Tissue microarray (TMA) use in post mortem neuropathology.

BACKGROUND: Tissue microarrays (TMAs), where each block (and thus section) contains multiple tissue cores from multiple blocks potentially allow more efficient use of tissue, reagents and time in neuropathology. NEW METHOD: The relationship between data from TMA cores and whole sections was investigated using 'virtual' TMA cores. This involved quantitative assessments of microglial pathology in white matter lesions and motor neuron disease, alongside qualitative TDP-43 inclusion status in motor neuron disease cases. Following this, a protocol was developed for TMA construction. RESULTS: For microglial pathology we found good concordance between virtual cores and whole sections for volume density using one 1.75 mm core (equivalent to a 2 mm core after accounting for peripheral tissue loss). More sophisticated microglial cell size and measures required two cores. Qualitative results of pTDP-43 pathology showed use of one 1.75 mm core gave a 100 % sensitivity and specificity within grey matter, and 88.3 % sensitivity and 100 % specificity within white matter. A method of producing the TMAs was suitable for immunohistochemistry both manually and by autostainer, with the minimal core loss from the microscope slide. COMPARISON WITH EXISTING METHODS: TMAs have been used infrequently in post mortem neuropathology research. However, we believe TMAs give comparable tissue assessment results and can be constructed, sectioned and stained with relative ease. CONCLUSIONS: We found TMAs could be used to assess both quantitative (microglial pathology) and qualitative pathology (TDP-43 proteinopathy) with greatly reduced quantities of tissue, time and reagents. These could be used for further work to improve data acquisition efficiency.

Microbiological Quality of Commercial Tofu.

A study was done to investigate the microbiological quality of commercial tofu available in local retail outlets. A sampling method was first developed to obtain accurate and representative microbial counts of individual pieces of tofu. Plate count determination of total aerobic organisms, psychrotrophs, coliforms, sporeformers, yeasts and molds, and staphylococci were made on 60 tofu samples (representing three lots each of four different brands) obtained within 24 h after delivery to the retail store. In addition, for two brands that provided manufacturer's pull dates, the same microbial counts were obtained for samples stored in the laboratory at 10°C until the pull date. Of the tofu sampled immediately after purchase, 83% of the lots tested had total counts greater than 106 colony-forming units (CFU)/g and psychrotrophic counts greater than 104 CFU/g. In addition, 67% of the lots tested had confirmed coliform counts greater than 103 CFU/g. Very low levels (less than 10 CFU/g) of all other microbial groups tested for were found in the majority of lots. Samples held until the manufacturer's pull date contained higher total and psychrotrophic counts but lower or stable counts of other organisms compared with samples tested immediately after purchase. To improve the microbiological quality of tofu, processors need to reduce initial loads by improving sanitation and processing techniques, and retailers should provide more consistent and colder refrigerated storage.

Relating gastric scintigraphy and symptoms to motility capsule transit and pressure findings in suspected gastroparesis.

BACKGROUND: Wireless motility capsule (WMC) findings are incompletely defined in suspected gastroparesis. We aimed to characterize regional WMC transit and contractility in relation to scintigraphy, etiology, and symptoms in patients undergoing gastric emptying testing. METHODS: A total of 209 patients with gastroparesis symptoms at NIDDK Gastroparesis Consortium centers underwent gastric scintigraphy and WMCs on separate days to measure regional transit and contractility. Validated questionnaires quantified symptoms. KEY RESULTS: Solid scintigraphy and liquid scintigraphy were delayed in 68.8% and 34.8% of patients; WMC gastric emptying times (GET) were delayed in 40.3% and showed 52.8% agreement with scintigraphy; 15.5% and 33.5% had delayed small bowel (SBTT) and colon transit (CTT) times. Transit was delayed in ≥2 regions in 23.3%. Rapid transit was rarely observed. Diabetics had slower GET but more rapid SBTT versus idiopathics (P ≤ .02). GET delays related to greater scintigraphic retention, slower SBTT, and fewer gastric contractions (P ≤ .04). Overall gastroparesis symptoms and nausea/vomiting, early satiety/fullness, bloating/distention, and upper abdominal pain subscores showed no relation to WMC transit. Upper and lower abdominal pain scores (P ≤ .03) were greater with increased colon contractions. Constipation correlated with slower CTT and higher colon contractions (P = .03). Diarrhea scores were higher with delayed SBTT and CTT (P ≤ .04). CONCLUSIONS & INFERENCES: Wireless motility capsules define gastric emptying delays similar but not identical to scintigraphy that are more severe in diabetics and relate to reduced gastric contractility. Extragastric transit delays occur in >40% with suspected gastroparesis. Gastroparesis symptoms show little association with WMC profiles, although lower symptoms relate to small bowel or colon abnormalities.

