Miracle-dz/UniFAR-FTUs huggingface dataset:
Endemic Diseases and African Economic Growth: Challenges and Policy Responses.

I examine the economic effects of disease and disease control. I consider both the effect of disease on conventionally measured GDP and also the monetary equivalent of the utility benefits from lower mortality. Regarding the effects on conventional GDP, I evaluate a number of approaches including cross-country regression (with and without instruments for disease) and simulation based on microeconomic studies. I also discuss theoretically and empirically the different channels that link disease and economic outcomes, including effects that run through labour productivity, education and population growth. Different approaches yield somewhat different results, but the overall finding is that there is at best weak support for the claims that the disease burden in Africa significantly lowers GDP or that improving health would provide a big impetus to economic growth. In contrast, the monetary equivalent of the utility benefits from better health can be extremely large. For example, reduced mortality in many developing countries has made a contribution to utility of roughly the same value as the growth of conventional GDP over the last several decades. Copyright 2010 The author 2010. Published by Oxford University Press on behalf of the Centre for the Study of African Economies. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org, Oxford University Press.
Psychosocial correlation between diabetes mellitus and depression: a primary care study from a low income country

Background and aims . Systematic reviews and meta-analyses show an association between diabetes and depression. It is a major public health issue, as depression is generally associated with poor outcome of chronic illnesses, including diabetes and contributes to the high economic burden of health care costs. The purpose of this study is to explore the correlation between depression and diabetes in order to develop adequate interventions. The primary aim was to examine the prevalence of depression, social stress, health related quality of life, and social support among patients with diabetes attending primary care. Material and methods. This was a cross-sectional study conducted in participating primary care clinics in Karachi. All patients with diabetes attending these primary care clinics were invited to participate in the study. Patients with prior diagnosis of major depression, psychotic disorder, or substance abuse disorder, were excluded. Full confidentiality of the data collected was ensured to all the study participants and all interviews were completed only after obtaining informed consent. We used several questionnaires (socio-demographic, clinical, Patient Health Questionnaire - PHQ-9, self-report questionnaire EQ-5D, Life Events Checklist) and scales (7 items Generalized Anxiety Disorder - GAD-7, 3 items - Oslo-3 scale). Results and conclusion. Our results show that the rates of depression in adult patients with diabetes in Pakistan are high. The patients with diabetes who have depression reported higher social stress, poorer health related quality of life compared to the non depressed diabetic patients.
Parameterizing time in electronic health record studies

Abstract Background Fields like nonlinear physics offer methods for analyzing time series, but many methods require that the time series be stationary—no change in properties over time. Objective Medicine is far from stationary, but the challenge may be able to be ameliorated by reparameterizing time because clinicians tend to measure patients more frequently when they are ill and are more likely to vary. Methods We compared time parameterizations, measuring variability of rate of change and magnitude of change, and looking for homogeneity of bins of temporal separation between pairs of time points. We studied four common laboratory tests drawn from 25 years of electronic health records on 4 million patients. Results We found that sequence time—that is, simply counting the number of measurements from some start—produced more stationary time series, better explained the variation in values, and had more homogeneous bins than either traditional clock time or a recently proposed intermediate parameterization. Sequence time produced more accurate predictions in a single Gaussian process model experiment. Conclusions Of the three parameterizations, sequence time appeared to produce the most stationary series, possibly because clinicians adjust their sampling to the acuity of the patient. Parameterizing by sequence time may be applicable to association and clustering experiments on electronic health record data. A limitation of this study is that laboratory data were derived from only one institution. Sequence time appears to be an important potential parameterization.
Intentions to use cervical cancer screening services among women aged 42 and older in Malawi

