Miracle-dz/UniFAR-FTUs huggingface dataset:
Survey of the genomic landscape surrounding the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant Amaranthus palmeri from geographically distant populations in the USA.

BACKGROUND Glyphosate resistance in Amaranthus palmeri, one of the most prevalent herbicide-resistant weeds in the USA, is attributable to amplification and increased expression of the gene encoding the target site of glyphosate, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). The EPSPS gene and the surrounding 287 kilobases (kb) of amplified sequence are unique to glyphosate-resistant plants and termed the EPSPS cassette. It has only been sequenced in one A. palmeri population from Mississippi. This research compares EPSPS cassettes in seven resistant and five sensitive populations from geographically distant locations within the USA, including Mississippi, Arizona, Kansas, Maryland, Delaware and Georgia. RESULTS Polymerase chain reaction (PCR) products from 40 primer pairs specific to the cassette were similar in size and sequence in resistant populations. Several primer pairs failed to generate PCR products in sensitive populations. Regions of the cassette sequenced in the resistant populations were found to be nearly identical to those from Mississippi. Gene expression analysis showed that both EPSPS and another gene in the cassette, a reverse transcriptase, were elevated in all resistant populations tested relative to the sensitive populations. CONCLUSION EPSPS cassettes from distant resistant populations were nearly homologous. Considering the complexity of the cassette, and the degree of similarity among some cassette sequences, the results are consistent with the hypothesis that glyphosate resistance probably evolved once and then rapidly spread across the USA. © 2017 Society of Chemical Industry.
A comparison of four porewater sampling methods for metal mixtures and dissolved organic carbon and the implications for sediment toxicity evaluations

Evaluations of sediment quality conditions are commonly conducted using whole‐sediment chemistry analyses but can be enhanced by evaluating multiple lines of evidence, including measures of the bioavailable forms of contaminants. In particular, porewater chemistry data provide information that is directly relevant for interpreting sediment toxicity data. Various methods for sampling porewater for trace metals and dissolved organic carbon (DOC), which is an important moderator of metal bioavailability, have been employed. The present study compares the peeper, push point, centrifugation, and diffusive gradients in thin films (DGT) methods for the quantification of 6 metals and DOC. The methods were evaluated at low and high concentrations of metals in 3 sediments having different concentrations of total organic carbon and acid volatile sulfide and different particle‐size distributions. At low metal concentrations, centrifugation and push point sampling resulted in up to 100 times higher concentrations of metals and DOC in porewater compared with peepers and DGTs. At elevated metal levels, the measured concentrations were in better agreement among the 4 sampling techniques. The results indicate that there can be marked differences among operationally different porewater sampling methods, and it is unclear if there is a definitive best method for sampling metals and DOC in porewater. Environ Toxicol Chem 2017;36:2906–2915. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Prenatal exposure to neurotoxic metals is associated with increased placental glucocorticoid receptor DNA methylation

ABSTRACT Epigenetic alterations related to prenatal neurotoxic metals exposure may be key in understanding the origins of cognitive and neurobehavioral problems in children. Placental glucocorticoid receptor (NR3C1) methylation has been linked to neurobehavioral risk in early life, but has not been examined in response to neurotoxic metals exposure despite parallel lines of research showing metals exposure and NR3C1 methylation each contribute to a similar set of neurobehavioral phenotypes. Thus, we conducted a study of prenatal neurotoxic metals exposure and placental NR3C1 methylation in a cohort of healthy term singleton pregnancies from Rhode Island, USA (n = 222). Concentrations of arsenic (As; median 0.02 ug/g), cadmium (Cd; median 0.03 μg/g), lead (Pb; median 0.40 μg/g), manganese (Mn; median 0.56 μg/g), mercury (Hg; median 0.02 μg/g), and zinc (Zn; 145.18 μg/g) measured in infant toenails were categorized as tertiles. Multivariable linear regression models tested the independent associations for each metal with NR3C1 methylation, as well as the cumulative risk of exposure to multiple metals simultaneously. Compared to the lowest exposure tertiles, higher levels of As, Cd, Pb, Mn, and Hg were each associated with increased placental NR3C1 methylation (all P<0.02). Coefficients for these associations corresponded with a 0.71–1.41 percent increase in NR3C1 methylation per tertile increase in metals concentrations. For Zn, the lowest exposure tertile compared with the highest tertile was associated with 1.26 percent increase in NR3C1 methylation (P=0.01). Higher cumulative metal risk scores were marginally associated with greater NR3C1 methylation. Taken together, these results indicate that prenatal exposure to neurotoxic metals may affect the offspring's NR3C1 activity, which may help explain cognitive and neurodevelopmental risk later in life.
O2-sensitive K+ channels in neuroepithelial body-derived small cell carcinoma cells of the human lung.