Voyaging into the third dimension: A perspective on virtual methods and their application to studies of juvenile sex estimation and the ontogeny of sexual dimorphism.

In contrast to the well-established and highly accurate morphological methods available for sexing adult skeletons, juvenile sex estimation is widely recognised as a difficult task that faces a series of challenges. The acquisition of 3D data, and construction of 3D models from volume or surface scans, has become increasingly common in forensic sciences, and these data offer considerable opportunity for the development and refinement of methods in sex estimation. The suitability and potential of virtual methods for juvenile sex estimation are evaluated with the aims of identifying (1) the benefits and challenges associated with virtual data and quantitative analysis of 3D models, and (2) pathways that may lead to practical improvements for sexing juveniles. The issues associated with sex estimation in juveniles are discussed and approached in the context of a framework that unifies classification results for a given trait, which provide information on its capacity to discriminate between the sexes, with the underlying patterns of dimorphism over ontogeny. Virtual collections of 3D models are suggested as integral to this framework because they enable the magnitude and mode of sexual dimorphism to be comprehensively quantified for a chosen trait or set of traits. Those data can be used to inform decisions about how to apply a method for sex estimation to maximize its success. Virtual collections, through extending the scope of analyses and impacting the way in which questions on sexual dimorphism in juveniles may be answered, are undoubtedly set to play a central role in future research.

Experiment and simulation of novel liquid crystal plasma mirrors for high contrast, intense laser pulses.

We describe the first demonstration of plasma mirrors made using freely suspended, ultra-thin films formed dynamically and in-situ. We also present novel particle-in-cell simulations that for the first time incorporate multiphoton ionization and dielectric models that are necessary for describing plasma mirrors. Dielectric plasma mirrors are a crucial component for high intensity laser applications such as ion acceleration and solid target high harmonic generation because they greatly improve pulse contrast. We use the liquid crystal 8CB and introduce an innovative dynamic film formation device that can tune the film thickness so that it acts as its own antireflection coating. Films can be formed at a prolonged, high repetition rate without the need for subsequent realignment. High intensity reflectance above 75% and low-field reflectance below 0.2% are demonstrated, as well as initial ion acceleration experimental results that demonstrate increased ion energy and yield on shots cleaned with these plasma mirrors.

A new family of bizarre durophagous carnivorous marsupials from Miocene deposits in the Riversleigh World Heritage Area, northwestern Queensland.

A new specimen of the bizarrely specialised Malleodectes mirabilis from middle Miocene deposits in the Riversleigh World Heritage Area provides the first and only information about the molar dentition of this strange group of extinct marsupials. Apart from striking autapomorphies such as the enormous P3, other dental features such as stylar cusp D being larger than B suggest it belongs in the Order Dasyuromorphia. Phylogenetic analysis of 62 craniodental characters places Malleodectes within Dasyuromorphia albeit with weak support and without indication of specific relationships to any of the three established families (Dasyuridae, Myrmecobiidae and Thylacinidae). Accordingly we have allocated Malleodectes to the new family, Malleodectidae. Some features suggest potential links to previously named dasyuromorphians from Riversleigh (e.g., Ganbulanyi) but these are too poorly known to test this possibility. Although the original interpretation of a steeply declining molar row in Malleodectes can be rejected, it continues to seem likely that malleodectids specialised on snails but probably also consumed a wider range of prey items including small vertebrates. Whatever their actual diet, malleodectids appear to have filled a niche in Australia's rainforests that has not been occupied by any other mammal group anywhere in the world from the Miocene onwards.

