Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of the Rhizobium meliloti ntrC gene: R. meliloti has separate regulatory pathways for activation of nitrogen fixation genes in free-living and symbiotic cells

We show here that Rhizobium meliloti, the nitrogen-fixing endosymbiont of alfalfa (Medicago sativa), has a regulatory gene that is structurally homologous to previously characterized ntrC genes in enteric bacteria. DNA sequence analysis showed that R. meliloti ntrC is homologous to previously sequenced ntrC genes from Klebsiella pneumoniae and Bradyrhizobium sp. (Parasponia) and that an ntrB-like gene is situated directly upstream from R. meliloti ntrC. Similar to its counterparts in K. pneumoniae and Escherichia coli, R. meliloti ntrC is expressed when the cells are grown in nitrogen-limiting media. In addition, R. meliloti ntrC is required for growth on media containing nitrate as the sole nitrogen source and for the ex planta transcription of several R. meliloti nif genes. On the other hand, root nodules elicited by R. meliloti ntrC mutants fix nitrogen as well as nodules elicited by wild-type R. meliloti. These latter results indicate that R. meliloti has separate regulatory pathways for activating nif gene expression ex planta and during symbiotic nitrogen fixation.
Design Opportunities for AAC and Children with Severe Speech and Physical Impairments

Augmentative and alternative communication (AAC) technologies can support children with severe speech and physical impairments (SSPI) to express themselves. Yet, these seemingly 'enabling' technologies are often abandoned by this target group, suggesting a need to understand how they are used in communication. Little research has considered the interaction between people, interaction design and the material dimension of AAC. To address this, we report on a qualitative video study that examines the situated communication of five children using AAC in a special school. Our findings offer a new perspective on reconceptualising AAC design and use revealing four areas for future design: (1) incorporating an embodied view of communication, (2) designing to emphasise children's competence and agency, (3) regulating the presence, prominence and value of AAC, and (4) supporting a wider range of communicative functions that help address children's needs.
Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations

Abstract Although the catalog of cancer-associated mutations in protein-coding regions is nearly complete for all major cancer types, an assessment of regulatory changes in cancer genomes and their clinical significance remain largely preliminary. Adopting bottom-up approach, we quantify the effects of different sources of gene expression variation in a cohort of 3899 samples from 10 cancer types. We find that copy number alterations, epigenetic changes, transcription factors and microRNAs collectively explain, on average, only 31–38% and 18–26% expression variation for cancer-associated and other genes, respectively, and that among these factors copy number alteration has the highest effect. We show that the genes with systematic, large expression variation that could not be attributed to these factors are enriched for pathways related to cancer hallmarks. Integrating whole genome sequencing data and focusing on genes with systematic expression variation we identify novel, recurrent regulatory mutations affecting known cancer genes such as NKX2-1 and GRIN2D in multiple cancer types. Nonetheless, at a genome-wide scale proportions of gene expression variation attributed to recurrent point mutations appear to be modest so far, especially when compared to that attributed to copy number changes – a pattern different from that observed for other complex diseases and traits. We suspect that, owing to plasticity and redundancy in biological pathways, regulatory alterations show complex combinatorial patterns, modulating gene expression in cancer genomes at a finer scale.
Loss of Large Predatory Sharks from the Mediterranean Sea

Abstract: Evidence for severe declines in large predatory fishes is increasing around the world. Because of its long history of intense fishing, the Mediterranean Sea offers a unique perspective on fish population declines over historical timescales. We used a diverse set of records dating back to the early 19th and mid 20th century to reconstruct long‐term population trends of large predatory sharks in the northwestern Mediterranean Sea. We compiled 9 time series of abundance indices from commercial and recreational fishery landings, scientific surveys, and sighting records. Generalized linear models were used to extract instantaneous rates of change from each data set, and a meta‐analysis was conducted to compare population trends. Only 5 of the 20 species we considered had sufficient records for analysis. Hammerhead (Sphyrna spp.), blue (Prionace glauca), mackerel (Isurus oxyrinchus and Lamna nasus), and thresher sharks (Alopias vulpinus) declined between 96 and 99.99% relative to their former abundance. According to World Conservation Union (IUCN) criteria, these species would be considered critically endangered. So far, the lack of quantitative population assessments has impeded shark conservation in the Mediterranean Sea. Our study fills this critical information gap, suggesting that current levels of exploitation put large sharks at risk of extinction in the Mediterranean Sea. Possible ecosystem effects of these losses involve a disruption of top‐down control and a release of midlevel consumers.
Antiviral Activity and Resistance Analysis of NS3/4A Protease Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons

