Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Nitrite Reductase in the Denitrifying Bacterium Alcaligenes faecalis S-6

A potent denitrifying bacterium, Alcaligenes faecalis S-6, was isolated from activated sludge, and the regulatory mechanisms for dissimilatory nitrite reductase (NIR) were studied. NIR activity was controlled by oxygen and nitrite through dual regulatory mechanisms, i.e., induced synthesis and inactivation of the enzyme. Full induction of NIR synthesis required both low oxygen tension and the presence of nitrate or nitrite as inducer. Nitrite seemed to be the real inducer, since nitrate failed to induce synthesis with a nitrate reductase deficient mutant. Intracellular NIR was inactivated by oxygen, and the inactivation was stimulated by cysteine and prevented by nitrite.NIR in the crude cell free extract was inactivated by oxygen when cysteine was added, but that in the partially purified preparation was not. An inactivating factor which may possibly be a protein catalyzing the inactivation was found in the cell extract.
Gold Nanorod Assemblies: The Roles of Hot-Spot Positioning and Anisotropy in Plasmon Coupling and SERS

Plasmon-coupled colloidal nanoassemblies with carefully sculpted “hot-spots” and intense surface-enhanced Raman scattering (SERS) are in high demand as photostable and sensitive plasmonic nano-, bio-, and chemosensors. When maximizing SERS signals, it is particularly challenging to control the hot-spot density, precisely position the hot-spots to intensify the plasmon coupling, and introduce the SERS molecule in those intense hot-spots. Here, we investigated the importance of these factors in nanoassemblies made of a gold nanorod (AuNR) core and spherical nanoparticle (AuNP) satellites with ssDNA oligomer linkers. Hot-spot positioning at the NR tips was made possible by selectively burying the ssDNA in the lateral facets via controlled Ag overgrowth while retaining their hybridization and assembly potential at the tips. This strategy, with slight alterations, allowed us to form nanoassemblies that only contained satellites at the NR tips, i.e., directional anisotropic nanoassemblies; or satellites randomly positioned around the NR, i.e., nondirectional nanoassemblies. Directional nanoassemblies featured strong plasmon coupling as compared to nondirectional ones, as a result of strategically placing the hot-spots at the most intense electric field position of the AuNR, i.e., retaining the inherent plasmon anisotropy. Furthermore, as the dsDNA was located in these anisotropic hot-spots, this allowed for the tag-free detection down to ~10 dsDNA and a dramatic SERS enhancement of ~1.6 × 108 for the SERS tag SYBR gold, which specifically intercalates into the dsDNA. This dramatic SERS performance was made possible by manipulating the anisotropy of the nanoassemblies, which allowed us to emphasize the critical role of hot-spot positioning and SERS molecule positioning in nanoassemblies.
Nonsurgical treatment for peri-implant mucositis: A systematic review and meta-analysis.

PURPOSE To assess the effectiveness of different nonsurgical protocols for the treatment of peri-implant mucositis. MATERIALS AND METHODS The identification of randomised clinical trials (RCTs) was systematically performed in three databases and supplemented by a thorough manual search of the literature in periodontics/implantology-related journals. Studies investigating the effect of mechanical and/or chemical plaque control agents aimed at preventing the development of peri-implant mucositis were excluded. When comparable trials were found, a meta-analysis was performed. RESULTS Fourteen studies were included in the systematic review and three in the meta-analysis. None of the selected studies reported a complete resolution of the peri-implant mucositis lesions. A nonsurgical therapy alone showed an average reduction of: 0.57 mm (95% CI [0.30 to 0.83]) in probing pocket depth (PPD); 22.41% (95% CI [12.74 to 32.08]) in bleeding on probing (BOP); 17.28% (95% CI [3.99 to 30.58]) in the plaque index (PI); and 13.41% (95% CI [3.50 to 23.31]) in the bleeding index (BI). The meta-analysis failed to demonstrate significant improvements with the adjunct use of chlorhexidine disinfectant to nonsurgical mechanical debridement for PPD reduction (-0.07 mm; 95% CI [-0.33 to 1.15], P = 0.62), and relative attachment level (RAL) gain (-0.13 mm; 95% CI [-0.6 to 0.35]), P = 0.6). CONCLUSION Conventional nonsurgical mechanical therapy alone may be considered the standard treatment for peri-implant mucositis as there is still a lack of evidence supporting the use of additional chemical/mechanical agents for clinical and/or microbiological improvement.
Understanding the Detection Mechanisms and Ability of Molecular Hydrogen on Three-Dimensional Bicontinuous Nanoporous Reduced Graphene Oxide