A laser driven pulsed X-ray backscatter technique for enhanced penetrative imaging.

X-ray backscatter imaging can be used for a wide range of imaging applications, in particular for industrial inspection and portal security. Currently, the application of this imaging technique to the detection of landmines is limited due to the surrounding sand or soil strongly attenuating the 10s to 100s of keV X-rays required for backscatter imaging. Here, we introduce a new approach involving a 140 MeV short-pulse (< 100 fs) electron beam generated by laser wakefield acceleration to probe the sample, which produces Bremsstrahlung X-rays within the sample enabling greater depths to be imaged. A variety of detector and scintillator configurations are examined, with the best time response seen from an absorptive coated BaF2 scintillator with a bandpass filter to remove the slow scintillation emission components. An X-ray backscatter image of an array of different density and atomic number items is demonstrated. The use of a compact laser wakefield accelerator to generate the electron source, combined with the rapid development of more compact, efficient and higher repetition rate high power laser systems will make this system feasible for applications in the field. Content includes material subject to Dstl (c) Crown copyright (2014). Licensed under the terms of the Open Government Licence except where otherwise stated. To view this licence, visit http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3 or write to the Information Policy Team, The National Archives, Kew, London TW9 4DU, or email: psi@ nationalarchives.gsi.gov.uk.

NASH resolution is associated with improvements in HDL and triglyceride levels but not improvement in LDL or non-HDL-C levels.

BACKGROUND: Nonalcoholic steatohepatitis (NASH) is associated with dyslipidemia and cardiovascular disease (CVD). AIM: To determine the relationship between resolution of NASH and dyslipidemia. METHODS: Individuals in the Pioglitazone vs. Vitamin E vs. Placebo for the Treatment of Nondiabetic Patients with Nonalcoholic Steatohepatitis (PIVENS) trial with paired liver biopsies and fasting lipid levels were included (N = 222). In the PIVENS trial individuals were randomised to pioglitazone 30 mg, vitamin E 800 IU or placebo for 96 weeks. Change in lipid levels at 96 weeks was compared between those with and without NASH resolution. RESULTS: Dyslipidemia at baseline was frequent, with low high-density lipoprotein (HDL) (<40 mg/dL in men or <50 mg/dL in women) in 63%, hypertriglyceridaemia (≥150 mg/dL) in 46%, hypercholesterolaemia (≥200 mg/dL) in 47% and triglycerides (TG)/HDL >5.0 in 25%. Low-density lipoprotein (LD) ≥160 mg/dL was found in 16% and elevated non-HDL cholesterol (non-HDL-C) (≥130 mg/dL) in 73%. HDL increased with NASH resolution but decreased in those without resolution (2.9 mg/dL vs. -2.5 mg/dL, P < 0.001). NASH resolution was associated with significant decreases in TG and TG/HDL ratio compared to those without resolution (TG: -21.1 vs. -2.3 mg/dL, P = 0.03 and TG/HDL: -0.7 vs. 0.1, P = 0.003). Non-HDL-C, LDL and cholesterol decreased over 96 weeks in both groups, but there was no significant difference between groups. Treatment group did not impact lipids. CONCLUSIONS: NASH resolution is associated with improvements in TG and HDL but not in other cardiovascular disease risk factors including LDL and non-HDL-C levels. Individuals with resolution of NASH may still be at increased risk of cardiovascular disease. ClinicalTrials.gov identifier: NCT00063622.

Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs.

