Probabilistic modeling of ambient noise in single-cell omics data

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single cell CRISPR perturbations (e.g., CROP-seq) and single-cell protein and transcriptomic profiling (e.g., CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single cell resolution, yet these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current efforts to address this issue are highly specific to a certain technology, while a universal model to describe the noise across these technologies may reveal this common source thereby improving the denoising accuracy. To this end, we explicitly examined these unexpected signals and observed a predictable pattern in multiple datasets across different technologies. Based on the finding, we developed single cell Ambient Remover (scAR) which uses probabilistic deep learning to deconvolute the observed signals into native and ambient composition. scAR provides an efficient and universal solution to count denoising for multiple types of single-cell omics data, including single cell CRISPR screens, CITE-seq and scRNAseq. It will facilitate the application of single-cell omics technologies.

A 65 nm Duplex Transconductance Path Up-Conversion Mixer for 24 GHz Automotive Short-Range Radar Sensor Applications

A 24 GHz highly-linear upconversion mixer, based on a duplex transconductance path (DTP), is proposed for automotive short-range radar sensor applications using the 65-nm CMOS process. A mixer with an enhanced transconductance stage consisting of a DTP is presented to improve linearity. The main transconductance path (MTP) of the DTP includes a common source (CS) amplifier, while the secondary transconductance path (STP) of the DTP is implemented as an improved cross-quad transconductor (ICQT). Two inductors with a bypass capacitor are connected at the common nodes of the transconductance stage and switching stage of the mixer, which acts as a resonator and helps to improve the gain and isolation of the designed mixer. According to the measured results, at 24 GHz the proposed mixer shows that the linearity of output 1-dB compression point (OP1dB) is 3.9 dBm. And the input 1-dB compression point (IP1dB) is 0.9 dBm. Moreover, a maximum conversion gain (CG) of 2.49 dB and a noise figure (NF) of 3.9 dB is achieved in the designed mixer. When the supply voltage is 1.2 V, the power dissipation of the mixer is 3.24 mW. The mixer chip occupies an area of 0.42 mm2.

Clinical Trial Quality Assessment in Adult Spinal Surgery: What Do Publication Status, Funding Source, and Result Reporting Tell Us?

Study Design Narrative Review Objectives The objective of this study was to compare publication status of clinical trials in adult spine surgery registered on ClinicalTrials.gov by funding source as well as to identify other trends in clinical trials in adult spine surgery. Methods All prospective, comparative, therapeutic (intervention-based) trials of adult spinal disease that were registered on ClinicalTrials.gov with a start date of January 1, 2000 and completion date before December 17, 2018 were included. Primary outcome was publication status of published or unpublished. A bivariate analysis was used to compare publication status to funding source of industry vs non-industry. Results Our search identified 107 clinical trials. The most common source of funding was industry (62 trials, 57.9% of total), followed by University funding (26 trials, 24.3%). The results of 76 trials (71.0%) were published, with industry-funded trials less likely to be published compared to non–industry-funded trials (62.9% compared to 82.2%, P = .03). Of the 31 unpublished studies, 13 did not report any results on ClinicalTrials.gov , and of those with reported results, none was a positive trial. Conclusions Clinician researchers in adult spine surgery should be aware that industry-funded trials are less likely to go on to publication compared to non–industry-funded trials, and that negative trials are frequently not published. Future opportunities include improvement in result reporting and in publishing negative studies.

Ground Target Tracking Using an Airborne Angle-Only Sensor with Terrain Uncertainty and Sensor Biases

Airborne angle-only sensors can be used to track stationary or mobile ground targets. In order to make the problem observable in 3-dimensions (3-D), the height of the target (i.e., the height of the terrain) from the sea-level is needed to be known. In most of the existing works, the terrain height is assumed to be known accurately. However, the terrain height is usually obtained from Digital Terrain Elevation Data (DTED), which has different resolution levels. Ignoring the terrain height uncertainty in a tracking algorithm will lead to a bias in the estimated states. In addition to the terrain uncertainty, another common source of uncertainty in angle-only sensors is the sensor biases. Both these uncertainties must be handled properly to obtain better tracking accuracy. In this paper, we propose algorithms to estimate the sensor biases with the target(s) of opportunity and algorithms to track targets with terrain and sensor bias uncertainties. Sensor bias uncertainties can be reduced by estimating the biases using the measurements from the target(s) of opportunity with known horizontal positions. This step can be an optional step in an angle-only tracking problem. In this work, we have proposed algorithms to pick optimal targets of opportunity to obtain better bias estimation and algorithms to estimate the biases with the selected target(s) of opportunity. Finally, we provide a filtering framework to track the targets with terrain and bias uncertainties. The Posterior Cramer–Rao Lower Bound (PCRLB), which provides the lower bound on achievable estimation error, is derived for the single target filtering with an angle-only sensor with terrain uncertainty and measurement biases. The effectiveness of the proposed algorithms is verified by Monte Carlo simulations. The simulation results show that sensor biases can be estimated accurately using the target(s) of opportunity and the tracking accuracies of the targets can be improved significantly using the proposed algorithms when the terrain and bias uncertainties are present.