ABSTRACT Although genotype 4 (GT4)-infected patients represent a minor overall percentage of the global hepatitis C virus (HCV)-infected population, the high prevalence of the genotype in specific geographic regions coupled with substantial sequence diversity makes it an important genotype to study for antiviral drug discovery and development. We evaluated two direct-acting antiviral agents—grazoprevir, an HCV NS3/4A protease inhibitor, and elbasvir, an HCV NS5A inhibitor—in GT4 replicons prior to clinical studies in this genotype. Following a bioinformatics analysis of available GT4 sequences, a set of replicons bearing representative GT4 clinical isolates was generated. For grazoprevir, the 50% effective concentration (EC50) against the replicon bearing the reference GT4a (ED43) NS3 protease and NS4A was 0.7 nM. The median EC50 for grazoprevir against chimeric replicons encoding NS3/4A sequences from GT4 clinical isolates was 0.2 nM (range, 0.11 to 0.33 nM; n = 5). The difficulty in establishing replicons bearing NS3/4A resistance-associated substitutions was substantially overcome with the identification of a G162R adaptive substitution in NS3. Single NS3 substitutions D168A/V identified from de novo resistance selection studies reduced grazoprevir antiviral activity by 137- and 47-fold, respectively, in the background of the G162R replicon. For elbasvir, the EC50 against the replicon bearing the reference full-length GT4a (ED43) NS5A gene was 0.0002 nM. The median EC50 for elbasvir against chimeric replicons bearing clinical isolates from GT4 was 0.0007 nM (range, 0.0002 to 34 nM; n = 14). De novo resistance selection studies in GT4 demonstrated a high propensity to suppress the emergence of amino acid substitutions that confer high-potency reductions to elbasvir. Phenotypic characterization of the NS5A amino acid substitutions identified (L30F, L30S, M31V, and Y93H) indicated that they conferred 15-, 4-, 2.5-, and 7.5-fold potency losses, respectively, to elbasvir. The activity profiles of grazoprevir and elbasvir supported the testing of the direct-acting antivirals in clinical studies.
Mechanisms of Streptomycin Resistance: Selection of Mutations in the 16S rRNA Gene Conferring Resistance

ABSTRACT Chromosomally acquired streptomycin resistance is frequently due to mutations in the gene encoding the ribosomal protein S12,rpsL. The presence of several rRNA operons (rrn) and a single rpsL gene in most bacterial genomes prohibits the isolation of streptomycin-resistant mutants in which resistance is mediated by mutations in the 16S rRNA gene (rrs). Three strains were constructed in this investigation: Mycobacterium smegmatis rrnB,M. smegmatis rpsL3+, and M. smegmatis rrnB rpsL3+. M. smegmatis rrnB carries a single functional rrnoperon, i.e., rrnA (comprised of 16S, 23S, and 5S rRNA genes) and a single rpsL+gene; M. smegmatis rpsL3+ is characterized by the presence of two rrn operons (rrnA and rrnB) and threerpsL+ genes; and M. smegmatis rrnB rpsL3+ carries a single functionalrrn operon (rrnA) and threerpsL+ genes. By genetically altering the number of rpsL and rrs alleles in the bacterial genome, mutations in rrs conferring streptomycin resistance could be selected, as revealed by analysis of streptomycin-resistant derivatives of M. smegmatis rrnB rpsL3+. Besides mutations well known to confer streptomycin resistance, novel streptomycin resistance conferring mutations were isolated. Most of the mutations were found to map to a functional pseudoknot structure within the 530 loop region of the 16S rRNA. One of the mutations observed, i.e., 524G→C, severely distorts the interaction between nucleotides 524G and 507C, a Watson-Crick interaction which has been thought to be essential for ribosome function. The use of the single rRNA allelic M. smegmatis strain should help to elucidate the principles of ribosome-drug interactions.
Investigation of a potential drug-drug interaction between salbutamol and ambroxol and bioequivalence of a new fixed-dose combination containing these two drugs in healthy Chinese subjects.

