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Objectives To reduce the number of new HIV infections and improve HIV health care outcomes, the social conditions in which people live and work should be assessed. The objective of this study was to describe linkage to HIV medical care by selected demographic characteristics and social determinants of health (SDH) among US adults with HIV at the county level. Methods We used National HIV Surveillance System data from 42 US jurisdictions and data from the American Community Survey to describe differences in linkage to HIV medical care among adults aged ≥18 with HIV infection diagnosed in 2017. We categorized SDH variables into higher or lower levels of poverty (where Results Of 33 204 adults with HIV infection diagnosed in 2017, 78.4% were linked to HIV medical care ≤1 month after diagnosis. Overall, rates of linkage to care were significantly lower among men and women living in counties with higher versus lower poverty (PR = 0.96; 95% CI, 0.94-0.97), with lower versus higher health insurance coverage (PR = 0.93; 95% CI, 0.92-0.94), and with lower versus higher education levels (PR = 0.97; 95% CI, 0.96-0.98). Conclusions Increasing health insurance coverage and addressing economic and educational disparities would likely lead to better HIV care outcomes in these areas.

STUDY QUESTION Do women with polycystic ovary syndrome (PCOS) have a greater risk of adverse pregnancy complications (gestational diabetes, preeclampsia, cesarean section, placental abnormalities) and neonatal outcomes (preterm birth, small for gestational age, prolonged delivery hospitalization) compared to women without a PCOS diagnosis and does this risk vary by BMI, subfertility and fertility treatment utilization? SUMMARY ANSWER Deliveries to women with a history of PCOS were at greater risk of complications associated with cardiometabolic function, including gestational diabetes and preeclampsia, as well as preterm birth and prolonged length of delivery hospitalization. WHAT IS KNOWN ALREADY Prior research has suggested that women with PCOS may be at increased risk of adverse pregnancy outcomes. However, findings have been inconsistent possibly due to lack of consistent adjustment for confounding factors, small samples size and other sources of bias. STUDY DESIGN, SIZE, DURATION Massachusetts deliveries among women ≥18 years old during 2013–2017 from state vital records linked to hospital discharges, observational stays and emergency department visits were linked to the Society for Assisted Reproductive Technology Clinic Outcome Reporting System (SART CORS) and the Massachusetts All-Payers Claims Database (APCD). PARTICIPANTS/MATERIALS, SETTING, METHODS PCOS was identified by ICD9 and ICD10 codes in APCD prior to index delivery. Relative risks (RRs) and 95% CI for pregnancy and delivery complications were modeled using generalized estimating equations with a log link and a Poisson distribution to take multiple cycles into account and were adjusted a priori for maternal age, BMI, race/ethnicity, education, plurality, birth year, chronic hypertension and chronic diabetes. Tests for homogeneity investigated differences between maternal pre-pregnancy BMI categories ( MAIN RESULTS AND THE ROLE OF CHANCE Among 91 825 deliveries, 3.9% had a history of PCOS. Women with a history of PCOS had a 51% greater risk of gestational diabetes (CI: 1.38–1.65) and a 25% greater risk of preeclampsia (CI: 1.15–1.35) compared to women without a diagnosis of PCOS. Neonates born to women with a history of PCOS were more likely to be born preterm (RR: 1.17, CI: 1.06–1.29) and more likely to have a prolonged delivery hospitalization after additionally adjusting for gestational age (RR: 1.23, CI: 1.09–1.40) compared to those of women without a diagnosis of PCOS. The risk for gestational diabetes for women with PCOS was greater among women with a pre-pregnancy BMI LIMITATIONS, REASONS FOR CAUTION PCOS was defined by ICD documentation prior to delivery so there may be women with undiagnosed PCOS or PCOS diagnosed after delivery included in the unexposed group. The study population is limited to deliveries within Massachusetts among most private insurance payers and inpatient or observational hospitalization in Massachusetts during the follow-up window, therefore there may be diagnoses and or deliveries outside of the state or outside of our sample that were not captured. WIDER IMPLICATIONS OF THE FINDINGS In this population-based study, women with a history of PCOS were at greater risk of pregnancy complications associated with cardiometabolic function and preterm birth. Obstetricians should be aware of patients’ PCOS status and closely monitor for potential pregnancy complications to improve maternal and infant perinatal health outcomes. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the NIH (R01HD067270). S.A.M. receives grant funding from NIH, AbbVie and the Marriot Family Foundation; payment/honoraria from the University of British Columbia, World Endometriosis Research Foundation and Huilun Shanghai; travel support for attending meetings for ESHRE 2019, IASP 2019, National Endometriosis Network UK meeting 2019; SRI 2022, ESHRE 2022; participates on the data safety monitoring board/advisory board for AbbVie, Roche, Frontiers in Reproductive Health; and has a leadership role in the Society for Women’s Health Research, World Endometriosis Research Foundation, World Endometriosis Society, American Society for Reproductive Medicine and ESHRE. The other authors have no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.

The application of genetic relationships among individuals, characterized by a genetic relationship matrix (GRM), has far-reaching effects in human genetics. However, the current standard to calculate the GRM generally does not take advantage of linkage information and does not reflect the underlying genealogical history of the study sample. Here, we propose a coalescent-informed framework to infer the expected relatedness between pairs of individuals given an ancestral recombination graph (ARG) of the sample. Through extensive simulations we show that the eGRM is an unbiased estimate of latent pairwise genome-wide relatedness and is robust when computed using genealogies inferred from incomplete genetic data. As a result, the eGRM better captures the structure of a population than the canonical GRM, even when using the same genetic information. More importantly, our framework allows a principled approach to estimate the eGRM at different time depths of the ARG, thereby revealing the time-varying nature of population structure in a sample. When applied to genotyping data from a population sample from Northern and Eastern Finland, we find that clustering analysis using the eGRM reveals population structure driven by subpopulations that would not be apparent using the canonical GRM, and that temporally the population model is consistent with recent divergence and expansion. Taken together, our proposed eGRM provides a robust tree-centric estimate of relatedness with wide application to genetic studies.

In the present study, the various 28 hybrid molecules containing hydrazone and sulfonate moiety were synthesized and characterized by FTIR, 1H-NMR, 13C-NMR spectroscopy and LC-MS spectrometry, besides elemental analysis. The compounds were evaluated for their antiproliferative effects against six cancer cell lines, namely A549 (non-small cell lung cancer), MCF-7 (breast cancer), HT-29 (colorectal adenocarcinoma cancer), PC-3 (androgen-independent prostate adenocarcinoma), Hep3B (hepatocellular carcinoma cancer), and HeLa (epitheloid cervix carcinoma cancer). Among all the target compounds, compounds 4g and 4h exhibited more promising effects on MCF-7 cell lines (IC50=17.8 mM and 21.2 mM, respectively) with high selectivity. Further mechanistic studies proposed that compounds 4g and 4h induced apoptosis is mediated through the intrinsic apoptotic pathway with changes in mitochondrial membrane potential by finally activating caspase-9 and caspase-3. The results have been encouraging enough to merit further investigation.