Neuroepithelial bodies act as airway O2 sensors, but studies of their activity at the cellular level have been severely limited because they are present at such a low density in lung tissue. Small cell lung carcinoma (SCLC) cells are believed to be derived from neuroepithelial body cells and may represent a model system for investigating the mechanisms of airway chemoreception. Here we have used the whole cell patch-clamp technique to investigate the effects of acute hypoxia on voltage-gated ionic currents and membrane potential in H-146 SCLC cells. Step depolarizations evoked transient inward currents due to activation of Na+ and Ca2+ channels, followed by outward K+ currents. K+ currents were partially inhibited by 200 μM Cd2+(indicative of the presence of a Ca2+-dependent component of the K+ current) and were inhibited by tetraethylammonium (TEA) in a concentration-dependent manner, although even at 100 mM TEA, a residual K+current could be detected. Hypoxia ([Formula: see text] 15-20 mmHg) caused a reversible inhibition of outward K+ currents without affecting inward currents. Inhibition by hypoxia was also observed in the presence of Cd2+. Hypoxia and TEA caused membrane depolarization in H-146 cells, and their effects appeared additive. These findings indicate that H-146 cells possess O2-sensitive, Ca2+-independent K+ channels that can influence cell membrane potential. SCLC cells may, therefore, represent a good model for investigating the mechanisms underlying O2 sensing by airway chemoreceptor cells.
Rat gastroduodenal motility in vivo: involvement of NO and ATP in spontaneous motor activity.

Our studies of fasted anesthetized rats have shown that all spontaneous relaxations of the antrum are nitric oxide (NO) dependent. Duodenal motility is patterned into propagating "grouped" motor activity interposed with "intergroup" periods of nonpropagating motor activity; in the duodenum, only intergroup relaxations are NO dependent. We examined the involvement of NO and ATP in spontaneous motor activities of the gastroduodenum in vivo: contractions and relaxations were recorded and analyzed simultaneously from the antrum (S1) and proximal duodenum (D1) of anesthetized Sprague-Dawley rats ( n = 10/group), using extraluminal foil strain gauges. Treatment with the NO synthase inhibitor N G-nitro-l-arginine methyl ester (l-NAME; 10 mg/kg iv) attenuated ( P < 0.05) antral and intergroup relaxations, whereas grouped relaxations were enhanced ( P < 0.05). These effects were reversed with l-arginine (300 mg/kg iv). l-NAME also increased ( P < 0.05) the amplitude of duodenal contractions. ATP (8 mg ⋅ kg-1 ⋅ min-1iv) stimulated relaxations at S1and D1 that were blocked by the P2-purinoceptor antagonist suramin (60 mg/kg iv). This treatment did not affect spontaneous antral relaxations; however, duodenal grouped relaxations were attenuated. Desensitization to the P2x-purinoceptor agonist α,β-methylene ATP (300 μg/kg iv) gave results similar to suramin. In contrast, the P2y-purinoceptor agonist 2-methylthio-ATP (2-MeS-ATP; 360 μg/kg iv) evoked duodenal relaxations that were attenuated byl-NAME, and desensitization to 2-MeS-ATP attenuated intergroup relaxations. Spontaneous relaxations of the rat antrum and duodenal intergroup relaxations are NO dependent. Both gut regions relax in response to systemically administered ATP; this response is sensitive to suramin. Grouped duodenal relaxations display functional sensitivity to suramin and P2x- purinoceptor desensitization, indicative of the involvement of ATP and P2x purinoceptors. P2y purinoceptors must also be present; however, these occur on elements releasing NO. Although NO does not mediate grouped relaxations or duodenal contractions, the sensitivity of these responses tol-NAME indicates that the pathway(s) controlling these responses is modulated by NO.
A Visible Light-Driven Minisci-Type Reaction with N-Hydroxyphthalimide Esters

