First pandemic A (H1N1) pdm09 outbreak in a private school, Bangkok, Thailand, June 2009.

OBJECTIVE: On June 9, 2009, the Thailand Ministry of Public Health received their first report of an outbreak of the pandemic A (HIN1) pdm09 that occurred in a school. The authors conducted a study to describe the epidemiological characteristics of the outbreak and its resurgence, estimate the basic reproduction number (R) and review recommendations for prevention and control. MATERIAL AND METHOD: Active case finding in the school and reviewing reports to the national surveillance system identified 184 students infected by the new virus. A survey described the illness in the students and the prevention and control measures taken by the school. The basic reproduction number was estimated from data in the early epidemic phase. The other survey was done to assess factors contributing to the resurgence of the outbreak. RESULTS: Students with the pandemic A (HINI) pdm09 had a mild illness resembling seasonal influenza. Overcrowding in the classroom and activities that mixed students from different classes contributed to transmission in the school. The basic reproduction number for this school-based setting is 3.58. The second outbreak occurred because of poor monitoring of absenteeism and management of ill students. CONCLUSION: This was the first outbreak ofthepandemic A (HIN1) pdm09 in Thailand. The source could not be identified. Effective control measures monitoring, screening, strict personal hygiene and proper management of ill students.

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology.

A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Existing computational approaches focus on either scoring the pathogenicity of mutations or characterizing their effects at specific scales. Here, we established a unified computational framework, NetFlow3D, that systematically maps the multiscale mechanistic effects of somatic mutations in cancer. The establishment of NetFlow3D hinges upon the Human Protein Structurome, a complete repository we first compiled that incorporates the 3D structures of every single protein as well as the binding interfaces for all known PPIs in humans. The vast majority of 3D structural information was resolved by recent deep learning algorithms. By applying NetFlow3D to 415,017 somatic protein-altering mutations in 5,950 TCGA tumors across 19 cancer types, we identified 1,656 intra- and 3,343 inter-protein 3D clusters of mutations throughout the Human Protein Structurome, of which ~50% would not have been found if using only experimentally-determined protein structures. These 3D clusters have converging effects on 377 cellular subnetworks. Compared to canonical PPI network analyses, NetFlow3D achieved a 5.5-fold higher statistical power for identifying significantly dysregulated subnetworks. The majority of identified subnetworks were previously obscured by the overwhelming background noise of non-clustered passenger mutations, including portions of non-canonical PRC1, mediator complex, MCM2-7 complex, neddylation of cullins, complement system, TRiC, etc. NetFlow3D and our pan-cancer results can be accessed from http://netflow3d.yulab.org. This work shows that mapping how individual mutations act across scales requires the integration of their local spatial organization on protein structures and their global topological organization in the PPI network.

Lessons from the 2006 Louisiana health and population survey.

The 2005 hurricane season caused extensive damage and induced a mass migration of approximately 1.1 million people from southern Louisiana in the United States. Current and accurate estimates of population size and demographics and an assessment of the critical needs for public services were required to guide recovery efforts. Since forecasts using pre-hurricane data may produce inaccurate estimates of the post-hurricane population, a household survey in 18 hurricane-affected parishes was conducted to provide timely and credible information on the size of these populations, their demographics and their condition. This paper describes the methods used, the challenges encountered, and the key factors for successful implementation. This post-disaster survey was unique because it identified the needs of the people in the affected parishes and quantified the number of people with these needs. Consequently, this survey established new population and health indicator baselines that otherwise would have not been available to guide the relief and recovery efforts in southern Louisiana.

Oral anticoagulation in the hospital: analysis of patients at risk.

