Extracting information on pneumonia in infants using natural language processing of radiology reports

Natural language processing (NLP) is critical for improvement of the healthcare process because it can encode clinical data in patient documents. Many clinical applications such as decision support require coded data to function appropriately. However, in order to be applicable for healthcare, performance must be adequate. A valuable automated application is the detection of infectious diseases, such as surveillance of pneumonia in newborns (e.g., neonates) because the disease produces significant rates of morbidity and mortality, and manual surveillance is challenging. Studies have demonstrated that automated surveillance using NLP is a useful adjunct to manual surveillance and an effective tool for infection control practitioners. This paper presents a study evaluating the feasibility of an NLP-based monitoring system to screen for healthcare-associated pneumonia in neonates. We estimated sensitivity, specificity, and positive predictive value by comparing results with clinicians' judgments. Sensitivity was 71% and specificity was 99%. Our results demonstrated that the automated method was feasible.     

DiGeorge anomaly in a patient with isochromosome 18p born to a diabetic mother

The DiGeorge anomaly (DGA) is an etiologically heterogeneous developmental field defect in which cardiovascular malformations, hypocalcemia, thymic hypoplasia, and characteristic dysmorphisms are major clinical features. The 22q11.2 deletion is the most common single etiology of DGA, although a number of other chromosomal abnormalities and teratogens, including maternal diabetes, have been implicated as well. We present a patient, born to a diabetic mother, with interrupted aortic arch type B (IAA-B), neonatal hypocalcemia, thymic hypoplasia, and dysmorphic features including microcephaly, thick, overfolded helices, and anteriorly-placed anus. Cytogenetic studies showed the presence of a marker chromosome, identified by fluorescence in-situ hybridization (FISH) as an isochromosome 18p [i(18p)]. We did not detect a 22q11.2 deletion by FISH using a cosmid probe corresponding to locus D22S75. The patient is the first example of either DGA or IAA-B in a patient with i(18p). We review the genetic abnormalities associated with DGA, and discuss the potential contributions of maternal diabetes and i(18p) in our patient.     

Immunoglobulins in the egg,embryo and young chick

Current knowledge of the immunoglobulin classes identified in some avian species is reviewed. The distribution and fate of passively acquired immunoglobulins or specific antibodies in compartments of the egg and of the developing embryo and in the newly hatched chick are described, together with the ontogeny of active Ig biosynthesis.     

Prevention of mother-to-child transmission of HIV--successes, controversies and critical questions

In a relatively short period of time enormous strides have been made in the field of mother-to-child transmission (MTCT) of HIV. Timing, mechanisms and risk factors for transmission have been elucidated and a large number of drug regimens have been shown to effectively reduce the risk of HIV infection in the child. A number of observations can be gleaned from the work that has been done to design and implement HIV perinatal prevention programs. First, pregnancy is a critical time to identify women with HIV infection and to link them and their families to ongoing HIV care and treatment In addition to providing perinatal prevention intervention, pregnancy serves as an entry point into the health-care system. There is a unique opportunity to link prevention and treatment efforts, two programmatic areas often viewed as conflicting and competing. Second, the evolution of perinatal prevention in high-resource settings and, to an increasing extent, more resource-constrained areas, reflects the interplay of science and public-health policy. Results of clinical trials and epidemiologic studies have progressively provided recommendations and guidelines for HIV counseling, testing and treatment for perinatal prevention. In many ways, the successes of perinatal prevention in the USA attest to the success of the dynamic interaction between health, science, and public policy. There is great hope and expectation that the next decade will be equally successful as care and treatment becomes increasingly available in resource-constrained settings. Third, a key element of perinatal prevention is the provision of safe and effective family planning to women of childbearing years. Many women, particularly in low-resource settings, have multiple pregnancies, influenced by cultural imperatives and limited access to safe, affordable contraception. Enhancing these services will enable women to make informed decisions about their health, their families, and their futures. Finally, it is critical to remember that primary prevention of HIV infection in women holds the true key to perinatal prevention. While work must continue to identify more efficacious and safe regimens to prevent MTCT, preventing women from becoming HIV-infected should remain the true measure of success.     

The major peanut allergen,Ara h 2, functions as a trypsin inhibitor,and roasting enhances this function

BACKGROUND: The widespread use of peanut products, the severity of the symptoms, and its persistence in afflicted individuals has made peanut allergy a major health concern in western countries such as the United States, United Kingdom, and Canada. In a previous study, the authors showed that the allergenic properties of peanut proteins are enhanced as a result of thermal processing. OBJECTIVE: The purpose of this investigation was to determine whether any specific functions are associated with the major peanut allergen, Ara h 2, and whether the functionality of this protein is influenced by processing. An assay was developed and used to assess structure/function changes in Ara h 2 induced by roasting and the effect of these alterations on the allergenic properties of this major peanut allergen. METHODS: A protein domain homology search was used to determine possible functions for Ara h 2. One of the putative functions (protease inhibition) was tested by means of appropriate enzyme assays and protein gel electrophoresis. Circular dichroism was used to compare the structural properties of Ara h 2 purified from raw and roasted peanuts. RESULTS: Ara h 2 purified from peanuts is homologous to and functions as a trypsin inhibitor. Roasting caused a 3.6-fold increase in trypsin inhibitory activity. Functional and structural comparison of the Ara h 2 purified from roasted peanuts to native and reduced Ara h 2 from raw peanuts revealed that the roasted Ara h 2 mimics the behavior of native Ara h 2 in a partially reduced form. CONCLUSIONS: The data indicate that thermal processing might play an important role in enhancing the allergenic properties of peanuts. Not only has it previously been shown to affect the structural and allergic properties of peanut proteins but also, for the first time, the functional characteristics of an allergen. These structural and functional alterations are likely to influence the allergenicity of peanuts.     

