Validity of Normative Volumetric Estimates from Open Access Software in Amnestic Mild Cognitive Impairment.

BACKGROUND: Neurodegeneration in Alzheimer's disease (AD) is typically assessed through brain MRI. Although proprietary software can provide normative estimates of regional atrophy, such tools can be cost-prohibitive for research settings. Free software for generating normative estimates has recently been released but has yet to be validated in the context of amnestic mild cognitive impairment (aMCI). OBJECTIVES: Determine whether normative morphometric estimates generated from open-source software replicate established patterns of neurodegeneration in aMCI, and whether these metrics correlate with episodic memory performance. DESIGN: Observational study of brain MRI and cognition in aging and aMCI with two identical study visits occurring approximately 1.2 years apart. SETTING: Participants were recruited from the local community and outpatient clinical settings. PARTICIPANTS: Adults ages 60-85 with aMCI (n = 25) and cognitively normal controls (CN; n = 74). A subset returned for follow-up (aMCI n = 11, CN n = 52). MEASUREMENTS: Participants completed brain MRI and two neuropsychological tests of verbal episodic memory. FreeSurfer v6.0 and Normative Morphometry Image Statistics were used to generate normative morphometric estimates for AD-relevant regions (hippocampus, parahippocampus, entorhinal cortex, amygdala) and control regions (cuneus, lingual gyrus, pericalcarine gyrus), adjusting for age, sex, head size, scanner manufacturer, and field strength. We tested for baseline group differences in ROI volumes and memory and assessed their within-group associations. We also evaluated changes in ROI volumes over time and tested whether these changes corresponded to declines in memory. RESULTS: At baseline, the aMCI group exhibited poorer memory and smaller volumes in AD-relevant regions than the CN group. There were no group differences in control region volumes. Memory was associated with volumes in AD-relevant regions in the aMCI group only. The aMCI group exhibited greater declines than the CN group in hippocampal volume (17% vs. 8% annual decline) and entorhinal volume (54% vs. 5% annual decline). Decrease in hippocampal volume was marginally associated with decline in memory for the aMCI group. CONCLUSIONS: Normative morphometric values generated from freely available software demonstrated expected patterns of group differences in AD-related volumes and associations with memory. Significant effects were localized to AD-relevant brain regions and only occurred in the aMCI group. These findings support the validity of these free tools as reliable and cost-effective alternatives to proprietary software for use in research settings.

A new species of Proegernia from the Namba Formation in South Australia and the early evolution and environment of Australian egerniine skinks.

The diverse living Australian lizard fauna contrasts greatly with their limited Oligo-Miocene fossil record. New Oligo-Miocene fossil vertebrates from the Namba Formation (south of Lake Frome, South Australia) were uncovered from multiple expeditions from 2007 to 2018. Abundant disarticulated material of small vertebrates was concentrated in shallow lenses along the palaeolake edges, now exposed on the western of Lake Pinpa also known from Billeroo Creek 2 km northeast. The fossiliferous lens within the Namba Formation hosting the abundant aquatic (such as fish, platypus Obdurodon and waterfowl) and diverse terrestrial (such as possums, dasyuromorphs and scincids) vertebrates and is hereafter recognized as the Fish Lens. The stratigraphic provenance of these deposits in relation to prior finds in the area is also established. A new egerniine scincid taxon Proegernia mikebulli sp. nov. described herein, is based on a near-complete reconstructed mandible, maxilla, premaxilla and pterygoid. Postcranial scincid elements were also recovered with this material, but could not yet be confidently associated with P. mikebulli. This new taxon is recovered as the sister species to P. palankarinnensis, in a tip-dated total-evidence phylogenetic analysis, where both are recovered as stem Australian egerniines. These taxa also help pinpoint the timing of the arrival of scincids to Australia, with egerniines the first radiation to reach the continent.

Efficient and tunable spectral compression using frequency-domain nonlinear optics.

