Miracle-dz/UniFAR-FTUs huggingface dataset:
Gata6 is required for complete acinar differentiation and maintenance of the exocrine pancreas in adult mice

Objectives Previous studies have suggested an important role of the transcription factor Gata6 in endocrine pancreas, while GATA6 haploinsufficient inactivating mutations cause pancreatic agenesis in humans. We aimed to analyse the effects of Gata6 inactivation on pancreas development and function. Design We deleted Gata6 in all epithelial cells in the murine pancreas at the onset of its development. Acinar proliferation, apoptosis, differentiation and exocrine functions were assessed using reverse transcriptase quantitative PCR (RT-qPCR), chromatin immunoprecipitation, immunohistochemistry and enzyme assays. Adipocyte transdifferentiation was assessed using electron microscopy and genetic lineage tracing. Results Gata6 is expressed in all epithelial cells in the adult mouse pancreas but it is only essential for exocrine pancreas homeostasis: while dispensable for pancreatic development after e10.5, it is required for complete acinar differentiation, for establishment of polarity and for the maintenance of acinar cells in the adult. Gata6 regulates directly the promoter of genes coding for digestive enzymes and the transcription factors Rbpjl and Mist1. Upon pancreas-selective Gata6 inactivation, massive loss of acinar cells and fat replacement take place. This is accompanied by increased acinar apoptosis and proliferation, acinar-to-ductal metaplasia and adipocyte transdifferentiation. By contrast, the endocrine pancreas is spared. Conclusions Our data show that Gata6 is required for the complete differentiation of acinar cells through multiple transcriptional regulatory mechanisms. In addition, it is required for the maintenance of the adult acinar cell compartment. Our studies suggest that GATA6 alterations may contribute to diseases of the human adult exocrine pancreas.
Infants exposed to cocaine in utero: Implications for developmental assessment and intervention

Findings of developmental assessment in the newborn and early infancy periods are presented. The implications of abnormal state control and orientation as well as dysfunction in motor control are discussed as the basis for intervention. Intervention in the newborn phase includes information on positioning, handling, and feeding. Parent education to improve the infants' ability to interact with caregivers is emphasized. Improving the infants' movement patterns through play, carrying positions, and handling techniques is the focus of intervention in infancy. While intervention with cocaine-exposed infants is presently possible, these children should be followed by health care professionals through preschool and early school years to identify any behavior or learning disorders that may be associated with intrauterine cocaine exposure
Severe sepsis in the ICU is often missing in hospital discharge codes

Different International Classification of Diseases (ICD)‐based code abstraction strategies have been used when studying the epidemiology of severe sepsis. The aim of this study was to compare three previously used ICD code abstraction strategies to the American College of Chest Physicians/Society of Critical Care Medicine (ACCP/SCCM) consensus criteria for severe sepsis, in a setting of intensive care patients.
Geographical variability and environmental risk factors in inflammatory bowel disease

The changing epidemiology of inflammatory bowel disease (IBD) across time and geography suggests that environmental factors play a major role in modifying disease expression. Disease emergence in developing nations suggests that epidemiological evolution is related to westernisation of lifestyle and industrialisation. The strongest environmental associations identified are cigarette smoking and appendectomy, although neither alone explains the variation in incidence of IBD worldwide. Urbanisation of societies, associated with changes in diet, antibiotic use, hygiene status, microbial exposures and pollution have been implicated as potential environmental risk factors for IBD. Changes in socioeconomic status might occur differently in different geographical areas and populations and, consequently, it is important to consider the heterogeneity of risk factors applicable to the individual patient. Environmental risk factors of individual, familial, community-based, country-based and regionally based origin may all contribute to the pathogenesis of IBD. The geographical variation of IBD provides clues for researchers to investigate possible environmental aetiological factors. The present review aims to provide an update of the literature exploring geographical variability in IBD and to explore the environmental risk factors that may account for this variability.
Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C