Post-transcriptional control of gene expression is mediated by the interaction of RNA-binding proteins with their cognate mRNAs that specifically regulate their stability, localization and translation. mRNA-binding proteins are multifunctional and it has been proposed therefore that a combinatorial RNA-binding protein code exists that allows specific protein sub-complexes to control cytoplasmic gene expression under a range of pathophysiological conditions. We show that polypyrimidine tract-binding protein (PTB) is central to one such complex that forms in apoptotic cells. Thus, during apoptosis initiated by TNF-related apoptosis inducing ligand there is a change in the repertoire of RNA-binding proteins with which PTB interacts. We show that altering the cellular levels of PTB and its binding partners, either singly or in combination, is sufficient to directly change the rates of apoptosis with increased expression of PTB, YBX1, PSF and NONO/p54(nrb) accelerating this process. Mechanistically, we show that these proteins post-transcriptionally regulate gene expression, and therefore apoptotic rates, by interacting with and stimulating the activity of RNA elements (internal ribosome entry segments) found in mRNAs that are translated during apoptosis. Taken together, our data show that PTB function is controlled by a set of co-recruited proteins and importantly provide further evidence that it is possible to dictate cell fate by modulating cytoplasmic gene expression pathways alone.

The effect of pH and nitrite concentration on the antimicrobial impact of celery juice concentrate compared with conventional sodium nitrite on Listeria monocytogenes.

The objectives of this study were to evaluate the impact of pH and nitrite from celery juice concentrate (CJ) on the growth of Listeria monocytogenes in broth and on ham slices, and to evaluate the impact of pH and nitrite from CJ on quality attributes of the ham. The pH of both broth and ham were increased by the addition of CJ. The CJ was less effective than conventional nitrite at 100 mg/kg nitrite in broth, but in ham, the CJ treatments at both 100 and 200 mg/kg resulted in growth of L. monocytogenes (p>0.05) similar to that of the conventional nitrite at the same concentrations. Reducing the pH of CJ before addition to the ham had greater impact on L. monocytogenes growth at 200 mg/kg nitrite than at 100 mg/kg. Celery juice concentrate may increase meat product pH which could have implications for the antimicrobial impact of nitrite in some products.

Permeability of edible coatings.

The permeabilities of water vapour, O2 and CO2 were determined for 18 coating formulations. Water vapour transmission rate ranged from 98.8 g/m(2).day (6% beeswax) to 758.0 g/m(2).day (1.5% carboxymethyl cellulose with glycerol). O2 permeability at 14 ± 1°C and 55 ± 5% RH ranged from 1.50 to 7.95 cm(3)cm cm(-2)s(-1)Pa(-1), with CO2 permeability 2 to 6 times as high. Permeability to noncondensable gases (O2 and CO2) was higher for hydrophobic (peanut oil followed by beeswax) coatings as compared to hydrophilic (whey protein concentrate and carboxymethyl cellulose).

Factors related to abdominal pain in gastroparesis: contrast to patients with predominant nausea and vomiting.

BACKGROUND: Factors associated with abdominal pain in gastroparesis are incompletely evaluated and comparisons of pain vs other symptoms are limited. This study related pain to clinical factors in gastroparesis and contrasted pain/discomfort- with nausea/vomiting-predominant disease. METHODS: Clinical and scintigraphy data were compared in 393 patients from seven centers of the NIDDK Gastroparesis Clinical Research Consortium with moderate-severe (Patient Assessment of Upper Gastrointestinal Disorders Symptoms [PAGI-SYM] score ≥ 3) vs none-mild (PAGI-SYM < 3) upper abdominal pain and predominant pain/discomfort vs nausea/vomiting. KEY RESULTS: Upper abdominal pain was moderate-severe in 261 (66%). Pain/discomfort was predominant in 81 (21%); nausea/vomiting was predominant in 172 (44%). Moderate-severe pain was more prevalent with idiopathic gastroparesis and with lack of infectious prodrome (P ≤ 0.05) and correlated with scores for nausea/vomiting, bloating, lower abdominal pain/discomfort, bowel disturbances, and opiate and antiemetic use (P < 0.05), but not gastric emptying or diabetic neuropathy or control. Gastroparesis severity, quality of life, and depression and anxiety were worse with moderate-severe pain (P ≤ 0.008). Factors associated with moderate-severe pain were similar in diabetic and idiopathic gastroparesis. Compared to predominant nausea/vomiting, predominant pain/discomfort was associated with impaired quality of life, greater opiate, and less antiemetic use (P < 0.01), but similar severity and gastric retention. CONCLUSIONS & INFERENCES: Moderate-severe abdominal pain is prevalent in gastroparesis, impairs quality of life, and is associated with idiopathic etiology, lack of infectious prodrome, and opiate use. Pain is predominant in one fifth of gastroparetics. Predominant pain has at least as great an impact on disease severity and quality of life as predominant nausea/vomiting.