A visible light-promoted protocol for the redox-neutral coupling of N-hydroxyphthalimide esters with different N-heterocyclic compounds is described. The reaction proceeds through an alkyl radical intermediate generated by reductive decarboxylation of N-hydroxyphthalimide esters. In contrast to the original Minisci protocol, polyalkylation can largely be avoided. Mechanistic investigations revealed a radical chain mechanism which in some cases can proceed even if no photocatalyst is added. This valuable and functional group-tolerant reaction produces substituted heterocycles in moderate to excellent yield. The use of inexpensive starting materials and LEDs as the light source are key features of this C–C bond formation.
Mitochondrial haplogroup D4j specific variant m.11696G > a(MT-ND4) may increase the penetrance and expressivity of the LHON-associated m.11778G > a mutation in Chinese pedigrees

Abstract Leber's hereditary optic neuropathy (LHON) is one of the most common mitochondrial disorders. We report here the clinical, genetic and molecular analysis of mitochondrial DNA (mtDNA) in eight Han Chinese families carrying the known mitochondrial 11778G > A(MT-ND4) mutation. Thirty-seven (26 males/11 females) of 77 matrilineal relatives in these families exhibited the variable severity and age-at-onset of optic neuropathy. The penetrances were from 25% to 75%, with the average of 42%, and the age-at-onset for visual impairment varied from 10 to 25 years, with the average of 17 in these Chinese pedigrees. Molecular analysis of their mtDNA identified distinct sets of variants belonging to the Eastern Asian haplogroupD4j. Except the known m.11778G > A mutation, the m.11696G > A(MT-ND4) mutation caused the substitution of an isoleucine for valineat amino acid position 313, located in a predicted transmembrane region of ND4. And, it is reported that the m.11696G > A mutation was associated with LHON, and appeared to contribute to higher penetrance in these nine Chinese families than other Chinese families carrying only the m.11778G > A mutation. Therefore, the mitochondrial haplogroup D4j specific m.11696G > A mutation may act in synergy with the primary LHON-associated m.11778G > A mutation, thereby increasing the penetrance and expressivity of visual loss in these Chinese families.
The Influence of Behavioral Context on the Representation of a Perceptual Decision in Developing Oculomotor Commands

To make decisions about sensory stimuli, the brain must weigh the evidence that supports or opposes the alternative interpretations. In the present study, we evaluated the hypothesis that a quantity reflecting the weight of sensory evidence is represented in brain circuits responsible for the behavioral response used to indicate the decision. We trained monkeys to decide the direction of random-dot motion and to indicate their decision with an eye movement to one of two choice targets. We interrupted decision formation with electrical microstimulation of the frontal eye field, causing an evoked eye movement that is influenced by ongoing oculomotor activity. For the “pro-saccade” version of the task, in which the correct target was at a known location in the direction of motion, the microstimulus-evoked eye movement reflected both the impending pro-saccadic response and the temporal accumulation of motion information used to select that response. In contrast, for the “colored-target” task, in which the correct target was of a particular color but at an unpredictable location, little ongoing oculomotor activity was evident. The results suggest that formation of the decision and formation of the behavioral response share a common level of neural organization, but only when the decision is associated with a specific, predictable movement.
Quantifying Spatial Heterogeneity in Urban Landscapes: Integrating Visual Interpretation and Object-Based Classification