Objective Ribavirin improves treatment response to pegylated-interferon (PEG-IFN) in chronic hepatitis C but the mechanism remains controversial. We studied correlates of response and mechanism of action of ribavirin in treatment of hepatitis C. Design 70 treatment-naive patients were randomised to 4 weeks of ribavirin (1000–1200 mg/d) or none, followed by PEG-IFNα-2a and ribavirin at standard doses and durations. Patients were also randomised to a liver biopsy 24 h before or 6 h after starting PEG-IFN. Hepatic gene expression was assessed by microarray and interferon-stimulated gene (ISG) expression quantified by nCounter platform. Temporal changes in ISG expression were assessed by qPCR in peripheral-blood mononuclear cells (PBMC) and by serum levels of IP-10. Results After 4 weeks of ribavirin monotherapy, hepatitis C virus (HCV) levels decreased by 0.5±0.5 log10 (p=0.009 vs controls) and ALT by 33% (p<0.001). Ribavirin pretreatment, while modestly augmenting ISG induction by PEG-IFN, did not modify the virological response to subsequent PEG-IFN and ribavirin treatment. However, biochemical, but not virological, response to ribavirin monotherapy predicted response to subsequent combination treatment (rapid virological response, 71% in biochemical responders vs 22% non-responders, p=0.01; early virological response, 100% vs 68%, p=0.03; sustained virological response 83% vs 41%, p=0.053). Ribavirin monotherapy lowered serum IP-10 levels but had no effect on ISG expression in PBMC. Conclusions Ribavirin is a weak antiviral but its clinical effect seems to be mediated by a separate, indirect mechanism, which may act to reset IFN-responsiveness in HCV-infected liver.
Risk of HBV reactivation in patients with B-cell lymphomas receiving obinutuzumab or rituximab immunochemotherapy.

Risk of hepatitis B virus (HBV) reactivation was assessed in B-cell non-Hodgkin lymphoma (NHL) patients with resolved HBV infection (hepatitis B surface antigen negative, hepatitis B core antibody positive) who received obinutuzumab- or rituximab-containing immunochemotherapy in the phase 3 GOYA and GALLIUM studies. HBV DNA monitoring was undertaken monthly to 1 year after the last dose of study drug. In case of HBV reactivation (confirmed, HBV DNA ≥29 IU/mL), immunochemotherapy was withheld and nucleos(t)ide analog treatment (preemptive NAT) started. Immunochemotherapy was restarted if HBV DNA became undetectable or reactivation was not confirmed, and discontinued if HBV DNA exceeded 100 IU/mL on NAT. Prophylactic NAT was allowed by investigator discretion. Among 326 patients with resolved HBV infection, 27 (8.2%) had HBV reactivation, occurring a median of 125 days (interquartile range, 85-331 days) after the first dose. In 232 patients without prophylactic NAT, 25 (10.8%) had HBV reactivation; all received preemptive NAT. Ninety-four patients received prophylactic NAT; 2 (2.1%) had HBV reactivation. No patients developed HBV-related hepatitis. On multivariate Cox analysis, detectable HBV DNA at baseline was strongly associated with an increased risk of reactivation (adjusted hazard ratio [HR], 18.22; 95% confidence interval [CI], 6.04-54.93; P < .0001). Prophylactic NAT was strongly associated with a reduced risk (adjusted HR, 0.09; 95% CI, 0.02-0.41; P = .0018). HBV DNA monitoring-guided preemptive NAT was effective in preventing HBV-related hepatitis during anti-CD20-containing immunochemotherapy in B-cell NHL patients with resolved HBV infection. Antiviral prophylaxis was also effective and may be appropriate for high-risk patients. These trials were registered at www.clinicaltrials. gov as NCT01287741 (GOYA) and NCT01332968 (GALLIUM).
Heparin‐binding protein as a biomarker of acute kidney injury in critical illness

There is no biomarker with high sensitivity and specificity for the development of acute kidney injury (AKI) in a mixed intensive care unit (ICU) population. Heparin‐binding protein (HBP) is released from granulocytes and causes increased vascular permeability which plays a role in the development of AKI in sepsis and ischemia. The aim of this study was to investigate whether plasma levels of HBP on admission can predict the development of AKI in a mixed ICU population and in the subgroup with sepsis.
Bifunctional PD-1 × αCD3 × αCD33 fusion protein reverses adaptive immune escape in acute myeloid leukemia.