A key requirement in the field of ultrafast vibrational spectroscopy is to efficiently generate intense tunable narrowband picosecond laser pulses synchronized to a broadband femtosecond laser source. Current nonlinear methods for picosecond pulse generation suffer from complexities in both experimental implementation and pulse frequency tunability. We present here a straightforward method for spectral bandwidth compression that produces frequency tunable picosecond pulses with efficient power conversion. Broadband femtosecond laser pulses are compressed to narrowband picosecond pulses using frequency domain sum-frequency generation of spatially chirped pulses, achieving spectral bandwidths of <20 cm-1 and power conversion efficiency of ∼18%. The experimental design of the bandwidth compressor is presented and its application to stimulated Raman spectroscopy is demonstrated.

Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes.

Encoded microparticles have become a powerful tool for a wide array of applications, including high-throughput sample tracking and massively parallel biological multiplexing. Spectral encoding, where particles are encoded with distinct luminescence spectra, provides a particularly appealing encoding strategy because of the ease of reading codes and assay flexibility. To date, spectral encoding has been limited in the number of codes that can be accurately resolved. Here, we demonstrate an automated 5-dimensional spectral encoding scheme using lanthanide nanophosphors that is capable of producing isotropic spherical microparticles with up to 1,100 unique codes, which we term MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding). We further develop a quantitative framework for evaluating global ability to distinguish codes and demonstrate that for six different sets of MRBLEs ranging from 106 to 1,101 codes in size, > 98% of MRBLEs can be assigned to a code with 99.99% confidence. These > 1,000 code sets represent the largest spectral code libraries built to date. We expect that these MRBLEs will enable a wide variety of novel multiplexed assays.

Correction: Programmable microfluidic synthesis of spectrally encoded microspheres.

Correction for 'Programmable microfluidic synthesis of spectrally encoded microspheres' by R. E. Gerver et al., Lab Chip, 2012, 12, 4716-4723.

Programmable microfluidic synthesis of spectrally encoded microspheres.

Spectrally encoded fluorescent beads are an attractive platform for assay miniaturization and multiplexing in the biological sciences. Here, we synthesize hydrophilic PEG-acrylate polymer beads encoded with lanthanide nanophosphors using a fully automated microfluidic synthesis device. These beads are encoded by including varying amounts of two lanthanide nanophosphors relative to a third reference nanophosphor to generate 24 distinct ratios. These codes differ by less than 3% from their target values and can be distinguished from each other with an error rate of <0.1%. The encoded bead synthesis strategy we have used is readily extensible to larger numbers of codes, potentially up to millions, providing a new platform technology for assay multiplexing.

Detection of Streptococcus pneumoniae carriage by the Binax NOW test with nasal and nasopharyngeal swabs in young children.

The rapid detection of carriage of Streptococcus pneumoniae could assist in the management of pneumococcal infection, such as acute otitis media. We evaluated the reliability of the Binax NOW test in the exclusion and detection of pneumococcal carriage by nasal samples from 139 children and using nasopharyngeal samples from 250 children (aged 6-35 months) with respiratory infection with or without acute otitis media. The Binax NOW test results were compared with culture-based detection of carriage of S. pneumoniae. The Binax NOW test from the nasal samples had a sensitivity of 95%, a specificity of 78%, and the positive and negative predictive values were 83 and 93%, respectively; and for the nasopharyngeal samples the corresponding numbers were 88%, 95%, 96%, and 87%. When rapid knowledge of the carriage status of S. pneumoniae is needed, the Binax NOW test is a reliable method for the exclusion of carriage using nasal sampling, and in the detection of carriage using nasopharyngeal sampling.

Merkel cell carcinoma in Western Australia: a population-based study of incidence and survival.