Free cervical cancer screening services are provided in Malawi’s public healthcare institutionssince 1999. Few women aged 42 and older, utilise these services. Cervical cancer continues to be a major cause of morbidity and mortality among this group of women. Structured interviews were conducted with 381 women who attended three healthcare centers in Blantyre and semi-structured interviews with 14 nurse/midwives working at the same centers. The results for both phases arepresented within the Health Belief Model’s constructs. Phase 1 revealed that women had low levels of perceived susceptibility to cervical cancer. Although the interviewed women perceived cervical cancer to be a serious condition, they did not regard themselves to be at risk of suffering from cervical cancer. Knowledge that cervical cancer screening could detect this cancer at an early stage, embarrassment, stigma, social support, financial costs, traditional practices and available sources of information, influenced women’s intentions to be screened for cervical cancer. In phase 2, the nurse/midwives indicated that Malawian women lacked information about cervical cancer, available screening tests and the purpose of such screening.These women perceived cervical canceras being incurable and linked to witchcraft. Women’s utilisation of cervical screening services was hampered by barriers relating to healthcare institutions, women themselves and nurse/midwives. Local radio and television broadcasts, friends and nurse/midwives motivated individual women to use these screening services.Women preferred receiving information about cervical cancer screening during community activities. Health education should be intensified, nurse/midwives should be more empathetic, clinic days and hours should be extended. Misconceptions should be addressed and more service providers should be trained. This would enable more Malawian women to use cervical screening services, enhancing early detection and treatment of cervical cancer and reducing the morbidity and mortality statistics related to this condition in Malawi. KEY TERMS:Health Belief Model (HBM), perceived susceptibility to cervical cancer,perceived severity of cervical cancer, perceived benefits of cervical screening, perceived barriers to cervical screening, cues to taking action to use cervical screening services
Real-time prediction of mortality, readmission, and length of stay using electronic health record data

OBJECTIVE To develop a predictive model for real-time predictions of length of stay, mortality, and readmission for hospitalized patients using electronic health records (EHRs). MATERIALS AND METHODS A Bayesian Network model was built to estimate the probability of a hospitalized patient being "at home," in the hospital, or dead for each of the next 7 days. The network utilizes patient-specific administrative and laboratory data and is updated each time a new pathology test result becomes available. Electronic health records from 32 634 patients admitted to a Sydney metropolitan hospital via the emergency department from July 2008 through December 2011 were used. The model was tested on 2011 data and trained on the data of earlier years. RESULTS The model achieved an average daily accuracy of 80% and area under the receiving operating characteristic curve (AUROC) of 0.82. The model's predictive ability was highest within 24 hours from prediction (AUROC = 0.83) and decreased slightly with time. Death was the most predictable outcome with a daily average accuracy of 93% and AUROC of 0.84. DISCUSSION We developed the first non-disease-specific model that simultaneously predicts remaining days of hospitalization, death, and readmission as part of the same outcome. By providing a future daily probability for each outcome class, we enable the visualization of future patient trajectories. Among these, it is possible to identify trajectories indicating expected discharge, expected continuing hospitalization, expected death, and possible readmission. CONCLUSIONS Bayesian Networks can model EHRs to provide real-time forecasts for patient outcomes, which provide richer information than traditional independent point predictions of length of stay, death, or readmission, and can thus better support decision making.
Preparation of Adenovirus‐Polylysine‐DNA Complexes

This unit describes preparation of adenovirus‐polylysine‐DNA complexes, which is useful for transfection of DNA into a variety of cell types. A DNA complex is prepared with biotinylated adenovirus and streptavidin‐polylysine, coupled to transferrin, and used to transfect cells. Several support protocols describe methods for adenovirus growth and purification, biotinylation, inactivation with psoralen, and quantitation of the adenovirus particles. Additional support protocols descibes preparation of streptavidin‐polylysine and transferrin‐polylysine, necessary for the basic procedure. The DNA used for transfection must be free of lipopolysaccharide (LPS), and two methods for removing LPS are described. A more direct polylysine‐virus linkage that is simple and requires no exotic reagents can be used for transfection. This protocol requires polylysine‐modified adenovirus, prepared as described. An alternate protocol describes transfecting cells with free virus and DNA condensed with a polycation.
Applying probabilistic temporal and multisite data quality control methods to a public health mortality registry in Spain: a systematic approach to quality control of repositories