The CD33-targeting bispecific T-cell engager (BiTE) AMG 330 proved to be highly efficient in mediating cytolysis of acute myeloid leukemia (AML) cells in vitro and in mouse models. Yet, T-cell activation is correlated with upregulation of programmed cell death-ligand 1 (PD-L1) and other inhibitory checkpoints on AML cells that confer adaptive immune resistance. PD-1 and PD-L1 blocking agents may counteract T-cell dysfunction, however, at the expense of broadly distributed immune-related adverse events (irAEs). We developed a bifunctional checkpoint inhibitory T cell-engaging (CiTE) antibody that combines T-cell redirection to CD33 on AML cells with locally restricted immune checkpoint blockade. This is accomplished by fusing the extracellular domain of PD-1 (PD-1ex), which naturally holds a low affinity to PD-L1, to an αCD3. αCD33 BiTE-like scaffold. By a synergistic effect of checkpoint blockade and avidity-dependent binding, the PD-1ex attachment increases T-cell activation (3.3-fold elevation of interferon-γ) and leads to efficient and highly selective cytotoxicity against CD33+PD-L1+ cell lines (50% effective concentration = 2.3-26.9 pM) as well as patient-derived AML cells (n = 8). In a murine xenograft model, the CiTE induces complete AML eradication without initial signs of irAEs as measured by body weight loss. We conclude that our molecule preferentially targets AML cells, whereas high-affinity blockers, such as clinically approved anticancer agents, also address PD-L1+ non-AML cells. By combining the high efficacy of T-cell engagers with immune checkpoint blockade in a single molecule, we expect to minimize irAEs associated with the systemic application of immune checkpoint inhibitors and suggest high therapeutic potential, particularly for patients with relapsed/ refractory AML.
Telephone-based re-education on the day before colonoscopy improves the quality of bowel preparation and the polyp detection rate: a prospective, colonoscopist-blinded, randomised, controlled study

Background Despite advances in bowel preparation methods, the quality of bowel preparation in some patients undergoing colonoscopy remains unsatisfactory. The effect of telephone re-education (TRE) on the day before colonoscopy on the quality of bowel preparation and other outcome measures had not been studied. Methods A prospective colonoscopist-blinded study was conducted. All patients received regular instructions during a visit to discuss colonoscopy. Those scheduled for colonoscopy were randomly assigned to receive TRE on the day before colonoscopy (TRE group) for bowel preparation or no TRE (control group). The primary outcome was the rate of adequate bowel preparation. The secondary outcomes included polyp detection rate (PDR), non-compliance with instructions, and willingness to repeat bowel preparation. Results A total of 605 patients were randomised, 305 to the TRE group and 300 to the control group. In an intention-to-treat analysis of the primary outcome, adequate preparation was found in 81.6% vs 70.3% of TRE and control patients, respectively (p=0.001). PDR was 38.0% vs 24.7% in the TRE and control group, respectively (p<0.001). Among patients with successful colonoscopy, the Ottawa scores were 3.0±2.3 in the TRE group and 4.9±3.2 in the control group (p<0.001). Fewer patients who showed non-compliance with instructions were found in the TRE group (9.4% vs 32.6%, p<0.001). No significant differences were observed between the two groups with regard to willingness to have a repeat bowel preparation (p=0.409). Conclusions TRE about the details of bowel preparation on the day before colonoscopy significantly improved the quality of bowel preparation and PDR.
Attenuated arsenic trioxide plus ATRA therapy for newly diagnosed and relapsed APL: long-term follow-up of the AML17 trial.