Record linkage aims to bring records together from two or more files that belong to the same statistical entity. Naively treating a linked file as if there are no linkage errors may lead to biased inference. We present two general approaches for compensating for linkage error when calculating and analysing a two-way contingency table for categorical data, and study the following question: under what conditions can a compensation approach improve on the naive approach, where linkage error is not compensated for? To this end, we compare estimation errors, bias, variance and mean square error for the naive approach and two compensation approaches by means of an analytical study as well as a simulation study.

This research aimed at looking at the linkage or relationship between learning independence, learning creativity, and English achievement; and finding out a significant effect of learning independence and learning creativity towards English achievement of the eighth-grade students of SMPN 1 Lumbis. Acorrelational research was employed at the eighth-grade students of SMP Negeri 1 Lumbis. 118 out of 168 students from five classes were the sample of this research by using the random sampling technique, where the Slovin formula was used to determine the students’ representation from each class. The data were gathered by utilizing questionnaires, interview, and document. The results of the analysis showed that: first, there was a simultaneous linkage or relationship between learningindependence, learningcreativity, and Englishachievement. It was proved by the value of probability from eithermultiple correlation or Pearson product moment correlation (0.000) was smaller than the level of significance (0.05). Second, learning independence and learning creativity simultaneously had a positive effect towards English achievement, in which the value of probability was smaller than the level of significance (0.000 0.05). However, there were differences in the direction of effect among the variables, where learning independence had a positive effect towards English achievement in which the value of probability was smaller than the level of significance (0.000 0.05), while learning creativity had an inconstant effect towards English achievement in which the value of probability was greater than the level of significance (0.141 0.05). The result of the determination coefficient was 30.50%, which means that learning independence and learning creativity during the covid-19 pandemic affected students’ English learning achievement by 30.50%. Other factors which influenced 69.50% were not investigated in this present study. One of these factors was the lack of online learning facilities such as unstable internet connection and internet data package.

Simple sequence repeat (SSR) markers have been proved to be a very powerful tool for quantitative trait locus (QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a high-density SSR genetic linkage map is still lacking because there are only a few SSR markers available in sweet potato. In this study, a total of 2545 simple sequence repeat (SSR) primer pairs, including 1215 genomic SSR (gSSR) primer pairs and 1330 BES-SSR (bSSR) primer pairs designed from the genome sequence and BAC-end sequence of sweet potato, respectively, were screened with sweet potato cultivars Luoxushu 8 and Zhengshu 20 and their randomly sampled two F1 individuals and 571 of them generated polymorphic bands. The selected 571 polymorphic SSR primer pairs and 35 EST-based SSR (eSSR) primer pairs developed at our laboratory were used to genotype 240 F1 individuals derived from a cross between Luoxushu 8 and Zhengshu 20. A double pseudo-test-cross strategy was applied for linkage analysis. The Luoxushu 8 map included 90 linkage groups with 5057 SSR markers and covered 13,299.9 cM with a marker density of 2.6 cM, and the Zhengshu 20 map contained 90 linkage groups with 3009 SSR markers and covered 11,122.9 cM with a marker density of 3.7 cM. Fifteen homologous groups were identified in both parent maps. These are the first SSR linkage maps consisting of the complete 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato, and are also the linkage maps with the highest SSR marker density reported to date. These results provide a basis for QTL mapping, marker-assisted breeding and comparative genomics research of sweet potato.

PURPOSE Non–small-cell lung cancer (NSCLC) is the most common type of lung cancer and accounts for 80%-90% of the cases. In Brazil, between 2018 and 2019, lung cancer was ranked as the second most frequent cancer among men and the fourth among women. The primary objectives were to describe the journey and survival rates of patients with advanced NSCLC treated in the Brazilian private health care system (HCS). MATERIALS AND METHODS A retrospective cohort study was based on the search in administrative databases to analyze the Brazilian private HCS. Patients with advanced NSCLC diagnosed between 2011 and 2016 were included. The data on demographics, cancer-related information, treatment-related information, and resources used were collected. Survival analyses were performed using the semiparametric Kaplan-Meier method to assess mortality by NSCLC stage, with NSCLC diagnosis as the index date. RESULTS A total of 5,016 patients were included. Most patients were between 60 and 69 years old (33.6%) and had completed elementary school (52.2%). There was a greater proportion of men (58.1% v 41.9%), and the majority of patients had stage IV NSCLC (67%). It took an average of 31 days, from the first consultation, to have diagnosis. In 44% of the cases, a clinical oncologist was the first specialist in the HCS that the patient was referred to. After the diagnosis, the median time to start of treatment was 35 days. Chemotherapy alone was the most common treatment regimen (32%). The median overall survival was 11.5 months and 6 months for stage II and IV NSCLC, respectively. CONCLUSION This study provides contemporary data on stage III and IV NSCLC in private health care in Brazil, which has shown a high rate of metastatic disease diagnoses, high health care–related costs, and low survival rates.

BackgroundSince the novel coronavirus SARS-COV-2 was first identified to be circulating in the US on January 20, 2020, some of the worst outbreaks have occurred within state and federal prisons. The vulnerability of inmate populations, and the additional threats posed to the health of prison staff and the people they contact in surrounding communities underline the need to better understand the dynamics of transmission in the inter-linked inmate/staff/community sub-populations to better inform optimal control of SARS-COV-2.MethodsWe examined SARS-CoV-2 case data from 101 non-administrative federal prisons between 5/18/2020 to 01/31/2021 and examined the per capita size of outbreaks in staff and inmates compared to outbreaks in the communities in the counties surrounding the prisons during the summer and winter waves of the SARS-COV-2 pandemic. We also examined the impact of decarceration, comparing inmate, staff and community SARS-COV-2 outbreak sizes during the winter wave to the summer wave.ResultsFor both the summer and winter waves we found significant inter-correlations between per capita rates in the outbreaks among inmates, staff, and the community.Over-all during the pandemic, per capita rates were significantly higher in inmates than in both the staff and community (paired Student’s t-test p=0.03 and pConclusionsWe found significant evidence of community/staff/inmate inter-linkage of SARS-COV-2 transmission. Decarceration ameliorates both prison and community SARS-COV-2 per capita rates. Further study is warranted to determine which control measures aimed at inmates and/or staff are most efficacious at preventing or controlling outbreaks.

