Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing

CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman’s risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg2+ ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target

Differentiating criminal networks in the illegal wildlife trade: organized, corporate and disorganized crime

Historically, the poaching of wildlife was portrayed as a small-scale local activity in which only small numbers of wildlife would be smuggled illegally by collectors or opportunists. Nowadays, this image has changed: criminal networks are believed to be highly involved in wildlife trafficking, which has become a significant area of illicit activity. Even though wildlife trafficking has become accepted as a major area of crime and an important topic and criminologists have examined a variety of illegal wildlife markets, research that specifically focusses on the involvement of different criminal networks and their specific nature is lacking. The concept of a ‘criminal network’ or ‘serious organized crime’ is amorphous – getting used interchangeably and describes all crime that is structured rather than solely reflecting crime that fits within normative definitions of ‘organized’ crime. In reality, criminal networks are diverse. As such, we propose categories of criminal networks that are evidenced in the literature and within our own fieldwork: (1) organized crime groups (2) corporate crime groups and (3) disorganized criminal networks. Whereas there are instances when these groups act alone, this article will (also) discuss the overlap and interaction that occurs between our proposed categories and discuss the complicated nature of the involved criminal networks as well as predictions as to the future of these networks

Referral Center Experience With Nonpalpable Contraceptive Implant Removals.

ObjectiveTo describe our experience with office removal of nonpalpable contraceptive implants at our referral center.MethodsWe performed a retrospective cohort study by reviewing the charts of patients referred to our family planning specialty center for nonpalpable or complex contraceptive implant removal from January 2015 through December 2018. We localized nonpalpable implants using high-frequency ultrasonography and skin mapping in radiology, followed by attempted removal in the office using local anesthesia and a modified vasectomy clamp. We abstracted information on demographics, implant location, and outcomes.ResultsOf 61 referrals, 55 patients attended their scheduled appointments. Seven patients had palpable implants; six elected removal. The other 48 patients had ultrasound localization, which identified 47 (98%) of the implants; the remaining patient had successful localization with computed tomography imaging. Nonpalpable implants were suprafascial (n=22), subfascial (n=25) and intrafascial (n=1); four of these patients opted to delay removal. Of 50 attempted office removals, all palpable (n=6), all nonpalpable suprafascial (n=21 [100%, 95% CI 83-100%]), and 19 out of 23 (83%, 95% CI 67-98%) subfascial implants were successful. Three of the four patients with failed subfascial implant office removal had successful operating room removal with a collaborative orthopedic surgeon; the other patient sought removal elsewhere. Transient postprocedure neuropathic complaints were noted in 7 out of 23 (30%, 95% CI 12-49%) subfascial and 1 out of 21 (5%, 95% CI 0-13%) suprafascial removals (P=.048). Nonpalpable implants were more likely to be subfascial in nonobese patients (24/34, 71%) as compared with obese (1/13, 8%) patients (P<.001). Seven (28%) of the 25 subfascially located implants had been inserted during a removal-reinsertion procedure through the same incision.ConclusionMost nonpalpable contraceptive implants can be removed in the office by an experienced subspecialty health care provider after ultrasound localization. Some patients may experience transient postprocedure neuropathic pain. Nonpalpable implants in thinner women are more likely to be in a subfascial location

Time-resolved spectral correlations of long-duration Gamma-Ray Bursts

For a sample of long GRBs with known redshift, we study the distribution of the evolutionary tracks on the rest-frame luminosity-peak energy Liso-Ep' diagram. We are interested in exploring the extension of the `Yonetoku' correlation to any phase of the prompt light curve, and in verifying how the high-signal prompt duration time, Tf, in the rest frame correlates with the residuals of such correlation (Firmani et al. 2006). For our purpose, we analyse separately two samples of time-resolved spectra corresponding to 32 GRBs with peak fluxes >1.8 phot cm^-2 s^-1 from the Swift-BAT detector, and 7 bright GRBs from the CGRO-BATSE detector previously processed by Kaneko et al. (2006). After constructing the Liso-Ep' diagram, we discuss the relevance of selection effects, finding that they could affect significantly the correlation. However, we find that these effects are much less significant in the Liso x Tf-Ep' diagram, where the intrinsic scatter reduces significantly. We apply further corrections for reducing the intrinsic scatter even more. For the sub-samples of GRBs (7 from Swift and 5 from CGRO) with measured jet break time, we analyse the effects of correcting Liso by jet collimation. We find that (i) the scatter around the correlation is reduced, and (ii) this scatter is dominated by the internal scatter of the individual evolutionary tracks. These results suggest that the time, integrated `Amati' and `Ghirlanda' correlations are consequences of the time resolved features, not of selection effects, and therefore call for a physical origin. We finally remark the relevance of looking inside the nature of the evolutionary tracks.Comment: 11 pages, 6 figures, 4 tables. Submitted to MNRAS (Sept 8th), after referee comment

