High Precision Detection of Change in Intermediate Range Order of Amorphous Zirconia-Doped Tantala Thin Films Due to Annealing.

Understanding the local atomic order in amorphous thin film coatings and how it relates to macroscopic performance factors, such as mechanical loss, provides an important path towards enabling the accelerated discovery and development of improved coatings. High precision x-ray scattering measurements of thin films of amorphous zirconia-doped tantala (ZrO_{2}-Ta_{2}O_{5}) show systematic changes in intermediate range order (IRO) as a function of postdeposition heat treatment (annealing). Atomic modeling captures and explains these changes, and shows that the material has building blocks of metal-centered polyhedra and the effect of annealing is to alter the connections between the polyhedra. The observed changes in IRO are associated with a shift in the ratio of corner-sharing to edge-sharing polyhedra. These changes correlate with changes in mechanical loss upon annealing, and suggest that the mechanical loss can be reduced by developing a material with a designed ratio of corner-sharing to edge-sharing polyhedra.

Survival analysis of carboplatin added to an anthracycline/taxane-based neoadjuvant chemotherapy and HRD score as predictor of response-final results from GeparSixto.

Background: In the neoadjuvant GeparSixto study, adding carboplatin to taxane- and anthracycline-based chemotherapy improved pathological complete response (pCR) rates in patients with triple-negative breast cancer (TNBC). Here, we present survival data and the potential prognostic and predictive role of homologous recombination deficiency (HRD). Patients and methods: Patients were randomized to paclitaxel plus nonpegylated liposomal doxorubicin (Myocet®) (PM) or PM plus carboplatin (PMCb). The secondary study end points disease-free survival (DFS) and overall survival (OS) were analyzed. Median follow-up was 47.3 months. HRD was among the exploratory analyses in GeparSixto and was successfully measured in formalin-fixed, paraffin-embedded tumor samples of 193/315 (61.3%) participants with TNBC. Homologous recombination (HR) deficiency was defined as HRD score ≥42 and/or presence of tumor BRCA mutations (tmBRCA). Results: A significantly better DFS (hazard ratio 0.56, 95% CI 0.34-0.93; P = 0.022) was observed in patients with TNBC when treated with PMCb. The improvement of OS with PMCb was not statistically significant. Additional carboplatin did not improve DFS or OS in patients with HER2-positive tumors. HR deficiency was detected in 136 (70.5%) of 193 triple-negative tumors, of which 82 (60.3%) showed high HRD score without tmBRCA. HR deficiency independently predicted pCR (ypT0 ypN0) [odds ratio (OR) 2.60, 95% CI 1.26-5.37, P = 0.008]. Adding carboplatin to PM significantly increased the pCR rate from 33.9% to 63.5% in HR deficient tumors (P = 0.001), but only marginally in HR nondeficient tumors (from 20.0% to 29.6%, P = 0.540; test for interaction P = 0.327). pCR rates with carboplatin were also higher (63.2%) than without carboplatin (31.7%; OR 3.69, 1.46-9.37, P = 0.005) in patients with high HRD score but no tmBRCA. DFS rates were improved with addition of carboplatin, both in HR nondeficient (hazard ratio 0.44, 0.17-1.17, P = 0.086) and HR deficient tumors (hazard ratio 0.49, 0.23-1.04, P = 0.059). Conclusions: The addition of carboplatin to neoadjuvant PM improved DFS significantly in TNBC. Long-term survival analyses support the neoadjuvant use of carboplatin in TNBC. HR deficiency in TNBC and HRD score in non-tmBRCA TNBC are predictors of response. HRD does not predict for carboplatin benefit.

Emergency oxygenator change-out after massive fat embolism.

We present a case with an unusually high transmembrane pressure gradient over the oxygenator during initiation of extracorporeal membrane oxygenation (ECMO). This necessitated an immediate emergency oxygenator exchange. A detailed inspection revealed a large lipid formation in the oxygenator. We hypothesize that this lipid was dislodged during the cannulation process.

Prolapsed sigmoid intussusception per anus in an elderly man: a case report.