Warfarin is one of the most commonly used medications associated with adverse events. Warfarin therapy is often initiated or continued in the hospital, yet hospitalization increases the risk of poor anticoagulation control with warfarin. To help understand this, we retrospectively reviewed the records of patients admitted to our hospital during a 6-month period who were given at least one dose of warfarin. To explore factors that may have contributed to poor anticoagulation control, we compared characteristics of patients with an international normalized ratio (INR) ≥ 5 at some point during hospitalization with those of a group of matched controls who also received warfarin and had INR <5. Among the 35 patients identified who had an INR ≥ 5, concomitant use of antibiotics was more common than among 105 matched controls; improper warfarin dosing also appeared to contribute to the high INRs. These findings indicate possible targets for intervention to improve patient safety.

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.

Orbital Inflammatory Syndrome and Anterior Uveitis: A Case Series.

PURPOSE: To describe four cases of orbital inflammatory syndrome (OIS) with associated anterior uveitis that have presented within 2 years to our practice. METHODS: Charts of patients diagnosed with OIS from June 2013 to May 2015 were reviewed. RESULTS: Four patients, three children and one adult, presented with orbital swelling, pain, and varying degrees of vision loss. Treatment with intravenous methylprednisolone resulted in significant symptomatic improvement in all cases initially; when symptoms recurred, the patients had evidence of anterior uveitis. With continued systemic therapy and the addition of topical prednisolone, the patients all achieved control of their uveitis and OIS and are well controlled with regular outpatient follow-up. CONCLUSIONS: Reports of OIS-associated with uveitis are relatively rare. The presentation of three pediatric patients and one adult patient to the same practice with OIS and secondary uveitis within a 2-year period may indicate that the association is underreported.

Maternal exposure to polybrominated and polychlorinated biphenyls: infant birth weight and gestational age.

Understanding the influence of maternal exposures on gestational age and birth weight is essential given that pre-term and/or low birth weight infants are at risk for increased mortality and morbidity. We performed a retrospective analysis of a cohort exposed to polybrominated biphenyls (PBB) through accidental contamination of cattle feed and polychlorinated biphenyls (PCB) through residual contamination in the geographic region. Our study population consisted of 444 mothers and their 899 infants born between 1975 and 1997. Using restricted maximum likelihood estimation, no significant association was found between estimated maternal serum PBB at conception or enrollment PCB levels and gestational age or infant birth weight in unadjusted models or in models that adjusted for maternal age, smoking, parity, infant gender, and decade of birth. For enrollment maternal serum PBB, no association was observed for gestational age. However, a negative association with high levels of enrollment maternal serum PBB and birth weight was suggested. We also examined the birth weight and gestational age among offspring of women with the highest (10%) PBB or PCB exposure, and observed no significant association. Because brominated compounds are currently used in consumer products and therefore, are increasingly prevalent in the environment, additional research is needed to better understand the potential relationship between in utero exposure to brominated compounds and adverse health outcomes.

Building confidence in quantitative systems pharmacology models: An engineer's guide to exploring the rationale in model design and development.

This tutorial promotes good practice for exploring the rationale of systems pharmacology models. A safety systems engineering inspired notation approach provides much needed rigor and transparency in development and application of models for therapeutic discovery and design of intervention strategies. Structured arguments over a model's development, underpinning biological knowledge, and analyses of model behaviors are constructed to determine the confidence that a model is fit for the purpose for which it will be applied.

Inorganic arsenic in cooked rice and vegetables from Bangladeshi households.

Many Bangladeshi suffer from arsenic-related health concerns. Most mitigation activities focus on identifying contaminated wells and reducing the amount of arsenic ingested from well water. Food as a source of arsenic exposure has been recently documented. The objectives of this study were to measure the main types of arsenic in commonly consumed foods in Bangladesh and estimate the average daily intake (ADI) of arsenic from food and water. Total, organic and inorganic, arsenic were measured in drinking water and in cooked rice and vegetables from Bangladeshi households. The mean total arsenic level in 46 rice samples was 358 microg/kg (range: 46 to 1,110 microg/kg dry weight) and 333 microg/kg (range: 19 to 2,334 microg/kg dry weight) in 39 vegetable samples. Inorganic arsenic calculated as arsenite and arsenate made up 87% of the total arsenic measured in rice, and 96% of the total arsenic in vegetables. Total arsenic in water ranged from 200 to 500 microg/L. Using individual, self-reported data on daily consumption of rice and drinking water the total arsenic ADI was 1,176 microg (range: 419 to 2,053 microg), 14% attributable to inorganic arsenic in cooked rice. The ADI is a conservative estimate; vegetable arsenic was not included due to limitations in self-reported daily consumption amounts. Given the arsenic levels measured in food and water and consumption of these items, cooked rice and vegetables are a substantial exposure pathway for inorganic arsenic. Intervention strategies must consider all sources of dietary arsenic intake.