Objective Reducing suicidal behavior among patients in the healthcare system requires accurate and explainable predictive models of suicide risk across diverse healthcare settings. Materials and Methods We proposed a general targeted fusion learning framework that can be used to build a tailored risk prediction model for any specific healthcare setting, drawing on information fusion from a separate more comprehensive dataset with indirect sample linkage through patient similarities. As a proof of concept, we predicted suicide-related hospitalizations for pediatric patients in a limited statewide Hospital Inpatient Discharge Dataset (HIDD) fused with a more comprehensive medical All-Payer Claims Database (APCD) from Connecticut. Results We built a suicide risk prediction model for the source data (APCD) and calculated patient risk scores. Patient similarity scores between patients in the source and target (HIDD) datasets using their demographic characteristics and diagnosis codes were assessed. A fused risk score was generated for each patient in the target dataset using our proposed targeted fusion framework. With this model, the averaged sensitivities at 90% and 95% specificity improved by 67% and 171%, and the positive predictive values for the combined fusion model improved 64% and 135% compared to the conventional model. Discussion and Conclusions We proposed a general targeted fusion learning framework that can be used to build a tailored predictive model for any specific healthcare setting. Results from this study suggest we can improve the performance of predictive models in specific target settings without complete integration of the raw records from external data sources.

According to WHO goals, the elimination of Hepatitis C Virus (HCV) by 2030 requires enhancing and simplifying HCV testing. Our aim was to create a model to assess and compare different strategies for HCV testing, linkage to care and treatment among people who access harm reduction centres (HRC) and Addiction Centres in Catalonia. A decision tree model was designed to evaluate two strategies: Hepatitis C Point-of-care (POC) "test and treat", at the community versus standard-of-care (SOC), in which HCV testing was performed at community and therapy at the hospital. Both strategies were assessed separately in HRCs (6,878 users) and Addiction Centres (13,778 users). with a time horizon of 18 months. Healthcare outcomes were HCV testing, linkage to care, treatment outcomes and reinfection rate. HCV testing was performed in 3,178 (46%) of the HRC users. Compared with SOC, POC increased access to treatment by 57% (63% vs. 6%). SVR rates were 64% in POC vs. 23% in SOC. Reinfection rates were 21% with POC compared to 24% with SOC. With POC, losses to follow-up were reduced by 41%. In the Addiction Centres, 12,566 users (91%) were screened using the two strategies. Compared to the SOC, POC increased access to treatment and linkage to care by 19% along with SVR at the same rate. Reinfection rates decreased by 6%. Thus, the implementation of a POC "test and treat" strategy at HRCs and Addiction Centres has shown to be an effective public health strategy to help eliminating HCV in accordance with WHO goal.

BackgroundNon-interventional large-scale research on real-world patients who had a stroke requires the use of multiple data sources ensuring access to longitudinal data from large populations with clinically-detailed information. We sought to establish a framework for longitudinal research on patients hospitalised with stroke by linking information-rich, deidentified inpatient data from the Paul Coverdell National Acute Stroke Program (PCNASP) to commercial and Medicare Advantage longitudinal claims data.MethodsAll stroke admissions in PCNASP between 2008 and 2015 were evaluated for linkage to longitudinal claims from a commercial insurer using an algorithm based on six available common data fields (patient age, gender, admission date, discharge date, discharge diagnosis and state) and a hospital match. We evaluated the linkage quality (via the percentage of unique records in the linked dataset) and the representativeness of the linked population. We also described medical history, stroke severity and patterns of medication use among the PCNASP-claims linked cohort.ResultsThe linkage produced uniqueness equal to 99.1%. We identified 5644 linked and 98 896 unlinked patients who had an ischaemic stroke hospitalisation in claims data. Linked patients were younger than unlinked (69.7 vs 72.5 years), but otherwise similar by medical history, prestroke medication use or lab values. Stroke severity was mild and most patients were discharged home. Prestroke and discharge use of antihypertensive and statins in the PCNASP were greater than their use as measured by filled prescriptions in claims.ConclusionsHigh-quality linkage between the PCNASP and commercial claims data is feasible. This linkage identified differences between reported or recommended versus actual out-of-hospital medication utilisation, highlighting the importance of longitudinal data availability for research aimed to improve the care of patients who had a stroke.

Background: Childhood obesity has been growing steadily, at an earlier age, and currently comprises a public health issue. A number of studies have pointed to perinatal factors as possible determinants in the development of childhood obesity. Objective: To evaluate the influence of perinatal factors on the development of obesity in children and adolescents in southern Brazil. Design: Retrospective cohort study in which a linkage was made between anthropometric data of children and adolescents aged 0 to 15 years who had been registered in the Food and Nutrition Surveillance System (SISVAN) from 2008 to 2016 and their perinatal data registered in the Live Birth Information System (SINASC) from 2000 to 2014. The SINASC was used to extract maternal covariables (age, schooling, marital status), prenatal variables (parity and number of prenatal visits), and perinatal variables (type of delivery, sex, and birth weight). Variables such as age, inclusion in the Bolsa Família income transfer program, and the number of anthropometric evaluations were extracted from SISVAN. Results: The sample comprised 537 children and adolescents. The median age was 8 years (interquartile range: 2-11 years). The prevalence of obesity was 15.1%. Poisson regression revealed a higher risk of obesity in children born via cesarean delivery (relative risk [RR] = 1.48; 95% CI: 1.01-2.17), children of primiparous mothers (RR = 1.72; 95% CI: 1.16-2.53), girls (RR = 1.77; 95% CI:1.21-2.60), and those aged between 5 and 9 years (RR = 26.8; 95% CI: 3.75-191.55) and older than 10 years (RR = 20.74; 95% CI: 2.89-148.61). Conclusions: The linkage between SINASC and SISVAN allowed identification of prenatal and perinatal risk factors for the development of childhood obesity. These findings should contribute to the development of health promotion and prevention policies.

This investigation concentrates on the association of intergenerational value similarity and adult children’s and parents’ subjective well-being, on the linkage between relationship quality and subjective well-being. Mediation effects of the relationship quality on the associations between value similarity and subjective well-being were focused. The sample consisted of 600 adult German children (53.8% women) and their parents. Dyadic correlations were constructed to determine the value similarity. In this study, the general value orientation and the family values were objects of research. We measured the subjective well-being with the Satisfaction with Life Scale and we used the Network of Relationships Inventory (NRI) to measure the relationship quality. Associations between subjective well-being and value similarity, and between subjective well-being and relationship quality, as well as mediation effects, were found. All effects depend on gender and perspective.

Barriers to conducting standardized behavioral health screening within pediatric primary care settings include engaging youth and families, limited time available for this activity, and difficulties related to obtaining behavioral health consultation and treatment from specialists. Child and adolescent psychiatrists may assist pediatric primary care practices with engaging youth and families around screening by assisting with identifying rating scales that have good psychometric characteristics across multiple languages and are validated in diverse samples and available within the public domain. Additionally, they may partner with pediatric primary care professionals to assist with optimizing screening workflows and linkage to specialized services.

