonstrate elimination of bacterial biofilm on membranes to represent wastewater treatment as well as biofilm formed by antibiotic‐resistant bacterial (ARB) to signify medical application, an antibiotic‐resistant bacterium and its lytic bacteriophage were isolated from a full‐scale wastewater treatment plant. Based on gram staining and complete 16 S rDNA sequencing, the isolated bacterium showed a more than 99% homology with Delftia tsuruhatensis, a gram‐negative bacterium belonging to β‐proteobacteria. The Delftia lytic phage's draft genome revealed the phage to be an N4‐like phage with 59.7% G + C content. No transfer RNAs were detected for the phage suggesting that the phage is highly adapted to its host Delftia tsuruhatensis ARB‐1 with regard to codon usage, and does not require additional tRNAs of its own. The gene annotation of the Delftia lytic phage found three different components of RNA polymerase (RNAP) in the genome, which is a typical characteristic of N4‐like phages. The lytic phage specific to D. tsuruhatensis ARB‐1 could successfully remove the biofilm formed by it on a glass slide. The water flux through the membrane of a prototype lab‐scale membrane bioreactor decreased from 47 L/h m2 to ∼15 L/h m2 over 4 days due to a biofilm formed by D. tsuruhatensis ARB‐1. However, the flux increased to 70% of the original after the lytic phage application. Overall, this research demonstrated phage therapy's great potential to solve the problem of membrane biofouling, as well as the problems posed by pathogenic biofilms in external wounds and on medical instruments. Biotechnol. Bioeng. 2015;112: 1644–1654. © 2015 Wiley Periodicals, Inc.
[Vocal effectiveness in speech and singing: acoustical, physiological and perceptive aspects. applications in speech therapy].

OBJECTIVE What is vocal effectiveness in lyrical singing in comparison to speech? Our study tries to answer this question, using vocal efficiency and spectral vocal effectiveness. MATERIAL AND METHODS Vocal efficiency was mesured for a trained and untrained subject. RESULTS According to these invasive measures, it appears that the trained singer uses her larynx less efficiently. Efficiency of the larynx in terms of energy then appears to be secondary to the desired voice quality. The acoustic measures of spectral vocal effectiveness of vowels and sentences, spoken and sung by 23 singers, reveal two complementary markers: The "singing power ratio" and the difference in amplitude between the singing formant and the spectral minimum that follows it. Magnetic resonance imaging and simulations of [a], [i] and [o] spoken and sung show laryngeal lowering and the role of the piriform sinuses as the physiological foundations of spectral vocal effectiveness, perceptively related to carrying power. CONCLUSION These scientifical aspects allow applications in voice therapy, such as physiological and perceptual foundations allowing patients to recuperate voice carrying power with or without background noise.
Periodontal Disease and Risk of Preeclampsia: A Meta-Analysis of Observational Studies

Background Many epidemiological studies have found a positive association between periodontal disease (PD) and the risk of preeclampsia, but the magnitude of this association varies and independent studies have reported conflicting findings. We performed a meta-analysis to ascertain the relationship between PD and preeclampsia. Methods The PubMed database was searched up to January 12, 2013, for relevant observational studies on an association between PD and the risk of preeclampsia. Data were extracted and analyzed independently by two authors. The meta-analysis was performed using comprehensive meta-analysis software. Results Thirteen observational case-control studies and two cohort studies, involving 1089 preeclampsia patients, were identified. Based on a random-effects meta-analysis, a significant association between PD and preeclampsia was identified (odds ratio = 2.79, 95% confidence interval CI, 2.01–3.01, P<0.0001). Conclusions Although the causality remains unclear, the association between PD and preeclampsia may reflect the induction of PD by the preeclamptic state, or it may be part of an overall exaggerated inflammatory response to pregnancy. Larger randomized controlled trials with preeclampsia as the primary outcome and pathophysiological studies are required to explore causality and to dissect the biological mechanisms involved.
Comparison of Sensitivity of Immunofluorescent Microscopy to That of a Combination of Immunofluorescent Microscopy and Immunomagnetic Separation for Detection of Cryptosporidium parvum Oocysts in Adult Bovine Feces

