Time-resolved density correlations as probe of squeezing in toroidal Bose-Einstein condensates

I study the evolution of mean field and linear quantum fluctuations in a toroidal Bose-Einstein condensate, whose interaction strength is quenched from a finite (repulsive) value to zero. The azimuthal equal-time density-density correlation function is calculated and shows temporal oscillations with twice the (final) excitation frequencies after the transition. These oscillations are a direct consequence of positive and negative frequency mixing during non-adiabatic evolution. I will argue that a time-resolved measurement of the equal-time density correlator might be used to calculate the moduli of the Bogoliubov coefficients and thus the amount of squeezing imposed on a mode, i.e., the number of atoms excited out of the condensate.Comment: 18 pages, IOP styl

Bringing order to protein disorder through comparative genomics and genetic interactions

Abstract Background Intrinsically disordered regions are widespread, especially in proteomes of higher eukaryotes. Recently, protein disorder has been associated with a wide variety of cellular processes and has been implicated in several human diseases. Despite its apparent functional importance, the sheer range of different roles played by protein disorder often makes its exact contribution difficult to interpret. Results We attempt to better understand the different roles of disorder using a novel analysis that leverages both comparative genomics and genetic interactions. Strikingly, we find that disorder can be partitioned into three biologically distinct phenomena: regions where disorder is conserved but with quickly evolving amino acid sequences (flexible disorder); regions of conserved disorder with also highly conserved amino acid sequences (constrained disorder); and, lastly, non-conserved disorder. Flexible disorder bears many of the characteristics commonly attributed to disorder and is associated with signaling pathways and multi-functionality. Conversely, constrained disorder has markedly different functional attributes and is involved in RNA binding and protein chaperones. Finally, non-conserved disorder lacks clear functional hallmarks based on our analysis. Conclusions Our new perspective on protein disorder clarifies a variety of previous results by putting them into a systematic framework. Moreover, the clear and distinct functional association of flexible and constrained disorder will allow for new approaches and more specific algorithms for disorder detection in a functional context. Finally, in flexible disordered regions, we demonstrate clear evolutionary selection of protein disorder with little selection on primary structure, which has important implications for sequence-based studies of protein structure and evolution

Analiza proteinskih adukata kao biomarkera kratkotrajne izloženosti etilen oksidu i rezultati biomonitoringa

An accidental exposure of six workers to ethylene oxide (EO) provided the rationale for a biomonitoring and follow-up study, whose aim was to analyse protein adduct kinetics and examine the differentiation between accidental and environmental exposure, e.g., from tobacco smoke. For this purpose, the decrease in the concentration of the haemoglobin adduct N-2-hydroxyethylvaline (HEV) was followed during a fi ve-month period after the accident, together with N-2-cyanoethylvaline (CEV) and urinary cotinine, two well-established biomarkers for smoking. The follow-up study showed that EO adduct concentrations significantly increased after a short but presumably high exposure. Initial biomonitoring revealed HEV levels above 500 pmol g-1 globin in all cases, with a maximum of about 2,400 pmol g-1 globin. This compares to a German EKA value (exposure equivalent for carcinogenic substances) for a daily 8-h-exposure to 1 ppm EO of 90 μg L-1 blood (~3,900 pmol g-1 globin). The adduct levels dropped in accordance with the expected zero-order kinetics for a single exposure. After the five-month observation interval, the HEV concentrations in blood refl ected the individual background from tobacco smoking. The results of this study show that even a short exposure to ethylene oxide may result in a signifi cant rise in haemoglobin adduct levels. Although protein adducts and their occupational-medical assessment values are considered for long-term exposure surveillance, they can also be used for monitoring accidental exposures. In these cases, the calculation of daily ‘ppm-equivalents’ may provide a means for a comparison with the existing assessment values.U radu su prikazani rezultati biomonitoringa provedenog neposredno nakon akcidentalnog izlaganja šestorice radnika etilen oksidu i studije praćenja (follow up) provedene u cilju procjene kinetike razgradnje proteinskih adukata i utvrđivanja razlika nakon kratkotrajne izloženosti i izlaganja čimbenicima iz okoliša kao što je duhanski dim. U tu smo svrhu tijekom petomjesečnoga razdoblja nakon nezgode pratili smanjenje koncentracije hemoglobinskog adukta N-2-hidroksietilvalina usporedo s mjerenjem razina N-2-cijanoetilvalina i kotinina u mokraći, koji su pouzdani biomarkeri za dokazivanje pušenja duhana. Studija praćenja je pokazala da su koncentracije adukata etilen oksida značajno porasle nakon kratkotrajnoga izlaganja visokoj razini etilen oksida. U početnom biomonitoringu svih radnika izmjerene su razine N-2-hidroksietilvalina iznad 500 pmol g-1 globina, s maksimalnom vrijednošću od oko 2400 pmol g-1 globina. Ti su podaci usporedivi s vrijednostima njemačkih normi ekvivalenata izlaganja kancerogenim tvarima (EKA) od 90 μg L-1 krvi (~3900 pmol g-1 globina) kroz osmosatno dnevno izlaganje koncentraciji od 1 ppm etilen oksida. Razine adukata smanjile su se u skladu s očekivanom kinetikom nultoga reda za jednokratno izlaganje. Koncentracije N-2-hidroksietilvalina izmjerene u krvi radnika nakon petomjesečnoga praćenja mogu se povezati s njihovim osobnim pušačkim navikama. Rezultati toga istraživanja pokazuju da čak i kratkotrajna izloženost etilen oksidu može znatno povisiti razine adukata hemoglobina. Premda se u zdravstvenom nadzoru u okviru medicine rada proteinski adukti i njihove vrijednosti razmatraju u procjeni dugotrajnoga izlaganja, oni se mogu koristiti i za praćenje akcidentalnih izlaganja. U tim slučajevima izračun dnevnih vrijednosti (tzv. ppm-ekvivalenata) može poslužiti za usporedbu s postojećim procijenjenim vrijednostima