OBJECTIVE To assess the variability in data distributions among data sources and over time through a case study of a large multisite repository as a systematic approach to data quality (DQ). MATERIALS AND METHODS Novel probabilistic DQ control methods based on information theory and geometry are applied to the Public Health Mortality Registry of the Region of Valencia, Spain, with 512 143 entries from 2000 to 2012, disaggregated into 24 health departments. The methods provide DQ metrics and exploratory visualizations for (1) assessing the variability among multiple sources and (2) monitoring and exploring changes with time. The methods are suited to big data and multitype, multivariate, and multimodal data. RESULTS The repository was partitioned into 2 probabilistically separated temporal subgroups following a change in the Spanish National Death Certificate in 2009. Punctual temporal anomalies were noticed due to a punctual increment in the missing data, along with outlying and clustered health departments due to differences in populations or in practices. DISCUSSION Changes in protocols, differences in populations, biased practices, or other systematic DQ problems affected data variability. Even if semantic and integration aspects are addressed in data sharing infrastructures, probabilistic variability may still be present. Solutions include fixing or excluding data and analyzing different sites or time periods separately. A systematic approach to assessing temporal and multisite variability is proposed. CONCLUSION Multisite and temporal variability in data distributions affects DQ, hindering data reuse, and an assessment of such variability should be a part of systematic DQ procedures.
Introduction to Basic Mouse Handling Techniques

Purification of DNA from fixed, paraffin‐embedded tissue (PET) requires the removal of paraffin, proteins, and, in some cases, heavy metal ions. The resulting DNA is not generally suitable for Southern blot analysis. However, the polymerase chain reaction (PCR) can be used to amplify short regions of this DNA. In this appendix, the basic protocol can be performed rapidly and involves only a small number of manipulations, thus minimizing the possibility of contamination. An alternate protocol involves additional steps including extractions with xylenes and phenol/chloroform. This procedure is recommended as the primary approach when tissue has not been fixed in an optimal manner or as a secondary approach when the basic protocol has failed to produce satisfactory DNA.
Health information exchange associated with improved emergency department care through faster accessing of patient information from outside organizations

Objective: To assess whether electronic health information exchange (HIE) is associated with improved emergency department (ED) care processes and utilization through more timely clinician viewing of information from outside organizations. Materials and Methods: Our data included 2163 patients seen in the ED of a large academic medical center for whom clinicians requested and viewed outside information from February 14, 2014, to February 13, 2015. Outside information requests w.ere fulfilled via HIE (Epic’s Care Everywhere) or fax/scan to the electronic health record (EHR). We used EHR audit data to capture the time between the information request and when a clinician accessed the data. We assessed whether the relationship between method of information return and ED outcomes (length of visit, odds of imaging [computed tomography (CT), magnetic resonance imaging (MRI), radiographs] and hospitalization, and total charges) was mediated by request-to-access time, controlling for patient demographics, case mix, and acuity. Results: In multivariate analysis, there was no direct association between return of information via HIE vs fax/scan and ED outcomes. HIE was associated with faster outside information access (58.5 minutes on average), and faster access was associated with changes in ED care. For each 1-hour reduction in access time, visit length was 52.9 minutes shorter, the likelihood of imaging was lower (by 2.5, 1.6, and 2.4 percentage points for CT, MRI, and radiographs, respectively), the likelihood of admission was 2.4 percentage points lower, and average charges were $1187 lower (P ⩽ .001 for all). Conclusion: The relationship between HIE and improved care processes and reduced utilization in the ED is mediated by faster accessing of information from outside organizations.
Titering Antibodies