Energy transport in short-pulse-laser-heated targets measured using extreme ultraviolet laser backlighting.

The accurate characterization of thermal electron transport and the determination of heating by suprathermal electrons in laser driven solid targets are both issues of great importance to the current experiments being performed at the National Ignition Facility, which aims to achieve thermonuclear fusion ignition using lasers. Ionization, induced by electronic heat conduction, can cause the opacity of a material to drop significantly once bound-free photoionization is no longer energetically possible. We show that this drop in opacity enables measurements of the transmission of extreme ultraviolet (EUV) laser pulses at 13.9 nm to act as a signature of the heating of thin (50 nm) iron layers with a 50-nm thick parylene-N (CH) overlay irradiated by 35-fs pulses at irradiance 3×10(16) Wcm(-2). Comparing EUV transmission measurements at different times after irradiation to fluid code simulations shows that the target is instantaneously heated by hot electrons (with approximately 10% of the laser energy), followed by thermal conduction with a flux limiter of ≈0.05.

The Teamwork Study: enhancing the role of non-GP staff in chronic disease management in general practice.

There is evidence for a team-based approach in the management of chronic disease in primary health care. However, the standard of care is variable, probably reflecting the limited organisational capacity of health services to provide the necessary structured and organised care for this group of patients. This study aimed to evaluate the impact of a structured intervention involving non-GP staff in GP practices on the quality of care for patients with diabetes or cardiovascular disease. A cluster randomised trial was undertaken across 60 GP practices. The intervention was implemented in 30 practices with staff and patients interviewed at baseline and at 12-15 months follow up. The change in team roles was evaluated using a questionnaire completed by practice staff. The quality of care was evaluated using the Patient Assessment of Chronic Illness Care questionnaire. We found that although the team roles of staff improved in the intervention practices and there were significant differences between practices, there was no significant difference between those in the intervention and control groups in patient-assessed quality of care after adjusting for baseline-level score and covariates at the 12-month follow up. Practice team roles were not significantly associated with change in Patient Assessment of Chronic Illness Care scores. Patients with multiple conditions were more likely to assess their quality of care to be better. Thus, although previous research has shown a cross-sectional association between team work and quality of care, we were unable to replicate these findings in the present study. These results may be indicative of insufficient time for organisational change to result in improved patient-assessed quality of care, or because non-GP staff roles were not sufficiently focussed on the aspects of care assessed. The findings provide important information for researchers when designing similar studies.

Bacterial DNA uptake sequences can accumulate by molecular drive alone.

Uptake signal sequences are DNA motifs that promote DNA uptake by competent bacteria in the family Pasteurellaceae and the genus Neisseria. The genomes of these bacteria contain many copies of their canonical uptake sequence (often >100-fold overrepresentation), so the bias of the uptake machinery causes cells to prefer DNA derived from close relatives over DNA from other sources. However, the molecular and evolutionary forces responsible for the abundance of uptake sequences in these genomes are not well understood, and their presence is not easily explained by any of the current models of the evolution of competence. Here we describe use of a computer simulation model to thoroughly evaluate the simplest explanation for uptake sequences, that they accumulate in genomes by a form of molecular drive generated by biased DNA uptake and evolutionarily neutral (i.e., unselected) recombination. In parallel we used an unbiased search algorithm to characterize genomic uptake sequences and DNA uptake assays to refine the Haemophilus influenzae uptake specificity. These analyses showed that biased uptake and neutral recombination are sufficient to drive uptake sequences to high densities, with the spacings, stabilities, and strong consensus typical of uptake sequences in real genomes. This result greatly simplifies testing of hypotheses about the benefits of DNA uptake, because it explains how genomes could have passively accumulated sequences matching the bias of their uptake machineries.