Measuring health-relevant businesses over 21 years: refining the National Establishment Time-Series (NETS), a dynamic longitudinal data set

Background The densities of food retailers, alcohol outlets, physical activity facilities, and medical facilities have been associated with diet, physical activity, and management of medical conditions. Most of the research, however, has relied on cross-sectional studies. In this paper, we assess methodological issues raised by a data source that is increasingly used to characterize change in the local business environment: the National Establishment Time Series (NETS) dataset. Discussion Longitudinal data, such as NETS, offer opportunities to assess how differential access to resources impacts population health, to consider correlations among multiple environmental influences across the life course, and to gain a better understanding of their interactions and cumulative health effects. Longitudinal data also introduce new data management, geoprocessing, and business categorization challenges. Examining geocoding accuracy and categorization over 21 years of data in 23 counties surrounding New York City (NY, USA), we find that health-related business environments change considerably over time. We note that re-geocoding data may improve spatial precision, particularly in early years. Our intent with this paper is to make future public health applications of NETS data more efficient, since the size and complexity of the data can be difficult to exploit fully within its 2-year data-licensing period. Further, standardized approaches to NETS and other “big data” will facilitate the veracity and comparability of results across studies

Correlation effects in MgO and CaO: Cohesive energies and lattice constants

A recently proposed computational scheme based on local increments has been applied to the calculation of correlation contributions to the cohesive energy of the CaO crystal. Using ab-initio quantum chemical methods for evaluating individual increments, we obtain 80% of the difference between the experimental and Hartree-Fock cohesive energies. Lattice constants corrected for correlation effects deviate by less than 1% from experimental values, in the case of MgO and CaO.Comment: LaTeX, 4 figure

Quality control in colorectal cancer screening: Systematic microbiological investigation of endoscopes used in the NORCCAP (Norwegian Colorectal Cancer Prevention) trial

BACKGROUND: Endoscopic colorectal cancer (CRC) screening is currently implemented in many countries. Since endoscopes cannot be sterilised, the transmission of infectious agents through endoscopes has been a matter of concern. We report on a continuous quality control programme in a large-scale randomised controlled trial on flexible sigmoidoscopy screening of an average-risk population. Continuously, throughout a two-year screening period, series of microbiological samples were taken from cleaned ready-to-use endoscopes and cultured for bacterial growth. RESULTS: 8573 endoscopies were performed during the trial period. Altogether, 178 microbiological samples (2%) were taken from the biopsy channels and surfaces from the endoscopes. One sample (0.5%) showed faecal contamination (Enterobacter cloacae), and 25 samples (14%) showed growth of environmental bacteria. CONCLUSIONS: Growth of bacteria occurs in a clinical significant number of samples from ready-to-use endoscopes. Pathogenic bacteria, however, were found only in one sample. Improvement of equipment design and cleaning procedures are desirable and continuous microbiological surveillance of endoscopes used in CRC screening is recommended

Microfluidic Fabrication of Colloidal Nanomaterials-Encapsulated Microcapsules for Biomolecular Sensing

Implantable sensors that detect biomarkers in vivo are critical for early disease diagnostics. Although many colloidal nanomaterials have been developed into optical sensors to detect biomolecules in vitro, their application in vivo as implantable sensors is hindered by potential migration or clearance from the implantation site. One potential solution is incorporating colloidal nanosensors in hydrogel scaffold prior to implantation. However, direct contact between the nanosensors and hydrogel matrix has the potential to disrupt sensor performance. Here, we develop a hollow-microcapsule-based sensing platform that protects colloidal nanosensors from direct contact with hydrogel matrix. Using microfluidics, colloidal nanosensors were encapsulated in polyethylene glycol microcapsules with liquid cores. The microcapsules selectively trap the nanosensors within the core while allowing free diffusion of smaller molecules such as glucose and heparin. Glucose-responsive quantum dots or gold nanorods or heparin-responsive gold nanorods were each encapsulated. Microcapsules loaded with these sensors showed responsive optical signals in the presence of target biomolecules (glucose or heparin). Furthermore, these microcapsules can be immobilized into biocompatible hydrogel as implantable devices for biomolecular sensing. This technique offers new opportunities to extend the utility of colloidal nanosensors from solution-based detection to implantable device-based detection. Keywords: biomolecular sensing; Microcapsules; microfluidic fabrication; nanosensorsJuvenile Diabetes Research Foundation International (Award 17-2013-507

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year