Environmental safety has become increasingly important with respect to hydrogen use in society. Monitoring techniques for explosive gaseous hydrogen are essential to ensure safety in sustainable hydrogen utilization. Here, we reveal molecular hydrogen detection mechanisms with monolithic three-dimensional nanoporous reduced graphene oxide under gaseous hydrogen flow and at room temperature. Nanoporous reduced graphene oxide significantly increased molecular hydrogen physisorption without the need to employ catalytic metals or heating. This can be explained by the significantly increased surface area in comparison to two-dimensional graphene sheets and conventional reduced graphene oxide flakes. Using this large surface area, molecular hydrogen adsorption behaviors were accurately observed. In particular, we found that the electrical resistance firstly decreased and then gradually increased with higher gaseous hydrogen concentrations. The resistance decrease was due to charge transfer from the molecular hydrogen to the reduced graphene oxide at adsorbed molecular hydrogen concentrations lower than 2.8 ppm; conversely, the resistance increase was a result of Coulomb scattering effects at adsorbed molecular hydrogen concentrations exceeding 5.0 ppm, as supported by density functional theory. These findings not only provide the detailed adsorption mechanisms of molecular hydrogen, but also advance the development of catalyst-free non-heated physisorption-type molecular detection devices.
Effect of condensed tannins upon the performance of lambs grazing Lotus corniculatus and lucerne (Medicago sativa)

SUMMARY A grazing experiment, conducted for 22 weeks in 1992/93 at Aorangi Research Station, AgResearch Grasslands, Manawatu, New Zealand, compared the productivity of weaned lambs grazing Lotus corniculatus (birdsfoot trefoil) and lucerne (Medicago sativa). Effects of condensed tannins (CT) in lotus were evaluated by studying the responses of lambs to twice daily oral supplementation with polyethylene glycol (PEG). A rotational grazing system with restricted feed allowance was used. Measurements were made of pre- and post-grazing herbage mass, the composition of the feed on offer and diet selected, voluntary feed intake (VFI), liveweight gain (LWG), carcass growth, wool growth and the concentration of metabolites in rumen fluid. For both lotus and lucerne swards, the diet selected was mainly leaf. Lotus contained 34 g total CT/kg dry matter in the diet selected, whilst there were essentially no CT in lucerne. Compared to lambs grazing lucerne, lambs grazing lotus had slightly lower VFI, and higher LWG, carcass weight gain, carcass dressing-out percentage and wool growth. PEG supplementation had no effect on these measurements or upon the composition of rumen fluid in lambs grazing lucerne. However, in lambs grazing lotus, PEG supplementation reduced wool growth (10·9 ν. 12·1 g/day), slightly reduced LWG (188 ν. 203 g/day), increased rumen ammonia concentration, and increased the molar proportions of /. so-butyric, isovaleric and n-valeric acids and protozoa numbers in rumen fluid. PEG supplementation did not affect carcass gain, carcass fatness or the molar proportion of rumen acetic, propionic or n-butyric acids in lambs grazing lotus. It was concluded that the principal effect of CT in growing lambs grazing lotus was to increase wool growth without affecting VFI, thereby increasing the efficiency of wool production, that the greater rate of carcass gain of lambs grazing lotus than those grazing lucerne was mainly caused by factors other than CT and that CT did not affect the rumen fermentation of carbohydrate to major volatile fatty acids.
Role of MicroRNAs in Host Defense against Infectious Bursal Disease Virus (IBDV) Infection: A Hidden Front Line

Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive avian disease caused by infectious bursal disease virus (IBDV). In recent years, remarkable progress has been made in the understanding of the pathogenesis of IBDV infection and the host response, including apoptosis, autophagy and the inhibition of innate immunity. Not only a number of host proteins interacting with or targeted by viral proteins participate in these processes, but microRNAs (miRNAs) are also involved in the host response to IBDV infection. If an IBDV–host interaction at the protein level is taken imaginatively as the front line of the battle between invaders (pathogens) and defenders (host cells), their fight at the RNA level resembles the hidden front line. miRNAs are a class of non-coding single-stranded endogenous RNA molecules with a length of approximately 22 nucleotides (nt) that play important roles in regulating gene expression at the post-transcriptional level. Insights into the roles of viral proteins and miRNAs in host response will add to the understanding of the pathogenesis of IBDV infection. The interaction of viral proteins with cellular targets during IBDV infection were previously well-reviewed. This review focuses mainly on the current knowledge of the host response to IBDV infection at the RNA level, in particular, of the nine well-characterized miRNAs that affect cell apoptosis, the innate immune response and viral replication.
Nonlinear Relationship Between the Yield of Solar-Induced Chlorophyll Fluorescence and Photosynthetic Efficiency in Senescent Crops

It has been demonstrated that solar-induced chlorophyll fluorescence (SIF) is linearly related to the primary production of photosynthesis (GPP) in various ecosystems. However, it is unknown whether such linear relationships have been established in senescent crops. SIF and GPP can be expressed as the products of absorbed photosynthetically active radiation (APAR) with the SIF yield and photosystem II (PSII) operating efficiency, respectively. Thus, the relationship between SIF and GPP can be represented by the relationship between the SIF yield and PSII operating efficiency when the APAR has the same value. Therefore, we analyzed the relationship between the SIF yield and the PSII operating efficiency to address the abovementioned question. Here, diurnal measurements of the canopy SIF (760 nm, F760) of soybean and sweet potato were manually measured and used to calculate the SIF yield. The PSII operating efficiency was calculated from measurements of the chlorophyll fluorescence at the leaf level using the FluorImager chlorophyll fluorescence imaging system. Meanwhile, field measurements of the gas exchange and other physiological parameters were also performed using commercial-grade devices. The results showed that the SIF yield was not linearly related to the PSII operating efficiency at the diurnal scale, reflecting the nonlinear relationship between SIF and GPP. This nonlinear relationship mainly resulted from the heterogeneity and diurnal dynamics of the PSII operating efficiency and from the intrinsic diurnal changes in the maximum efficiency of the PSII photochemistry and the proportion of opened PSII centers. Intensifying respiration was another factor that complicated the response of photosynthesis to the variation in environmental conditions and negatively impacted the relationship between the SIF yield and the PSII operating efficiency. The nonlinear relationship between the SIF yield and PSII efficiency might yield errors in the estimation of GPP using the SIF measurements of senescent crops.
RNF8 has both KU-dependent and independent roles in chromosomal break repair

Abstract Chromosomal double strand breaks (DSBs) can initiate several signaling events, such as ubiquitination, however the precise influence of such signaling on DSB repair outcomes remains poorly understood. With an RNA interference screen, we found that the E3 ubiquitin ligase RNF8 suppresses a deletion rearrangement mediated by canonical non-homologous end joining (C-NHEJ). We also found that RNF8 suppresses EJ without insertion/deletion mutations, which is a hallmark of C-NHEJ. Conversely, RNF8 promotes alternative EJ (ALT-EJ) events involving microhomology that is embedded from the edge of the DSB. These ALT-EJ events likely require limited end resection, whereas RNF8 is not required for single-strand annealing repair involving extensive end resection. Thus, RNF8 appears to specifically facilitate repair events requiring limited end resection, which we find is dependent on the DSB end protection factor KU. However, we also find that RNF8 is important for homology-directed repair (HDR) independently of KU, which appears linked to promoting PALB2 function. Finally, the influence of RNF8 on EJ is distinct from 53BP1 and the ALT-EJ factor, POLQ. We suggest that RNF8 mediates both ALT-EJ and HDR, but via distinct mechanisms, since only the former is dependent on KU.
Seeing yourself clearly: Self‐identification of a body image problem in adolescents with an eating disorder

Many adolescents who meet diagnostic criteria for an eating disorder do not self‐identify as having a problem and may consequently be less likely to seek help. Extant research investigating self‐identification has been limited to specific populations (ie, girls meeting criteria for bulimic‐type eating disorders). This study investigated how self‐identification varied across sex, eating disorder diagnoses, and the presence of extreme eating behaviours, and how self‐identification was related to help‐seeking in adolescents.
Improving Land Cover Classification Using Extended Multi-Attribute Profiles (EMAP) Enhanced Color, Near Infrared, and LiDAR Data

Hyperspectral (HS) data have found a wide range of applications in recent years. Researchers observed that more spectral information helps land cover classification performance in many cases. However, in some practical applications, HS data may not be available, due to cost, data storage, or bandwidth issues. Instead, users may only have RGB and near infrared (NIR) bands available for land cover classification. Sometimes, light detection and ranging (LiDAR) data may also be available to assist land cover classification. A natural research problem is to investigate how well land cover classification can be achieved under the aforementioned data constraints. In this paper, we investigate the performance of land cover classification while only using four bands (RGB+NIR) or five bands (RGB+NIR+LiDAR). A number of algorithms have been applied to a well-known dataset (2013 IEEE Geoscience and Remote Sensing Society Data Fusion Contest). One key observation is that some algorithms can achieve better land cover classification performance by using only four bands as compared to that of using all 144 bands in the original hyperspectral data with the help of synthetic bands generated by Extended Multi-attribute Profiles (EMAP). Moreover, LiDAR data do improve the land cover classification performance even further.
A SINGLE ORIGIN OF PLASTIDS REVISITED: CONVERGENT EVOLUTION IN ORGANELLAR GENOME CONTENT 1

In recent years a consensus has emerged from molecular phylogenetic investigations favoring a common endosymbiotic ancestor for all chloroplasts. It is within this conceptual framework that most comparative analyses of eukaryotic biochemistry and genetics now are interpreted. One of the first and most influential sources of data leading to this consensus is the remarkable similarity in genome content among all major plastid lineages. Here we report statistical analyses of two sequence data sets, genes encoding ribosomal proteins and transfer RNAs, from representatives of the three primary plastid lineages and a mitochondrion. The latter almost certainly originated in an independent endosymbiotic association and serves as a control for similarity due to convergent evolution. When genes related to organelle‐specific function are factored out, plastid genomes appear to be no more similar to each other than they are to the mitochondrion. Total similarities in gene content, measured as deviations from the expectation from a process of random gene loss, are correlated with the extent of reduction in the two genomes compared. They do not appear to reflect putative evolutionary relationships among plastids. These analyses indicate that similarities in plastid genome content are better explained by convergent evolution due to constraint on gene loss than by a shared evolutionary history. A review of other data cited as support for a single plastid origin suggests that the alternative hypothesis of multiple origins is at least equally consistent in most cases.
Patient Inspiratory Maneuver Performance; Peak Lungpower, Acceleration and Volume

Background: Use of drug delivery devices between nebulizers, dry powder inhalers (DPIs), or metered dose inhalers (MDIs), for treating patients with asthma and chronic obstructive pulmonary disease (COPD), is based on patients' capability of coordinating the inhalation maneuver and achieving sufficient airflow. There are limited data available with regard to how patients meet the requirements of successful inhalation performance, and how the concept of inspiratory lungpower could be applied. The aim of this work was to study the patient inspiratory airflow profile performance in large data sets. We analyzed how the Kamin-Haidl inhalation criteria were met by patients with DPIs such as Easyhaler for combination therapy (EH-combi), Easyhaler for monotherapy (EH-mono), Diskus, and Turbuhaler (TH), and applied peak lungpower instead of peak inspiratory flow rate as an indicator of patient performance. Materials and Methods: Data sets gathered in two previous studies for DPIs, that is, EH-combi, EH-mono, Diskus, and TH, were used to analyze how inspiratory lungpower representing inspiratory muscle power, flow acceleration, and volume after peak met the inhalation criteria. The measured patient airflow profiles through inhalers were assessed for patients with asthma or COPD. Results: Based on the Kamin-Haidl inhalation criteria, successful inhalation requirements were met with EH-combi in 96.1% and with EH-mono in 92.6% of patients. The success rates were 89.5% and 84.6% with Diskus and TH, respectively, (p < 0.0001 between devices). In patients with asthma or COPD, the mean lungpower was 7.51 and 6.15 W for EH-combi, 8.79 and 6.88 W for EH-mono, 7.18 and 4.36 W for Diskus, and 9.65 and 6.86 W for TH, respectively, when patients followed the manufacturer's written instructions. Conclusions: Lungpower applied to the Kamin-Haidl inhalation criteria concept could be an applicable method for reviewing patient performance for different DPIs despite DPIs' characteristic differences in airflow resistance. In light of these results, DPIs provide a feasible treatment option for a large majority of respiratory patients.
Soil Nitrogen Status as Affected by Tillage, Crops, amd Crop Sequences

Conservation tillage practices, including no-till (NT), reduce soil erosion and increase precipitation storage efficiency, but many decrease available soil N. We conducted studies at two sites to determine the comparative effects of NT and stubble mulch (SM) on the N supplying capacity of Pullman clay loam (fine, mixed, thermic torrertic Paleustolls) cropped to continuous wheat (Triticum aestivum L.) (CW), continuous grain sorghum [Sorghum bicolor (L.) Moench] (CS), wheat-sorghum-fallow (WSF), and wheat-fallow (WF) sequences (.)
In Vitro Digestibility of Thermally Processed Diafiltered Whey as Influenced by Water Activity

Abstract Diafiltered whey protein concentrates of varying water activity were heated at 121°C for 83.3 min (5000 s). Nitrogen and amino acid digestibilities were determined by the digestion cell technique. Whey nitrogen digestibility significantly decreased only at a water activity of . 97. Although this heat treatment did not affect the amino acid profile of the protein, the relative digestibility of most amino acids was slightly increased at a water activity of . 3 but relative digestibility decreased at a water activity of . 5 and . 97. At a water activity of . 7, digestibility slightly increased for aspartic acid, threonine, glutamic acid, proline, cysteine, isoleucine, histidine, and arginine and decreased or remained unchanged for the other amino acids. At a water activity of . 97, the relative digestibility of aspartic acid, threonine, serine, glutamic acid, glycine isoleucine, leucine, and phenylalanine, significantly decreased. Water activity plays a role in the structural organization of heated whey, which in turn affects the enzymatic liberation of amino acids.
Assimilation of sulphur into the cell-wall polysaccharide of the red microalga Porphyridium sp. (Rhodophyta)

M. Keidan, H. Broshy, D. van Moppes and S. (Malis) Arad. 2006. Assimilation of sulphur into the cell-wall polysaccharide of the red microalga Porphyridium sp. (Rhodophyta). Phycologia 45: 505–511. DOI: 10.2216/05-57.1 The cell walls of red algae contain sulphated polysaccharides. It is believed that the bioactivity of such natural sulphated polysaccharides may be attributed to the sulphate groups. Knowledge of the mode of sulphation of these polysaccharides is, however, very limited. The current study forms part of our efforts to elucidate the mode of sulphation of the cell-wall polysaccharide of the red microalga Porphyridium sp. Although this microalga is an obligatory photoautotroph, under conditions of sulphate starvation it can assimilate the sulphur-containing amino acid cysteine (but not methionine) and incorporate sulphur from [35S]cysteine into the cell-wall polysaccharide. The ratio between 35S uptake to the soluble polysaccharide complex and to the cells was threefold higher from [35S]cysteine than that from Na235SO4, although the uptake of 35S to the cells was higher when Na235SO4 was used as the sulphur source. Pulse–chase experiments demonstrated that differences in the incorporation of 35S from the two sulphur sources were greater for the soluble polysaccharide complex (45.1% from [35S]cysteine vs. 13.9% from Na235SO4) than for the cellular fractions (bound polysaccharide, protein and low-molecular-weight fraction). SDS-PAGE analysis showed that the 35S label resided predominantly in the polysaccharide of the soluble complex and not in the glycoprotein. The effect of sodium chlorate, a sulphation inhibitor, on 35S incorporation into the soluble polysaccharide complex and the different cellular fractions depended on the 35S source: significant inhibition of sulphation of the soluble polysaccharide complex was found for [35S]cysteine as the source of sulphate, i.e. 87% vs.36. 4% for Na235SO4. This study suggests that in addition to the commonly accepted sulphate pathway, there is another sulphation pathway in which cysteine serves as the sulphur source.