Isotropy of Cosmic Rays beyond 10

We report an estimation of the injected mass composition of ultrahigh energy cosmic rays (UHECRs) at energies higher than 10 EeV. The composition is inferred from an energy-dependent sky distribution of UHECR events observed by the Telescope Array surface detector by comparing it to the Large Scale Structure of the local Universe. In the case of negligible extragalactic magnetic fields (EGMFs), the results are consistent with a relatively heavy injected composition at E∼10 EeV that becomes lighter up to E∼100 EeV, while the composition at E>100 EeV is very heavy. The latter is true even in the presence of highest experimentally allowed extragalactic magnetic fields, while the composition at lower energies can be light if a strong EGMF is present. The effect of the uncertainty in the galactic magnetic field on these results is subdominant.

Metal doped polyaniline as neuromorphic circuit elements for in-materia computing.

Polyaniline-based atomic switches are material building blocks whose nanoscale structure and resultant neuromorphic character provide a new physical substrate for the development next-generation, nanoarchitectonic-enabled computing systems. Metal ion-doped devices consisting of a Ag/metal ion doped polyaniline/Pt sandwich structure were fabricated using an in situ wet process. The devices exhibited repeatable resistive switching between high (ON) and low (OFF) conductance states in both Ag+ and Cu2+ ion-doped devices. The threshold voltage for switching was>0.8 V and average ON/OFF conductance ratios (30 cycles for 3 samples) were 13 and 16 for Ag+ and Cu2+ devices, respectively. The ON state duration was determined by the decay to an OFF state after pulsed voltages of differing amplitude and frequency. The switching behaviour is analagous to short-term (STM) and long-term (LTM) memories of biological synapses. Memristive behaviour and evidence of quantized conductance were also observed and interpreted in terms of metal filament formation bridging the metal doped polymer layer. The successful realization of these properties within physical material systems indicate polyaniline frameworks as suitable neuromorphic substrates for in materia computing.

Assessment of feline hospitalization environment using a one-way mirror.

A separate, cat-specific hospitalization room away from dogs is recommended to reduce stress in cats; however, this can be difficult for some hospitals to provide. In such cases, measures are undertaken to reduce the cat's stress by providing a place to hide. However, inability to observe the cat's condition may be an obstacle to providing veterinary care. The use of a one-way mirror to create a sheltered environment while allowing observation of the cats was assessed. Five healthy cats were assessed using the Cat Stress Score (CSS) while in a cage with either a transparent panel or a one-way mirror. No significant differences in the CSS between the transparent panel and one-way mirror were observed. Variations in the CSS scores depended on the cat's personality, with friendlier and more sociable cats showing a lower CSS with the one-way mirror. A one-way mirror may be useful to reduce stress in hospitalized cats.

An extremely energetic cosmic ray observed by a surface detector array.

Cosmic rays are energetic charged particles from extraterrestrial sources, with the highest-energy events thought to come from extragalactic sources. Their arrival is infrequent, so detection requires instruments with large collecting areas. In this work, we report the detection of an extremely energetic particle recorded by the surface detector array of the Telescope Array experiment. We calculate the particle's energy as [Formula: see text] (~40 joules). Its arrival direction points back to a void in the large-scale structure of the Universe. Possible explanations include a large deflection by the foreground magnetic field, an unidentified source in the local extragalactic neighborhood, or an incomplete knowledge of particle physics.

High-resolution, high-throughput HLA genotyping by next-generation sequencing.