BACKGROUND: Intussusception in pediatrics is widely documented and well described. On the basis of the literature, however, adult intussusception is a rare entity with a prevalence of from 1% to 5%. The majority of adult patients with intussusception have an underlying pathology that needs to be identified by performing a proper physical examination and a wide array of investigations. CASE PRESENTATION: We present a case of a 66-year-old African man who presented to our emergency department with a mass protruding per anus with obstipation. During laparotomy, we found that the sigmoid colon had intussuscepted into the rectum and out from the anus. Other abdominal viscera were normal and without any obvious mesenteric lymphadenopathy. Sigmoid colectomy and spectacle colostomy were performed. Grossly, the excised bowel looked normal, but the histologic results showed features of necrosis and chronic inflammation. CONCLUSION: While 70% to 90% of cases of adult intussusception have an identifiable cause or lesion, most pediatric intussusceptions are idiopathic. The presentation in an adult described herein was of an uncommon idiopathic type with no identifiable cause found on the basis of the history, physical examination, or histological findings.

Detection of human viral RNA via a combined fluorescence and SERS molecular beacon assay.

A dual-mode molecular beacon on a multiplexed substrate has been developed and applied to the measurement of unlabeled human viral RNA. The detection system is based on a combined surface-enhanced Raman scattering (SERS) and fluorescent molecular beacon assay that is assembled on Nanobarcodes™ particles. In this assay, a molecular beacon probe terminated with a fluorescent Raman label dye is conjugated to the metallic Nanobarcodes™ particles. The molecular beacon probe is a single-stranded oligonucleotide that has been designed with a hairpin structure that holds the dye at 3'-end close to the particle surface when the probe is attached through a 5'-thiol group. In this configuration, the SERS spectrum of the label was obtained and its fluorescence quenched because the dye is in very close proximity to a noble metal surface with nanoscale features (Nanobarcodes™ particles). The SERS signal decreased and the fluorescence signal increased when target viral RNA was captured by this molecular beacon probe. In addition, a hepatitis C virus reverse transcriptase-polymerase chain reaction (HCV RT-PCR) product was detected using this dual-mode beacon. The development of a multiplexed, label-free assay system with the reassurance offered by detection of two distinctly separate signals offers significant benefits for rapid molecular diagnostics.

Identification of toxicologically predictive gene sets using cDNA microarrays.

We have developed an approach to classify toxicants based upon their influence on profiles of mRNA transcripts. Changes in liver gene expression were examined after exposure of mice to 24 model treatments that fall into five well-studied toxicological categories: peroxisome proliferators, aryl hydrocarbon receptor agonists, noncoplanar polychlorinated biphenyls, inflammatory agents, and hypoxia-inducing agents. Analysis of 1200 transcripts using both a correlation-based approach and a probabilistic approach resulted in a classification accuracy of between 50 and 70%. However, with the use of a forward parameter selection scheme, a diagnostic set of 12 transcripts was identified that provided an estimated 100% predictive accuracy based on leave-one-out cross-validation. Expansion of this approach to additional chemicals of regulatory concern could serve as an important screening step in a new era of toxicological testing.

Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants.

DNA arrays containing 260 unique genes involved in phase I and II metabolism, heat shock, DNA repair, inflammation, transcription, and housekeeping were used to examine gene expression patterns in liver and kidney in response to five classes of chemicals (polyaromatic hydrocarbons: benzo(a)pyrene, 3-methylcholanthrene; DNA alkylators: dimethylnitrosamine, ethylnitrosourea; peroxisome proliferators: diethylhexylphthalate, clofibrate; heavy metals: CdCl(2), HgCl(2); and oxidative stressors: CCl(4), bromobenzene). Time course experiments in mice were carried out in both tissues for each chemical and dose-response studies were used to further evaluate several of these chemicals. Each pair of chemicals yielded a similar pattern of gene expression distinct from the other four classes of chemicals. Both peroxisome proliferators up-regulated Cyp4a10, acyl-CoA thioesterase, and insulin-like growth factor binding protein-1, whereas the DNA alkylators altered the expression of monokine induced by gamma-interferon, the metallothioneins, p21, and several acute phase proteins. For each of the five classes of chemicals tested, several genes that were induced or repressed were common in each chemical exposure, whereas other genes were unique for that specific class of compound. Both time and dose are important factors in differentiating between chemical classes. Likewise, comparison of changes in messenger RNA expression between the kidney and liver of treated animals indicates that gene arrays may be useful in determining the comparative toxicity of chemicals in various tissues but that exposure to uncharacterized chemicals will have to be monitored in several tissues.