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation.

Tetramethylenedisulfotetramine: old agent and new terror.

Tetramethylenedisulfotetramine has accounted for numerous intentional and unintentional poisonings in China. In May 2002, the first known case of human illness in the United States caused by tetramethylenedisulfotetramine, a banned neurotoxic rodenticide from China, occurred in New York City. The clinical presentation after tetramethylenedisulfotetramine exposure is dose dependent, and the most recognized complication is status epilepticus. Poisonings may be fatal within hours. No known antidote exists, and treatment is mainly supportive. Anecdotal reports, case reports, and 2 animal studies suggest possible success with certain pharmacologic interventions, including pyridoxine and chelation therapy. Pesticide and rodenticide poisonings, whether intentional or unintentional, pose a serious threat to populations, and the availability of a banned rodenticide such as tetramethylenedisulfotetramine, with its associated morbidity and lethality, is a serious public health concern. Given the recent case report that confirms the presence of tetramethylenedisulfotetramine in the United States, the toxicity of the compound, its unique physical properties, the absence of an antidote, and the history of its use as an agent of intentional mass poisoning, public health entities have undertaken educational efforts to inform the public, health care providers, and emergency personnel of this potentially lethal rodenticide.

Menstrual function among women exposed to polybrominated biphenyls: a follow-up prevalence study.

BACKGROUND: Alteration in menstrual cycle function is suggested among rhesus monkeys and humans exposed to polybrominated biphenyls (PBBs) and structurally similar polychlorinated biphenyls (PCBs). The feedback system for menstrual cycle function potentially allows multiple pathways for disruption directly through the hypothalamic-pituitary-ovarian axis and indirectly through alternative neuroendocrine axes. METHODS: The Michigan Female Health Study was conducted during 1997-1998 among women in a cohort exposed to PBBs in 1973. This study included 337 women with self-reported menstrual cycles of 20-35 days (age range: 24-56 years). Current PBB levels were estimated by exponential decay modeling of serum PBB levels collected from 1976-1987 during enrollment in the Michigan PBB cohort. Linear regression models for menstrual cycle length and the logarithm of bleed length used estimated current PBB exposure or enrollment PBB exposure categorized in tertiles, and for the upper decile. All models were adjusted for serum PCB levels, age, body mass index, history of at least 10% weight loss in the past year, physical activity, smoking, education, and household income. RESULTS: Higher levels of physical activity were associated with shorter bleed length, and increasing age was associated with shorter cycle length. Although no overall association was found between PBB exposure and menstrual cycle characteristics, a significant interaction between PBB exposures with past year weight loss was found. Longer bleed length and shorter cycle length were associated with higher PBB exposure among women with past year weight loss. CONCLUSION: This study suggests that PBB exposure may impact ovarian function as indicated by menstrual cycle length and bleed length. However, these associations were found among the small number of women with recent weight loss suggesting either a chance finding or that mobilization of PBBs from lipid stores may be important. These results should be replicated with larger numbers of women exposed to similar lipophilic compounds.

Agent-Based Modeling in Systems Pharmacology.

Modeling and simulation (M&S) techniques provide a platform for knowledge integration and hypothesis testing to gain insights into biological systems that would not be possible a priori. Agent-based modeling (ABM) is an M&S technique that focuses on describing individual components rather than homogenous populations. This tutorial introduces ABM to systems pharmacologists, using relevant case studies to highlight how ABM-specific strengths have yielded success in the area of preclinical mechanistic modeling.