The human leukocyte antigen (HLA) class I and class II loci are the most polymorphic genes in the human genome. Hematopoietic stem cell transplantation requires allele-level HLA typing at multiple loci to select the best matched unrelated donors for recipient patients. In current methods for HLA typing, both alleles of a heterozygote are amplified and typed or sequenced simultaneously, often making it difficult to unambiguously determine the sequence of the two alleles. Next-generation sequencing methods clonally propagate in parallel millions of single DNA molecules, which are then also sequenced in parallel. Recently, the read lengths obtainable by one such next-generation sequencing method (454 Life Sciences, Inc.) have increased to >250 nucleotides. These clonal read lengths make possible setting the phase of the linked polymorphisms within an exon and thus the unambiguous determination of the sequence of each HLA allele. Here we demonstrate this capacity as well as show that the throughput of the system is sufficiently high to enable a complete, 7-locus HLA class I and II typing for 24 or 48 individual DNAs in a single GS FLX sequencing run. Highly multiplexed amplicon sequencing is facilitated by the use of sample-specific internal sequence tags (multiplex identification tags or MIDs) in the primers that allow pooling of samples yet maintain the ability to assign sequences to specific individuals. We have incorporated an HLA typing software application developed by Conexio Genomics (Freemantle, Australia) that assigns HLA genotypes for these 7 loci (HLA-A, -B, -C, DRB1, DQA1, DQB1, DPB1), as well as for DRB3, DRB4, and DRB5 from 454 sequence data. The potential of this HLA sequencing system to analyze chimeric mixtures is demonstrated here by the detection of a rare HLA-B allele in a mixture of two homozygous cell lines (1/100), as well as by the detection of the rare nontransmitted maternal allele present in the blood of a severe combined immunodeficiency disease syndrome (SCIDS) patient.

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.

A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.

In silico mapping of complex disease-related traits in mice.

Experimental murine genetic models of complex human disease show great potential for understanding human disease pathogenesis. To reduce the time required for analysis of such models from many months down to milliseconds, a computational method for predicting chromosomal regions regulating phenotypic traits and a murine database of single nucleotide polymorphisms were developed. After entry of phenotypic information obtained from inbred mouse strains, the phenotypic and genotypic information is analyzed in silico to predict the chromosomal regions regulating the phenotypic trait.

Plasma angiotensin II concentrations in the early neonatal period.

BACKGROUND: There have been only a few reports on the renin-angiotensin system in low birthweight infants; in particular, plasma angiotensin II concentrations have not been studied. AIM: To investigate plasma angiotensin II concentrations in early neonatal infants including low birthweight infants. METHODS: Forty six patients were studied, of whom 14 weighed not less than 2500 g (normal birth weight), 16 weighed less than 2500 g but not less than 1500 g (moderately low birth weight), and 16 weighed less than 1500 g (very low birth weight). Blood samples were collected twice, on day 0 and day 7. Angiotensin II concentration was assayed using an enzyme immunoassay kit with a microplate. RESULTS: Geometric means of angiotensin II concentrations on day 7 were 19 pg/ml in the normal birthweight group, 28 pg/ml in the moderately low birthweight group, and 76 pg/ml in the very low birthweight group. The concentrations on day 7 in the very low birthweight group were significantly higher than those in the normal birthweight and moderately low birthweight groups (p = 0.005, p = 0.031). There were significant correlations between angiotensin II concentration on day 7 and gestational age (r(s) = -0.4, p = 0.007) and birth weight (r(s) = -0.36, p = 0.016). CONCLUSIONS: Specific physiological conditions associated with a very low birth weight are thought to be responsible for the increased concentration of angiotensin II on day 7. It is necessary to measure angiotensin II concentration for a longer period after birth and study the factors that could influence it.

Transcript quantitation in total yeast cellular RNA using kinetic PCR.

Kinetically monitored, reverse transcriptase-initiated PCR (kinetic RT-PCR, kRT-PCR) is a novel application of kinetic PCR for high throughput transcript quantitation in total cellular RNA. The assay offers the simplicity and flexibility of an enzyme assay with distinct advantages over DNA microarray hybridization and SAGE technologies for certain applications. The reproducibility, sensitivity and accuracy of the kRT-PCR were assessed for yeast transcripts previously quantitated by a variety of methods including SAGE analysis. Changes in transcript levels between different genetic or physiological cell states were reproducibly quantitated with an accuracy of +/-20%. The assay was sufficiently sensitive to quantitate yeast transcripts over a range of more than five orders of magnitude, including low abundance transcripts encoding cell cycle and transcriptional regulators.