Jitter radiation images, spectra, and light curves from a relativistic spherical blastwave

We consider radiation emitted by the jitter mechanism in a Blandford-McKee self-similar blastwave. We assume the magnetic field configuration throughout the whole blastwave meets the condition for the emission of jitter radiation and we compute the ensuing images, light curves and spectra. The calculations are performed for both a uniform and a wind environment. We compare our jitter results to synchrotron results. We show that jitter radiation produces slightly different spectra than synchrotron, in particular between the self-absorption and the peak frequency, where the jitter spectrum is flat, while the synchrotron spectrum grows as \nu^{1/3}. The spectral difference is reflected in the early decay slope of the light curves. We conclude that jitter and synchrotron afterglows can be distinguished from each other with good quality observations. However, it is unlikely that the difference can explain the peculiar behavior of several recent observations, such as flat X-ray slopes and uncorrelated optical and X-ray behavior.Comment: 11 pages, 7 postscript figures. Accepted for publication in MNRA

Transition from Townsend to glow discharge: subcritical, mixed or supercritical

The full parameter space of the transition from Townsend to glow discharge is investigated numerically in one space dimension in the classical model: with electrons and positive ions drifting in the local electric field, impact ionization by electrons ($\alpha$ process), secondary electron emission from the cathode ($\gamma$ process) and space charge effects. We also perform a systematic analytical small current expansion about the Townsend limit up to third order in the total current that fits our numerical data very well. Depending on $\gamma$ and system size pd, the transition from Townsend to glow discharge can show the textbook subcritical behavior, but for smaller values of pd, we also find supercritical or some intermediate ``mixed'' behavior. The analysis in particular lays the basis for understanding the complex spatio-temporal patterns in planar barrier discharge systems.Comment: 12 pages, 10 figures, submitted to Phys. Rev.

A multiwavelength study of Swift GRB 060111B constraining the origin of its prompt optical emission

In this work, we present the results obtained from a multi-wavelength campaign, as well as from the public Swift/BAT, XRT, and UVOT data of GRB 060111B for which a bright optical emission was measured with good temporal resolution during the prompt phase. We identified the host galaxy at R~25 mag; its featureless spectral continuum and brightness, as well as the non-detection of any associated supernova 16 days after the trigger and other independent redshift estimates, converge to z~1-2. From the analysis of the early afterglow SED, we find that non-negligible host galaxy dust extinction, in addition to the Galactic one, affects the observed flux in the optical regime. The extinction-corrected optical-to-gamma-ray spectral energy distribution during the prompt emission shows a flux density ratio $F_{\gamma}/F_{opt}$=0.01-0.0001 with spectral index $\beta_{\gamma,opt}> \beta_{\gamma}$, strongly suggesting a separate origin of the optical and gamma-ray components. This result is supported by the lack of correlated behavior in the prompt emission light curves observed in the two energy domains. The properties of the prompt optical emission observed during GRB 060111B favor interpretation of this optical light as radiation from the reverse shock in a thick shell limit and in the slow cooling regime. The expected peak flux is consistent with the observed one corrected for the host extinction, likely indicating that the starting time of the TAROT observations is very near to or coincident with the peak time. The estimated fireball initial Lorentz factor is >260-360 at z=1-2, similar to the Lorentz factors obtained from other GRBs. GRB 060111B is a rare, good test case of the reverse shock emission mechanism in both the X-ray and optical energy ranges.Comment: Accepted for publication in Astronomy and Astrophysics, 15 pages,10 figures and 7 table