Establishing a colorectal cancer research database from routinely collected health data: the process and potential from a pilot study.

OBJECTIVE: Colorectal cancer is a common cause of death and morbidity. A significant amount of data are routinely collected during patient treatment, but they are not generally available for research. The National Institute for Health Research Health Informatics Collaborative in the UK is developing infrastructure to enable routinely collected data to be used for collaborative, cross-centre research. This paper presents an overview of the process for collating colorectal cancer data and explores the potential of using this data source. METHODS: Clinical data were collected from three pilot Trusts, standardised and collated. Not all data were collected in a readily extractable format for research. Natural language processing (NLP) was used to extract relevant information from pseudonymised imaging and histopathology reports. Combining data from many sources allowed reconstruction of longitudinal histories for each patient that could be presented graphically. RESULTS: Three pilot Trusts submitted data, covering 12 903 patients with a diagnosis of colorectal cancer since 2012, with NLP implemented for 4150 patients. Timelines showing individual patient longitudinal history can be grouped into common treatment patterns, visually presenting clusters and outliers for analysis. Difficulties and gaps in data sources have been identified and addressed. DISCUSSION: Algorithms for analysing routinely collected data from a wide range of sites and sources have been developed and refined to provide a rich data set that will be used to better understand the natural history, treatment variation and optimal management of colorectal cancer. CONCLUSION: The data set has great potential to facilitate research into colorectal cancer

sox9b Is a Key Regulator of Pancreaticobiliary Ductal System Development

The pancreaticobiliary ductal system connects the liver and pancreas to the intestine. It is composed of the hepatopancreatic ductal (HPD) system as well as the intrahepatic biliary ducts and the intrapancreatic ducts. Despite its physiological importance, the development of the pancreaticobiliary ductal system remains poorly understood. The SRY-related transcription factor SOX9 is expressed in the mammalian pancreaticobiliary ductal system, but the perinatal lethality of Sox9 heterozygous mice makes loss-of-function analyses challenging. We turned to the zebrafish to assess the role of SOX9 in pancreaticobiliary ductal system development. We first show that zebrafish sox9b recapitulates the expression pattern of mouse Sox9 in the pancreaticobiliary ductal system and use a nonsense allele of sox9b, sox9bfh313, to dissect its function in the morphogenesis of this structure. Strikingly, sox9bfh313 homozygous mutants survive to adulthood and exhibit cholestasis associated with hepatic and pancreatic duct proliferation, cyst formation, and fibrosis. Analysis of sox9bfh313 mutant embryos and larvae reveals that the HPD cells appear to mis-differentiate towards hepatic and/or pancreatic fates, resulting in a dysmorphic structure. The intrahepatic biliary cells are specified but fail to assemble into a functional network. Similarly, intrapancreatic duct formation is severely impaired in sox9bfh313 mutants, while the embryonic endocrine and acinar compartments appear unaffected. The defects in the intrahepatic and intrapancreatic ducts of sox9bfh313 mutants worsen during larval and juvenile stages, prompting the adult phenotype. We further show that Sox9b interacts with Notch signaling to regulate intrahepatic biliary network formation: sox9b expression is positively regulated by Notch signaling, while Sox9b function is required to maintain Notch signaling in the intrahepatic biliary cells. Together, these data reveal key roles for SOX9 in the morphogenesis of the pancreaticobiliary ductal system, and they cast human Sox9 as a candidate gene for pancreaticobiliary duct malformation-related pathologies

Contraceptive use among HIV-infected women and men receiving antiretroviral therapy in Lusaka, Zambia: a cross-sectional survey

Abstract Background Family planning (FP) is an essential health service and an important part of comprehensive HIV care. However, there is limited information about the contraceptive needs of people living with HIV in sub-Saharan Africa, which in turn has hampered efforts to expand and integrate FP services into existing HIV programs. Methods We performed a cross-sectional survey to determine FP prevalence and predictors among HIV-positive women and men attending 18 public antiretroviral therapy (ART) clinics in Lusaka, Zambia. Trained peer counselors administered the 10-question survey to those seeking care for five days at each of the target sites. Results From February to April 2014, we surveyed 7,046 HIV-infected patients receiving routine HIV services. Use of modern contraception was reported by 69 % of female ART patients and 79 % of male ART patients. However, highly effective contraceptive use and dual method use were low among women (38 and 25 %, respectively) and men (19 and 14 %, respectively). HIV disclosure status (adjusted odds ratio (AOR) = 4.91, 95 % confidence interval (CI) = 3.32–7.24 for women, AOR = 3.58, 95 % CI = 2.39–5.38 for men) and sexual activity in the last 6 months (AOR = 5.80, 95 % CI = 4.51–7.47 for women, AOR = 6.24, 95 % CI = 3.51–11.08 for men) were associated with modern contraceptive use in multivariable regression. Most respondents said they would access FP services if made available within ART clinic. Conclusions While FP-ART integration may be a promising strategy for increasing FP service uptake, such services must focus on assessing sexual activity and advocating for dual method use to increase effective contraceptive use and prevent unintended pregnancies

<i>sox9b</i> mutants display defective HPD patterning during organ development.