Polybrominated biphenyl exposure and benign breast disease in a cohort of US women.

PURPOSE: We examined the relation between serum polybrominated biphenyl (PBB) levels and the risk of benign breast disease in a cohort of Michigan women unintentionally exposed to PBBs in 1973 and interviewed in 1997. METHODS: We used extended Cox models to generate adjusted hazard ratios; models included polychlorinated biphenyls (PCBs) and risk factors for benign breast disease reported in the literature. RESULTS: Two hundred fourteen (23%) of 951 women reported benign breast disease diagnosed by a physician. Compared with women with low PBB exposure, benign breast disease was not reported more frequently among those with moderate (>1-12 parts per billion [ppb]), (odds ratio [OR] 1.08, 95% confidence interval [CI] = 0.80-1.45), or high (>12 ppb), (OR 0.79, 95% CI = 0.46-1.38) PBB exposure. PCB exposure was also not associated with self-reported physician-diagnosed benign breast disease. Age, smoking, and annual number of health-care provider visits were significantly associated with benign breast disease. CONCLUSIONS: Our analysis did not demonstrate an association between serum PBB level and self- reported physician-diagnosed benign breast disease. We did observe an increased risk of benign breast disease for women who smoked, an association that has not been consistently found in previous studies.

Effect of aminoguanidine on plasma nitric oxide by-products and blood flow during chronic peritoneal sepsis.

We hypothesized that plasma nitric oxide (NO), generated via inducible NO synthase (iNOS) or endothelial constitutive NO synthase and measured via its by-products NO2- and NO3- (NO2- + NO3- = NOx) would increase and remain elevated during chronic peritoneal sepsis. We further hypothesized that treatment with aminoguanidine (AG; 50 mg/kg), a selective iNOS inhibitor, would decrease NO production and alter blood flow. Sprague Dawley rats were randomized to septic and nonseptic groups. Septic rats received an intraperitoneal cecal slurry (200 mg of cecal material/5 mL 5% dextrose-H2O/kg); control rats received sterile 5% dextrose-H2O (5 mL/kg) only. Plasma NOx and hemodynamics were measured 0, 4, 12, 24, and 48 h after sepsis or sham induction. We also examined the effect of AG, an iNOS inhibitor, on plasma NOx levels and tissue blood flow at 24 h. Septic rats uniformly displayed signs of sepsis, including lethargy, piloerection, and diarrhea. NOx levels were significantly elevated compared with controls at 4, 12, 24, and 48 h (p < or = .05). Septic rats also demonstrated hypotension (t = 12, 24, and 48 h) and tachycardia (t = 4, 12, 24, and 48 h). The infusion of AG (50 mg/kg intravenously for 30 min) at 24 h significantly decreased plasma NOx in septic animals. Plasma NOx concentrations returned to basal levels by 90 min after infusion of AG. In addition, blood flow studies demonstrated that AG treatment in nonseptic rats resulted in a significant decrease in blood flow to the stomach, skin, and adipose tissue, whereas AG infusion did not significantly alter the regional perfusion profile in septic animals. Furthermore, treatment with AG did not significantly alter mean arterial pressure in either group; however, nonseptic animals exhibited a decrease in stroke volume, and septic animals demonstrated an increase in heart rate. In contrast to the rise and fall of NOx levels in endotoxemia, this study demonstrates that the initial rise is sustained during 48 h of peritoneal sepsis. This sustained increase in NOx levels in this model correlated with the observable signs of systemic infection and may relate to enhanced iNOS activity. AG infusion demonstrated variable effects on regional tissue blood flow profiles in septic and nonseptic animals and attenuated the increase in plasma NOx levels in septic animals, an index of iNOS activity.

Central versus peripheral mediation of naloxone's perfusion effects in endotoxic rats.