Epidemiological and outcome characteristics of major burns in Tokyo.

The Tokyo Burn Unit Association (TBUA) was established in 1983 funded by the Tokyo Metropolitan Government, and is organized by 13 burn units in Tokyo. TBUA covers more than 90% of severe burn patients occurring in Tokyo, and all of the cases are registered according to the burn injury registration format. The purpose of this study is to analyze the registered data and to elucidate epidemiological and outcome characteristics of major burn injuries in Tokyo. The total of 6988 hospitalized patients had data for epidemiological analysis, and 6401 patients had complete data for outcome analysis as well, and were included in this study. The characteristic profiles for the analysis included age, sex, cause of burns, inhalation injury, %BSA, burn index (BI), length of burn unit stay, and outcome, and were analyzed by age groups. The mean age of the patients was 40.4 years, and 63% of them were male. It was noteworthy that 25% of the total patients were elderly patients over 60 years of age. Flame was the most common cause making up 45.6% followed by scalding (32.0%). The overall mortality rate was 15.4%. Inhalation injury was accompanied in 27.3% of burn patients. The mortality rate was 34.6% with inhalation injury, and 8.2% without inhalation injury. Causes of death showed that multiple organ failure made up 36.9% of total mortality, followed by sepsis 25.2 and shock 19.0%. The burn size (%BSA and BI) and inhalation injury were the factors for high mortality rate in all age groups whereas age was a predictor for high mortality in the patients older than 16 years of age. Gender was not a factor for high mortality in any age group. The mortality rate showed mildly decreasing tendency since 1995 for which implementation of skin bank was thought to be responsible.

Human ribosomal RNA gene spacer sequences are found interspersed elsewhere in the genome.

A cloned EcoRI fragment containing human 18 S rRNA gene sequences was used to screen a gene library to obtain a set of 8 overlapping cloned DNA segments extending into the non-transcribed spacer region of the human ribosomal RNA gene cluster. 19.4 kb of the approx. 43-kb rDNA repeat was obtained in cloned form and mapped with restriction endonucleases. None of the clones obtained extended into 28 S rRNA sequences. A 7-kb region of non-transcribed spacer DNA shared in common between five independent clones was subjected to comparative restriction digests. It was estimated that sequences among the five different spacer isolated varied by not more than 1.0%, if all the observed differences are assumed due to point mutation. HaeII-restriction fragments from within this same 7-kb region contain sequences carried not only within the tandem repeats of the gene cluster but interspersed elsewhere in the genome. Some of these sequences correspond to the Alu family of highly repeated interspersed sequences.

Identification of a mislabeled fixed specimen by DNA analysis.

Formalin-fixed, paraffin embedded surgical specimens can be identified by genotypic analysis. DNA was extracted from single sections of fixed tissue and amplified by the polymerase chain reaction for the human leukocyte antigen (HLA) DQ alpha and low density lipoprotein receptor genes. These two loci are polymorphic and fixed specimens can be distinguished based on differences between these alleles. The examination can be performed in 2 days and the HLA DQ alpha test utilized a nonisotopic color detection method. In this case report, a mislabeled specimen was identified as a section from a mastectomy because they had identical genotypes. Molecular genetic analysis of the DNA present in fixed specimens can yield information not otherwise evident from the histology.

Synthesis and biological activity of a novel series of nonsteroidal, peripherally selective androgen receptor antagonists derived from 1,2-dihydropyridono[5,6-g]quinolines.