Introduction: Tajikistan is scaling up molecular diagnostic and digital technologies to strengthen its fight against drug-resistant TB (DR-TB). The study aimed to document national scale-up GeneXpert/GxAlert and Open MRS from 2012-2019 and compare time taken from TB diagnosis to treatment and quality of data recording before and after the introduction of GxAlert. Methodology: This was a longitudinal study that included a comparison of historical cohorts. Continuous variables were compared using Wilcoxon Rank-Sum test and categorical variables using the chi square test. Results: GeneXpert was introduced in 2011 and scaled up to 46 instruments in 43 (51%) diagnostic laboratories by May 2019. GxAlert was introduced in August 2018 and connected with all GeneXpert instruments by February 2019. Open MRS was introduced in 2014 and implemented in all 108 treatment centers by mid-2018. Time from diagnosis to treatment pre-GxAlert (range 0-749, median 3, days) was significantly longer than with GxAlert (range 0-273, median 3, days) (p 2 weeks was 16% (282/1740) pre-GxAlert and 11% (206/1902) with GxAlert (p < 0.001). Between 31%-34% of patients with DR-TB results in Open MRS did not have results available in GeneXpert/GxAlert systems. Where results were present in both systems, there were discrepancies in 8.2% of patients pre-GxAlert and 4.3% with GxAlert (p = 0.25). Conclusions: The scale-up of GeneXpert and digital technologies in Tajikistan was associated with a reduction in the proportion of patients with delays more than 2 weeks between diagnosis and treatment, but data quality recording improved only slightly.

Male sexual orientation is influenced by environmental and complex genetic factors. Childhood gender nonconformity (CGN) is one of the strongest correlates of homosexuality with substantial familiality. We studied brothers in families with two or more homosexual brothers (409 concordant sibling pairs in 384 families, as well as their heterosexual brothers), who self-recalled their CGN. To map loci for CGN, we conducted a genome-wide linkage scan (GWLS) using SNP genotypes. The strongest linkage peaks, each with significant or suggestive two-point LOD scores and multipoint LOD score support, were on chromosomes 5q31 (maximum two-point LOD = 4.45), 6q12 (maximum two-point LOD = 3.64), 7q33 (maximum two-point LOD = 3.09), and 8q24 (maximum two-point LOD = 3.67), with the latter not overlapping with previously reported strongest linkage region for male sexual orientation on pericentromeric chromosome 8. Family-based association analyses were used to identify associated variants in the linkage regions, with a cluster of SNPs (minimum association p = 1.3 × 10–8) found at the 5q31 linkage peak. Genome-wide, clusters of multiple SNPs in the 10–6 to 10–8p-value range were found at chromosomes 5p13, 5q31, 7q32, 8p22, and 10q23, highlighting glutamate-related genes. This is the first reported GWLS and genome-wide association study on CGN. Further increasing genetic knowledge about CGN and its relationships to male sexual orientation should help advance our understanding of the biology of these associated traits.

Let $(A,\mathfrak{m})$ be a Gorenstein local ring and let $M$, $N$ be two Cohen-Macaulay $A$-modules with $M$ linked to $N$ via a Gorenstein ideal $\mathfrak{q}$. Let $L$ be another finitely generated $A$-module. We show that $\mathrm{Ext}^i_A(L,M) = 0 $ for all $i \gg 0$ if and only if $\mathrm{Tor}^A_i(L,N) = 0$ for all $i \gg 0$. If $D$ is a Cohen-Macaulay module then we show that $\mathrm{Ext}^i_A(M, D) = 0 $ for all $i \gg 0$ if and only if $\mathrm{Ext}^i_A(D^\dagger , N) = 0$ for all $i \gg 0$, where $D^\dagger = \mathrm{Ext}^r_A(D,A)$ and $r = \mathrm{codim}(D)$. As a consequence we get that $\mathrm{Ext}^i_A(M, M) = 0 $ for all $i \gg 0$ if and only if $\mathrm{Ext}^i_A(N, N) = 0$ for all $i \gg 0$. We also show that $\mathrm{End}_A(M)/\mathrm{rad}\,\mathrm{End}_A(M) \cong (\mathrm{End}_A(N)/\mathrm{rad}\,\mathrm{End}_A(N))^{\mathrm{op}}$. We also give a negative answer to a question of Martsinkovsky and Strooker.

Background The SEARCH study provided community-based HIV and multi-disease testing and antiretroviral therapy (ART) to 32 communities in East Africa and reported no statistically significant difference in three-year HIV incidence. We used mathematical modelling to estimate the effect of control arm viral suppression and community mixing on SEARCH trial outcomes. Setting Uganda and Kenya. Methods Using the individual-based HIV modeling software EMOD-HIV, we configured a new model of SEARCH communities. The model was parameterized using demographic, HIV prevalence, male circumcision, and viral suppression data, and calibrated to HIV prevalence, ART coverage, and population size. Using assumptions about ART scale-up in the control arm, degree of community mixing, and effect of baseline testing, we estimated comparative HIV incidence under multiple scenarios. Results Prior to the trial results, we predicted that SEARCH would report a 4-40% reduction between arms, depending on control arm ART linkage rates and community mixing. With universal baseline testing followed by rapidly expanded ART eligibility and uptake, modelled effect sizes were smaller than the study was powered to detect. Using interim viral suppression data, we estimated three-year cumulative incidence would have been reduced by up to 27% in the control arm and 43% in the intervention arm compared to a counterfactual without universal baseline testing. Conclusions Our model suggests that the active control arm substantially reduced expected effect size and power of the SEARCH study. However, compared to a counterfactual "true control" without increased ART linkage due to baseline testing, SEARCH reduced HIV incidence by up to 43%.

BACKGROUND: Probabilistic linkage can link patients from different clinical databases without the need for personal information. If accurate linkage can be achieved, it would accelerate the use of linked datasets to address important clinical and public health questions. OBJECTIVE: We developed a step-by-step process for probabilistic linkage of national clinical and administrative datasets without personal information, and validated it against deterministic linkage using patient identifiers. STUDY DESIGN AND SETTING: We used electronic health records from the National Bowel Cancer Audit and Hospital Episode Statistics databases for 10,566 bowel cancer patients undergoing emergency surgery in the English National Health Service. RESULTS: Probabilistic linkage linked 81.4% of National Bowel Cancer Audit records to Hospital Episode Statistics, vs. 82.8% using deterministic linkage. No systematic differences were seen between patients that were and were not linked, and regression models for mortality and length of hospital stay according to patient and tumour characteristics were not sensitive to the linkage approach. CONCLUSION: Probabilistic linkage was successful in linking national clinical and administrative datasets for patients undergoing a major surgical procedure. It allows analysts outside highly secure data environments to undertake linkage while minimizing costs and delays, protecting data security, and maintaining linkage quality.

Objective: Studies examining posttraumatic growth (PTG) rely on surveys evaluating PTG in relation to prior traumatic experiences, resulting in psychometric problems due to the linkage of the depen...