ABSTRACT A direct immunofluorescence assay (DFA) (Merifluor; Meridian Diagnostics, Inc., Cincinnati, Ohio) was compared to an immunomagnetic separation (IMS) assay (Dynabeads; Dynal, Inc., Lake Success, N.Y.) coupled with immunofluorescent microscopy (Waterborne, Inc., New Orleans, La.) for their ability to detect low concentrations ofCryptosporidium parvum oocysts in adult bovine fecal material. IMS-DFA resulted in a 2-log-unit increase in sensitivity (10 oocysts/g) compared to DFA alone (1,000 oocysts/g). The higher sensitivity obtained with IMS-DFA resulted from testing 2 g of fecal material instead of the 13 to 19 mg of fecal material tested in the DFA; the increased sensitivity was not attributable to a higher percent recovery.
Actomyosin Contraction at the Cell Rear Drives Nuclear Translocation in Migrating Cortical Interneurons

Neuronal migration is a complex process requiring the coordinated interaction of cytoskeletal components and regulated by calcium signaling among other factors. Migratory neurons are polarized cells in which the largest intracellular organelle, the nucleus, has to move repeatedly. Current views support a central role for pulling forces that drive nuclear movement. The participation of actomyosin driven forces acting at the nucleus rear has been suggested, however its precise contribution has not been directly addressed. By analyzing interneurons migrating in cortical slices of mouse brains, we have found that nucleokinesis is associated with a precise pattern of actin dynamics characterized by the initial formation of a cup-like actin structure at the rear nuclear pole. Time-lapse experiments show that progressive actomyosin contraction drives the nucleus forward. Nucleokinesis concludes with the complete contraction of the cup-like structure, resulting in an actin spot at the base of the retracting trailing process. Our results demonstrate that this actin remodeling requires a threshold calcium level provided by low-frequency spontaneous fast intracellular calcium transients. Microtubule stabilization with taxol treatment prevents actin remodeling and nucleokinesis, whereas cells with a collapsed microtubule cytoskeleton induced by nocodazole treatment, display nearly normal actin dynamics and nucleokinesis. In summary, the results presented here demonstrate that actomyosin forces acting at the rear side of the nucleus drives nucleokinesis in tangentially migrating interneurons in a process that requires calcium and a dynamic cytoskeleton of microtubules.
Assessment of hepatitis C virus RNA and genotype from 6807 patients with chronic hepatitis C in the United States

Hepatitis C virus (HCV) RNA status and HCV genotype have become important tools in the diagnosis and monitoring of therapy in chronic HCV infection. To establish a database with respect to HCV genotype and serum HCV RNA concentrations in chronic hepatitis C patients in the United States, we analysed 6807 chronic hepatitis C patients who had HCV RNA and HCV genotype tests conducted at a central laboratory. The HCV RNA concentration cut‐off for the lower 25th percentile of this population (low titre) was 0.9 × 106 copies ml–1. The median HCV RNA concentration was 3.5 × 106 copies ml–1 and the cut‐off for the upper 25th percentile (high titre) was 5 × 106 copies ml–1. Male patients had a median HCV RNA concentration of 3.9 × 106 copies ml–1, which was significantly higher than the median HCV RNA level for females (2.75 × 106 copies ml–1; P < 0.001). HCV genotype 1 was detected in 73% of patients; genotype 2 in 14%; genotype 3 in 8%; mixed genotype in 4%; and genotypes 4, 5 and 6 with a frequency of < 1%. Patients from the Northeast, Southeast and Midwest had significantly (P < 0.001) more infections with genotype 1 than patients from the Western and Southern regions. African–American patients were more likely to be infected with genotype 1 when compared with Caucasian, Hispanic or Asian Pacific Islanders (P < 0.001). Patients infected with HCV genotype 1 and mixed HCV genotypes had significantly higher serum HCV RNA concentrations when compared with HCV genotypes 2 and 3 (P < 0.001 for all comparisons).
The zebrafish fgf24 mutant identifies an additional level of Fgf signaling involved in vertebrate forelimb initiation

The development of vertebrate limb buds is triggered in the lateral plate mesoderm by a cascade of genes, including members of the Fgf and Wnt families, as well as the transcription factor tbx5. Fgf8, which is expressed in the intermediate mesoderm, is thought to initiate forelimb formation by activating wnt2b, which then induces the expression of tbx5 in the adjacent lateral plate mesoderm. Tbx5, in turn, is required for the activation of fgf10, which relays the limb inducing signal to the overlying ectoderm. We show that the zebrafish fgf24 gene, which belongs to the Fgf8/17/18 subfamily of Fgf ligands, acts downstream of tbx5 to activate fgf10 expression in the lateral plate mesoderm. We also show that fgf24 activity is necessary for the migration of tbx5-expressing cells to the fin bud, and for the activation of shh, but not hand2, expression in the posterior fin bud.
Unveiling the Organisms behind Novel Eukaryotic Ribosomal DNA Sequences from the Ocean