A new nonsteroidal antiandrogenic pharmacophore has been discovered using cell-based cotransfection assays with human androgen receptor (hAR). This series of AR antagonists is structurally characterized by a linear tricyclic 1,2-dihydropyridono[5,6-g]quinoline core. Analogues inhibit AR-mediated reporter gene expression and bind to AR as potently as or better than any known AR antagonists. Several analogues also showed excellent in vivo activity in classic rodent models of AR antagonism, inhibiting growth of rat ventral prostate and seminal vesicles, without accompanying increases in serum gonadotropin and testosterone levels, as is seen with other AR antagonists. Investigations of structure-activity relationships surrounding this pharmacophore resulted in molecules with complete specificity for AR, antagonist activity on an AR mutant commonly observed in prostate cancer patients, and improved in vivo efficacy. Molecules based on this series of compounds have the potential to provide unique and effective clinical opportunities for treatment of prostate cancer and other androgen-dependent diseases.

Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.

Procedures utilizing Chelex 100 chelating resin have been developed for extracting DNA from forensic-type samples for use with the PCR. The procedures are simple, rapid, involve no organic solvents and do not require multiple tube transfers for most types of samples. The extraction of DNA from semen and very small bloodstains using Chelex 100 is as efficient or more efficient than using proteinase K and phenol-chloroform extraction. DNA extracted from bloodstains seems less prone to contain PCR inhibitors when prepared by this method. The Chelex method has been used with amplification and typing at the HLA DQ alpha locus to obtain the DQ alpha genotypes of many different types of samples, including whole blood, bloodstains, seminal stains, buccal swabs, hair and post-coital samples. The results of a concordance study are presented in which the DQ alpha genotypes of 84 samples prepared using Chelex or using conventional phenol-chloroform extraction are compared. The genotypes obtained using the two different extraction methods were identical for all samples tested.

Influenza A virus-binding activity of glycoglycerolipids of aquatic bacteria.

As the aqueous sphere has been proposed to be an important source medium for the virus infection of land animals, the glycolipids of some aquatic organisms were examined for human influenza A virus-binding activity. Active compounds were not found among the eight echinoderm gangliosides, but two active non-sialylated glycoglycerolipids were isolated from an aquatic bacterium, Corynebacterium aquaticum. The structural formula of one of them, H632A, was elucidated to be 1-14-methyl-hexadecanoyl-3-alpha-D-galactopyranosyl-(1-->3)-6-(12-met hyl-tetradecanoyl)-1-alpha-D-mannopyranosyl]-sn-glycerol. The latter together with reported one elsewhere, S365A, 1-14-methyl-hexadecanoyl-3-[alpha-D-mannopyranosyl-(1-->3)-6-(12-meth yl-tetradecanoyl)-1-alpha-D-mannopyranosyl]-sn-glycerol, apparently bound to three human influenza viruses, A/PR/8/34 (H1N1), A/Aichi/2/68 (H3N2), and A/Memphis/1/71 (H3N2), exhibiting 7-12% (H632A) and 10-22% (S365A) of the activities of the control substances (Neu5Acalpha2-3-paragloboside and Neu5Acalpha2-6- paragloboside). Additionally, these glycolipids were assumed to have virus-neutralizing activities for the following two reasons: (i) The hemagglutination and hemolysis activities of the viruses were inhibited by the glycolipid. (ii) The leakage of a cytosolic enzyme (lactate dehydrogenase) from Madin-Darby canine kidney cells on virus infection was prevented by the glycolipids to nearly the same extent as by fetuin. This is the first evidence of the binding- and neutralizing-abilities of native glycoglycerolipids as to influenza viruses.

Nebulized vs. instilled exogenous surfactant in an adult lung injury model.