Null mutation in human ciliary neurotrophic factor gene confers higher body mass index in males

Ciliary neurotrophic factor (CNTF) administration reduces weight in leptin-resistant mice via the signalling pathway normally activated by leptin. A G>A null mutation in the CNTF gene results in complete absence of protein. We hypothesised that absence of CNTF could lead to diminished initiation of anorectic pathways, with consequent increase in body mass. In 575 Caucasian men aged 59-73 years, the A/A genotype (frequency 1.9%) was associated with a 10 kg increase in weight (P=0.03, 2 df) and 3 kg/m(2) greater BMI (P=0.02, 2 df). There was no effect in women. The CNTF G>A null mutation therefore confers a moderate effect on obesity in males of A/A genotype, who represent 1% of the general population.     

Bacterial superantigen-treated intestinal epithelial cells upregulate heat shock proteins 25 and 72 and are resistant to oxidant cytotoxicity

While the pathological events evoked by infection are commonly described, effective host responses to bacteria and their products should primarily be protective. Heat shock protein (Hsp) expression is upregulated by many stimuli and serves to maintain intracellular protein integrity. The ability of the prototypic superantigen, Staphylococcus aureus enterotoxin B (SEB) to induce Hsps was investigated with BALB/c mice and by in vitro addition to the murine small intestinal epithelial cell line MSIE. SEB-treated (5 or 100 microg intraperitoneally) mice revealed increased Hsp25 and Hsp72, but not Hsc73, in jejunal lymphocytes and epithelial cells. A similar Hsp response to SEB occurred in MSIE cells and was preceded by activation of the ERK1/2 and p38 mitogen-activated protein kinases but not the SAPK/JNK pathway; pharmacological inhibition of ERK1/2, but not p38, significantly reduced SEB-induced Hsps. Moreover, SEB-treated MSIE cells were protected against oxidant-induced cytotoxicity (measured by 51Cr release) and F-actin depolymerization. Thus, SEB exposure results in a rapid induction of the Hsp25 and Hsp72 in intestinal epithelial cells, both directly and through lymphocyte activation, and we suggest that this event is important in protecting the gut from damage by Staphylococcus infection or in the reparatory process and may be a generalized response to lumen-derived bacterial toxins.     

Abnormalities of cholesterol metabolism in autism spectrum disorders.

Although Smith-Lemli-Opitz Syndrome (SLOS), a genetic condition of impaired cholesterol biosynthesis, is associated with autism [Tierney et al., 2001; Am J Med Genet 98:191-200.], the incidence of SLOS and other sterol disorders among individuals with autism spectrum disorders (ASD) is unknown. This study investigated (1) the incidence of biochemically diagnosed SLOS in blood samples from a cohort of subjects with ASD from families in which more than one individual had ASD and (2) the type and incidence of other sterol disorders in the same group. Using gas chromatography/mass spectrometry, cholesterol, and its precursor sterols were quantified in 100 samples from subjects with ASD obtained from the Autism Genetic Resource Exchange (AGRE) specimen repository. Although no sample had sterol levels consistent with SLOS, 19 samples had total cholesterol levels lower than 100 mg/dl, which is below the 5th centile for children over age 2 years. These findings suggest that, in addition to SLOS, there may be other disorders of sterol metabolism or homeostasis associated with ASD.     

Nucleotide sequence of RNA segment 3 of the avian influenza A/FPV/Rostock/34 and its comparison with the corresponding segment of human strains A/PR/8/34 and A/NT/60/68

The nucleotide sequence of RNA segment 3 of A/FPV/Rostock/34 (H7N1), an avian strain of influenza A virus, has been determined from a cloned DNA copy. Segment 3 codes for the PA polypeptide and the sequence specifies an acidic polypeptide of 716 amino acid residues. Comparison of the sequence with the corresponding segment of two human strains A/PR/8/34 and A/NT/60/68 indicates significant divergence of the avian sequence from the human sequences at the nucleotide level. At the amino acid level there is considerably greater homology between the avian and human strains. This presumably reflects a constraint on divergence of the PA polypeptide imposed by a common functional requirement of PA in all influenza virus strains.     

Study of carrier frequency of Warsaw breakage syndrome in the Ashkenazi Jewish population and presentation of two cases

Warsaw breakage syndrome (WABS), caused by bi‐allelic variants in the DDX11 gene, is a rare cohesinopathy characterized by pre‐ and postnatal growth retardation, microcephaly, intellectual disability, facial dysmorphia, and sensorineural hearing loss due to cochlear hypoplasia. The DDX11 gene codes for an iron–sulfur DNA helicase in the Superfamily 2 helicases and plays an important role in genomic stability and maintenance. Fourteen individuals with WABS have been previously reported in the medical literature. Affected individuals have been of various ethnic backgrounds with different pathogenic variants. We report two unrelated individuals of Ashkenazi Jewish descent affected with WABS, who are homozygous for the c.1763‐1G>C variant in the DDX11 gene. Their phenotype is consistent with previously reported individuals. RNA studies showed that this variant causes an alternative splice acceptor site leading to a frameshift in the open reading frame. Carrier screening of the c.1763‐1G>C variant in the Jewish population revealed a high carrier frequency of 1 in 68 in the Ashkenazi Jewish population. Due to the high carrier frequency and the low number of affected individuals, we hypothesize a high rate of miscarriage of homozygous fetuses and/or subfertility for carrier couples. If the carrier frequency is reproducible in additional Ashkenazi Jewish populations, we suggest including DDX11 to Ashkenazi Jewish carrier screening panels.