Classification of Daily Crop Phenology in PhenoCams Using Deep Learning and Hidden Markov Models

Near-surface cameras, such as those in the PhenoCam network, are a common source of ground truth data in modelling and remote sensing studies. Despite having locations across numerous agricultural sites, few studies have used near-surface cameras to track the unique phenology of croplands. Due to management activities, crops do not have a natural vegetation cycle which many phenological extraction methods are based on. For example, a field may experience abrupt changes due to harvesting and tillage throughout the year. A single camera can also record several different plants due to crop rotations, fallow fields, and cover crops. Current methods to estimate phenology metrics from image time series compress all image information into a relative greenness metric, which discards a large amount of contextual information. This can include the type of crop present, whether snow or water is present on the field, the crop phenology, or whether a field lacking green plants consists of bare soil, fully senesced plants, or plant residue. Here, we developed a modelling workflow to create a daily time series of crop type and phenology, while also accounting for other factors such as obstructed images and snow covered fields. We used a mainstream deep learning image classification model, VGG16. Deep learning classification models do not have a temporal component, so to account for temporal correlation among images, our workflow incorporates a hidden Markov model in the post-processing. The initial image classification model had out of sample F1 scores of 0.83–0.85, which improved to 0.86–0.91 after all post-processing steps. The resulting time series show the progression of crops from emergence to harvest, and can serve as a daily, local-scale dataset of field states and phenological stages for agricultural research.

Do the Child Welfare and Protection Services Involve Children in Cases With Parental Mental Health Problems? A Norwegian Case-File Study

Background: Parental mental health problems is a common source of concern reported to child welfare and protection services (CWPS). In this study we explored to what extent the child was invited to participate in the investigation process. We aimed to study: (a) what was the current practice in the child protection service in Norway when the CWPS received a report of concern about children whose parents were affected by mental health problems or substance abuse, (b) to what extent were children involved and consulted, (c) which factors predicted the decision to involve the children, and (d) in cases in which conversations with children were conducted: what was the main content of the conversations.Method: The study was a cross-sectional case file study (N = 1,123). Data were collected retrospectively from case records in 16 different child protection agencies. The cases were randomly drawn from all referrals registered in the participating agencies. Differences in how investigations were conducted in cases with and without concerns about parental mental health were analyzed using t-tests and chi-square testes. Predictors of child involvement in cases with parental mental health problems (N = 324) were estimated by logistic regression analyses.Results: When the referral to the CWPS contained concerns about parental mental health, there were more consultations with parents, more frequent home visits and the investigation took longer to conclude. The children, however, were less likely to be involved. Children in such cases were consulted in 47.5% of cases. Predictors for involving the children in those cases were child age, concern about the child's emotional problems and if the child was known from previous referrals.Conclusion: In Norwegian child protection investigations, in which there were concerns about the parent's mental health, conversations with children were conducted to a significantly lower degree compared to cases where the child's problem was the main concern. In such cases, the CWPS workers have to overcome a threshold before they consult with the child. The threshold decreases with child age and when case worker already knows the child.

Awareness about sexually transmitted diseases in women related to their age, education and income

Objective: To assess the level of awareness about sexually transmitted diseases in females coming from different age groups and to investigate the role that education and social status may play on their knowledge. Methods: Study design: Cross Sectional Setting: CMH Lahore Gynaecology Out Patient Department Time frame: June 2019 till July 2019. Sample size: 337 Inclusion criteria: Patients included in this study presented to the CMH Gynaecology OPD during June to July 2019 and gave an informed consent about participation in the research. Exclusion criteria: Anyone who did not give consent. Data collection: Patients were given a hard copy of the questionnaire to fill. Any queries were answered on the spot. Data Analysis: SPSS version 23. Results: Of the 337 patients interviewed, 158 were aged 26-35 years. 71 patients were undergraduates and 99 had completed post graduate studies. 205 patients belonged to families with an income of less than RS.50, 000. 229 females had presented for a routine pregnancy checkup. 244 of the 337 patients had attested to know about STD’s. The most common source of their knowledge was through TV (142), followed by the internet (137). 251 of the 337 patients were familiar with limited STDs such as AIDS and Hepatitis B. Conclusion: Age, level of education and income had a profound effect on the knowledge regarding Sexually transmitted diseases amongst the women in Pakistan. Keywords: Sexually transmitted diseases, sexual and reproductive health, STD’s, STI’s, venereal diseases.