TO THE EDITOR: We have previously reported on the results of the United Kingdom National Cancer Research Institute (NCRI) AML17 trial, which, for acute promyelocytic leukemia (APL) of all risk groups, compared anthracycline + all- trans retinoic acid (ATRA) (AIDA) vs arsenic trioxide (ATO) + ATRA
Residential Aged-Care Workers and the Palliative Approach: Tensions in the Field

Despite the recognition of the importance of the palliative approach for older adults in residential aged-care facilities, the provision of palliative care remains suboptimal. Strategies to improve palliative care education have targeted those health carers who provide direct physical care, namely, registered nurses and unlicensed personal care attendants. While ancillary (laundry, lifestyle, food services, maintenance, and administrative) staff have been identified as an important part of the aged-care team, they have been largely absent from such studies. This article reports the experiences and perceptions of palliative care by the entire care team in an Australian aged-care facility. With few exceptions, staff perceived palliative care to be synonymous with terminal care and to be primarily physically focused. Teamwork was found to be threatened by poor communication strategies between physical care and ancillary staff, with ancillary staff simultaneously reluctant to engage in, and frustrated by their exclusion from, care-related discussions. In addition to identifying key areas for education for all levels of health carers, along with the potential of focus groups as a strategy in this endeavor, this study highlights the importance of team cohesion for enacting the palliative approach in the aged-care context.
Estimating the Level of Abortion In the Philippines and Bangladesh

In both the Philippines and Bangladesh a lack of reliable data on induced abortion requires the use of various estimation techniques to assess the number of procedures performed. The Philippine penal code contains a general prohibition on abortion yet about one-third of such procedures are performed by nurses or physicians. In Bangladesh abortion is permitted only to save a womans life; however menstrual regulation is not covered by the penal code and this procedure accounts for about two-thirds of all voluntary pregnancy terminations. Estimation techniques suggest that the abortion rate in the Philippines is within the range of 20-30 induced abortions per 1000 women 15-49 years old while the rate in Bangladesh is 26-30 per 1000 women. An estimated 400000 abortions are performed each year in the Philippines; in Bangladesh the annual number is approximately 730000. In the Philippines about 80000 women are treated in hospitals each year for complications of abortion; in Bangladesh 52000 women are treated for abortion-related complications and another 19000 receive hospital care for complications related to menstrual regulation procedures. Each year 45% of pregnancies in Bangladesh and 53% of those in the Philippines are unwanted; only 18% and 16% of these pregnancies respectively are resolved through abortion indicating a large unmet need for family planning services.
Development and validation of a survival staging system incorporating BNP in patients with light chain amyloidosis.

Immunoglobulin light chain amyloidosis (AL amyloidosis) is caused by misfolded light chains that form soluble toxic aggregates that deposit in tissues and organs, leading to organ dysfunction. The leading determinant of survival is cardiac involvement. Current staging systems use N-terminal pro-brain natriuretic peptide (NT-proBNP) and cardiac troponins T and I (TnT and TnI) for prognostication, but many centers do not offer NT-proBNP. We sought to derive a new staging system using brain natriuretic peptide (BNP) that would correlate with the Mayo 2004 staging system and be predictive for survival in AL amyloidosis. Two cohorts of patients were created: a derivation cohort of 249 consecutive patients who had BNP, NT-proBNP, and TnI drawn simultaneously to create the staging system and a complementary cohort of 592 patients with 10 years of follow-up to determine survival. In the derivation cohort, we found that a BNP threshold of more than 81 pg/mL best associated with Mayo 2004 stage and also best identified cardiac involvement. Three stages were developed based on a BNP higher than 81 pg/mL and a TnI higher than 0.1 ng/mL and compared with Mayo 2004 with high concordance (κ = 0.854). In the complementary cohort, 25% of patients had stage I, 44% had stage II, 15% had stage III, and 16% had stage IIIb disease with a median survival not reached in stage I, 9.4 years in stage II, 4.3 years in stage III, and 1 year in stage IIIb. This new Boston University biomarker scoring system will allow centers without access to NT-proBNP the ability to appropriately stage patients with AL amyloidosis. This trial was registered at www.clinicaltrials. gov as #NCT00898235.
Mortality and causes of death in Crohn's disease: results from 20 years of follow-up in the IBSEN study