Applications of gene arrays in environmental toxicology: fingerprints of gene regulation associated with cadmium chloride, benzo(a)pyrene, and trichloroethylene.

Toxicity testing of unknown chemicals currently uses a number of short-term bioassays. These tests are costly and time consuming, require large numbers of animals, and generally focus on a single end point. The recent development of DNA arrays provides a potential mechanism for increasing the efficiency of standard toxicity testing through genome-wide assessments of gene regulation. In this study, we used DNA arrays containing 148 genes for xenobiotic metabolizing enzymes, DNA repair enzymes, heat shock proteins, cytokines, and housekeeping genes to examine gene expression patterns in the liver in response to cadmium chloride, benzo(a)pyrene (BaP), and trichloroethylene (TCE). Dose-response studies were carried out in mice for each chemical; each produced a unique pattern of gene induction. As expected, CdCl2 markedly up-regulated metallothionine I and II (5- to 10,000-fold at the highest doses) and several of the heat shock/stress response proteins and early response genes. In contrast, administration of BaP up-regulated only Cyp1a1 and Cyp1a2 genes and produced no significant increases in any of the stress response genes or any of the DNA repair genes present on the array. Likewise, TCE-induced gene induction was highly selective; only Hsp 25 and 86 and Cyp2a were up-regulated at the highest dose tested. Microarray analysis with a highly focused set of genes is capable of discriminating between different classes of toxicants and has potential for differentiating highly noxious versus more subtle toxic agents. These data suggest that use of microarrays to evaluate the potential hazards of unknown chemicals or chemical mixtures must include multiple doses and time points to provide effective assessments of potential toxicity of these substances.

Mining the human genome using microarrays of open reading frames.

To test the hypothesis that the human genome project will uncover many genes not previously discovered by sequencing of expressed sequence tags (ESTs), we designed and produced a set of microarrays using probes based on open reading frames (ORFs) in 350 Mb of finished and draft human sequence. Our approach aims to identify all genes directly from genomic sequence by querying gene expression. We analysed genomic sequence with a suite of ORF prediction programs, selected approximately one ORF per gene, amplified the ORFs from genomic DNA and arrayed the amplicons onto treated glass slides. Of the first 10,000 arrayed ORFs, 31% are completely novel and 29% are similar, but not identical, to sequences in public databases. Approximately one-half of these are expressed in the tissues we queried by microarray. Subsequent verification by other techniques confirmed expression of several of the novel genes. Expressed sequence tags (ESTs) have yielded vast amounts of data, but our results indicate that many genes in the human genome will only be found by genomic sequencing.

The role of submacular surgery in the treatment of choroidal neovascular membranes.

The growth of choroidal neovascular membranes (CNVM) beneath the macula can cause significant disturbances of central vision. Conditions such as age-related macular degeneration (AMD) and presumed ocular histoplasmosis syndrome (POHS) are the most common etiologies. The Macular Photocoagulation Study group presented data that clearly showed laser photocoagulation to be beneficial in the treatment of CNVM. Poor visual results and a high rate of recurrence have prompted clinicians to seek out alternative treatments. Experiences with CNVM removal utilizing submacular surgical techniques have shown that central visual function may be restored or preserved in POHS, multifocal choroiditis and idiopathic causes. The Submacular Surgery Trials were designed to investigate whether submacular surgery is more effective in retaining central acuity in patients with subfoveal CNVM, than observation alone. The goal of this paper is to review the role of submacular surgery in the treatment of subfoveal choroidal neovascular membranes.

Adult onset foveomacular vitelliform dystrophy: a case report.

BACKGROUND: Pattern dystrophies of the retinal pigment epithelium, an arrangement of a pattern of dots, lines, or branches, are infrequent fundus abnormalities. Adult onset foveomacular vitelliform dystrophy (AOFVD) is considered a subtype of pattern dystrophy. Onset occurs during middle age, with an accumulation of yellow-gray macular deposits in the deeper retinal layers. Typically electro-oculograms are mildly subnormal or normal. Genetic studies suggest an autosomal dominant inheritance with variable penetrance. CASE REPORT: A case of a 56-year-old Hispanic women with a 1-month onset of "wavy moving vision" in both eyes is presented. Previous ocular and family history were unremarkable. Ophthalmoscopic examination revealed yellow circumscribed subretinal lesions of one-third to one-half disk diameter in the foveal centers of both eyes. Fluorescein angiography revealed a circumscribed area of mottled hyperfluorescence surrounding a central hypofluorescent spot. The patient was diagnosed with AOFVD. Examination of the patient's children revealed retinal pigment epithelial disturbances in the two oldest daughters, consistent with pattern dystrophies. CONCLUSION: Our investigation supports an autosomal dominant inheritance pattern, as seen on pedigree. The presence of different pattern dystrophies within the same family suggests a common etiologic continuum.