Flow cytometry using fluorochrome‐conjugated antibodies has emerged as a major approach to automated cellular identification. One of the most important issues in immunophenotyping is using the correct amount of antibody. This unit presents techniques for ascertaining the optimal titer for individual, dual, and multiple antibodies used for simultaneous phenotyping, stressing the importance of quality control in making batches of antibody for routine use. Keywords: flow cytometry; monoclonal antibodies; antibody titration; immunophenotyping.
Automated classification of eligibility criteria in clinical trials to facilitate patient-trial matching for specific patient populations

Objective To develop automated classification methods for eligibility criteria in ClinicalTrials.gov to facilitate patient-trial matching for specific populations such as persons living with HIV or pregnant women. Materials and Methods We annotated 891 interventional cancer trials from ClinicalTrials.gov based on their eligibility for human immunodeficiency virus (HIV)-positive patients using their eligibility criteria. These annotations were used to develop classifiers based on regular expressions and machine learning (ML). After evaluating classification of cancer trials for eligibility of HIV-positive patients, we sought to evaluate the generalizability of our approach to more general diseases and conditions. We annotated the eligibility criteria for 1570 of the most recent interventional trials from ClinicalTrials.gov for HIV-positive and pregnancy eligibility, and the classifiers were retrained and reevaluated using these data. Results On the cancer-HIV dataset, the baseline regex model, the bag-of-words ML classifier, and the ML classifier with named entity recognition (NER) achieved macro-averaged F2 scores of 0.77, 0.87, and 0.87, respectively; the addition of NER did not result in a significant performance improvement. On the general dataset, ML + NER achieved macro-averaged F2 scores of 0.91 and 0.85 for HIV and pregnancy, respectively. Discussion and Conclusion The eligibility status of specific patient populations, such as persons living with HIV and pregnant women, for clinical trials is of interest to both patients and clinicians. We show that it is feasible to develop a high-performing, automated trial classification system for eligibility status that can be integrated into consumer-facing search engines as well as patient-trial matching systems.
Dual‐Pulse Labeling Using 5‐Ethynyl‐2′‐Deoxyuridine (EdU) and 5‐Bromo‐2′‐Deoxyuridine (BrdU) in Flow Cytometry

Changes in DNA replication during S‐phase can give insights into mechanisms of cell growth, cell cycle kinetics, and cytotoxicity. A common method for detection of cell proliferation utilizes the incorporation of a thymidine analog during DNA synthesis. Incorporation of multiple analogs at different time points can further define cell cycle kinetics. Traditionally, the dual‐pulse method has been done by combining 5‐bromo‐2′‐deoxyuridine (BrdU) with iododeoxyuridine or chlorodeoxyuridine, with detection using multiple cross‐reacting BrdU antibodies. This unit presents a dual‐pulse method using the thymidine analog 5‐ethyl‐2′‐deoxyuridine (EdU), detected by click chemistry, combined with BrdU labeling and detection. No cross reactivity with incorporated EdU is observed using the BrdU antibody clone MoBU‐1. EdU detection using click chemistry does not cross‐react with incorporated BrdU. Cells are first pulsed with EdU, and then pulsed with BrdU; sequential pulses of EdU, followed by BrdU, are done without removing or washing out EdU. Curr. Protoc. Cytom. 55:7.38. 1‐7.38. 15. © 2011 by John Wiley & Sons, Inc.
Analysis of Intracellular Organelles by Flow Cytometry or Microscopy

Functional analysis of cellular organelles can be accomplished by staining cells with suitable organelle‐specific dyes and analyzing the fluorescence of the stained cells with a flow cytometer. With this methodology it is possible to resolve suspected heterogeneity in organelle function or content within a population of cells. Morphological information can be provided by quantitative microscopy (confocal microscope or video microscope with digital image‐analysis system). The thirteen protocols cover flow cytometry and microscopy for both live and fixed cells.
Flow Cytometric Analysis of Cell Division by Dilution of CFSE and Related Dyes

