Complex wavelet filter improves FLIM phasors for photon starved imaging experiments

Fluorescence lifetime imaging microscopy (FLIM) with phasor analysis provides easy visualization and analysis of fluorophores' lifetimes which is valuable for multiple applications including metabolic imaging, STED imaging, FRET imaging and functional imaging. However, FLIM imaging typically suffers from low photon budgets, leading to unfavorable signal to noise ratios which in many cases prevent extraction of information from the data. Traditionally, median filters are applied in phasor analysis to tackle this problem. This unfortunately degrades high spatial frequency FLIM information in the phasor analysis. These high spatial frequency components are typically edges of features and puncta, which applies to membranes, mitochondria, granules and small organelles in a biological sample. To tackle this problem, we propose a filtering strategy with complex wavelet filtering and Anscombe transform for FLIM phasor analysis. This filtering strategy preserves fine structures and reports accurate lifetimes in photon starved FLIM imaging. Moreover, this filter outperforms median filters and makes FLIM imaging with lower laser power and faster imaging possible.

Mechanics of soft epithelial keratin networks depend on modular filament assembly kinetics

Structural adaptability is a pivotal requirement of cytoskeletal structures, enabling their reorganization to meet the cellular needs. Shear stress, for instance, results in large morphological network changes of the human soft epithelial keratin pair K8:K18, and is accompanied by an increase in keratin phosphorylation levels. Yet the mechanisms responsible for the disruption of the network structure in vivo remain poorly understood. To understand the effect of the stress-related site-specific phosphorylation of the K8:K18 pair, we created phosphomimicry mutants - K8(S431E), K8(S73E), K18(S52E) - in vitro, and investigated the various steps of keratin assembly from monomer to network structure using fluorescence and electron microscopy, and using rheology characterized their network mechanical properties. We find that the addition of a charged group produces networks with depleted intra-connectivity, which translates to a mechanically weaker and more deformable network. This large variation in network structure is achieved by the formation of shorter mutant filaments, which exhibit differing assembly kinetics and a manifestly reduced capacity to form the extended structures characteristic of the wild-type system. The similarity in outcome for all the phosphomimicry mutants explored points to a more general mechanism of structural modulation of intermediate filaments via phosphorylation. Understanding the role of kinetic effects in the construction of these cytoskeletal biopolymer networks is critical to elucidating their structure-function properties, providing new insight for the design of keratin-inspired biomaterials.

STATEMENT OF SIGNIFICANCE

Structural remodeling of cytoskeletal networks accompanies many cellular processes. Interestingly, levels of phosphorylation of the human soft epithelial keratin pair K8:K18 increase during their stress-related structural remodeling. Our multi-scale study sheds light on the poorly understood mechanism with which site-specific phosphorylation induces disruption of the keratin network structure in vivo. We show how phosphorylation reduces keratin filament length, an effect that propagates through to the mesoscopic structure, resulting in the formation of connectivity-depleted and mechanically weaker networks. We determine that the intrinsically-set filament-to-filament attractions that drive bundle assembly give rise to the structural variability by enabling the formation of kinetically-arrested structures. Overall, our results shed light on how self-assembled intermediate filament structures can be tailored to exhibit different structural functionalities.

Assessing the ecological long-term impact of wastewater irrigation on soil and water based on bioassays and chemical analyses

The reuse of treated wastewater for irrigation and groundwater recharge can counteract water scarcity and reduce pollution of surface waters, but assessing its environmental risk should likewise consider effects associated to the soil. The present study therefore aimed at determining the impact of wastewater irrigation on the habitat quality of water after soil passage and of soil after percolation by applying bioassays and chemical analysis. Lab-scale columns of four different soils encompassing standard European soil and three field soils of varying characteristics and pre-contamination were continuously percolated with treated wastewater to simulate long-term irrigation. Wastewater and its percolates were tested for immobilization of Daphnia magna and growth inhibition of green algae (Pseudokirchneriella subcapitata) and water lentils (Lemna minor). The observed phytotoxicity of the treated wastewater was mostly reduced by soil passage, but in some percolates also increased for green algae. Chemical analysis covering an extensive set of wastewater-born organic pollutants demonstrated that many of them were considerably reduced by soil passage, particularly through peaty soils. Taken together, these results indicated that wastewater-born phytotoxic substances may be removed by soil passage, while existing soil pollutants (e.g. metals) may leach and impair percolate quality. Soils with and without wastewater irrigation were tested for growth of plants (Avena sativa, Brassica napus) and soil bacteria (Arthrobacter globiformis) and reproduction of collembolans (Folsomia candida) and oligochaetes (Enchytraeus crypticus, Eisenia fetida). The habitat quality of the standard and two field soils appeared to be deteriorated by wastewater percolation for at least one organism (enchytraeids, plants or bacteria), while for two pre-contaminated field soils it also was improved (for plants and/or enchytraeids). Wastewater percolation did not seem to raise soil concentrations of classical organic pollutants and priority substances, while a significant retention was found for zinc and several organic micropollutants, particularly in the peaty soils, thus matching these soils' observed higher removal efficiency. Overall, our results demonstrate that benefits of wastewater irrigation can come with the cost of deteriorating soil habitat quality and depend on the respective soil and considered test organism. The approach employed here represents a feasible tool to assess these integrated effects at lab-scale while being predictive for scenarios at field-scale.