BACKGROUND: Merkel cell carcinoma (MCC) is an uncommon but aggressive cutaneous skin cancer. Even with the appropriate treatment, MCC is prone to recurrence, and metastases are common. Exposure to ultraviolet radiation has been suggested as contributing towards the development of MCC. MCC has not been extensively investigated in Australia, even though Australia has the highest incidence of sun-related cancers in the world. OBJECTIVES: To describe the demographics and determine trends of incidence and survival of MCC cases in Western Australia (WA). METHODS: All reported invasive cases of MCC incident between 1 January 1993 and 31 December 2007 were extracted from the WA Cancer Registry. Age-adjusted incidence rates for MCC were calculated using direct standardization to the U.S. standard 2000 population. Cause-specific survival was investigated using Kaplan-Meier and Cox proportional hazards analysis. results: Two hundred and fifteen cases were confirmed by pathological review as being definite cases of MCC. Patients were mainly males (65%) and elderly (median age 77 years). Standardized age-adjusted incidence rates were higher in men (1·0/100,000) than in women (0·63/100,000) and higher in older ages (15·5/100,000 in the 85+year age group) than younger ages (0·1/100,000 in the 30-34 year age group). Five-year cause-specific survival was 64%. CONCLUSIONS: Incidence of MCC in WA is the highest reported in the literature. In addition, MCC has worse survival than melanoma. The high rates and demographic and anatomical distribution are consistent with sun exposure playing a causal role.

The effects on the lower esophageal sphincter of sevoflurane induction and increased intra-abdominal pressure during laparoscopy.

BACKGROUND: Today sevoflurane is one of the most frequently used volatile anesthetics. The speed of induction can approach that of intravenous anesthetics, and case reports using sevoflurane induction for emergency anesthesia have been published. The purpose of this study in laparoscopic cholecystectomy patients was to investigate the effects of sevoflurane during inhalation induction on the lower esophageal sphincter pressure (LESP) and barrier pressure (BrP). The effects on lower esophageal sphincter (LES) and BrP of increased intra-abdominal pressure during laparoscopy were also evaluated. METHODS: We recorded LESP and BrP in nine patients using a Dent sleeve device. Recordings were made before and after inhalation induction of anesthesia with 8% sevoflurane, as well as before and after insufflation of CO(2) into the abdomen. RESULTS: After induction with sevoflurane, LESP (P= 0.039) and BrP (P= 0.020) decreased. Nevertheless, BrP was kept positive in all patients. Insufflation of CO(2) into the abdomen during laparoscopy induced a significant increase in LESP (P= 0.02) and gastric pressure (P= 0.004). However, there was no significant change in BrP (P= 0.66); it increased in four patients and decreased in five. CONCLUSION: BrP was kept positive in all patients after induction of anesthesia. Therefore, we believe that in combination with cricoid pressure, inhalation induction with sevoflurane might be a safe choice. As the adaptive increase in LESP during laparoscopy was not enough to retain a barrier pressure in all patients, it is important to be aware of the risk of regurgitation throughout the anesthesia.

15N NMR investigation of the covalent binding of reduced TNT amines to soil humic acid, model compounds, and lignocellulose.

The five major reductive degradation products of TNT-4ADNT (4-amino-2,6-dinitrotoluene), 2ADNT (2-amino-4,6-dinitrotoluene), 2,4DANT (2,4-diamino-6-nitrotoluene), 2,6DANT (2,6-diamino-4-nitrotoluene), and TAT (2,4,6-triaminotoluene)-labeled with 15N in the amine positions, were reacted with the IHSS soil humic acid and analyzed by 15N NMR spectrometry. In the absence of catalysts, all five amines underwent nucleophilic addition reactions with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and nonheterocyclic condensation products. Imine formation via 1,2-addition of the amines to quinone groups in the soil humic acid was significant with the diamines and TAT but not the monoamines. Horseradish peroxidase (HRP) catalyzed an increase in the incorporation of all five amines into the humic acid. In the case of the diamines and TAT, HRP also shifted the binding away from heterocyclic condensation product toward imine formation. A comparison of quantitative liquid phase with solid-state CP/MAS 15N NMR indicated that the CP experiment underestimated imine and heterocyclic nitrogens in humic acid, even with contact times optimal for observation of these nitrogens. Covalent binding of the mono- and diamines to 4-methylcatechol, the HRP catalyzed condensation of 4ADNT and 2,4DANT to coniferyl alcohol, and the binding of 2,4DANT to lignocellulose with and without birnessite were also examined.