OBJECTIVES The aims of the study were to investigate the potential drug-drug interaction between salbutamol and ambroxol, the bioequivalence of the new fixed-dose combination containing salbutamol and ambroxol compared with co-administration of the two separate formulations, and to describe the safety and tolerability of the fixed-dose combination formulation in healthy Chinese volunteers. MATERIALS AND METHODS An open-label, single-dose, four-treatment, four-period crossover study for evaluation of drug-drug interaction and bioequivalence (n = 24) was performed. Each participant received salbutamol 4 mg, ambroxol 15 mg, salbutamol 4 mg co-administered with ambroxol 15 mg or fixed-dose combination formulation (salbutamol 4 mg and ambroxol 15 mg). Plasma concentrations of two analytes were determined with the use of validated LC-MS/MS method. Safety and tolerability were assessed by recording adverse events. RESULTS Co-administration of salbutamol and ambroxol was not associated with a significant influence on single salbutamol or ambroxol pharmacokinetics. After statistical comparisons of log-transformed Cmax and AUC of salbutamol and ambroxol between fixed-dose combination and concomitant treatments, all 90% confidence intervals of geometric mean ratios were within the predefined equivalence range of 80 - 125%. No serious adverse events were reported, and all treatments were safe and well tolerated in Chinese healthy subjects. CONCLUSION There were no significant drug-drug pharmacokinetic interactions between salbutamol and ambroxol after oral administration. The new formulation was bioequivalent to the co-administration of two drugs in separate dosage forms.
Fluorescent Probe DCVJ Shows High Sensitivity for Characterization of Amyloid β‐Peptide Early in the Lag Phase

The aggregation of intrinsically disordered and misfolded proteins in the form of oligomers and fibrils plays a crucial role in a number of neurological and neurodegenerative diseases. Currently, most probes and biophysical techniques that detect and characterize fibrils at high resolution fail to show sensitivity and binding for oligomers. Here, we show that 9‐(dicyano‐vinyl)julolidine (DCVJ), a class of molecular rotor, binds amyloid beta (Aβ) early aggregates, and we report the kinetics as well as packing of the oligomer formation. The binding of DCVJ to Aβ40 increased its emission intensity with time at 510 nm and produced a second excimer peak at 575 nm. However, DCVJ did not bind to the prefibrillar aggregates of Aβ42, which indicated that the oligomers formed by Aβ40 and Aβ42 were not the same. The F4C F19W mutant of Aβ40, which did not form fibrils, also bound DCVJ, but the emission spectral profile varied from that of the wild‐type (WT). Atomic force microscopy images of WT Aβ40, the F4C F19W mutant, and Aβ42 oligomers displayed differences in size and shape, confirming the difference in their DCVJ spectra. The effect of epigallocatechin‐3‐gallate (EGCG) on the reduction of Aβ42 fibrils was also observed with finer detail than with other techniques. The results of this study show that DCVJ detects early aggregates and provides valuable information regarding the oligomer kinetics, packing, and mechanism of formation.
The influence of traffic on heavy-duty vehicle platoon formation

Heavy-duty vehicle (HDV) platooning is a mean to significantly reduce the fuel consumption for the trailing vehicle. By driving close to the vehicle in front, the air drag is reduced tremendously. Due to each HDV being assigned with different transport missions, platoons will need to be frequently formed, merged, and split. Driving on the road requires interaction with surrounding traffic and road users, which will influence how well a platoon can be formed. In this paper, we study how traffic may affect a merging maneuver of two HDVs trying to form a platoon. We simulate this for different traffic densities and for different HDV speeds. Even on moderate traffic density, a platoon merge could be delayed with 20 % compared to the ideal case with no traffic.
Presumptive BSE cases with an aberrant prion protein phenotype in Switzerland, 2011: Lack of prion disease in experimentally inoculated cattle and bovine prion protein transgenic mice