Search for over 2000 current and legacy micropollutants on a wastewater infiltration site with a UPLC-high resolution MS target screening method

A target screening method using ultra high performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) was developed. The method was applied to 14 groundwater and 11 surface water samples of a former wastewater infiltration site, where raw wastewater was applied until 1985 and treated wastewater is applied since 2005. The measured data are compared with mass spectrometric data of over 2000 organic micropollutants (OMPs), including pharmaceuticals, personal care products, pesticides, industrial chemicals and metabolites of these classes. A total number of 151 and 159 OMPs were detected in groundwater and surface water, respectively, of which 12 have not been reported before in these matrices. Among these 12 compounds were 11 pharmaceuticals and one personal care product. The identity of 55 of the detected OMPs (35%) was verified by analysis of standard compounds. Based on the distribution in the study area, two groups of OMPs were clearly distinguished: current OMPs introduced with treated municipal wastewater since 2005 and legacy OMPs originating from infiltration of untreated wastewater until 1985. A third group included OMPs contained in historic as well as in current wastewater. During infiltration, OMPs with molecular mass >500 g/mol and log DOW > 3.9 were preferentially removed. Speciation had a strong impact with cationic OMPs showing high, neutral OMPs medium and anionic OMPs lowest elimination during infiltration. This target screening method proved useful to study a wide range of compounds, even in retrospect and at sites with poorly documented history and with a complex and variable hydrological situation.

A confirmatory factor analysis of the WISC-III in a clinical sample with cross-validation in the standardization sample

Maximum likelihood confirmatory factor analysis was applied to the Wechsler Intelligence Scale for Children-Third Edition (WISC-III; Wechsler, 1991) data of a mixed clinical sample of 318 children. Analyses were designed to determine which of nine hypothesized oblique factor solutions could best explain intelligence as measured by the WISC-III in the clinical sample. Competing latent variable models were identified in previous studies, and results in the clinical sample were cross-validated by testing all models in the WISC-III standardization sample (n = 2200). Findings in both the clinical and standardization samples supported a five-factor model including Verbal Comprehension, Constructional Praxis, Visual Reasoning, Freedom from Distractibility, and Processing Speed factors. The Visual Reasoning factor was defined primarily by Picture Arrangement, whereas Mazes did not appear to improve model fit. Potential opportunities and pitfalls with regard to the interpretation of the proposed Visual Reasoning factor are discussed.

Postexposure prophylaxis after nonoccupational HIV exposure: clinical, ethical, and policy considerations

In the wake of recent breakthroughs in antiviral therapies and Centers for Disease Control and Prevention (CDC) recommendations advocating occupational postexposure prophylaxis (PEP), health care workers are increasingly receiving inquiries about PEP following exposures to the human immunodeficiency virus (HIV) through sex and injection drug use. The probability of HIV transmission by certain sexual or injection drug exposures is of the same order of magnitude as percutaneous occupational exposures for which the CDC recommends PEP. In such cases, if the exposure is sporadic, it seems appropriate to extrapolate from the data on occupational PEP and recommend prophylaxis. However, for individuals with continuing or low-risk exposures, we instead recommend referrals to state-of-the-art risk reduction programs. Clinicians, using local HIV seroprevalence data and their knowledge of transmission probabilities, can help exposed patients make an informed decision regarding PEP. Because of the large number of risky encounters that will not be treated prophylactically, even after significant outreach efforts, public health interventions that emphasize PEP as part of a comprehensive HIV prevention program should be confined to cities with highest HIV prevalences.