15N NMR investigation of the reduction and binding of TNT in an aerobic bench scale reactor simulating windrow composting.

T15NT was added to a soil of low organic carbon content and composted for 20 days in an aerobic bench scale reactor. The finished whole compost and fulvic acid, humic acid, humin, and lignocellulose fractions extracted from the compost were analyzed by solid-state CP/MAS and DP/MAS 15N NMR. 15N NMR spectra provided direct spectroscopic evidence for reduction of TNT followed by covalent binding of the reduced metabolites to organic matter of the composted soil, with the majority of metabolite found in the lignocellulose fraction, by mass also the major fraction of the compost. In general, the types of bonds formed between soil organic matter and reduced TNT amines in controlled laboratory reactions were observed in the spectra of the whole compost and fractions, confirming that during composting TNT is reduced to amines that form covalent bonds with organic matter through aminohydroquinone, aminoquinone, heterocyclic, and imine linkages, among others. Concentrations of imine nitrogens in the compost spectra suggest that covalent binding by the diamines 2,4DANT and 2,6DANT is a significant process in the transformation of TNT into bound residues. Liquid-phase 15N NMR spectra of the fulvic acid and humin fractions provided possible evidence for involvement of phenoloxidase enzymes in covalent bond formation.

Determination of bending-induced strain in optical fibers by use of quantitative phase imaging.

Quantitative phase microscopy with polarized light has been used to determine the change in refractive index introduced into an optical fiber when the fiber is bent through a constant radius of curvature. By obtaining phase images for two orthogonal directions of the polarization of the incident light, one can infer the induced axial strain profile within the fiber. Radii of curvature from 1 to 8 cm were considered, and in each case excellent agreement, within lambda/100, was obtained between experimental results and theory.

Interaction of the human adenovirus proteinase with its 11-amino acid cofactor pVIc.

The interaction of the human adenovirus proteinase (AVP) and AVP-DNA complexes with the 11-amino acid cofactor pVIc was characterized. The equilibrium dissociation constant for the binding of pVIc to AVP was 4.4 microM. The binding of AVP to 12-mer single-stranded DNA decreased the K(d) for the binding of pVIc to AVP to 0.09 microM. The pVIc-AVP complex hydrolyzed the substrate with a Michaelis constant (K(m)) of 3.7 microM and a catalytic rate constant (k(cat)) of 1.1 s(-1). In the presence of DNA, the K(m) increased less than 2-fold, and the k(cat) increased 3-fold. Alanine-scanning mutagenesis was performed to determine the contribution of individual pVIc side chains in the binding and stimulation of AVP. Two amino acid residues, Gly1' and Phe11', were the major determinants in the binding of pVIc to AVP, while Val2' and Phe11' were the major determinants in stimulating enzyme activity. Binding of AVP to DNA greatly suppressed the effects of the alanine substitutions on the binding of mutant pVIcs to AVP. Binding of either or both of the cofactors, pVIc or the viral DNA, to AVP did not dramatically alter its secondary structure as determined by vacuum ultraviolet circular dichroism. pVIc, when added to Hep-2 cells infected with adenovirus serotype 5, inhibited the synthesis of infectious virus, presumably by prematurely activating the proteinase so that it cleaved virion precursor proteins before virion assembly, thereby aborting the infection.

ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions.

The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein-protein, protein-nucleic acid, and protein-small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studying the contribution of single amino acids to the energetics of protein interactions, and can be updated by researchers as new data are generated.

Engineering the processive run length of the kinesin motor.