Eastern filbert blight (EFB), caused by Anisogramma anomala, is a fungal disease threatening the european hazelnut (Corylus avellana) industry in the Willamette Valley of Oregon. The pathogen is endemic to the eastern United States where it causes little damage to the wild Corylus americana but causes severe cankers on most cultivars of the commercially important european hazelnut. The host genetic resistance in ‘Gasaway’ is conferred by a dominant allele at a single locus on linkage group 6 (LG6), and resistance from several other sources has been mapped to the same region. Some fungal isolates can overcome ‘Gasaway’ resistance, prompting a search for other sources of resistance. Resistance from other sources has been mapped to LG2 and LG7, for which additional simple sequence repeat (SSR) markers would facilitate marker-assisted selection (MAS). In this study, an in silico approach was used to develop new polymorphic SSR markers in the EFB resistance regions on LG2 and LG7. Starting with a search of 17 contigs of the ‘Jefferson’ genome sequence, 45 new polymorphic SSR markers were developed, characterized, and placed on the linkage map. The new SSR markers had an average of 10.18 alleles per locus, and average values for expected heterozygosity, observed heterozygosity, polymorphism information content, and frequency of null alleles of 0.72, 0.65, 0.68, and 0.068, respectively. Of the 42 new polymorphic SSRs segregating in the mapping population, 24 were on LG2, 12 were on LG7, and six were placed on other LGs. The new and previously developed SSR markers were used to study six new sources of EFB resistance, four from Russia and two from Crimea. Six resistant selections were crossed with susceptible selections, resulting in 7 progenies. Phenotyping for disease response revealed that segregation in progenies of the two Moscow selections (#2 and #27), one Russian selection (OSU 1187.101), and one Crimean selection (H3R12P62) fit the 1:1 segregation ratio expected for control of resistance by a dominant allele at a single locus; but in progenies of the other Russian selection (OSU 1166.123) and the other Crimean selection (H3R07P11), there was an excess of resistant seedlings. Correlation of disease scores and alleles at SSR loci indicated that resistance from three Russian selections (Moscow selections #2 and #27 and OSU 1166.123) and the Crimean selection H3R12P62 was on LG7, while resistance from Russian selection OSU 1187.101 was on LG2. Resistance from Crimean selection H3R07P11 was not correlated with markers on LG6, or LG2, or LG7. These sources and new SSR markers will be useful in MAS and the pyramiding of resistance genes in the breeding of new EFB-resistant cultivars.

Fredrik Nyberg,1 Stefan Franzén,1,2 Magnus Lindh,3,4 Lowie Vanfleteren,5,6 Niklas Hammar,7 Björn Wettermark,8 Johan Sundström,9,10 Ailiana Santosa,1 Staffan Björck,11 Magnus Gisslén3,12 1School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; 2National Diabetes Register, Centre of Registers Västra Götaland, Gothenburg, Sweden; 3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; 4Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden; 5COPD Center, Department of Respiratory Medicine and Allergology, Sahlgrenska University Hospital, Gothenburg, Sweden; 6Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; 7Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden; 8Pharmacoepidemiology & Social Pharmacy, Department of Pharmacy, Uppsala University, Uppsala, Sweden; 9Clinical Epidemiology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden; 10The George Institute for Global Health, University of New South Wales, Sydney, Australia; 11Centre of Registers Västra Götaland, Gothenburg, Sweden; 12Region Västra Götaland, Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, SwedenCorrespondence: Fredrik NybergSchool of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Box 463, Gothenburg, 405 30, SwedenTel +46 31 7866289; +46 76 6186289Email Fredrik.Nyberg.2@gu.seBackground: In response to the Covid-19 pandemic, we designed and initiated a nationwide linked multi-register, regularly updated, observational study for timely response to urgent scientific questions.Aim: To describe the SCIFI-PEARL (Swedish Covid-19 Investigation for Future Insights – a Population Epidemiology Approach using Register Linkage) linked database encompassing essentially all known diagnosed Swedish Covid-19 patients plus a large general population comparison cohort and outline its utility in the current and future phases of the pandemic.Methods: Individuals with Covid-19 from the entire country are identified on a regularly updated basis, from different sources: all individuals from SmiNet, the national database of notifiable diseases, with positive SARS-CoV-2 polymerase chain reaction (PCR) test results; patients identified in the healthcare system by condition (ICD-10) or procedure codes in the National Patient Register or Cause-of-Death Register; patients identified through several disease-specific national quality registers (NQRs); and in two regions additionally patients identified in primary care. A comparison population was obtained by stratified random sampling from Swedish national population registers. Data from all these registers plus the National Prescribed Drug Register, the Cancer Register, national sociodemographic registers, some additional NQRs, the National Vaccination Register, and further data sources, are then linked to all study subjects (Covid-19 cases and population cohort). New cases in the study population and all data for all subjects are updated every few months, as required.Conclusion and Utility: The SCIFI-PEARL study cohort captures Swedish residents with Covid-19 on an ongoing basis, includes a representative general population comparison cohort, and links to a broad range of national and regional healthcare data for a comprehensive longitudinal view of the Covid-19 pandemic. By combining high-quality national registers with short time delay and continuous repeated linkage and updating, the project brings timely and internationally relevant data for epidemiological research on SARS-CoV-2. Our efforts provide an example and important learnings for similar efforts internationally in the future.Keywords: SARS-CoV-2, population cohort, data updates, observational research, longitudinal

Broomrape (Orobanche cumana Wallr.) is one of the main biotic factors limiting high sunflower yield formation. The most effective and environmentally safe method of protection is cultivation of resistant varieties and hybrids of sunflower. Development of resistant sunflower genotypes includes search and usage of sources of resistance in breeding process as well as accurate and productive procedures of material assessment. The purpose of the research is to analyze a linkage of a gene Or7 with microsatellite loci of the line-donor of resistance to broomrape race G from the VNIIMK’s collection. The objects of the research are the line RGP1 – a donor of resistance to broomrape race G and a susceptible to this race line VR 678 from the VNIIMK’s collection. Sunflower plants were crossed in field to produce F1. Also we conducted self-pollination of F1 plants to obtain F2 progeny. Plants were tested in a greenhouse in soil infected with seeds of broomrape race G using a method of early diagnostic. Sunflower DNA was extracted from the top leaves of the young sprouts of the vegetative plants. For PCR-analysis we used three SSR-primers demonstrated polymorphism in parental lines: ORS 683, ORS 1040, and ORS 1112. We tested joint inheritance of the gene Or7 and these loci, and inheritance between SSR-loci. An independent inheritance of the gene Or7 with DNA-loci ORS 683, ORS 1040, and ORS 1112, as well as SSR-loci between ORS 1040 and ORS 1112, ORS 1040 and ORS 683 was showed. Loci ORS683 – ORS 1112 are linked with a frequency of recombination of 0.27 ± 0.41 (27 cM). As a result of our research location of the gene Or7 in the nearest area to microsatellite loci ORS 683, ORS 1040, and ORS 1112 was excluded. Basing on studied literary sources and a representative sunflower genome HanXRQr2.0-SUNRISE we made a partial physical map LG3 for determination of an area for the further search of a localization of the Or7 and DNAmarkers co-segregating with this gene.