The journal "impact factor": a misnamed, misleading, misused measure

The Institute for Scientific Information (ISI), a database publishing company that publishes Current Contents and Science Citation Index, has devised and promulgated what it terms the journal "impact factor." ISI describes this factor as a "measure of the frequency with which the 'average article' in a journal has been cited in a particular year." The factor is a ratio between citations and recent citable published items calculated by dividing the number of all current citations of items published in a journal during the preceding 2 years by the number of articles published in those 2 years by that journal. What, if anything, is wrong with the "impact factor"? There is absolutely nothing incorrect with the calculation of the ratio itself. However, the "impact factor" is misnamed and misleading. Being misnamed and misleading, the "impact factor" has been misused. It is being held out as a measure of the importance of a specific journal article and the journal in which the article appeared. By extension, the "impact factor" is also being misused to gauge the relative importance of individual researchers, research programs, and even the institution hosting the research. We recommend that the term "impact factor" be abolished and that this measure be renamed in keeping with its actual role, that merely of a time-specific "citation rate index" and nothing more. What is currently called the "impact factor" should not be misused to evaluate journals or to validate the scientific relevance of a particular researcher or research program, especially in decisions regarding employment, funding, and tenure.

[Reevaluation of surgical treatment of cancers of the anus. Therapeutic proposals based on an experience with 33 patients]

Radiotherapy remains the basic treatment of anal cancer especially for epidermoid carcinomas. Tumorectomy and rectal amputation still have indications in the many others histological types and also in aguamous cell carcinomas (> T2) which cannot be totally healed by radiotherapy or after recurrences.

Mapping FRA11A, a folate-sensitive fragile site in human chromosome band 11q13.3

FRA11A, a rare folate-sensitive fragile site assigned to 11q13.3, lies in an area of genomic instability associated with several diseases and amplification events. To map FRA11A, we used fluorescence in situ hybridization with yeast artificial chromosome and cosmid probes on metaphase chromosomes of patients expressing the fragile site. FRA11A was found situated centromeric to ACTN3 and telomeric to D11S913, these markers being within an interval of approximately 1 Mb in the 11q13.3 region.

Cytogenetics of malignant gliomas. II. The sex chromosomes with reference to X isodisomy and the role of numerical X/Y changes

Sex chromosomal monosomy with total loss of an X or Y is frequently observed in malignant gliomas. Beyond that, not much is known about the behavior of the sex chromosomes in these tumors. We noted loss of the X from 3 of 13 gliomas from women (23%) compared to loss of the Y from 16 of 28 gliomas from men (57%). There were two structural rearrangements of the Y (an inversion and a translocation with chromosome 4). Most unexpectedly, clones with sex chromosome reversal were encountered in 3 cases. These XX clones in gliomas from men are perforce the consequence of Y loss coupled with X isodisomy, a nonrandom sequence of sex chromosome changes. We examined the company kept by numerical X and Y changes in clones and found that clones with numerical sex chromosome changes had fewer autosomal abnormalities, reflecting a distinct tendency to clonal separation of sex chromosome from autosomal abnormalities. We conclude that the sex chromosome changes are not a necessary part of the neoplastic process in malignant gliomas but that they must be of biologic significance to the brain since they are highly nonrandom in frequency, type, and sequence in brain cells.

Cytogenetics of malignant gliomas: I. The autosomes with reference to rearrangements

Autosomal chromosome abnormalities are far from always detectable and, when detected, far from fully consistent in malignant gliomas. In 15 of 41 malignant gliomas, we found autosomal chromosome aberrations ranging from solitary trisomy to a wildly abnormal polyploid complement. The sequence of chromosome events appears to proceed from the normal to the near-diploid state (via structural and numerical changes) to near-tetraploidy (via polyploidization), and finally toward near-triploidy (via chromosome loss and additional rearrangements). Characteristic chromosome changes of trisomy 7 and monosomy 10 were repeatedly found, usually together in the same cell clones. In only one case was trisomy 7 an isolated change. We observed structural rearrangements of chromosomes 7 and 10 which may be of some use in mapping specific genes duplicated or deleted by the whole-chromosome changes of chromosomes 7 and 10. Nonrandom structural changes of other autosomes, including chromosomes 1, 5, and 11, fit with the model of malignant glioma as a process involving multiple genes. An unusual concentration of breakpoints in 12q13, juxtaposing it to at least five other regions, reflects the presence of genetic information in 12q13 important to the development of malignant gliomas.

