The effect of culture preservation techniques on patulin and citrinin production by Penicillium expansum Link

Aims: To study the influence of culture preservation methods and culture conditions on the production of the mycotoxins patulin and citrinin by Penicillium expansum. Methods and results: Ten strains of Penicillium expansum were preserved using subculture and maintenance at 4 ºC, mineral oil, drying on silica gel and freeze-drying. Patulin and citrinin production was assessed on yeast extract sucrose agar (YES) and grape juice agar (GJ), using TLC before and after 0.5, 2–3, 6 and 12 months preservation. Citrinin was detected in all cultures for all preservation techniques on YES. The patulin profiles obtained differed with strain and culture media used. Conclusions: Citrinin production seems to be a stable character for the tested strains. There is a tendency for patulin detection with time apparently more consistent for silica gel storage and freeze-drying, especially when the strains are grown on GJ. Significance and Impact of the Study: Variability in the profiles of the mycotoxins tested seems to be more strain-specific than dependent on the preservation technique used

A comprehensive platform for highly multiplexed mammalian functional genetic screens

<p>Abstract</p> <p>Background</p> <p>Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens.</p> <p>Results</p> <p>Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens.</p> <p>Conclusion</p> <p>Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.</p

A multi-centric, single-blinded, randomized, parallel-group study to evaluate the effectiveness of nasoalveolar moulding treatment in non-syndromic patients with complete unilateral cleft lip, alveolus and palate (NAMUC study): a study protocol for a randomized controlled trial.

BACKGROUND Cleft lip and palate (CLP) are among the most common congenital anomaly that affects up to 33,000 newborns in India every year. Nasoalveolar moulding (NAM) is a non-surgical treatment performed between 0 and 6 months of age to reduce the cleft and improve nasal aesthetics prior to lip surgery. The NAM treatment has been a controversial treatment option with 51% of the cleft teams in Europe, 37% of teams in the USA and 25 of cleft teams in India adopting this methodology. This treatment adds to the already existing high burden of care for these patients. Furthermore, the supporting evidence for this technique is limited with no high-quality long-term clinical trials available on the effectiveness of this treatment. METHOD The NAMUC study is an investigator-initiated, multi-centre, single-blinded randomized controlled trial with a parallel group design. The study will compare the effectiveness of NAM treatment provided prior to lip surgery against the no-treatment control group in 274 patients with non-syndromic unilateral complete cleft lip and palate. The primary endpoint of the trial is the nasolabial aesthetics measured using the Asher McDade index at 5 years of age. The secondary outcomes include dentofacial development, speech, hearing, cost-effectiveness, quality of life, patient perception, feeding and intangible benefits. Randomization will be carried out via central online system and stratified based on cleft width, birth weight and clinical trial site. DISCUSSION We expect the results from this study on the effectiveness of treatment with NAM appliance in the long term along with the cost-effectiveness evaluation can eliminate the dilemma and differences in clinical care across the globe. TRIAL REGISTRATION ClinicalTrials.gov CTRI/2022/11/047426 (Clinical Trials Registry India). Registered on 18 November 2022. The first patient was recruited on 11 December 2022. CTR India does not pick up on Google search with just the trial number. The following steps have to be carried out to pick up. How to search: ( https://ctri.nic.in/Clinicaltrials/advsearch.php -use the search boxes by entering the following details: Interventional trial > November 2022 > NAMUC)