Three days after subcutaneous injection of N-nitroso-N-methylurethane (NNNMU) to induce lung injury, adult rabbits were mechanically ventilated and lung function was evaluated. Each animal then received either nebulized Survanta (Neb Surv), nebulized saline (Neb Saline), nebulized gas alone (Neb Gas), or tracheally instilled Survanta (Inst Surv). The ventilation efficiency index (VEI) value increased significantly compared with pretreatment values (P less than 0.01) over a 3-h treatment period for the Neb Surv animals, whereas VEI values for the other three groups decreased after treatment (P less than 0.05). Arterial PO2-to-fraction of inspired O2 ratios and dynamic compliance values significantly decreased after treatment for the Inst Surv group (P less than 0.05). Pressure-volume curves demonstrated a significantly greater volume at maximal pressure for the Neb Surv group compared with each of the other groups studied (P less than 0.01). The calculated quantity of surfactant recovered in lung tissue for the Neb Surv group was only 4.9 +/- 1.0 mg lipid/kg compared with 100 mg lipid/kg delivered to the Inst Surv group. Surfactant administered as an aerosol resulted in modest physiological improvements in this model of lung injury and was superior to the tracheal instillation technique.

A patient with undifferentiated carcinoma of gallbladder presenting with hemobilia.

Hemobilia is relatively rare among hemorrhages in the digestive tract, and hemobilia caused by tumors of the biliary tract is particularly rare. We treated a 74-year-old-man with undifferentiated carcinoma of the gallbladder presenting with hemobilia. During hospitalization for neurogenic bladder at the Department of Urology, he showed progressive anemia. Since hemorrhage in the digestive tract was suspected, endoscopy of the upper gastrointestinal tract was performed, and bleeding from the papilla of Vater was observed. On ultrasound examination, findings were indicative of cholecystic cancer, and hemorrhage from the cystic duct was found on percutaneous transhepatic cholangioscopy. On perioral cholecystoscopy, however, masses of coagulated blood were found only in the gallbladder. Abnormalities such as dense staining of tumors or extravasation were not found on angiography. The patient died of hepatic failure due to rapid invasion of the liver by the tumor, associated with biliary infection and disseminated intravascular coagulation. At autopsy, a nodal tumor was found in the gallbladder, and the cavity of the gallbladder was filled with coagulated masses of blood. Direct invasion of the tumor to the liver, diaphragm, and transverse colon was found. The histopathological diagnosis was undifferentiated carcinoma (pleomorphic large-cell type).

Quantification of human mitochondrial DNA in a real time PCR.

Recently, a moderately priced machine for real-time quantitative PCR has become available, the Perkin Elmer 5700. The rapid and quantitative assay of mitochondrial DNA (mtDNA) copy number is potentially useful in a variety of molecular, evolutionary and forensic fields. Using this new tool, we have evaluated the precision and reliability of the real time PCR to quantify undeleted mitochondrial genome copy number, and to determine the frequency of an age-associated deletion of 4977 base pairs in length, in 42 human iliopsoas muscle DNA samples from persons of known age. We have evaluated the accuracy with which age can be predicted, knowing only the frequency of this common 4977 bp deletion, and derived a statistical formula which describes the confidence with which the 4977 bp frequency predicts age. The results indicate that the mutation frequency could be used to distinguish between tissue from young and old individuals. However in this data set, while there was considerable agreement of 4977 bp frequency among replicates from the same individual sample, there was substantial diversity of mean mutation frequency between individuals of the same or similar ages. The simplest interpretation of these results is that there are biological modifiers of 4977 bp frequency that are age-independent, which are potentially interesting but may limit the usefulness of this deletion frequency alone as a "molecular forensic clock."

Glyceroglycolipids preventing tert-butylhydroperoxide-induced cell death from Microbacterium sp. and Corynebacterium aquaticum strains.

Galactosyl diacylglycerols M874B and S365B obtained from the recently isolated bacteria identified as Microbacterium sp. M874 and Corynebacterium aquaticum S365 were found to prevent oxidative cell death induced by tert-butylhydroperoxide. Their structures were determined to be 1,2-di-O-(12-methyltetradecanoyl)-3-O-beta-D-galactopyranosyl-sn-glycerol and 1-O-(14-methylhexadecanoyl)-2-O-(12-methyltetradecanoyl)-3-O-beta-D-galactopyranosyl-sn-glycerol, respectively.