Bovine spongiform encephalopathy (BSE) is caused by different prion strains that are discriminated by the molecular characteristics of the pathological prion protein. In 2011, Switzerland reported two presumptive cases of BSE in cattle with a prion protein phenotype different from previously described strains, and it was unclear whether these findings were related to a transmissible disease and have implications on animal and public health. In this study, brain tissues of these cases were inoculated into transgenic mice expressing the bovine prion protein (BoPrP-Tg110) and into cattle. Clinical and pathological investigations as well as molecular testing did not provide evidence for the presence of BSE in the Swiss cases after two passages in BoPrP-Tg110 mice and a challenge period of 3.5 years in cattle. This lack of disease transmission suggests that the Swiss 2011 cases were not affected by a prion disease and were unrelated to the feed-born BSE epidemic.
High-Contrast Imaging of Cholesterol Crystals in Rabbit Arteries Ex Vivo Using LED-Based Polarization Microscopy

Detection of cholesterol crystals (Chcs) in atherosclerosis disease is important for understanding the pathophysiology of atherosclerosis. Polarization microscopy (PM) has been in use traditionally for detecting Chcs, but they have difficulty in distinguishing Chcs with other crystalline materials in tissue, such as collagens. Thus, most studies using PM have been limited to studying cell-level samples. Although various methods have been proposed to detect Chcs with high specificity, most of them have low signal-to-noise ratios, a high system construction cost, and are difficult to operate due to a complex protocol. To address these problems, we have developed a simple and inexpensive universal serial bus (USB) PM system equipped with a 5700 K cool-white light-emitting diode (LED). In this system, Chcs are shown in a light blue color while collagen is shown in a yellow color. More importantly, the contrast between Chcs and collagens is improved by a factor of 2.3 under an aqueous condition in these PM images. These imaging results are well-matched with the ones acquired with two-photon microscopy (TPM). The system can visualize the features of atherosclerosis that cannot be visualized by the conventional hematoxylin and eosin and oil-red-o staining methods. Thus, we believe that this simple USB PM system can be widely used to identify Chcs in atherosclerosis.
NADPH oxidase 2 does not contribute to early reperfusion-associated reactive oxygen species generation following transient focal cerebral ischemia

Excess production of reactive oxygen species (ROS) critically contributes to occurrence of reperfusion injury, the paradoxical response of ischemic brain tissue to restoration of cerebral blood flow. However, the enzymatic sources of ROS generation remain to be unclear. This study examined Nox2-containing NADPH oxidase (Nox2) expression and its activity in ischemic brain tissue following post-ischemic reperfusion to clarify the mechanism of enzymatic reaction of ROS. Male Sprague-Dawley rats were subjected to 90-minute middle cerebral artery occlusion, followed by 3 or 22.5 hours of reperfusion. Quantitative reverse transcriptase PCR and western blot assay were performed to measure mRNA and protein expression of Nox2. Lucigenin fluorescence assays were performed to assess Nox activity. Our data showed that Nox2 mRNA and protein expression levels were significantly increased (3.7-fold for mRNA and 3.6-fold for protein) in ischemic brain tissue at 22.5 hours but not at 3 hours following post-ischemic reperfusion. Similar results were obtained for the changes of NADPH oxidase activity in ischemic cerebral tissue at the two reperfusion time points. Our results suggest that Nox2 may not contribute to the early burst of reperfusion-related ROS generation, but is rather an important source of ROS generation during prolonged reperfusion.
Wood of Giant Sequoia: properties and unique characteristics