Fundamental optical processes in armchair carbon nanotubes

Single-wall carbon nanotubes provide ideal model one-dimensional (1-D) condensed matter systems in which to address fundamental questions in many-body physics, while, at the same time, they are leading candidates for building blocks in nanoscale optoelectronic circuits. Much attention has been recently paid to their optical properties, arising from 1-D excitons and phonons, which have been revealed via photoluminescence, Raman scattering, and ultrafast optical spectroscopy of semiconducting carbon nanotubes. On the other hand, dynamical properties of metallic nanotubes have been poorly explored, although they are expected to provide a novel setting for the study of electronﾖhole pairs in the presence of degenerate 1-D electrons. In particular, (n,n)-chirality, or armchair, metallic nanotubes are truly gapless with massless carriers, ideally suited for dynamical studies of TomonagaﾖLuttinger liquids. Unfortunately, progress towards such studies has been slowed by the inherent problem of nanotube synthesis whereby both semiconducting and metallic nanotubes are produced. Here, we use post-synthesis separation methods based on density gradient ultracentrifugation and DNA-based ion-exchange chromatography to produce aqueous suspensions strongly enriched in armchair nanotubes. Through resonant Raman spectroscopy of the radial breathing mode phonons, we provide macroscopic and unambiguous evidence that density gradient ultracentrifugation can enrich ensemble samples in armchair nanotubes. Furthermore, using conventional, optical absorption spectroscopy in the nearinfrared and visible range, we show that interband absorption in armchair nanotubes is strongly excitonic. Lastly, by examining the G-band mode in Raman spectra, we determine that observation of the broad, lower frequency (G!) feature is a result of resonance with non-armchair “metallic” nanotubes. These !ndings regarding the fundamental optical absorption and scattering processes in metallic carbon nanotubes lay the foundation for further spectroscopic studies to probe many-body physical phenomena in one dimension

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Are iPhones really better for privacy? A comparative study of iOS and Android apps

While many studies have looked at privacy properties of the Android and Google Play app ecosystem, comparatively much less is known about iOS and the Apple App Store, the most widely used ecosystem in the US. At the same time, there is increasing competition around privacy between these smartphone operating system providers. In this paper, we present a study of 24k Android and iOS apps from 2020 along several dimensions relating to user privacy. We find that third-party tracking and the sharing of unique user identifiers was widespread in apps from both ecosystems, even in apps aimed at children. In the children’s category, iOS apps tended to use fewer advertising-related tracking than their Android counterparts, but could more often access children’s location. Across all studied apps, our study highlights widespread potential violations of US, EU and UK privacy law, including 1) the use of third-party tracking without user consent, 2) the lack of parental consent before sharing personally identifiable information (PII) with third-parties in children’s apps, 3) the non-data-minimising configuration of tracking libraries, 4) the sending of personal data to countries without an adequate level of data protection, and 5) the continued absence of transparency around tracking, partly due to design decisions by Apple and Google. Overall, we find that neither platform is clearly better than the other for privacy across the dimensions we studied

Goodbye tracking? Impact of iOS app tracking transparency and privacy labels

Tracking is a highly privacy-invasive data collection practice that has been ubiquitous in mobile apps for many years due to its role in supporting advertising-based revenue models. In defence of user privacy, Apple introduced two significant changes with iOS 14: App Tracking Transparency (ATT), a mandatory opt-in system for enabling tracking on iOS, and Privacy Nutrition Labels, which disclose what kinds of data each app processes. So far, the impact of these changes on individual privacy and control has not been well understood. This paper addresses this gap by analysing two versions of 1,759 iOS apps from the UK App Store: one version from before iOS 14 and one that has been updated to comply with the new rules. We find that Apple’s new policies, as promised, prevent the collection of the Identifier for Advertisers (IDFA), an identifier used to facilitate cross-app user tracking. Smaller data brokers, who used to engage in some of the most invasive data practices, will now face higher challenges in tracking users – a positive development for privacy. However, the number of tracking libraries has – on average – roughly stayed the same in the studied apps. Many apps still collect device information that can be used to track users at a group level (cohort tracking) or identify individuals probabilistically (fingerprinting). We find real-world evidence of apps computing and agreeing on a fingerprinting-derived identifier through the use of server-side code, thereby violating Apple’s policies and exposing the limits of what ATT can do against tracking on iOS. This is especially concerning because we explicitly refused opt-in to tracking in our study, and consent is a legal requirement for tracking under EU and UK data protection law. We find that Apple itself engages in some forms of tracking and exempts invasive data practices like first-party tracking and credit scoring from its new rules, and that the new Privacy Nutrition Labels were often inaccurate. This is in conflict with the company’s marketing claims and the resulting expectations of many iOS users. Overall, our observations suggest that, while Apple’s changes make tracking individual users more difficult, they motivate a counter-movement, and reinforce existing market power of gatekeeper companies with access to large troves of first-party data. Making the privacy properties of apps transparent through large-scale analysis remains a difficult target for independent researchers, and a key obstacle to meaningful, accountable and verifiable privacy protections