Conventional kinesin is a highly processive molecular motor that takes several hundred steps per encounter with a microtubule. Processive motility is believed to result from the coordinated, hand-over-hand motion of the two heads of the kinesin dimer, but the specific factors that determine kinesin's run length (distance traveled per microtubule encounter) are not known. Here, we show that the neck coiled-coil, a structure adjacent to the motor domain, plays an important role in governing the run length. By adding positive charge to the neck coiled-coil, we have created ultra-processive kinesin mutants that have fourfold longer run lengths than the wild-type motor, but that have normal ATPase activity and motor velocity. Conversely, adding negative charge on the neck coiled-coil decreases the run length. The gain in processivity can be suppressed by either proteolytic cleavage of tubulin's negatively charged COOH terminus or by high salt concentrations. Therefore, modulation of processivity by the neck coiled-coil appears to involve an electrostatic tethering interaction with the COOH terminus of tubulin. The ability to readily increase kinesin processivity by mutation, taken together with the strong sequence conservation of the neck coiled-coil, suggests that evolutionary pressures may limit kinesin's run length to optimize its in vivo function.

ATPase kinetic characterization and single molecule behavior of mutant human kinesin motors defective in microtubule-based motility.

Conventional kinesin is a microtubule-based motor protein that is an important model system for understanding mechanochemical transduction. To identify regions of the kinesin protein that participate in microtubule binding and force production, Woehlke et al. [(1997) Cell 90, 207-216] generated 35 alanine mutations in solvent-exposed residues. Here, we have performed presteady-state kinetic and single molecule motility analyses on three of these mutants [Y138A, loop 11 triple (L248A/D249A/E250A), and E311A] that exhibited a similar approximately 3-fold reduction in both microtubule gliding velocity and microtubule-stimulated ATPase activity. All mutants showed normal second-order ATP binding kinetics, indicating correct folding of the active site. The Y138A and loop 11 triple mutants were defective both in nucleotide hydrolysis and in microtubule-stimulated ADP release rates, the latter suggesting a defect in allosteric communication between the microtubule and the active site. A single molecule fluorescence assay further revealed that the loop 11 mutant is defective in initiating processive motion, suggesting that this loop is important for the initial contact between kinesin and the microtubule. Y138A, on the other hand, can bind to the microtubule normally but cannot move processively. For E311A, neither the rate of nucleotide hydrolysis nor ADP release could account for its slower ATPase and gliding velocity, which suggests that either phosphate release or a conformational transition is rate-limiting in this mutant. The single molecule assay showed that E311A has a reduced velocity of movement, but is not defective in processivity. Thus, while these mutants behave similarly in solution ATPase and multiple motor gliding assays, kinetic and single molecule analyses reveal defects in distinct processes in kinesin's mechanochemical cycle.

A novel method of affinity-purifying proteins using a bis-arsenical fluorescein.

Genetically-encoded affinity tags constitute an important strategy for purifying proteins. Here, we have designed a novel affinity matrix based on the his-arsenical fluorescein dye FlAsH, which specifically recognizes short alpha-helical peptides containing the sequence CCXXCC (Griffin BA, Adams SR, Tsien RY, 1998, Science 281:269-272). We find that kinesin tagged with this cysteine-containing helix binds specifically to FlAsH resin and can be eluted in a fully active form. This affinity tag has several advantages over polyhistidine, the only small affinity tag in common use. The protein obtained with this single chromatographic step from crude Escherichia coli lysates is purer than that obtained with nickel affinity chromatography of 6xHis tagged kinesin. Moreover, unlike nickel affinity chromatography, which requires high concentrations of imidazole or pH changes for elution, protein bound to the FlAsH column can be completely eluted by dithiothreitol. Because of these mild elution conditions, FlAsH affinity chromatography is ideal for recovering fully active protein and for the purification of intact protein complexes.

Hepatitis C: the lurking dragon.

Hepatitis C virus (HCV) is the most common chronic blood-borne infection in the United States. An estimated 3.9 million Americans (1.4%) are infected with HCV. The 10th leading cause of death in U.S. adults is chronic liver disease (CLD), which accounts for 25,000 deaths annually. Approximately 40% of all CLD is related to HCV, causing 8000 to 10,000 deaths annually. In addition, approximately 60% of people with HIV are believed to be coinfected with HCV, which hastens their progression to AIDS.