Opioid receptor antagonists can act centrally and peripherally. It is unclear if these 2 pathways differentially mediate the perfusion-associated effects of opioid antagonism during endotoxemia. Male, Sprague-Dawley rats (340-390 g) were surgically prepared with left ventricular, tail artery, and jugular vein catheters 24 h before experiments were begun. Conscious, unrestrained rats were challenged with Escherichia coli lipopolysaccharide (LPS; 2 mg/kg/hr over 30 min) infusion. Measurements of regional blood flows were made using radioactive microspheres prior to (baseline), and at 60 and 120 min after LPS infusion. Saline (1 mL/kg bolus + 0.5 mL/kg/h infusion), naloxone (Nlx; 4 mg/kg bolus + 2 mg/kg/h infusion), or naloxone methyl bromide (Nlx-mb; 4.64 mg/kg, bolus + 2.32 mg/kg/h infusion) were administered 40 min after LPS infusion was begun. Nlx-mb does not cross the blood-brain barrier, and was thus used to differentiate central from peripherally mediated responses. At the end of each experiment, blood samples were collected for determination of ET-1 and nitric oxide metabolites (NOx = NO3 + NO2) using enzyme-linked immunosorbent assay (ELISA) and Griess reaction methods, respectively. Endotoxemia produced a significant decrease in cardiac output and an increase in systemic vascular resistance. Treatment with Nlx or Nlx-mb significantly attenuated the endotoxin-induced elevation in systemic vascular resistance and the decrease in cardiac output at 60 min after induction of endotoxemia compared with their respective baseline values. Nlx and Nlx-mb also attenuated the endotoxin-induced increases in hepatic portal and skeletal vascular resistances. These observations suggested that the ameliorative effect of Nlx on endotoxemia-induced regional vascular resistance alterations was mediated via peripheral opioid receptor mechanisms. However, although Nlx attenuated the endotoxin-induced decreases in the blood flow to the stomach and pancreas, Nlx-mb attenuated the endotoxin-induced decreases in the blood flow to the small intestine and cecum, in addition to the pancreas and, to some extent, the stomach. As such, separate central and peripherally mediated actions of opioid receptor antagonism were indicated. Nlx also resulted in an increase in the plasma levels of ET-1 only, whereas Nlx-mb increased the plasma levels of ET-1 and NOx. These observations suggest that separate central and peripheral effects of opioids during endotoxemia play a role in the associated circulatory alterations, and may differentially affect the release and/or synthesis of vasoactive mediators that might be related to their varied hepatosplanchnic vascular response during endotoxemia.

Elevated coronary endothelin-1 but not nitric oxide in diabetics during CABG.

BACKGROUND: After coronary artery bypass grafting procedures, a higher incidence of morbidity and mortality has been reported in diabetic patients. We tested whether coronary artery bypass grafting in diabetics affects the endothelin-1 and nitric oxide coronary effluent profile during reperfusion. METHODS: Twenty-one consecutive patients (9 with type II diabetes mellitus, 12 non-diabetics) underwent coronary artery bypass grafting by one surgeon. The two groups did not differ in preoperative ejection fraction, Parsonnet score, number of vessels bypassed, or cross-clamp time. Each patient was treated in the same intraoperative manner with single atrial, aortic, and antegrade and retrograde cardioplegia (CPL) cannulas. Cold CPL arrest was by antegrade and retrograde infusion of modified Buckberg CPL solution. Warm CPL solution was infused before reperfusion. Coronary sinus blood samples were obtained for estimation of endothelin-1 and nitrite plus nitrate before CPL arrest and at 1 and 15 minutes after each of 2 reperfusion periods. RESULTS: In diabetics, endothelin-1 was significantly increased at all reperfusion times as compared with non-diabetics. Nitrite plus nitrate levels were significantly higher in patients with diabetes than in those without, but did not change with time in either of the groups. CONCLUSIONS: Reperfusion after CPL during coronary artery bypass grafting procedure can trigger the release of endothelin-1 in patients with diabetes mellitus. This may favor increased vascular tone or positive inotropic responses after coronary artery bypass grafting and may contribute to significant cardiovascular consequences in diabetic patients.