Alkaline degradation of oligosaccharides coupled with matrix-assisted laser desorption/ionization Fourier transform mass spectrometry: a method for sequencing oligosaccharides.

A new technique for determining sequence and linkage information of underivatized oligosaccharides is developed using alkaline degradation and matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Alkaline degradation (also known as the "peeling" reaction) is a chemical degradation technique that only cleaves the glycosidic bond at the reducing end by beta-elimination to yield a new reducing end. The reaction products are sampled directly with minimal cleanup and monitored by MALDI-FTMS to elucidate the oligosaccharide sequence. Linkage information is provided by cross-ring cleavage fragmentation of the new reducing ends, created by either MALDI source fragmentation or sustained off-resonance irradiation collision-induced dissociation. This method is illustrated by the successful sequence and linkage determination of neutral, branched, fucosylated, and sialylated oligosaccharides. Experiments on differently linked disaccharides are also performed to determine the specificity of the cross-ring cleavage reactions. The power of this technique is enhanced by the Fourier transform mass analyzer, which provides high-resolution, exact mass, and facile tandem mass spectrometry experiments of MALDI-produced ions.

A modular lymphographic magnetic resonance imaging contrast agent: contrast enhancement with DNA transfection potential.

A gadolinium-chelated liposomal contrast agent has been prepared, and magnetic resonance imaging (MRI) efficacy has been examined by indirect magnetic resonance lymphography. A lipidic N,N'-dimethylethylenediamine derivative (4) containing a 10,12-diyne-diacyl domain was treated with DTPA anhydride followed by GdCl3 complexation. The complex was confirmed using MALDI spectrometry. An equimolar mixture of the Gd-chelate lipid and a commercially available diyne-PE was formulated as a liposome suspension and irradiated with UV light prior to imaging experiments. Subcutaneous injection of the liposomal gadolinium agent and subsequent MRI of rabbit axillary and popliteal lymph nodes revealed significant contrast enhancement up to 4 h postinjection. To explore the possibility of imaging a DNA transfection event, the gadolinium contrast mixture was formulated with the cationic transfection lipid DOTAP and complexed with the reporter gene encoding luciferase. DNA transfection studies on the NIH3T3 cell line confirmed the transfection activity of the dual-purpose contrast agent and exemplified the potential toward development of an imaging and DNA delivery vehicle.

Characterization of neutral oligosaccharide-alditols from Xenopus laevis egg jelly coats by matrix-assisted laser desorption Fourier transform mass spectrometry.

Neutral oligosaccharides were released by alkaline sodium borohydride reduction of the jelly coating from the South African clawed toad, Xenopus laevis. The oligosaccharides were isolated by HPLC and analyzed by matrix-assisted laser desorption ionization (MALDI)-Fourier transform mass spectrometry (FTMS). The mass spectrometry analysis allowed confirmation of 12 structures first proposed by Strecker et al. using nuclear magnetic resonance. In addition, seven new oligosaccharides with weak abundances were found and characterized by mass spectrometry. A method for discriminating metastable fragments from quasimolecular ions is described. It involves doping the sample with cesium chloride. Cesium-coordinated oligosaccharides do not fragment as readily as those coordinated to sodium. Tandem MS experiments are performed on an unknown oligosaccharide illustrating the potential of MALDI-collision-induced dissociation-FTMS.

Direct analysis of sugar alcohol borate complexes in plant extracts by matrix-assisted laser desorption/ionization fourier transform mass spectrometry.

Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI/FTMS), operating in the negative ion mode, is used to directly observe sugar alcohol borate complexes in a number of plant fractions. The method involves virtually no sample workup and, in the case of celery phloem sap, requires only 40 nL of sap to observe the borate complex. The isolation and characterization of such soluble borate complexes is important in understanding the distribution of boron in plants. The results show that the complexes are composed of two mannitol or sorbitol ligands (L) complexed to a single borate center (B). In some cases, the boron is complexed to non-alditol monosaccharides. Sustained off-resonance collision irradiation dissociation of the BL2- complex, where L is a mannitol, gives fragments that confirm the proposed structure. Complexes of larger oligosaccharides have also been successfully observed using MALDI/FTMS. Semiempirical molecular orbital calculations (AM1) of the mannitol BL2- complex show that the most favorable configuration is with carbons 3 and 4 of both mannitol residues complexed to the borate. This allows maximum interaction of the remaining hydroxyls with the borate center.