Chromosomes in gliomatosis cerebri

Gliomatosis cerebri is a rare brain tumor which histologically resembles a diffuse cerebral astrocytoma. It can simultaneously infiltrate multiple sites in the cerebrum, cerebellum, brainstem, and spinal cord. This remarkable diffuseness has led to the idea that gliomatosis cerebri does not derive from a solitary focus but must arise from a broad field of glial cells. We studied the chromosomes from gliomatosis cerebri in a 12-year-old boy by conventional cytogenetics and fluorescence in situ hybridization (FISH). Aside from normal cells, we found a majority of cells with the karyotype 44,XY,del(6)(q25),del(14)(q21), der(15;21)(q10;q10),add(18)(q22),del(19)(p12),add(20)(p13),-21. A smaller proportion of cells had 88 chromosomes with a doubling of this abnormal karyotype. These findings are consistent with a clonal neoplasm stemming from a single cell. The chromosome changes we observed, with the possible exception of the chromosome 6 deletion, did not resemble those frequently found in astrocytomas. Gliomatosis cerebri may therefore belong to a separate category of brain tumors.

Ring 22 chromosomes in dermatofibrosarcoma protuberans are low-level amplifiers of chromosome 17 and 22 sequences

Ring chromosomes have been found with some regularity as solid tumors have come increasingly under cytogenetic study. The full genetic content and significance of these rings remain unclear. Dermatofibrosarcoma protuberans, a tumor of the deep dermis, consistently has supernumerary ring chromosomes, sometimes as the sole detectable cytogenetic change. Using a modified method for comparative genomic hybridization and fluorescent in situ hybridization with a panel of various probes, we found that these ring chromosomes consistently contain the chromosome 22 centromere along with interstitial sequences from chromosomes 17 and 22, specifically from regions 17q23-24 and 22q11-12. The ring chromosomes in dermatofibrosarcoma protuberans are vehicles for a particular pattern of relatively low-level genomic amplification of selected sequences.

Immunophenotyping and metastatic localization of breast cancer

Monoclonal antibody SM 92 is involved in the immunophenotype of gastrointestinal and liver cells, SM 43 in ovarian cells, and SM 13 in lung cells. Based on a study of 61 breast adenocarcinoma patients, we found that tumors reacting with SM 92 appear associated with liver metastases, SM 43 with ovarian metastases, and SM 13 with lung metastases. These associations are highly significant. They lend some support to the concept that tumor cells that metastasize tend to go to sites where cells normally have the same surface antigens.

Supernumerary ring chromosomes containing chromosome 17 sequences. A specific feature of dermatofibrosarcoma protuberans?

Mystery surrounds the mechanisms by which the uncommon cutaneous tumor dermatofibrosarcoma protuberans (DP) arises and progresses. A clue may be at hand in the form of extra abnormal chromosomes (one of three ring chromosomes per case with or without other chromosome abnormalities) seen in some 10 cases, including five cases in our experience. The specificity of the rings to DP would be enhanced if the rings were found to contain a contribution from a constant chromosome. We here report fluorescence in situ hybridization (FISH) results bearing on the chromosomal content of DP rings, together with clinical, pathologic, and cytogenetic documentation of our first two cases, which were briefly reported earlier, and three new DP cases. To dissect a translocation (in our 2nd case), we probed by FISH and discovered chromosome 17 sequences in the rings in all five DP cases. Nonfluorescent bands were seen on some rings painted with a whole chromosome 17 probe, indicating the presence in these rings of foreign chromosome sequences. The complexity of the rings was underscored by the detection in only one case of chromosome 17 centromeric sequences. The situation in DP seems to have parallels to that in well-differentiated liposarcoma, another tumor of intermediate malignancy with extra abnormal marker chromosome containing contributions from a constant chromosome and variable donors. In DP the supernumerary rings are clearly specific and significant.

Prenatal detection of de novo paracentric inversion 46, XX inv (14) (q22q32.1) in a normal child: report and review of the literature

We present prenatal diagnosis and follow-up examination of an individual with a de novo paracentric inversion of the long are of chromosome 14. A literature search documented 19 other cases of paracentric inversion of 14q. The outcome of each of these cases is specified together with that of this current case. Four of the 20 cases, all XY, manifested significant abnormalities with mental retardation and microcephaly present in 3 of the 4 cases; 15% (2/13) of familial cases had abnormalities and 40% (2/5) of de novo cases had abnormalities.

Numerical simulation of steady flow in a model of the aortic bifurcation

The governing equations of steady flow of an incompressible viscous fluid through a 3-D model of the aortic bifurcation are solved with the finite element method. The effect of Reynolds number on the flow was studied for a range including the physiological values (200 < or = Re < or = 1600). The symmetrical bifurcation, with a branch angle of 70 degrees and an area ratio of 0.8, includes a tapered transition zone. Secondary flows induced by the tube curvature are observed in the daughter tubes. Transverse currents in the transition zone are generated by the combined effect of diverging and converging walls. Flow separation depends on both the Reynolds number and the inlet wall shear.