ABSTRACT Despite the fact that the smallest eukaryotes (cells less than 5 μm in diameter) play key roles in marine food webs, particularly in open oligotrophic areas, the study of their in situ diversity started just one year ago. Perhaps the most remarkable finding of the most recent studies has been the discovery of completely new phylogenetic lineages, such as novel clades belonging to the stramenopile and alveolate phyla. The two new groups account for a significant fraction of clones in genetic libraries from North Atlantic, equatorial Pacific, Antarctic, and Mediterranean Sea waters. However, the identities and ecological relevance of these organisms remain unknown. Here we investigate the phylogenetic relationships, morphology, in situ abundance, and ecological role of novel stramenopiles. They form at least eight independent clades within the stramenopile basal branches, indicating a large phylogenetic diversity within the group. Two lineages were visualized and enumerated in field samples and enrichments by fluorescent in situ hybridization using specific rRNA-targeted oligonucleotide probes. The targeted organisms were 2- to 3-μm-diameter, round-shaped, nonpigmented flagellates. Further, they were found to be bacterivorous. One lineage accounted for up to 46% (average during an annual cycle, 19%) of heterotrophic flagellates in a coastal environment, providing evidence that novel stramenopiles are important and unrecognized components of the total stock of bacterial grazers.
The Small Molecule, LLL12, Inhibits STAT3 Phosphorylation and Induces Apoptosis in Medulloblastoma and Glioblastoma Cells

Tumors of the central nervous system represent a major source of cancer-related deaths, with medulloblastoma and glioblastoma being the most common malignant brain tumors in children and adults respectively. While significant advances in treatment have been made, with the 5-year survival rate for medulloblastoma at 70–80%, treating patients under 3 years of age still poses a problem due to the deleterious effects of radiation on the developing brain, and the median survival for patients with glioblastoma is only 15 months. The transcription factor, STAT3, has been found constitutively activated in a wide variety of cancers and in recent years it has become an attractive therapeutic target. We designed a non-peptide small molecule STAT3 inhibitor, LLL12, using structure-based design. LLL12 was able to inhibit STAT3 phosphorylation, decrease cell viability and induce apoptosis in medulloblastoma and glioblastoma cell lines with elevated levels of p-STAT3 (Y705). IC50 values for LLL12 were found to be between 1.07 µM and 5.98 µM in the five cell lines expressing phosphorylated STAT3. STAT3 target genes were found to be downregulated and a decrease in STAT3 DNA binding was observed following LLL12 treatment, indicating that LLL12 is an effective STAT3 inhibitor. LLL12 was also able to inhibit colony formation, wound healing and decreased IL-6 and LIF secretion. Our results suggest that LLL12 is a potent STAT3 inhibitor and that it may be a potential therapeutic treatment for medulloblastoma and glioblastoma.
Reset of human neocortical oscillations during a working memory task

Both amplitude and phase of rhythmic slow-wave electroencephalographic activity are physiological correlates of learning and memory in rodents. In humans, oscillatory amplitude has been shown to correlate with memory; however, the role of oscillatory phase in human memory is unknown. We recorded intracranial electroencephalogram from human cortical and hippocampal areas while subjects performed a short-term recognition memory task. On each trial, a series of four list items was presented followed by a memory probe. We found agreement across trials of the phase of oscillations in the 7- to 16-Hz range after randomly timed stimulus events, evidence that these events either caused a phase shift in the underlying oscillation or initiated a new oscillation. Phase locking in this frequency range was not generally associated with increased poststimulus power, suggesting that stimulus events reset the phase of ongoing oscillations. Different stimulus classes selectively modulated this phase reset effect, with topographically distinct sets of recording sites exhibiting preferential reset to either probe items or to list items. These findings implicate the reset of brain oscillations in human working memory.
Learning from one example in machine vision by sharing probability densities