Isolation and characterization of soluble boron complexes in higher plants. The mechanism of phloem mobility of boron.

Boron (B) polyol complexes have been isolated and characterized from the phloem sap of celery (Apium graveolens L.) and the extrafloral nectar of peach (Prunus persica L.). In celery the direct analysis of untreated phloem sap by matrix-assisted laser desorption-Fourier transform mass spectrometry, with verification by high-performance liquid chromagraphy and gas chromatography-mass spectrometry, revealed that B is present in the phloem as the mannitol-B-mannitol complex. Molecular modeling further predicted that this complex is present in the 3,4 3',4' bis-mannitol configuration. In the extrafloral nectar of peach, B was present as a mixture of sorbitol-B-sorbitol, fructose-B-fructose, or sorbitol-B-fructose. To our knowledge, these findings represent the first successful isolation and characterization of soluble B complexes from higher plants and provide a mechanistic explanation for the observed phloem B mobility in these species.

Bastadin 20 and bastadin O-sulfate esters from Ianthella basta: novel modulators of the Ry1R FKBP12 receptor complex.

New compounds bastadin 20 (9), 15,34-O-disulfatobastadin 7 (10), and 10-O-sulfatobastadin 3 (11) were isolated from Ianthella basta collected in Exmouth Gulf, Western Australia. Compounds 10 and 11 exhibited moderate differential activity as SR Ca2+ channel agonists (EC50 13.6 and 100 microM, respectively) of the Ry1R FKBP12 complex, while the potency of 9 was almost half that of 10 (EC50 20.6 microM). The problem of dereplication of bastadins was addressed using 1H-NMR "fingerprinting" of MeO signals in the corresponding permethyl bastadin derivatives.

Collision-induced dissociation of branched oligosaccharide ions with analysis and calculation of relative dissociation thresholds.

Collision-induced dissociation (CID) is used in an external source Fourier transform mass spectrometer (FTMS) equipped with matrix-assisted laser desorption/ionization (MALDI) to study a number of complex, branched oligosaccharides. The relative dissociation thresholds for various oligosaccharide fragmentation pathways have been calculated in terms of kinetic and center-of-mass frame energy. For two isomers of difucosyllacto-N-hexaose, the loss of the fucose sugar is always the lowest energy fragment observed and occurs at the same energy for both isomers when the oligosaccharide is coordinated to a sodium ion. When the oligosaccharide is complexed to cesium, the threshold for the removal of the fucose moiety increases, indicating that the cesium is involved in a coordination complex that stabilizes the sugar. MS/ MS/MS is performed on a sugar, mannose core, which does not readily fragment during MALDI. In all the sugars examined, CID produces additional structural information relative to MALDI/FTMS.

A dual vacuum chamber fourier transform mass spectrometer with rapidly interchangeable LSIMS, MALDI, and ESI sources: initial results with LSIMS and MALDI.

A design is presented involving two separate vacuum chambers to provide nearly simultaneous capabilities of liquid secondary ion mass spectrometry (LSIMS), matrix-assisted laser desorption/ionization (MALDI), and electrospray ionization (ESI) in an external source Fourier transform mass spectrometer. The instrument consists of two vacuum chambers, one with five stages of differential pumping for a combined LSIMS/MALDI source. The chamber dedicated to ESI was formerly a three-stage chamber with LSIMS and electron ionization. Two additional stages were added with the ESI source. LSIMS and MALDI have similar vacuum requirements and were moved to a newly built chamber with two stages of pumping. We present our first results obtained on the new vacuum chamber. Data presented for the MALDI source show that, with only two stages of pumping, and with shorter radio frequency-only quadrupole rods for ion injection, spectra comparable to those obtained on the formerly three-stage instrument can be obtained. Characterization of the MALDI source and data on linear, cyclic, and branched oligosaccharides are given. Finally, the design of the secon chamber is proposed as a low-cost prototype for an external source FTMS instrument.