Perceptions of cervical cancer care among Ethiopian women and their providers: a qualitative study

Background Cervical cancer is the second most commonly diagnosed cancer among Ethiopian women, killing an estimated 4700 women each year. As the government rolls out the country’s first national cancer control strategy, information on patient and provider experiences in receiving and providing cervical cancer screening, diagnosis, and treatment is critical. Methods This qualitative study aimed to assess the availability of cervical cancer care; explore care barriers and sources of delay; and describe women’s and providers’ perceptions and experiences of care. We analyzed data from 45 informants collected at 16 health centers, district hospitals and referral hospitals in East Gojjam Zone and a support center in Addis Ababa. Thirty providers and ten women receiving care were interviewed, and five women in treatment or post-treatment participated in a focus group discussion. Deductive and inductive codes were used to thematically analyze data. Results Providers lacked equipment and space to screen and treat patients and only 16% had received in-service cervical cancer training. Consequently, few facilities provided screening or preventative treatment. Patients reported low perceptions of risk, high stigma, a lack of knowledge about cervical cancer, and delayed care initiation. All but one patient sought care only when she became symptomatic, and, pre-diagnosis, only half of the patients knew about cervical cancer. Even among those aware of cervical cancer, many assumed they were not at risk because they were not sexually active. Misdiagnosis was another common source of delay experienced by half of the patients. Once diagnosed, women faced multiple-month waits for referrals, and, once in treatment, broken equipment and shortages of hospital beds resulted in additional delays. Barriers to therapeutic treatment included a lack of housing and travel funds. Patient-provider communication of cancer diagnosis was often lacking. Conclusions In-service provider training should be intensified and should include discussions of cervical cancer symptoms. Better distribution of screening and diagnostic supplies to lower-level facilities and better maintenance of treatment equipment at tertiary facilities are also a priority. Expanded cervical cancer health education should focus on stigma reduction and emphasize a broad, wide-spread risk of cervical cancer.

Birds Kept in the German Zoo “Tierpark Berlin” Are a Common Source for Polyvalent Yersinia pseudotuberculosis Phages

Yersinia pseudotuberculosis is an important animal pathogen, particularly for birds, rodents, and monkeys, which is also able to infect humans. Indeed, an increasing number of reports have been published on zoo animals that were killed by this species. One option to treat diseased animals is the application of strictly lytic (virulent) phages. However, thus far relatively few phages infecting Y. pseudotuberculosis have been isolated and characterized. To determine the prevalence of Y. pseudotuberculosis phages in zoo animals, fecal samples of birds and some primates, maras, and peccaries kept in the Tierpark Berlin were analyzed. Seventeen out of 74 samples taken in 2013 and 2017 contained virulent phages. The isolated phages were analyzed in detail and could be allocated to three groups. The first group is composed of 10 T4-like phages (PYps2T taxon group: Myoviridae; Tevenvirinae; Tequatrovirus), the second group (PYps23T taxon group: Chaseviridae; Carltongylesvirus; Escherichia virus ST32) consists of five phages encoding a podovirus-like RNA polymerase that is related to an uncommon genus of myoviruses (e.g., Escherichia coli phage phiEcoM-GJ1), while the third group is comprised of two podoviruses (PYps50T taxon group: Autographiviridae; Studiervirinae; Berlinvirus) which are closely related to T7. The host range of the isolated phages differed significantly. Between 5.5 and 86.7% of 128 Y. pseudotuberculosis strains belonging to 20 serotypes were lysed by each phage. All phages were additionally able to lyse Y. enterocolitica B4/O:3 strains, when incubated at 37°C. Some phages also infected Y. pestis strains and even strains belonging to other genera of Enterobacteriaceae. A cocktail containing two of these phages would be able to lyse almost 93% of the tested Y. pseudotuberculosis strains. The study indicates that Y. pseudotuberculosis phages exhibiting a broad-host range can be isolated quite easily from zoo animals, particularly birds.