<p>(A–B) Labeling for the hepatocyte marker <i>Tg(fabp10:</i>ras-GFP) (green) and the HPD marker 2F11 (red) in wild-type and <i>sox9b</i> mutant embryos at 50 hpf. 2F11 labeling in the HPD primordium is noticeably reduced in <i>sox9b</i> mutants. (A′–B′) Same views as (A–B), but only showing the 2F11 immunostaining. (C–D) In wild-type, Prox1 expression marks the liver and pancreas and is largely absent from the HPD primordium (C). In contrast, Prox1 is abnormally expressed in the HPD primordium in <i>sox9b</i> mutants (D). (A′–B′, C–D) Brackets mark the HPD primordium. (E) By 80 hpf, different compartments of the HPD system, including the cystic duct (CD), common bile duct (CBD), gallbladder (GB), extrahepatic duct (EHD) have become evident in wild-type. (F) In <i>sox9b</i> mutants, the HPD system is dysmorphic and its compartments are indistinguishable based on morphology. The gallbladder is also often missing. (E′–F′) Same views as (E–F), but only showing 2F11 immunostaining. (G–H) Whole-mount <i>in situ</i> hybridization showing <i>sox17</i> expression in the gallbladder primordium in wild-type and <i>sox9b</i> mutants at 52 (G) and 72 (H) hpf. <i>sox17</i> expression is greatly reduced or absent in <i>sox9b</i> mutants. The proportion of mutants showing the corresponding phenotype is indicated. Arrows point to the gallbladder primordium. (A–F, A′–F′) All images are projections of confocal z-stacks. Ventral views. (G–H) Dorsal views. Anterior (A) to the top. Pa, pancreas; Li, liver; EPD, extrapancreatic duct. Scale bars, 20 µm.</p

The pattern of Notch signaling activity is altered in <i>sox9b</i> mutants.

<p>(A–F) Expression of <i>Tg(Tp1bglob</i>:H2B-mCherry) (red), 2F11 (blue), and <i>Tg(Tp1bglob:</i>VenusPest) (green) in wild-type (A–C) and <i>sox9b</i> mutant (D–F) larvae at 75 (A, D), 99 (B, E), and 123 hpf (C, F). At each time point, 6 larvae of each genotype were analyzed. (A′–F′) Diagrams showing the distribution of <i>Tg(Tp1bglob:</i>H2B-mCherry);<i>Tg(Tp1bglob:</i>VenusPest)-double positive cells (yellow) and <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells (red) in (A–F). Livers are outlined by solid white line. In wild-type livers, expression of <i>Tg(Tp1bglob:</i>H2B-mCherry) and <i>Tg(Tp1bglob:</i>VenusPest) largely overlaps at 75 hpf (A, A′). At 99 and 123 hpf (B–B′, C–C′), a few <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells (arrows) appear along the intrahepatic duct that connects to the extrahepatic system. In <i>sox9b</i> mutants, <i>Tg(Tp1bglob:</i>H2B-mCherry);<i>Tg(Tp1bglob:</i>VenusPest)-double positive cells and <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells show similar distribution as in wild-type at 75 and 99 hpf (D–D′, E–E′). However, at 123 hpf (F, F′), we observed big clusters of <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells in the mutant livers (arrows). (G) Percentages (average±SEM) of <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells relative to the total number of <i>Tg(Tp1bglob:</i>H2B-mCherry)-expressing cells. Whereas wild-type and <i>sox9b</i> heterozygous livers contained similar percentages of <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells at all stages examined (p>0.4), this percentage was significantly higher in <i>sox9b</i> mutants at 123 hpf (p<0.0005). (H) Percentages (average±SEM) of <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells or <i>Tg(Tp1bglob:</i>H2B-mCherry);<i>Tg(Tp1bglob:</i>VenusPest)-double positive cells that were labeled by EdU. EdU incubation was conducted from 96 to 120 hpf or from 120 to 148 hpf. Under both conditions, the hepatic Notch responsive cells in <i>sox9b</i> mutants showed higher EdU incorporation compared to wild-type, and the difference was more pronounced for <i>Tg(Tp1bglob:</i>H2B-mCherry)-single positive cells. 7 wild-types and 7 <i>sox9b</i> mutants were examined for each experimental condition. Asterisks indicate statistical significance: *, p<0.05. (A–F) All images are projections of confocal z-stacks. Ventral views, anterior (A) to the top. Scale bar, 20 µm.</p

<i>sox9b</i> is expressed in the pancreaticobiliary ductal system, and the <i>sox9b^fh313</i> lesion is a nonsense mutation.