Upregulated c-myc expression in multiple myeloma by internal ribosome entry results from increased interactions with and expression of PTB-1 and YB-1.

The 5' untranslated region of the proto-oncogene c-myc contains an internal ribosome entry segment (IRES) and c-myc translation can therefore be initiated by internal ribosome entry as well as by cap-dependent mechanisms. It has been shown previously that in patients with multiple myeloma (MM) and in MM-derived cell lines there is a C to T mutation in the c-myc IRES that increases IRES activity and the corresponding synthesis of c-myc protein although it is not fully understood how this occurs. Our data show that two recently identified c-myc IRES trans-acting factors, Y-box binding protein 1 (YB-1) and polypyrimidine tract-binding protein 1 (PTB-1), bind more strongly (approximately 3.5- and 2-fold respectively) to the mutated version of the c-myc IRES and in vitro these proteins exert their effect synergistically to stimulate IRES activity of the mutant IRES 4.5-fold more than the wild-type version. Importantly, we show that there is a strong correlation between the expression of PTB-1, YB-1 and c-myc in MM-derived cell lines, suggesting that by reducing either PTB-1 or YB-1 protein levels it is possible to decrease c-myc expression and inhibit cell proliferation of MM-derived cell lines.

Changes of soybean quality during storage as related to soymilk and tofu making.

Soybeans are stored and transported under various humidity and temperature conditions. Soymilk and tofu are two of the most important foods made from whole soybeans. The objective of this study was to investigate the influence of storage conditions on soybean quality as related to soymilk and tofu-making properties. Soybeans of 3 different genotypes (Proto, IA2032, and Vinton 81) were stored in varying conditions: temperature ranging from 4 to 50 degrees C, relative humidity from 55% to 80%, initial moisture content from 6% to 14%, and storage time up to 15 mo depending upon storage conditions. The effects of different storage conditions on soybean color, solids and protein extractability, soymilk pH, tofu yield, tofu solids and protein contents, tofu color, and texture were investigated. While no significant changes occurred for the soybeans stored at 4 degrees C, the soybeans stored at high temperatures (30 to 50 degrees C) exhibited significant quality loss (P < 0.05). The degradation of soybean lightness (Hunter L), color difference (Delta E), and solid extractability exhibited a linear relationship with time. Soak weight decreased at high temperature and relative humidity, but increased at mild storage conditions. Several combinations of storage conditions at temperatures exceeding 30 degrees C produced a drastic loss in tofu yield. Storage also affected the tofu making process by reducing optimum mixing time to produce the highest tofu yield. Varietal difference in soybean storability was observed. The results provided useful information for the soybean processing industry to store soybeans using the optimal storage conditions and to estimate soybean quality after storage.

Utilization of okara, a byproduct from soymilk production, through the development of soy-based snack food.

This study was conducted to develop a new soy-based food product that could utilize okara (a byproduct from soymilk production) and maximize the health benefits of okara for the consumer. A Japanese commercial okara snack product was used as a standard reference. Two types of dried okara powder, a commercially dried okara powder with 7.7% moisture content made from regular (lipoxygenase-present) soybeans and a partially dried okara with 44.3% moisture content made from lipoxygenase-free (LOX-null) soybeans, were used in this study. Commercial low saturated soybean oil and commercial low linolenic acid soybean oil were also used in the same formulation to compare and find the best formulation for a baked or deep-fat-fried soy-based food product. Two descriptive analysis studies were performed with a minimum of 15 trained panelists. Instrumental analyses with a Hunter Lab system and a TA.XT2i texture analyzer and chemical analysis were performed to compare with the sensory results. All the results were statistically analyzed. The baked product made from commercial low saturated soybean oil and the partially dried LOX-null okara powder gave the closest flavor, texture, and appearance to the reference standard. The final product contained 11.4% protein and 7.4% dietary fiber, which were, respectively, 1.5 and 2.0 times higher than the reference. The calcium content was also 4.3 times higher than the reference. The objectives of this study were achieved by developing a new soy-based snack food, which has more health benefits with an enjoyable flavor and texture than the existing commercial product.