Male sexual orientation is a scientifically and socially important trait shown by family and twin studies to be influenced by environmental and complex genetic factors. Individual genome-wide linkage studies (GWLS) have been conducted, but not jointly analyzed. Two main datasets account for > 90% of the published GWLS concordant sibling pairs on the trait and are jointly analyzed here: MGSOSO (Molecular Genetic Study of Sexual Orientation; 409 concordant sibling pairs in 384 families, Sanders et al. (2015)) and Hamer (155 concordant sibling pairs in 145 families, Mustanski et al. (2005)). We conducted multipoint linkage analyses with Merlin on the datasets separately since they were genotyped differently, integrated genetic marker positions, and combined the resultant LOD (logarithm of the odds) scores at each 1 cM grid position. We continue to find the strongest linkage support at pericentromeric chromosome 8 and chromosome Xq28. We also incorporated the remaining published GWLS dataset (on 55 families) by using meta-analytic approaches on published summary statistics. The meta-analysis has maximized the positional information from GWLS of currently available family resources and can help prioritize findings from genome-wide association studies (GWAS) and other approaches. Although increasing evidence highlights genetic contributions to male sexual orientation, our current understanding of contributory loci is still limited, consistent with the complexity of the trait. Further increasing genetic knowledge about male sexual orientation, especially via large GWAS, should help advance our understanding of the biology of this important trait. Supplementary Information The online version contains supplementary material available at 10.1007/s10508-021-02035-3.

Background: Growing evidence highlights the linkage between body image, eating, and exercise behaviors among adolescents. Objective: This study aims to determine the association between body image perception, nutritional status, and dietary and physical activity behaviors among adolescents in Indonesia. Methods: A cross-sectional household survey was conducted among a representative sample (n = 2160) of adolescent girls and boys aged 12 to 18 years in Klaten and Lombok Barat districts. The association between adolescents’ body image, their diets, and physical activity patterns was determined using complex samples Cox’s regression analysis. Separate multivariate models were developed for adolescent girls and boys. Results: Physical appearance was considered important to nearly all adolescents. Approximately 11% of girls and 14% of boys were overweight or obese, the majority of whom (∼70%) correctly perceived themselves as overweight or obese. More of overweight or obese adolescents felt unhappy about their perceived weight than their thin counterparts. With respect to the overweight/obese girls, the adolescents’ perceptions of being overweight or obese was associated with a 63% reduction in the prevalence of overweight/obese girls consuming fatty snacks, such as deep-fried crackers (adjusted prevalence ratio (PR): 0.37, 95% confidence interval (CI): 0.19-0.71) and a 40% reduction in the prevalence of overweight/obese girls engaging in moderate-intensity physical activity (adjusted PR: 0.60, 95% CI: 0.38-0.94), after adjusting for potential confounders. No association between body image and eating and physical activity behaviors was observed among adolescent boys. Conclusions: Body image may be one of the most important determinants of dietary and physical activity behaviors, and thus future efforts to foster healthy eating and physical activity behaviors among Indonesian adolescents need to address body image concerns.

Record linkage - i.e. the use and linkage of electronic, mainly administrative databases - has been utilizedin epidemiologic research for over three decades now, starting from the system implemented in a fewUS health maintenance organizations (HMO, i.e. the Kaiser Permanente network), a few Nordic countriessystems, or the UK general practice research database (UK GPRD, now clinical practice research datalink,CPRD) [1, 2]...

Psychological disturbance (PD) or cerebral dysfunction (CD) covers several clinical areas, and has defining features of mental retardation. Recently, we conducted a study to investigate heritable heterogeneity in Pakistani consanguineous couples with recessive autosomal intellectual abnormalities. A cohort of three consanguineous families with multiple birth defects, belonging two to district lower Dir and one to district Lodhra, were selected for molecular analysis. All the affected individuals in the cohort showed autosomal recessive non-syndromic mental disturbances. DNA was extracted and subjected to Single tagged sequence (STS) marker analyses to all known non-syndromic autosomal recessive mental retardation (NS-ARMR) genes, while autozygosity mapping was performed by advanced SNP techniques. Fragment analyses of the NS-ARMR disease genes CRBN, CC2D2A, PRSS12, GRIK2, TUSC3, and CC2D1A using polymorphic STS markers confirmed these to be contender genes for the alteration. Mapping of autozygosity in all the study subjects using genome study revealed nine novel linkage intervals, i.e. four intervals for MR4, two intervals for MR8 and three intervals for MR13. In spite of being a monogenic condition, autosomal recessive mental retardation shows genetic heterogeneity and several genes are involved in different families; hence, there is a chance for involvement of separate gene in each family.

In Lima, Perú, HIV prevalence is estimated to be 15% among men who have sex with men (MSM) and 30% among transgender women (TW). We investigated timely linkage of MSM and TW to HIV care, provided through a nationally funded program, as linkage to antiretroviral therapy (ART) is critical to protect the health of those living with HIV and to prevent onward transmission. We investigated linkage to care within 90 days of diagnosis among HIV-positive MSM and TW matching data from two studies conducted in Lima between 2013 and 2015 to national ART program records. Generalized linear modeling was used to assess predictors of timely linkage and late presentation to care based on viral load and CD4 count at first visit to an ART program clinic. Of 487 MSM and TW newly diagnosed with HIV infection, only 44% presented for care at an HIV clinic within 90 days. Timely linkage was less common among TW (aPR 0.7, 95% CI 0.5–1.0), those younger than 24 (aPR 0.8, 95% CI 0.6–1.0), and those reporting a history of sex work (aPR 0.7, 95% CI 0.6–0.9). Proximity to an ART program clinic was not associated with linkage; most participants linked to clinics offering ‘LGBTQ-friendly’ care. Timely linkage to care was low in these MSM and TW study participants, especially among youth and sex workers. The pattern of clinics selected by participants suggests the importance of concerns about confidentiality and stigma as determinants of decisions about where to link to care.

Objective: To determine the frequency of raised low density lipoproteins (LDL) in subjects with ischemic stroke (IS) in our local population. Study Design: Cross-sectional study. Setting: Medical Unit-III, Nishtar Medical College, Multan. Period: 12 March 2016 to 12 September 2016. Material & Methods: Eligibility criteria include subjects with age limit between 40-70 year of both sex surfing with ischemic stroke. Raised-LDL means serum fasting LDL level ≥ 100 mg/dl was deemed as raised LDL on two different reading 24 hours apart (both was raised). Results: Our study registered a total of 205 patients out of this 92 (44.9%) were male patients while 113 (55.1%) were female with ischemic stroke. Mean height and weight of our study cases was 159.94 ± 11.21 and 68.43 ± 6.33 respectively. Mean BMI was noted to be 23.17± 2.85 kg/m2. Mean LDL level noted in our study was 109.59 ± 49.15 mg/dl and raised level of LDL was seen in 88 (42.9%) of our study cases. Raised level of LDL was observed significant in gender, diabetes, obesity, hypertension, family history and previous history of stoke. Conclusion: Very high frequency of raised serum LDL levels was noted in our study. Raised LDL were positively linked with male gender, hypertension, family history of stroke, diabetes, obesity and past event of stroke. Our study determines the initial diagnosis of stoke that eventually lead to suitable management to enhance clinical result in such subjects.