Wood properties of giant sequoia (Sequoia gigantea [Lindl.] Decne.) were compared with those for other coniferous tree species. Wood properties such as specific gravity, various mechanical properties, extractive content, and decay resistance of young-growth giant sequoia are comparable to or more fa­ vorable than those of coast redwood (Sequoia sempervirens [D. Don] Endl.). It is recommended that giant sequoia be considered for planting stock in managed production forests to increase future supplies of wood having the characteristics so highly valued in coast redwood and other decay-resistant species. Giant sequoia (Sequoia gigantea [Lindl.] Decne.) is one of the oldest and certainly the largest living organism on earth. I have been studying giant sequoia and coast redwood (Sequoia sempervirens [D. Don] Endl.) since 1970. Although knowledge of both species is steadily improving, the focus has been on coast redwood, primarily because of its commercial importance. For this reason, correcting the many misleading generalizations about giant sequoia has been a slow and sometimes agonizing process. The wood from giant sequoia trees has had the repu­ tation of being very brash (brittle) and of little use for lumber products. This belief fails to distinguish differences between oldand young-growth trees, and it fails to recognize the wide range of wood products obtainable from forest trees besides lumber, e.g., particleboard, plywood, and paper (Piirto and Wilcox 1981). This paper has two objectives: First, to compare the wood properties of native grown giant sequoia to coast redwood, in­ cense cedar (Libocedrus decurrens Torn), white fir (Abies concolor [Gord. and Glend.] Lindl. ex Hildebr.) and western redcedar (Thuja plicata Donn). And, second, to emphasize the value of giant sequoia in both National Parks and in production forestry (e.g., plantations containing giant sequoia). It also highlights key points in the following subject areas: (1) general char­ acteristics and minute anatomy (2) physical and mechanical properties (3) chemical composition (4) natural decay resistance, and (5) utilization. Several excellent studies on the wood properties of giant se­ quoia grown outside of its native range have been and are being conducted in several foreign countries (Finogeev and Kuznecov 1969, Liubimirescu and others 1972, Knigge 1983, Knigge and Wenzel 1982, Knigge and others 1983). Presented at the Workshop on Management of Giant Sequoia, May 24-25, 1985, Reedley, California. Associate professor, California Polytechnic State University, San Luis
Reduction of severe visual loss and complications following intra-arterial chemotherapy (IAC) for refractory retinoblastoma

Background Intra-arterial chemotherapy (IAC) for retinoblastoma has been documented as causing visual loss and ocular motility problems. A lack of safety data has precluded its acceptance in all centres. Methods Retrospective cohort study of patients with retinoblastoma from 2013 to 2015 who had a healthy foveola and relapsed following systemic chemotherapy. All required IAC. The correlation of complications with doses of melphalan +/− topotecan used and putative catheterisation complications was assessed. Ocular complications were determined using vision, macular (including pattern visual evoked potentials (PVEPs)), retinal electroretinograms (ERGs) and ocular motility functions. Efficacy (tumour control) was also assessed. Results All eyes had age appropriate doses of melphalan with five having additional doses of topotecan. Severe physiological reactions requiring adrenaline were seen in six patients during the catheterisation procedure. Difficulty was documented in accessing the ophthalmic artery in 7/27 catheterisations. The median/mean number of courses of chemotherapy was three. No child had severe visual loss as assessed by age appropriate tests (median follow-up 20.9 months, range 3.7–35.2 months). One child had nasal choroidal ischaemia and a sixth nerve palsy. Post-IAC PVEPs were performed in eight and reported as normal. All post-IAC ERGs were normal apart from one (total dose 20 mg melphalan 0.8 mg topotecan). Tumour control was achieved in six of nine cases. Conclusion The proportion of visual and ocular motility complications may be reduced by providing age-adjusted doses of melphalan. Dose rather than complications from catheterisation is the most important risk factor for ocular injury.
Diffusion and near-equilibrium distribution of MRI and CT contrast agents in articular cartilage

Charged contrast agents have been used both in vitro and in vivo for estimation of the fixed charge density (FCD) in articular cartilage. In the present study, the effects of molecular size and charge on the diffusion and equilibrium distribution of several magnetic resonance imaging (MRI) and computed tomography (CT) contrast agents were investigated. Full thickness cartilage disks (Ø = 4.0 mm, n = 64) were prepared from fresh bovine patellae. Contrast agent (gadopentetate: Magnevist®, gadodiamide: Omniscan™, ioxaglate: Hexabrix™ or sodium iodide: NaI) diffusion was allowed either through the articular surface or through the deep cartilage. CT imaging of the samples was conducted before contrast agent administration and after 1, 5, 9, 16, 25 and 29 h (and with three samples after 2, 3, 4 and 5 days) diffusion using a clinical peripheral quantitative computed tomography (pQCT) instrument. With all contrast agents, the diffusion through the deep cartilage was slower when compared to the diffusion through the articular surface. With ioxaglate, gadopentetate and gadodiamide it took over 29 h for diffusion to reach the near-equilibrium state. The slow diffusion of the contrast agents raise concerns regarding the validity of techniques for FCD estimation, as these contrast agents may not reach the equilibrium state that is assumed. However, since cartilage composition, i.e. deep versus superficial, had a significant effect on diffusion, imaging of the nonequilibrium diffusion process might enable more accurate assessment of cartilage integrity.