Objective Population-based studies have shown a slightly decreased life expectancy in patients with Crohn's disease (CD). The primary aim of the present study was to evaluate mortality and causes of death 20 years after the diagnosis in a well defined population-based cohort of CD patients in Norway. Design The Inflammatory Bowel South-Eastern Norway study has prospectively followed all patients diagnosed with CD in the period between 1 January 1990 and 31 December 1993 in four geographically well-defined areas. All patients (n=237) were age and sex matched with 25 persons from the same county selected at random from the general population. Data on death and causes of deaths were collected from the Norwegian Causes of Death Register. All causes and cause-specific mortality (gastrointestinal cancer, cancer and heart disease) were modelled with Cox regression model stratified by matched sets. Results are expressed as HRs with 95% CIs. Results There was no significant difference between CD patients and controls in overall mortality (HR=1.35, 95% CI 0.94 to 1.94, p=0.10). Furthermore, there were no marked differences in deaths from gastrointestinal cancer, other cancers or cardiovascular diseases in the CD group compared with the controls. In the CD group, 13.9% had died compared with 12.7% in the control group (p=0.578). Conclusions In our population-based inception cohort followed for 20 years, there was no increased mortality or more deaths from cancer compared with the general population.
Color Atlas of Clinical Oral Pathology

Developmental disturbances of the oral and maxillofacial region pathology of the teeth pulpal, periapical and periodontal pathology infections physical and chemical injuries allergies and immunologic diseases benign and malignant lesions of epithelial origin salivary gland pathology soft tissue tumours lymphoreticular and haematopoietic diseases diseases and tumours of bone odontogenic cysts and tumours dermatologic diseases oral manifestations of systemic diseases.
Five-year PFS from the AETHERA trial of brentuximab vedotin for Hodgkin lymphoma at high risk of progression or relapse.

The phase 3 AETHERA trial established brentuximab vedotin (BV) as a consolidative treatment option for adult patients with classical Hodgkin lymphoma (cHL) at high risk of relapse or progression after autologous hematopoietic stem-cell transplantation (auto-HSCT). Results showed that BV significantly improved progression-free survival (PFS) vs placebo plus best supportive care alone. At 5-year follow-up, BV continued to provide patients with sustained PFS benefit; 5-year PFS was 59% (95% confidence interval [CI], 51-66) with BV vs 41% (95% CI, 33-49) with placebo (hazard ratio [HR], 0.521; 95% CI, 0.379-0.717). Similarly, patients with ≥2 risk factors in the BV arm experienced significantly higher PFS at 5 years than patients in the placebo arm (HR, 0.424; 95% CI, 0.302-0.596). Upfront consolidation with BV significantly delayed time to second subsequent therapy, an indicator of ongoing disease control, vs placebo. Peripheral neuropathy, the most common adverse event in patients receiving BV, continued to improve and/or resolve in 90% of patients. In summary, consolidation with BV in adult patients with cHL at high risk of relapse or progression after auto-HSCT confers a sustained PFS benefit and is safe and well tolerated. Physicians should consider each patient's HL risk factor profile when making treatment decisions. This trial was registered at www.clinicaltrials. gov as #NCT01100502.
Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints.

Follicular lymphoma (FL) is a low-grade B-cell malignancy that transforms into a highly aggressive and lethal disease at a rate of 2% per year. Perfect isolation of the malignant B-cell population from a surgical biopsy is a significant challenge, masking important FL biology, such as immune checkpoint coexpression patterns. To resolve the underlying transcriptional networks of follicular B-cell lymphomas, we analyzed the transcriptomes of 34 188 cells derived from 6 primary FL tumors. For each tumor, we identified normal immune subpopulations and malignant B cells, based on gene expression. We used multicolor flow cytometry analysis of the same tumors to confirm our assignments of cellular lineages and validate our predictions of expressed proteins. Comparison of gene expression between matched malignant and normal B cells from the same patient revealed tumor-specific features. Malignant B cells exhibited restricted immunoglobulin (Ig) light chain expression (either Igκ or Igλ), as well the expected upregulation of the BCL2 gene, but also downregulation of the FCER2, CD52, and major histocompatibility complex class II genes. By analyzing thousands of individual cells per patient tumor, we identified the mosaic of malignant B-cell subclones that coexist within a FL and examined the characteristics of tumor-infiltrating T cells. We identified genes coexpressed with immune checkpoint molecules, such as CEBPA and B2M in regulatory T (Treg) cells, providing a better understanding of the gene networks involved in immune regulation. In summary, parallel measurement of single-cell expression in thousands of tumor cells and tumor-infiltrating lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development.