Human beings exhibit rapid learning when presented with a small number of images of a new object. A person can identify an object under a wide variety of visual conditions after having seen only a single example of that object. This ability can be partly explained by the application of previously learned statistical knowledge to a new setting. This thesis presents an approach to acquiring knowledge in one setting and using it in another. Specifically, we develop probability densities over common image changes. Given a single image of a new object and a model of change learned from a different object, we form a model of the new object that can be used for synthesis, classification, and other visual tasks. We start by modeling spatial changes. We develop a framework for learning statistical knowledge of spatial transformations in one task and using that knowledge in a new task. By sharing a probability density over spatial transformations learned from a sample of handwritten letters, we develop a handwritten digit classifier that achieves 88.6% accuracy using only a single hand-picked training example from each class. The classification scheme includes a new algorithm, congealing , for the joint alignment of a set of images using an entropy minimization criterion. We investigate properties of this algorithm and compare it to other methods of addressing spatial variability in images. We illustrate its application to binary images, gray-scale images, and a set of 3-D neonatal magnetic resonance brain volumes. Next, we extend the method of change modeling from spatial transformations to color transformations. By measuring statistically common joint color changes of a scene in an office environment, and then applying standard statistical techniques such as principal components analysis, we develop a probabilistic model of color change. We show that these color changes, which we call color flows, can be shared effectively between certain types of scenes. That is, a probability density over color change developed by observing one scene can provide useful information about the variability of another scene. We demonstrate a variety of applications including image synthesis, image matching, and shadow detection. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Ieee Transactions on Visualization and Computer Graphics Interpenetration Free Simulation of Thin Shell Rigid Bodies

—We propose a new algorithm for rigid body simulation that guarantees each body is in an interpenetration free state, both increasing the accuracy and robustness of the simulation as well as alleviating the need for ad hoc methods to separate bodies for subsequent simulation and rendering. We cleanly separate collision and contact resolution such that objects move and collide in the first step, with resting contact handled in the second step. The first step of our algorithm guarantees that each time step produces geometry that does not intersect or overlap by using an approximation to the continuous collision detection (and response) problem and thus is amenable to thin shells and degenerately flat objects moving at high speeds. In addition we introduce a novel failsafe which allows us to resolve all interpenetration without iterating to convergence. Since the first step guarantees a non-interfering state for the geometry, in the second step we propose a contact model for handling thin shells in proximity considering only the instantaneous locations at the ends of the time step.
Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex

The assembly of the preinitiation complex (PIC) occurs upstream of the +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled with the histone variant H2A.Z. To understand the contribution of the transcription machinery in the disassembly of the +1 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A quantitative ChIP-seq approach, which allows detection of global occupancy change, was employed to measure H2A.Z occupancy. Blocking PIC assembly resulted in promoter-specific H2A.Z accumulation, indicating that the PIC is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected upon depletion of INO80, a remodeler previously reported to displace nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at active and infrequently transcribed genes, indicating that constitutive H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z turnover precisely mark transcript starts, providing a new metric for identifying cryptic and alternative sites of initiation. DOI: http://dx.doi. org/10.7554/eLife.14243. 001
Scaling of the Raman gain coefficient: applications to germanosilicate fibers

This paper presents a comprehensive analysis of the temperature dependence of a Raman amplifier and the scaling of the Raman gain coefficient with wavelength, modal overlap, and material composition. The temperature dependence is derived by applying a quantum theoretical description, whereas the scaling of the Raman gain coefficient is derived using a classical electromagnetic model. We also present experimental verification of our theoretical findings.
One-cell biopsy significantly improves the outcome of preimplantation genetic diagnosis (PGD) treatment: retrospective analysis of 569 PGD cycles at the Stockholm PGD centre.

STUDY QUESTION What are the significant factors that influence the outcome of a PGD treatment? SUMMARY ANSWER The age of the woman and the number of biopsied cells per embryo are of significant importance for a successful PGD treatment. WHAT IS KNOWN ALREADY Younger women are more likely to succeed with an IVF treatment. STUDY DESIGN, SIZE, DURATION Cohort study, retrospective analysis of 569 PGD cycles, 1996-2009. PARTICIPANTS, SETTING, METHODS 256 couples and 569 PGD treatments at 'Stockholm PGD centre'. At this centre after 2003, a 1-cell policy was applied, when possible, with respect to the reliability of the diagnostic test and since 2009, 1-cell biopsy policy was also applied for monogenic disorders. MAIN RESULTS AND THE ROLE OF CHANCE The women under 36 years of age were three times more likely to get pregnant after PGD treatment, P = 0.003 and odds ratio 3.1 [95% confidence interval (CI) 1.5-6.5]. The 1-cell biopsy cycles were twice as likely to result in a pregnancy in comparison with cycles were 2 cells were removed from the embryo, P = 0.0013 and odds ratio 2.55 (95% CI 1.44-4.52). No other factors were found to be significant for the outcome. LIMITATIONS, REASONS FOR CAUTION Retrospective analysis with 1- and 2-cell biopsies at different times. WIDER IMPLICATIONS OF THE FINDINGS The results will have an impact on the implementation of PGD in general, thereby making it possible to significantly improve the treatment outcome.
Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study

Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of 1H-13C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae.