Computer-aided nanodrug discovery: recent progress and future prospects.

Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.

Number of COVID-19 cases required in a population to detect SARS-CoV-2 RNA in wastewater in the province of Alberta, Canada: Sensitivity assessment.

With a unique and large size of testing results of 1,842 samples collected from 12 wastewater treatment plants (WWTP) for 14 months through from low to high prevalence of COVID-19, the sensitivity of RT-qPCR detection of SARS-CoV-2 RNA in wastewater that correspond to the communities was computed by using Probit analysis. This study determined the number of new COVID-19 cases per 100,000 population required to detect SARS-CoV-2 RNA in wastewater at defined probabilities and provided an evidence-based framework of wastewater-based epidemiology surveillance (WBE). Input data were positive and negative test results of SARS-CoV-2 RNA in wastewater samples and the corresponding new COVID-19 case rates per 100,000 population served by each WWTP. The analyses determined that RT-qPCR-based SARS-CoV-2 RNA detection threshold at 50%, 80% and 99% probability required a median of 8 (range: 4-19), 18 (9-43), and 38 (17-97) of new COVID-19 cases /100,000, respectively. Namely, the positive detection rate at 50%, 80% and 99% probability were 0.01%, 0.02%, and 0.04% averagely for new cases in the population. This study improves understanding of the performance of WBE SARS-CoV-2 RNA detection using the large datasets and prolonged study period. Estimated COVID-19 burden at a community level that would result in a positive detection of SARS-CoV-2 in wastewater is critical to support WBE application as a supplementary warning/monitoring system for COVID-19 prevention and control.

Significant Roles of a Particularly Stable Two-Center Two-Electron Lu-Lu σ Bond in Lu2@C86: Electronic Structure of Lu and Radius of Lu2.

There is still dispute over the stability of endohedral metallofullerenes (EMFs) M2C2n, and recently, multiform lutetium-based dimetallofullerenes have been dropped in experiments. The thermodynamic stabilities of Lu2C86 EMFs are revealed by density functional theory (DFT) in conjunction with statistical thermodynamic analyses. Inevitably, besides the experimentally reported Lu2@C2v(63751)-C86, Lu2@Cs(63750)-C86, and Lu2@Cs(63757)-C86, other three metal carbide clusterfullerenes, Lu2C2@D2d(51591)-C84, Lu2C2@C1(51383)-C84, and Lu2C2@Cs(id207430)-C84, rather than Lu2@C86 are first characterized as thermodynamically stable isomers of Lu2C86. Specially, the Cs(id207430)-C84 is a newly non-classical fullerene containing one heptagon, which is stabilized via encaging Lu2C2. Another interesting phenomenon is that the outer fullerene cages of thermodynamically stable Lu2C82-88 molecules are geometrically connected through C2 addition/loss and Stone-Wales (SW) transformation, suggesting a special relationship between thermodynamic stabilities and geometries of Lu2C82-88 EMFs. Furthermore, the electronic configurations of (Lu2)4+@C864- and (Lu2C2)4+@C844- were confirmed. A significantly stable two-center two-electron (2c-2e) Lu-Lu σ single bond is formed in Lu2@C86. By comparing M-M bonds in M2@C2v(63751)-C86 (M = Sc, Y, La, and Lu), two significant factors, the valence atomic orbital (ns) of metal atoms and radius of M2+, are found to determine the stability of the M-M bond in the C2v(63751)-C86. Additionally, the simulated UV-vis-NIR spectra of thermodynamically stable Lu2C86 isomers were simulated, which further disclose their electronic features.

Pathogen performance testing of a natural swimming pool using a cocktail of microbiological surrogates and QMRA-derived management goals.

In recent decades, natural swimming pools (NSPs) have gained popularity in Europe, especially in Germany and Austria. NSPs differ from swimming pools in that they utilize biological treatment processes based on wetland processes with no disinfection residual. However, data are missing on the specific log-reduction performance of NSPs to address enteric virus, bacteria, and parasitic protozoa removal considered necessary to meet the North American risk-based benchmark (<35 illnesses per 1,000 swimming events) set by the USEPA for voluntary swimming. In this study, we examined Canada's first NSP at Borden Park, Edmonton, Canada, to address the following three questions: (1) Given normal faecal shedding rates by bathers, what is the total log reduction (TLR) theoretically needed to meet the EPA benchmark? (2) what is the in-situ performance of the NSP based on spiking suitable microbial surrogates (MS2 coliphage, Enterococcus faecalis, and Saccharomyces cerevisiae [Baker's yeast])? and (3) how much time is required to reach acceptable bather risk levels under different representative volume-turnover rates? A reverse-quantitative microbial risk assessment (QMRA) revealed that of the four reference pathogens selected (Norovirus, Campylobacter, Cryptosporidium, and Giardia), only Norovirus was estimated to exceed the risk benchmark at the 50th, 75th, and 95th percentiles, while Campylobacter was the only other reference pathogen to exceed at the 95th percentile. Log-reduction values (LRVs) were similar to previous reports for bacterial indicators, and novel LRVs were estimated for the other two surrogates. A key finding was that more than 24 h treatment time would be necessary to provide acceptable bather protection following heavy bather use (378 bathers/day for main pool and 26 bathers/day for children's pool), due to the mixing dynamics of the treated water diluting out possible residual pool faecal contamination. The theoretical maximum number of people in the pool per day to be below USEPA's 35 gastro cases in 1,000 swimming events was 113, 47, and 8, at the 50th, 75th, and 95th percentiles. Further, the use of ultra-violet disinfection to the pool return flow had little effect on reducing the treatment time required.

Magnesiation of Aryl Fluorides Catalyzed by a Rhodium-Aluminum Complex.

We report the magnesiation of aryl fluorides catalyzed by an Al-Rh heterobimetallic complex. We show that the complex is highly reactive to cleave the C-F bonds across the polarized Al-Rh bond under mild conditions. The reaction allows the use of an easy-to-handle magnesium powder to generate a range of arylmagnesium reagents from aryl fluorides, which are conventionally inert to such metalation compared with other aryl halides.

Coordination Flexibility of the Rh(PXP) Complex to NH3, CO, and C2H4 (PXP = Diphosphine-Based Pincer Ligand; X = B, Al, and Ga): Theoretical Insight.

The recently synthesized rhodium-aluminum bimetallic complex Rh(PAlP) 1 (PAlP = pincer-type diphosphino-aluminyl ligand Al{[N(C6H4)]2NMe}[CH2P(iPr)2]2) containing a unique Rh-Al direct bond exhibits coordination flexibility because Rh and Al can play the role of coordination site for the substrate. DFT calculations of NH3, CO, and C2H4 adducts with 1 show that the Rh atom is favorable for all these substrate but the Al atom is as favorable as the Rh atom for NH3 and unfavorable for CO and C2H4. NH3 and CO prefer the coordination at the Rh-axial (Ax) site to the Rh-equatorial (Eq) site, but C2H4 prefers coordination at the Rh-Eq site to the Rh-Ax site. Consequently, two CO and C2H4 molecules coordinate with 1 at the Rh-Ax and Rh-Eq sites to afford trigonal bipyramidal complexes Rh(PAlP)(CO)2 and Rh(PAlP)(C2H4)2, which is consistent with the experimental observation of Rh(PAlP)(CO)2. Energy decomposition analysis reveals that an electrostatic term plays an important role for NH3 coordination with the Al atom of 1, because Al has a significantly large positive charge and NH3 has a much negatively charged N atom and exhibits a considerably negative electrostatic potential at the Al position. In B and Ga analogues Rh(PBP) 2 and Rh(PGaP) 3, B and Ga atoms are not good for CO and C2H4 like the Al atom in 1. NH3 adducts with 2 and 3 at the B and Ga sites are less stable than those adducts at the Rh-Ax site unlike the NH3 adduct with 1 at the Al site. This difference in the NH3 adduct between Rh(PAlP) and others (Rh(PBP) and Rh(PGaP)) arises from much less positive charges of B and Ga and a smaller atomic size of B than that of Al. These results indicate that the significantly large electropositive nature and appropriate atomic size of Al are responsible for the characteristic coordination flexibility of Rh(PAlP).

Theoretical Investigations of Lu2C84: Unexpected Impact of Metal Electronic Configuration toward the Metal-Metal σ-Bond in Fullerene.

Recent experimental works recovered multiformity of lutetium-involved dimetallofullerenes. On the basis of density functional theory (DFT) combined with statistical thermodynamic analyses, the relative stabilities of Lu2C84 dimetallofullerene were clarified. Besides the experimentally acknowledged Lu2@D2d(51591)-C84 and Lu2@C2v(51575)-C84, another four isomers metallofullerenes, Lu2@C1(51580)-C84, Lu2C2@Cs(39715)-C82, Lu2C2@C3v(39717)-C82, and Lu2C2@C2v(39718)-C82, are first proposed as thermodynamically stable structures. Interestingly, the geometric relationships among the pristine cages of stable Lu2C84 isomers through Stone-Wales transformation or C2 lose/insertion reveal important clues of the fullerene formation mechanism. The ionic interaction in the stable Lu2C84 isomers is revealed, and their valence states are Lu24+@C844- or (Lu2C2)4+@C824-. In the Lu2@C84 isomers, the results of frontier molecular orbital and natural bond orbital analyses suggest that a Lu-Lu single bond is formed, which is mainly composed of the 6s and 6p orbitals of the Lu atoms. Further analyses of the M2@C84 (M = Sc, Y, La, and Yb) structures disclose the importance of the electron configuration of metal element toward the formation of a single metal-metal bond in C84. Moreover, the covalent interaction between the Lu2 moiety and the C84 cages is disclosed, which is a supplement to the ionic model.

Spiked Virus Level Needed To Correctly Assess Enteric Virus Recovery in Water Matrices.

Quantitative microbial risk assessment (QMRA) identifies human enteric viruses in municipal wastewater as the pathogen group requiring the highest log reductions for various reuse applications. However, the performance of methods for estimating virus concentration is not well understood, and without performance assessment, actual risks are likely severely underestimated. To evaluate the efficiency of virus recovery from water, a water sample is often spiked with "known" amounts of virus, and the virus is then recovered after a series of analytical procedures. Yet for water matrices such as wastewater, due to the unknown background concentrations of targeted viruses in the matrix and the variable recovery efficiency between individual processes, only an approximation of the recovery efficiency may be obtained from such spike-and-recovery experiments. In this study, we demonstrated theoretically that for two widely used approximations, the error in estimating virus recovery should be less than the ratio of the amount of target virus in the background sample to that in the spike. Furthermore, we developed an applicable method, based on this new understanding, for deciding on the amount of virus for spiking before conducting a spike-and-recovery experiment, so that the approximation error is restricted to an acceptable level for each individual process. Finally, we applied the method to a set of experimental data for viruses in wastewater, demonstrating its utility and noting its general applicability to other pathogens or water matrices.IMPORTANCE The performance of procedures for pathogen log reduction is at the heart of new risk-based guidance/regulation globally, yet the methods for undertaking assessments of pathogen recovery are not standardized despite their fundamental impacts on assessing log reductions. Here we describe the level of spiking agent(s) that is necessary to correctly assess spiked pathogen/surrogate recovery with whatever method is deployed. The significance of our research lies in identifying the importance of the amount of spiking agents for reducing uncertainty in recovery estimates, which will allow the development of a recommendation for spiking experiments, proactively applying this understanding.

Encapsulation of Monometal Uranium into Fullerenes C2n (2n = 70-74): Important Ionic U4+C2n4- Characters and Covalent U-Cage Bonding Interactions.

By using density functional theory calculations combined with statistical thermodynamic analyses, the stabilization performance of a series of fullerene cages C2n (2n = 70-74) via encapsulating monometal uranium was systematically and thoroughly investigated. Results indicate that fullerene cages D5h(8149)-C70 and D3h(14246)-C74 obeying the isolated pentagon rule and C2(10612)-C72 featured with one pentalene moiety were the most promising candidates to encage uranium. Subsequent Mulliken spin density distribution and frontier molecular orbital analyses suggest that four formal electron transfer occurs from monometal U to above the carbon cages. There also exists a high degree of covalent character between the atom U and fullerenes C2n based on Mayer bond order and quantum theory of atoms in molecule (QTAIM) analyses, indicative of the cooperative stabilization by both ionic and covalent bonding interactions. In addition, investigations on the above-mentioned U@C2n isomers and other favorable candidates (U@Cs(8094)-C70, U@C1(10610)-C72, U@C1(13393)-C74, and U@C1(14049)-C74) reveal that these isomers could be closely linked via simple C2 addition and Stone-Wales transformation. These results will provide a systematic understanding on U-based endohedral metallofullerenes (EMFs) and also might be helpful for further exploration of EMF growth mechanisms.

La-La bonded dimetallofullerenes [La2@C2n]-: species for stabilizing C2n (2n = 92-96) besides La2C2@C2n.

Recent reports pointed out that the formal La2C2n (2n = 92-106) series can exist stably as carbide cluster metallofullerenes (CCMFs) La2C2@C2n-2 with their successful crystallographic characterization. Herein, we suggest that the corresponding dimetallofullerenes (di-EMFs) La2@C2n possessing the lowest potential energies are also plausible candidates because of their favorability in statistical thermodynamics. This can be demonstrated in our present theoretical investigations on La2C94 and previously reported other La2C2n (2n = 92, 96-100) series by density functional theory calculations and statistical mechanics analyses. Nevertheless, it was noted that these thermodynamically favorable La2@C2n isomers turned out to be kinetically unstable radicals due to the presence of one unpaired electron on the carbon cage, making them missing fullerenes and difficult to be captured in their pristine forms, except for the experimentally obtained La2@D5(450)-C100 that has no unpaired electron. Such kinetic instability could be modified by electron reduction (the products were denoted as [La2@C2n]-) or other similar exterior functionalization with ˙CF3 and benzyl radicals, resulting in La-La bonded and paramagnetic species capable of being captured. On the basis of these approaches, carbon cages D3(85)-C92, Cs(120)-C94, D2(186)-C96, and C2(157)-C96 are predicted to be feasibly captured as both pristine CCMF species and electron reduced di-EMF derivatives.

Andrographolide Induces Autophagic Cell Death and Inhibits Invasion and Metastasis of Human Osteosarcoma Cells in An Autophagy-Dependent Manner.

BACKGROUND/AIMS: Osteosarcoma (OS) is the most common primary malignant tumor of bone tissue. Although treatment effectiveness has improved, the OS survival rate has fluctuated in recent years. Andrographolide (AG) has been reported to have antitumor activity against a variety of tumors. Our aim was to investigate the effects and potential mechanisms of AG in human osteosarcoma. METHODS: Cell viability and morphological changes were assessed by MTT and live/dead assays. Apoptosis was detected using Annexin V-FITC/PI double staining, DAPI, and caspase-3 assays. Autophagy was detected with mRFP-GFP-LC3 adenovirus transfection and western blot. Cell migration and invasion were detected by wound healing assay and Transwell® experiments. RESULTS: AG dose-dependently reduced the viability of osteosarcoma cells. No increase in apoptosis was detected in AG-treated human OS MG-63 and U-2OS cells, and the pan-caspase inhibitor z-VAD did not attenuate AG-induced cell death. However, AG induced autophagy by suppressing PI3K/Akt/mTOR and enhancing JNK signaling pathways. 3-MA and Beclin-1 siRNA could reverse the cytotoxic effects of AG. In addition, AG inhibited the invasion and metastasis of OS, and this effect could be reversed with Beclin-1 siRNA. CONCLUSION: AG inhibits viability and induces autophagic death in OS cells. AG-induced autophagy inhibits the invasion and metastasis of OS.

Epoxy and Oxidoannulene Oxidation Mechanisms of Fused-Pentagon Chlorofullerenes: Oxides Linked by a Pirouette-Type Transition State.

Recently, the oxidative functionalization of double-fused-pentagon (DFP)-containing chlorofullerenes #271C50Cl10 and #913C56Cl10 was carried out, resulting in two monoepoxides with the oxygen atom added at the ortho site of pentalene on the DFP moiety. To uncover the reactivity of isolated-pentagon-rule violating fullerenes upon oxidation, two possible formation processes (ozone molecule and oxygen radical served as oxidation reagents) of these two oxides were systematically investigated through density functional theory calculations. For the ozone oxidation, two possible pathways were explored, and the results indicate that the biradical mechanism Pathos-RACDP is kinetically more favorable than Pathos-RABP, where R, A, and P represent reactants, ozonide intermediates, and oxidation products and B, C, and D represent another three oxygen-containing intermediates. The products obtained by ozone oxidation ([6,6]-55-closed epoxides P-C3-C29 for #271C50Cl10 and P-C42-C43 for #913C56Cl10 with oxygen atom added at the shortest and highest HOMO-contribution bonds) are consistent with experimental observations. However, the oxygen radical additions on these two chlorofullerenes favor generation of the [5,6]-66-open oxidoannulene adducts P-C3-C2 and P-C42-C54, respectively. Subsequent analyses of their geometrical features and structural stabilities suggest that these two oxidoannulene adducts are energetically unfavorable and could be converted to more stable epoxides mentioned above by undergoing a pirouette-type transition state. In these two diverse oxidation procedures, the favorable C-C bonds for ozone attacking and C atoms for oxygen-adsorption are rationalized in terms of their bond lengths and HOMO contributions as well as pyramidalization angles.

Photoreactions of Endohedral Metallofullerene with Siliranes: Electronic Properties of Carbosilylated Lu3N@Ih-C80.

Photochemical carbosilylation of Lu3N@Ih-C80 was performed using siliranes (silacyclopropanes) to afford the corresponding [5,6]- and [6,6]-adducts. Electrochemical studies indicated that the redox potentials of the carbosilylated derivatives were shifted cathodically in comparison with those of the [5,6]-pyrrolidino adducts. The electronic effect of the silirane addends on Lu3N@Ih-C80 was verified on the basis of density functional theory calculations.

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants.

UNLABELLED: Escherichia coli has been proposed to have two habitats-the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains of E. coli have evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the surviving E. coli strains were found to contain a genetic insertion element (IS30) located within the uspC-flhDC intergenic region. The positional location of the IS30 element was not observed across a library of 845 E. coli isolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animal E. coli isolates (n = 1,177). Phylogenetics clustered the IS30 element-containing wastewater E. coli isolates into a distinct clade, and biomarker analysis revealed that these wastewater isolates contained a single nucleotide polymorphism (SNP) biomarker pattern that was specific for wastewater. These isolates belonged to phylogroup A, possessed generalized stress response (RpoS) activity, and carried the locus of heat resistance, features likely relevant to nonhost environmental survival. Isolates were screened for 28 virulence genes but carried only the fimH marker. Our data suggest that wastewater contains a naturalized resident population of E. coli We developed an endpoint PCR targeting the IS30 element within the uspC-flhDC intergenic region, and all raw sewage samples (n = 21) were positive for this marker. Conversely, the prevalence of this marker in E. coli-positive surface and groundwater samples was low (≤5%). This simple PCR assay may represent a convenient microbial source-tracking tool for identification of water samples affected by municipal wastewater. IMPORTANCE: The results of this study demonstrate that some strains of E. coli appear to have evolved to become naturalized populations in the wastewater environment and possess a number of stress-related genetic elements likely important for survival in this nonhost environment. The presence of non-host-adapted strains in wastewater challenges our understanding of using E. coli as a microbial indicator of wastewater treatment performance, suggesting that the E. coli strains present in human and animal feces may be very different from those found in treated wastewater.

An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli.

Several studies have demonstrated that E. coli appears to display some level of host adaptation and specificity. Recent studies in our laboratory support these findings as determined by logic regression modeling of single nucleotide polymorphisms (SNP) in intergenic regions (ITGRs). We sought to determine the degree of host-specific information encoded in various ITGRs across a library of animal E. coli isolates using both whole genome analysis and a targeted ITGR sequencing approach. Our findings demonstrated that ITGRs across the genome encode various degrees of host-specific information. Incorporating multiple ITGRs (i.e., concatenation) into logic regression model building resulted in greater host-specificity and sensitivity outcomes in biomarkers, but the overall level of polymorphism in an ITGR did not correlate with the degree of host-specificity encoded in the ITGR. This suggests that distinct SNPs in ITGRs may be more important in defining host-specificity than overall sequence variation, explaining why traditional unsupervised learning phylogenetic approaches may be less informative in terms of revealing host-specific information encoded in DNA sequence. In silico analysis of 80 candidate ITGRs from publically available E. coli genomes was performed as a tool for discovering highly host-specific ITGRs. In one ITGR (ydeR-yedS) we identified a SNP biomarker that was 98% specific for cattle and for which 92% of all E. coli isolates originating from cattle carried this unique biomarker. In the case of humans, a host-specific biomarker (98% specificity) was identified in the concatenated ITGR sequences of rcsD-ompC, ydeR-yedS, and rclR-ykgE, and for which 78% of E. coli originating from humans carried this biomarker. Interestingly, human-specific biomarkers were dominant in ITGRs regulating antibiotic resistance, whereas in cattle host-specific biomarkers were found in ITGRs involved in stress regulation. These data suggest that evolution towards host specificity may be driven by different natural selection pressures on the regulome of E. coli among different animal hosts.

Stabilization of a Chlorinated (#4348)C66:C2v Cage by Encapsulating Monometal Species: Coordination between Metal and Double Hexagon-Condensed Pentalenes.

Carbon cages in endohedral and exohedral fullerene derivatives are usually different. A recent report suggested that chlorofullerene C66Cl10:Cs and endohedral metallofullerene (EMF) Sc2@C66 shared the same cage (#4348)C66:C2v, while it was denied by the definitive characterization of Sc2@C66, which actually possesses the (#4059)C66:C2v isomer. Here, we show that a (#4348)C66:C2v cage with a double hexagon-condensed pentalene (DHCP) moiety, which was captured by exohedral chlorination, is also capable of being stabilized by encapsulating tri- or divalent monometal (M) species. On the basis of density functional theory calculations combined with statistical mechanics analyses, (#4348)C66:C2v-based mono-EMFs M@C2v(4348)-C66 (M = Tb, La, Y, and Yb) were demonstrated to be the most stable and predominant isomers at the fullerene formation temperature region, while another chlorinated cage (#4169)C66:Cs, featured with triple sequentially fused pentagon (TSFP) moiety, is less favorable to be obtained in the form of EMFs, although these two cages can be interconverted by a simple Stone-Wales transformation. The superiority of M@C2v(4348)-C66 over M@Cs(4169)-C66 comes from the stronger interaction of M-DHCP over that of M-TSFP in both ionic and covalent bonding aspects. In addition, size-selective complexation of host [n]cycloparaphenylene ([n]CPP) and Tb@C2v(4348)-C66 was simulated, showing that [10]CPP exhibits the best affinity toward Tb@C66, which provides a new opportunity for isolation and characterization of C66-based mono-EMFs.

Evaluating the Auto-MODS assay, a novel tool for tuberculosis diagnosis for use in resource-limited settings.

There is an urgent need for simple, rapid, and affordable diagnostic tests for tuberculosis (TB) to combat the great burden of the disease in developing countries. The microscopic observation drug susceptibility assay (MODS) is a promising tool to fill this need, but it is not widely used due to concerns regarding its biosafety and efficiency. This study evaluated the automated MODS (Auto-MODS), which operates on principles similar to those of MODS but with several key modifications, making it an appealing alternative to MODS in resource-limited settings. In the operational setting of Chiang Rai, Thailand, we compared the performance of Auto-MODS with the gold standard liquid culture method in Thailand, mycobacterial growth indicator tube (MGIT) 960 plus the SD Bioline TB Ag MPT64 test, in terms of accuracy and efficiency in differentiating TB and non-TB samples as well as distinguishing TB and multidrug-resistant (MDR) TB samples. Sputum samples from clinically diagnosed TB and non-TB subjects across 17 hospitals in Chiang Rai were consecutively collected from May 2011 to September 2012. A total of 360 samples were available for evaluation, of which 221 (61.4%) were positive and 139 (38.6%) were negative for mycobacterial cultures according to MGIT 960. Of the 221 true-positive samples, Auto-MODS identified 212 as positive and 9 as negative (sensitivity, 95.9%; 95% confidence interval [CI], 92.4% to 98.1%). Of the 139 true-negative samples, Auto-MODS identified 135 as negative and 4 as positive (specificity, 97.1%; 95% CI, 92.8% to 99.2%). The median time to culture positivity was 10 days, with an interquartile range of 8 to 13 days for Auto-MODS. Auto-MODS is an effective and cost-sensitive alternative diagnostic tool for TB diagnosis in resource-limited settings.

Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions.

Host specificity in E. coli is widely debated. Herein, we used supervised learning logic-regression-based analysis of intergenic DNA sequence variability in E. coli in an attempt to identify single nucleotide polymorphism (SNP) biomarkers of E. coli that are associated with natural selection and evolution toward host specificity. Seven-hundred and eighty strains of E. coli were isolated from 15 different animal hosts. We utilized logic regression for analyzing DNA sequence data of three intergenic regions (flanked by the genes uspC-flhDC, csgBAC-csgDEFG, and asnS-ompF) to identify genetic biomarkers that could potentially discriminate E. coli based on host sources. Across 15 different animal hosts, logic regression successfully discriminated E. coli based on animal host source with relatively high specificity (i.e., among the samples of the non-target animal host, the proportion that correctly did not have the host-specific marker pattern) and sensitivity (i.e., among the samples from a given animal host, the proportion that correctly had the host-specific marker pattern), even after fivefold cross validation. Permutation tests confirmed that for most animals, host specific intergenic biomarkers identified by logic regression in E. coli were significantly associated with animal host source. The highest level of biomarker sensitivity was observed in deer isolates, with 82% of all deer E. coli isolates displaying a unique SNP pattern that was 98% specific to deer. Fifty-three percent of human isolates displayed a unique biomarker pattern that was 98% specific to humans. Twenty-nine percent of cattle isolates displayed a unique biomarker that was 97% specific to cattle. Interestingly, even within a related host group (i.e., Family: Canidae [domestic dogs and coyotes]), highly specific SNP biomarkers (98% and 99% specificity for dog and coyotes, respectively) were observed, with 21% of dog E. coli isolates displaying a unique dog biomarker and 61% of coyote isolates displaying a unique coyote biomarker. Application of a supervised learning method, such as logic regression, to DNA sequence analysis at certain intergenic regions demonstrates that some E. coli strains may evolve to become host-specific.

Boosting activation of oxygen molecules on C60 fullerene by boron doping.

The activation of oxygen molecules on boron-doped C60 fullerene (C59 B) and the subsequent water formation reaction are systematically investigated by using hybrid density functional calculations. Results indicate that C59 B shows a favorable ability to activate oxygen molecules both kinetically and thermodynamically. The oxygen molecule is first adsorbed on the boron atom, which is identified to be the most reactive site in C59 B for O2 adsorption because of its high positive charge and spin density. The adsorption structure C59 BO2 can further isomerize to form two products with small reaction barriers. Water formation reactions upon these two structures are energetically favorable and suggest a four-electron mechanism for the oxygen reduction reaction catalyzed by C59 B. This work provides a reliable theoretical insight into the catalytic properties of boron-doped fullerene, which is believed to be helpful to explore fullerene catalysts.

Azide addition to Sc2@C66: favorable activity on unsaturated linear triquinanes and dramatic reactivity difference compared with the free C66 cage.

Density functional theory calculations on methyl azide additions to C66 and Sc2@C2v(4059)-C66 suggest that the best addition sites type E[5,6]-56 bond e2 and the new type D[5,6]-55 bond d for C66 and type G[5,5]-66 bond g for Sc2@C66 are located on the unsaturated linear triquinane moieties.