Describing and quantifying the spatial heterogeneity of land cover in urban systems is crucial for developing an ecological understanding of cities. This paper presents a new approach to quantifying the fine-scale heterogeneity in urban landscapes that capitalizes on the strengths of two commonly used approaches—visual interpretation and object-based image analysis. This new approach integrates the ability of humans to detect pattern with an object-based image analysis that accurately and efficiently quantifies the components that give rise to that pattern. Patches that contain a mix of built and natural land cover features were first delineated through visual interpretation. These patches served as pre-defined boundaries for finer-scale segmentation and classification of within-patch land cover features which were classified using object-based image analysis. Patches were then classified based on the within-patch proportion cover of features. We applied this approach to the Gwynns Falls watershed in Baltimore, Maryland, USA. The object-based classification approach proved to be effective for classifying within-patch land cover features. The overall accuracy of the classification maps of 1999 and 2004 were 92.3% and 93.7%, respectively. This exercise demonstrates that by integrating visual interpretation with object-based classification, the fine-scale spatial heterogeneity in urban landscapes and land cover change can be described and quantified in a more efficient and ecologically meaningful way than either purely automated or visual methods alone. This new approach provides a tool that allows us to quantify the structure of the urban landscape including both built and non-built components that will better accommodate ecological research linking system structure to ecological processes.
Flaky and fullerene-like WS2 nanoparticles as tribologic and toughening additives for epoxy

Just like MoS2, WS2 is known for its outstanding tribologic properties. When used as additives, both were found to considerably improve the tribologic behavior of epoxy, i.e., its coefficient of friction and wear resistance. The best improvements were obtained with WS2 or MoS2 nanoparticles, in particular if they had a fullerene-like morphology. Likewise, fullerene-like WS2 nanoparticles were shown to considerably enhance the fracture toughness of epoxy. It was thus hypothesized that the improved wear resistance could be due to the toughening effect rather than due to reduced friction. Our investigations showed that both flaky and fullerene-like WS2 nanoparticles can improve the fracture toughness of certain epoxy systems, while they can embrittle others. The beneficial effect on the epoxy’s wear resistance could not be confirmed either: The coefficient of friction and wear measured in pin-on-disc tests correlated insignificantly with the type or amount of nanoparticles used or the dispersion technique applied. The fact that the fracture toughness did not correlate with the measured wear suggests that the investigated epoxy system wears by adhesion rather than by abrasion. It is thus possible that tribologic additives like WS2 are unsuited for counteracting this wear mechanism. In a nutshell, both the toughening and the wear-reducing effect of flaky and fullerene-like WS2 nanoparticles seem to depend strongly on the particular epoxy system investigated.
INVESTIGATION INTO THE USE OF FONIO (DIGITARIA EXILIS) STARCH AS A TABLET DISINTEGRANT

This study aims at evaluating a tablet excipient from local sources fonio (Digitaria exilis) starch which is used locally as food because of its high carbohydrate content, it was thought that the starch of fonio (Digitaria exilis) may serve as a tablet disintegrant. The results showed that Fonio (Digitaria exilis) starch and maize starch BP have similar Angle of repose, Carrs index, moisture content, true density, tapped density, bulk density, Hausner ratio and mean particle size, however, fonio (Digitaria exilis) starch showed superiority in some properties such as moisture sorption capacity and swelling power. Tablets produced with fonio (Digitaria exilis) starch disintegrated quicker and faster than those produced with maize starch BP at all concentrations employed. It was also found that the dissolution time for tablets containing the two starches had similar profiles. The ability of fonio (Digitaria exilis) starch to swell better than maize starch in the presence of water might be the reason for its ability to function as a good tablet disintegrant. Therefore, the study confirmed the suitability of fonio (Digitaria exilis) starch as an alternative to maize starch BP as a tablet disintegrant especially in paracetamol tablet formulation.
Comparisons of physical activity, adipokines, vitamin D status and dietary vitamin D intake among adolescents