Purpose The linkage between patient-reported data and medico-administrative claims is of great interest for epidemiologic research. The goal of this study was to assess the willingness of people living with chronic pain to share personal identifiers on the web for the linkage of medico-administrative and patient-reported data. Methods This methodological investigation was achieved in the context of the implementation of the COPE Cohort. A web-based recruitment initiative targeting adults living with chronic pain was conducted in the province of Quebec (Canada). Results A total of 1935 participants completed the questionnaire (mean age: 49.86 ± 13.27; females: 83.69%), 921 (47.60%) of which agreed to data linkage and shared their personal identifiers (name, date of birth, health insurance number) online. The most common reasons for refusal were: concerns regarding data security/privacy (25.71%), and the belief that the requested data were too personal/intrusive (13.52%). Some participants did not understand the relevance of data linkage (11.81%). Participants from the COPE Cohort and those from the subsample who agreed to data linkage were comparable to other random samples of chronic pain individuals in terms of age and pain characteristics. Conclusions Although approximately half of the participants refused data linkage, our approach allowed for the implementation of a data platform that contains a diverse and substantial sample. This investigation has also led to the formulation of recommendations for web-based data linkage, including placing items designed to assess willingness to share personal identifiers at the end of the questionnaire, adding explanatory videos, and using a mixed-mode questionnaire. This article is protected by copyright. All rights reserved.

BACKGROUND Early antiretroviral therapy (ART) is necessary for HIV epidemic control and depends on early diagnosis and successful linkage to care. Since 2014, annual household-based HIV testing and counseling and linkage services have been provided through the Chokwe Health and Demographic Surveillance System for residents testing HIV positive in this high HIV-burden district. METHODS District-wide Test and Start [T&S, ART for all people living with HIV (PLHIV)] began in August 2016, supported by systematic interventions to improve linkage to care and treatment. Annual rounds (R) of random household surveys were conducted to assess trends in population prevalence of ART use and viral load suppression (

Haplotype-based variant callers, which consider physical linkage between variant sites, are currently among the best tools for germline variation discovery and genotyping from short-read sequencing data. However, almost all such tools were designed specifically for detecting common germline variation in diploid populations, and give sub-optimal results in other scenarios. Here we present Octopus, a versatile haplotype-based variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. We show that Octopus accurately calls de novo mutations in parent-offspring trios and germline variants in individuals, including SNVs, indels, and small complex replacements such as microinversions. In addition, using a carefully designed synthetic-tumour data set derived from clean sequencing data from a sample with known germline haplotypes, and observed mutations in large cohort of tumour samples, we show that Octopus accurately characterizes germline and somatic variation in tumours, both with and without a paired normal sample. Sequencing reads and prior information are combined to phase called genotypes of arbitrary ploidy, including those with somatic mutations. Octopus also outputs realigned evidence BAMs to aid validation and interpretation.

Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.

Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00619-0.

To identify risk factors associated with severe COVID-19 infection in a defined Midwestern US population overall and within different age groups.We used the Rochester Epidemiology Project research infrastructure to identify persons residing in a defined 27-county Midwestern region who had positive results on polymerase chain reaction tests for COVID-19 between March 1, 2020, and September 30, 2020 (N=9928). Age, sex, race, ethnicity, body mass index, smoking status, and 44 chronic disease categories were considered as possible risk factors for severe infection. Severe infection was defined as hospitalization or death caused by COVID-19. Associations between risk factors and severe infection were estimated using Cox proportional hazard models overall and within 3 age groups (0 to 44, 45 to 64, and 65+ years).Overall, 474 (4.8%) persons developed severe COVID-19 infection. Older age, male sex, non-White race, Hispanic ethnicity, obesity, and a higher number of chronic conditions were associated with increased risk of severe infection. After adjustment, 36 chronic disease categories were significantly associated with severe infection. The risk of severe infection varied significantly across age groups. In particular, persons 0 to 44 years of age with cancer, chronic neurologic disorders, hematologic disorders, ischemic heart disease, and other endocrine disorders had a greater than 3-fold increased risk of severe infection compared with persons of the same age without those conditions. Associations were attenuated in older age groups.Older persons are more likely to experience severe infections; however, severe cases occur in younger persons as well. Our data provide insight regarding younger persons at especially high risk of severe COVID-19 infection.

Using the CRISPR-Cas system, it has been possible to introduce different kinds of mutations in single or multiple genes for trait improvement in crops. Last year, for the first time, the CRISPR-Cas-mediated induction of different kinds of targeted heritable chromosomal rearrangements has been achieved in plants. This novel application has the potential to revolutionize plant breeding as genetic exchange and linkage drag are now becoming controllable in a targeted manner.

We explore trends in linkage to HIV care following diagnosis and investigate the impact of diagnosis setting on linkage in the era of expanded testing.All adults (aged ≥ 15 years) diagnosed with HIV between 2005 and 2014 in England, Wales and Northern Ireland (EWNI) were followed up until the end of 2017. People who died within 1 month of diagnosis were excluded (n = 1009). Trends in linkage to outpatient care (time to first CD4 count) were examined by sub-population and diagnosis setting. Logistic regression identified predictors of delayed linkage of 1 month, 3 months and 1 year post-diagnosis (2012-2014).Overall, 97% (60 250/62 079) of people linked to care; linkage ≤ 1 month was 75% (44 291/59 312), ≤ 3 months was 88% (52 460) and ≤ 1 year was 95% (56 319). Median time to link declined from 15 days [interquartile range (IQR): 4-43] in 2005 to 6 (IQR: 0-20) days in 2014 (similar across sub-populations/diagnosis settings). In multivariable analysis, delayed linkage to care was associated with acquiring HIV through injecting drug use, heterosexual contact or other routes compared with sex between men ( 1 month/3 months/1 year), being diagnosed in earlier years ( 1 month/3 months/1 year) and having a first CD4 ≥ 200 cells/μL ( 3 months/1 year). Diagnosis outside of sexual health clinics, antenatal services and infectious disease units predicted delays of 1 month. By 3 months, only diagnosis in 'other' settings (prisons, drug services, community and other medical settings) was significant.Linkage to care following HIV diagnosis is relatively timely in EWNI. However, non-traditional testing venues should have well-defined referral pathways established to facilitate access to care and treatment.