<p>(A–D) <i>sox9b</i> expression is observed in the head and fin buds (arrowheads in A–C), as well as the notochord (n) and part of the foregut endoderm (bracket) at 30 hpf (A). At 48 hpf, <i>sox9b</i> expression is observed in the liver bud (arrow) and hepatopancreatic duct primordium (bracket) (B). At 60 hpf, <i>sox9b</i> expression covers the intra- (arrow) and extrahepatic (bracket) ducts (C), and extends to the intrapancreatic ducts by 72 hpf (white arrow, D). Dorsal views, anterior (A) to the left. (E) Genomic DNA sequence of wild-type (left panel) and <i>sox9b^fh313</i> mutant (right panel) showing an A>T transversion at position 302 of the coding sequence. This mutation leads to a stop codon at amino acid Lys68. (F) Schema of Sox9b depicting the localization of the amino acid affected by the <i>fh313</i> mutation leading to a stop codon upstream of the HMG box DNA-binding domain. IPD, intrapancreatic duct; IHD, intrahepatic duct; HPD, hepatopancreatic duct; HMG, high-mobility group; aa, amino acid.</p

Intrahepatic biliary network morphogenesis and bile canaliculi formation are impaired in <i>sox9b</i> mutants.

<p>(A–B) Distribution of hepatocytes and biliary cells in 96 hpf wild-type and <i>sox9b</i> mutant larvae as revealed by Prox1 (red) and <i>Tg(Tp1bglob:</i>GFP) (green) expression. In wild-type, the cell bodies of biliary cells are separated from one another and interconnected via cellular processes (A). In <i>sox9b</i> mutants, the biliary cells are clustered together (B). Dashed lines mark the long bile ducts and arrows in (A) point to the short interconnecting ducts that are missing in the mutants. (C) Percentage (average±SEM) of biliary cells that exist as single cells, doubles, triples, or clusters of four or more at 96 hpf. 6 wild-type and 6 <i>sox9b</i> mutant larvae were analyzed. (D) Number (average±SEM) of branching points observed along the bile ducts per liver. 7 wild-type and 7 mutants were analyzed. (C–D) Asterisks indicate statistical significance: *p<0.05; ****p<0.0001; *****p<0.00001. (E, G) Wild-type and <i>sox9b</i> mutant livers stained for BSEP (red) which marks the canaliculi, Alcam (blue) which marks the apical side of the hepatocytes, and <i>Tg(fabp10:</i>ras-GFP) (green) which labels the hepatocytes. The hepatocytes in wild-type livers are organized in parallel arrays (highlighted by pseudo-colors), while the <i>sox9b</i> mutant hepatocytes are arranged in rosettes (highlighted by pseudo-colors). (F, H) High magnification confocal images showing the morphology of biliary cells and bile canaliculi. The canaliculi (arrows) in <i>sox9b</i> mutant livers appear shorter and wider compared to wild-type. (A–B) All images are projections of confocal z-stacks. (E–H) Single confocal plane images. (A–B, E–H) Ventral views, anterior (A) to the top. Scale bars, 20 µm.</p

Notch signaling regulates <i>sox9b</i> expression in the intrahepatic and intrapancreatic ducts.