BACKGROUND Considering that lifestyle and diet are key factors responsible for the increases in adiposity in youth, it is important to understand how vitamin D, adipokines and markers of glucose metabolism are related to physical activity level (PAL) during growth. The present study aimed to investigate associations between physical activity level, adiponectin/leptin ratio, vitamin D status and dietary vitamin D intake among adolescents. METHODS A cross-sectional study was conducted with adolescents aged 14-18 years old who were living in São Paulo, Brazil. Serum 25 hydroxyvitamin D [25(OH)D], adiponectin (A), leptin (L), glucose and insulin were obtained after 12 h of fasting. Dietary calcium and vitamin D intake were measured by 24-h food record, as repeated in 62.6% of the sample. PAL was measured by the International Physical Activity Questionnaire (IPAQ). Pearson's chi-square test, Pearson correlation and linear regression analysis were performed. RESULTS A total of 198 subjects, mean (SD) age 16.3 (1.4) years, 51% male, were enrolled in the study. Some 9% of participants were sedentary, 22% were insufficiently active (IA), 51% were active and 18% were very active (VA). The A/L ratio was lower among sedentary/IA subjects [2.2 (4.0) versus 5.6 (12.3); P = 0.01] compared to active/VA subjects. PAL was not associated with vitamin D status or markers of glucose metabolism. Serum 25(OH)D positively associated with vitamin D intake, after adjusting for sex, sun exposure and season of the year in regression analysis (partial r2 =0.026, P = 0.02). CONCLUSIONS Low PAL was associated with a lower A/L ratio. Vitamin D status was not associated with sun exposure habits, although it was positively correlated with vitamin D intake.
A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

MicroRNAs (miRNAs) are endogenous small RNAs playing an important regulatory function in plant development and stress responses. Among them, some are evolutionally conserved in plant and others are only expressed in certain species, tissue or developmental stages. Cucumber is among the most important greenhouse species in the world, but only a limited number of miRNAs from cucumber have been identified and the experimental validation of the related miRNA targets is still lacking. In this study, two independent small RNA libraries from cucumber leaves and roots were constructed, respectively, and sequenced with the high-throughput Illumina Solexa system. Based on sequence similarity and hairpin structure prediction, a total of 29 known miRNA families and 2 novel miRNA families containing a total of 64 miRNA were identified. QRT-PCR analysis revealed that some of the cucumber miRNAs were preferentially expressed in certain tissues. With the recently developed ‘high throughput degradome sequencing’ approach, 21 target mRNAs of known miRNAs were identified for the first time in cucumber. These targets were associated with development, reactive oxygen species scavenging, signaling transduction and transcriptional regulation. Our study provides an overview of miRNA expression profile and interaction between miRNA and target, which will help further understanding of the important roles of miRNAs in cucumber plants.
Amino Acid Metabolism and Transport Mechanisms as Potential Antifungal Targets

Discovering new drugs for treatment of invasive fungal infections is an enduring challenge. There are only three major classes of antifungal agents, and no new class has been introduced into clinical practice in more than a decade. However, recent advances in our understanding of the fungal life cycle, functional genomics, proteomics, and gene mapping have enabled the identification of new drug targets to treat these potentially deadly infections. In this paper, we examine amino acid transport mechanisms and metabolism as potential drug targets to treat invasive fungal infections, including pathogenic yeasts, such as species of Candida and Cryptococcus, as well as molds, such as Aspergillus fumigatus. We also explore the mechanisms by which amino acids may be exploited to identify novel drug targets and review potential hurdles to bringing this approach into clinical practice.