The complexity of sweetpotato genome, including hexaploidy and heterozygosity, has hindered genetic studies on agronomically important traits such as storage root formation and thickening. Ipomoea trifida (H. B. K.) G. Don. (2n = 2x = 30) is closely related to and cross-compatible with sweetpotato. The diploid I. trifida has been developed as a model plant for sweetpotato genetic research, due to its low ploidy and simple genetic background. In order to reveal the molecular mechanisms underlying storage root development in sweetpotato, F1 mapping population derived from diploid I. trifida was screened for root diameter by genotyping-by-sequencing method. A total of 11,555 raw polymorphic SNPs were identified, in which 8454 SNPs can be used in this F1 population. The SNP genotyping data was utilized to construct the genetic linkage map of I. trifida. The maternal and paternal linkage maps were produced, and 904 maternal and 2034 paternal markers resulted in 13 and 15 LGs respectively. The total length of the maternal maps covered 842.34 cM, while the paternal maps spanned 1540.98 cM. The integrated genetic map consisted of 2892 SNPs (average of 193 markers/linkage group) on 15 linkage groups (LGs) covering 1550.22 cM of the whole genome at an average inter marker distance of 0.55 cM. By using the phenotypic data obtained in this study, three significant QTL were detected for root diameter. These QTL were distributed among three LGs at three independent positions, and each QTL explained significant amount of phenotypic trait variation ranged from 6.1 to 12.0%. The qRD-2 QTL explained 12.0% of the phenotypic variation. This study results will assist in the map-based cloning of genes controlling storage root-related traits and further helps to reveal the genetic basis of root development in sweetpotato.

Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.

Coupled with the reduction in sequencing costs, the number of RAD-seq analysis have been surging, generating vast genetic knowledge in relation with many crops. Specialized platforms might be intimidating to non-expert users and difficult to implement on each computer despite the growing interest in the usage of the dataset obtained by high-throughput sequencing. Therefore, RAD-R scripts were developed on Windows10 for RAD-seq analysis, allowing users who are not familiar with bioinformatics to easily analyze big sequence data. These RAD-R scripts that run a flow from raw sequence reads of F2 population for the self-fertilization plants to the linkage map construction as well as the QTL analysis can be also useful to many users with limited experience due to the simplicity of copying Excel cells into the R console. During the comparison of linkage maps constructed by RAD-R scripts and Stacks, RAD-R scripts were shown to construct the linkage map with less missing genotype data and a shorter total genetic distance. QTL analysis results can be easily obtained by selecting the reliable genotype data that is visually inferred to be appropriate for error correction from the genotype data files created by RAD-R scripts.

Precision medicine, a popular treatment strategy, has become increasingly important to the development of targeted therapy. To correlate medical imaging with prognostic and genomic data, researches in radiomics and radiogenomics have provided many pre-defined image features to describe image information quantitatively or qualitatively. However, in previous researches, there are only statistical results which prove high correlation among multi-source medical data, but those can’t give intuitive and visual result. In this paper, a deep learning based radiogenomic framework is provided to construct the linkage from lung tumor images to genomic data and implement generation process in turn, which form a bi-direction framework to map multi-source medical data. The imaging features are extracted from autoencoder under the condition of genomic data. It can obtain much more relevant features than traditional radiogenomic methods. Finally, we use generative adversarial network to transform genomic data onto tumor images, which gives a cogent result to explain the linkage between them. As a result, our framework provides a deep learning method to do radiogenomic researches more functionally and intuitively.

Achieving the UNAIDS 90-90-90 targets by 2020 is contingent on identifying and addressing mental health challenges that may affect HIV testing and treatment-related behaviors. This study is based on survey data from KwaZulu-Natal, South Africa (2014–2015). HIV positive women who reported higher depression scores had a lower odds of having tested previously for HIV (15–25 years: AOR = 0.90, 95% CI [0.83, 0.98]; 26–49 years: AOR = 0.90, 95% CI [0.84, 0.96]). Because HIV testing behavior represents a gateway to treatment, the findings suggest mental health may be one challenge to attaining the UNAIDS 90-90-90 targets.

Background Low socioeconomic position (SEP) is related to higher healthcare use in out-of-hours primary care services (OPCSs). We aimed to determine whether inequalities persist when taking the generally poorer health status of socioeconomically vulnerable individuals into account. To put OPCS use in perspective, this was compared with healthcare use in daytime general practice (DGP). Methods Electronic health record (EHR) data of 988 040 patients in 2017 (251 DGPs, 27 OPCSs) from Nivel Primary Care Database were linked to socio-demographic data (Statistics, The Netherlands). We analyzed associations of OPCS and DGP use with SEP (operationalized as patient household income) using multilevel logistic regression. We controlled for demographic characteristics and the presence of chronic diseases. We additionally stratified for chronic disease groups. Results An income gradient was observed for OPCS use, with higher probabilities within each lower income group [lowest income, reference highest income group: odds ratio (OR) = 1.48, 95% confidence interval (CI): 1.45–1.51]. Income inequalities in DGP use were considerably smaller (lowest income: OR = 1.17, 95% CI: 1.15–1.19). Inequalities in OPCS were more substantial among patients with chronic diseases (e.g. cardiovascular disease lowest income: OR = 1.60, 95% CI: 1.53–1.67). The inequalities in DGP use among patients with chronic diseases were similar to the inequalities in the total population. Conclusions Higher OPCS use suggests that chronically ill patients with lower income had additional healthcare needs that have not been met elsewhere. Our findings fuel the debate how to facilitate adequate primary healthcare in DGP and prevent vulnerable patients from OPCS use.

PCORnet, the Patient-Centered Outcomes Research Network, is comprised of health systems and health plans that transform electronic health records (EHRs) and claims data to a common data model (CDM) to facilitate real-world clinical research. Because patients receive health care in multiple care delivery settings, linking health records across systems and health plan claims would provide a more comprehensive and accurate picture of health care for patients. The current study expanded on a PCORnet Antibiotics and Childhood Growth (ABX) study to (1) identify and implement a privacy-preserving patient linkage solution among a clinical data research network and a health plan network within the ABX Study, and (2) assess overlap in prescribed and dispensed antibiotics and additional data gained from claims among the linked patients. This manuscript describes the linkage process and resulting overlap analysis. The authors identified 549 patients from the EHR record study cohort who had claims records with the health plan. Sixty percent (n = 329) of patients had consistent antibiotic exposure data across the 2 sources, indicating antibiotic exposure (44.3%) or nonexposure (15.7%). Among total antibiotic prescribing records, 43.1% had a matched claims record for dispensing within 60 days. Among antibiotic dispense records 26.5% were not associated with a prescribing record in the linked health systems. These findings showcase the feasibility of linking health plan claims data to PCORnet CDM in a privacy-preserving manner while also demonstrating continued gaps in data that may occur. The study highlights the importance of combining multiple health data sources for comprehensive clinical research.

X-chromosomal STRs are a powerful tool to assess a broad variety of complex kinship scenarios. We introduce herewith the first Swiss X-STR dataset based on 1198 individuals (592 female, 606 male), characterized with the Qiagen Investigator® Argus X-12 QS multiplex kit. Anomalous allele patterns, allele and haplotype frequencies, and forensic and population genetic parameters are presented. We detected linkage disequilibrium within three out of the four designated linkage groups and no apparent intra-national population substructure. We compared the dataset to a global panel of X-STR datasets and it fits well in the European context, as expected.