<p>(A–D) Whole-mount <i>in situ</i> hybridization (ISH) showing <i>sox9b</i> expression in larvae obtained from a wild-type to <i>sox9b</i> heterozygote cross that were treated with DMSO control or 20 µM DAPT between 75 and 99 hpf. In DMSO-treated controls, <i>sox9b</i> was strongly expressed in the liver and pancreas at 99 hpf (A, Class I). In animals treated with 20 µM DAPT (B–D), some showed a slight reduction of <i>sox9b</i> expression in the liver (Li) and pancreas (Pa) (B, Class II), others only retained expression of <i>sox9b</i> in the liver (C, Class III), and the remaining ones did not exhibit any obvious expression of <i>sox9b</i> in either organ (D, Class IV). Dorsal views, anterior (A) to the top. (E) Percentages of larvae showing different classes of phenotypes. <i>sox9b</i> heterozygotes exhibited a more severe reduction in <i>sox9b</i> expression than wild-type upon DAPT treatment. The numbers of larvae analyzed are indicated at the bottom. (F–I) Larvae obtained from crossing <i>Tg(hsp70l:Gal4)</i>;<i>Tg(UAS:myc-Notch1a-intra)</i> hemizygous and <i>Tg(Tp1bglob:GFP);Tg(Tp1bglob:H2BmCherry)</i> parents were heat-shocked at 80 hpf to induce myc-Notch1a-intra expression and fixed 26 hours later. (myc-Notch1a-intra)-overexpressing larvae were selected based on the increased expression of both <i>Tg(Tp1bglob:</i>GFP) and <i>Tg(Tp1bglob:</i>H2BmCherry), and their genotype was confirmed by anti-myc antibody labeling (data not shown). (F–G) <i>in situ</i> hybridization showed an increased expression of <i>sox9b</i> in the liver (Li) and pancreas (Pa) as well as in the HPD system (bracket) including the gallbladder (arrowhead) in (myc-Notch1a-intra)-overexpressing larvae (G) compared to (myc-Notch1a-intra)-negative siblings (F). 10 larvae of each genotype were analyzed. Dorsal views, anterior (A) to the top. (H–I) Confocal images of (myc-Notch1a-intra)-negative (H) and (myc-Notch1a-intra)-overexpressing (I) larvae showing elevated expression of <i>Tg(Tp1bglob:</i>GFP) and <i>Tg(Tp1bglob:</i>H2BmCherry) in the liver (Li), pancreas (Pa), gut (g) and gallbladder (gb) in (myc-Notch1a-intra)-overexpressing larvae after heat-shock. Dashed lines in (I) mark the pancreas. All images are projections of confocal z-stacks. Ventral views, anterior (A) to the top. Scale bars, 50 µm.</p

<i>sox9b</i> mutant larvae fail to form a complex intrapancreatic ductal network.

<p>(A–F) Confocal images of <i>Tg(Tp1bglob:GFP);Tg(Tp1bglob:H2B-mCherry)</i> wild-type (top row) and <i>sox9b</i> mutant (bottom row) pancreata at 80 (A,B), 100 (C,D) and 120 (E,F) hpf. Elastase antibody staining (blue) labels acinar cells. Although acinar and endocrine tissues appear morphologically unaffected in <i>sox9b</i> mutants (data not shown), the intrapancreatic ductal network is less complex and secondary branches are missing in the mutants (D–D′) whereas they start to form by 100 hpf in wild-type larvae (arrowheads and insets, C–C′). (E′″–F′″) Higher magnifications of the area marked by dashed squares in (E–F′) show that at 120 hpf the main duct forms secondary branches (arrowheads) in wild-type larvae (E″–E′″), whereas in the mutants, secondary branches remain absent and clusters of ductal cells are sometimes observed (F″–F′″). (A–F) All images are projections of confocal z-stacks. Ventral views, anterior (A) to the top. Scale bars, 50 µm. (G) Graph representing the number of <i>Tg(Tp1bglob:</i>GFP<i>);Tg(Tp1bglob:</i>H2B-mCherry)-double positive cells (average±SEM) in the intrapancreatic ducts of wild-type and <i>sox9b</i> mutant larvae at different time points. 7 to 11 larvae of each genotype were counted at each stage. (H) Graph representing the area (in arbitrary unit, a.u.) of the primary islet (average±SEM) of <i>TgBAC(neurod:GFP)</i> wild-type and <i>sox9b</i> mutant larvae (7 dpf) and juvenile animals (2, 3 and 4 weeks (wks)). 6 to 11 animals of each genotype were analyzed at each stage. Area of primary islet was determined using ImageJ. (I) Graph representing the number of <i>TgBAC(neurod:</i>GFP)-positive cells/clusters (average±SEM) along the intrapancreatic ducts (IPD) in wild-type and <i>sox9b</i> mutant larvae (10 dpf) and juvenile animals. 7 to 11 animals of each genotype were analyzed at each stage. Asterisks indicate statistical significance: *p<0.05; **p<0.01; ***p<0.0005; ****p<0.0001; ******p<0.000005.</p

The Role of Spouses and Extended Family Members as Primary Caretakers of Children During a Parent's Drug Addiction

This qualitative study explores the experiences of five men and one woman who were parents, substance dependent, and receiving treatment at a year-long drug treatment program. The qualitative research methods of observation and in-depth interviewing were used to collect and analyze information about their experiences. This paper discusses themes related to the role of spouses and extended family members who assumed primary responsibility for children during a parent\u27s drug addiction. Participants reported how, when they were unable to care for their children, these responsibilities fell to other family members, giving rise to many conflicts. Initially they were grateful for the support, especially while the participants were actively using drugs, because this provided them with more opportunities to continue their addictive lifestyle. Eventually, power struggles emerged when the participants were in recovery and attempted to reenter their children\u27s lives as parental figures. Copyright © by The Haworth Press, Inc. All rights reserved