The technique described in this unit uses the intracellular fluorescent label carboxyfluorescein diacetate succinimidyl ester (CFSE) to track proliferating cells. Covalently bound CFSE is divided equally between daughter cells, allowing discrimination of successive rounds of cell division. The technique is applicable to in vitro cell division, as well as to in vivo division of adoptively transferred cells and can resolve eight or more successive generations. CFSE is long lived, permitting analysis for several months after cell transfer, and has the same spectral characteristics as fluorescein, so monoclonal antibodies conjugated to phycoerythrin or other compatible fluorochromes may be used to immunophenotype the dividing cells. In addition, information is given on a second‐generation dye, Cell Trace Violet (CTV), excited by 405‐nm blue laser light. CTV is chemically related to CFSE, but allows the 488‐nm line of the Argon laser to be used for other probes. Curr. Protoc. Cytom. 64:9.11. 1‐9.11. 12. © 2013 by John Wiley & Sons, Inc.
Isolation of Subcellular Fractions from the Yeast Saccharomyces cerevisiae

This unit presents detailed protocols for a range of centrifugation‐based subcellular fractionation procedures for the yeast Saccharomyces cerevisiae. Techniques include spheroplast preparation, glass‐bead lysis, differential centrifugation, and several density gradient procedures using a variety of gradient media. There are analytical procedures that are primarily designed to evaluate the association of proteins with organelles in the exocytic and endocytic pathways. Additionally, there are preparative protocols for isolation of yeast nuclei, vacuoles, mitochondria, peroxisomes, endoplasmic reticulum, plasma membrane, and cytosol. The unit also contains a table, with references, for alternative approaches to isolation of these organelles and fractions.
Isolation of Mast Cell Granules

The mast cell is a multipotent inflammatory cell that has been shown to participate in the pathogenesis of a variety of diseases, such as immediate hypersensitivity reactions, arthritis, atherosclerosis, and heart failure. Upon stimulation, mast cells exocytose cytoplasmic secretory granules into their extracellular microenvironment. These granules are modified lysosomes containing preformed mediators such as histamine, neutral proteases, cytokines, and growth factors embedded in a heparin proteoglycan matrix. When exposed to the extracellular fluid, the soluble components of the granules (e.g., histamine and cytokines) diffuse away, whereas the heparin proteoglycans and the mast cell–specific neutral proteases (e.g., chymase) remain tightly bound to each other, forming proteolytically active intra‐ and extracellular granule remnants. This unit describes a method to isolate rat serosa mast cell granule remnants in experiments aimed at determining the role of mast cell activation and degranulation in disease.
Isolation of Endoplasmic Reticulum, Mitochondria, and Mitochondria‐Associated Membrane Fractions from Transfected Cells and from Human Cytomegalovirus‐Infected Primary Fibroblasts

Increasingly mechanistic virology studies require dependable and sensitive methods for isolating purified organelles containing functional cellular sub‐domains. The mitochondrial network is, in part, closely apposed to the endoplasmic reticulum (ER). The mitochondria‐associated membrane (MAM) fraction provides direct physical contact between the ER and mitochondria. Characterization of the dual localization and trafficking of human cytomegalovirus (HCMV) UL37 proteins required establishing protocols in which the ER and mitochondria could be reliably separated. Because of its documented role in lipid and ceramide transfer from the ER to mitochondria, a method to purify MAM from infected cells was also developed. Two robust procedures were developed to efficiently isolate mitochondria, ER, and MAM fractions while providing the substantial protein yields from HCMV‐infected primary fibroblasts and from transfected HeLa cells. Moreover, this unit includes a protocol that allows visualization of the mitochondria network disruption that occurs in permissively infected cells by their optimal resolution in Percoll gradients. Curr. Protoc. Cell Biol. 37:3.27. 1‐3.27. 23. © 2007 by John Wiley & Sons, Inc.