Homology-directed repair involves multiple strand invasion cycles in fission yeast.

Homology-directed repair of DNA double-strand breaks (DSBs) represents a highly faithful pathway. Non-crossover repair dominates in mitotically growing cells, likely through a preference for synthesis-dependent strand annealing (SDSA). How homology-directed repair mechanism choice is orchestrated in time and space is not well understood. Here, we develop a microscopy-based assay in living fission yeast to determine the dynamics and kinetics of an engineered, site-specific interhomologue repair event. We observe highly efficient homology search and homology-directed repair in this system. Surprisingly, the initial distance between the DSB and the donor sequence does not correlate with the duration of repair. Instead, we observe that repair often involves multiple site-specific and Rad51-dependent colocalization events between the DSB and donor sequence. Upon loss of the RecQ helicase Rqh1 (BLM in humans) we observe rapid repair possibly involving a single strand invasion event, suggesting that multiple strand invasion cycles antagonized by Rqh1 could reflect ongoing SDSA. However, failure to colocalize with the donor sequence and execute repair is also more likely in rqh1Δ cells, possibly reflecting erroneous strand invasion. This work has implications for the molecular etiology of Bloom syndrome, caused by mutations in BLM and characterized by aberrant sister chromatid crossovers and inefficient repair.

Potential Association of Doxycycline With the Onset of Primary Sclerosing Cholangitis: A Case Series.

BACKGROUND: Primary sclerosing cholangitis (PSC) is linked to inflammatory bowel diseases (IBD). Evidence suggests an association between the gut microbiome and PSC. However, the putative relationship between exposure to antibiotics and onset of PSC has never been reported. We observed 3 cases in which patients without antecedent liver or bowel issues developed symptoms leading to diagnosis of IBD and subsequently PSC after being exposed to doxycycline. We aimed to identify, through the PSC Partners national patient registry, additional cases of PSC in which there is a temporal relationship between exposure to doxycycline and onset of PSC or PSC-IBD. AREAS OF UNCERTAINTY: The etiopathogenesis of PSC remains an enigma. DATA SOURCES: We collected data from patients with PSC and PSC-IBD in which there seemed to be a temporal relationship between exposure to doxycycline and PSC. Time from doxycycline exposure to: (1) onset of PSC or PSC-IBD symptoms and (2) diagnosis of PSC were documented for each patient. Descriptive statistical analyses were performed. RESULTS: We identified 6 additional patients with PSC or PSC-IBD in whom there was a temporal relationship between exposure to doxycycline and onset of PSC or PSC-IBD. The median age of these 9 patients was 20 years, 6 were female, and 7 had ulcerative colitis. The median time from doxycycline exposure to onset of first symptoms was 3 months, and median time from doxycycline exposure to diagnosis of PSC was 15 months. THERAPEUTIC HYPOTHESIS: We describe 9 cases of PSC and PSC-IBD in which there seem to be a temporal relationship between exposure to doxycycline and onset of PSC.

Financial costs to the U.S. Army for suicides by newly enlisted Soldiers.

OBJECTIVE: To estimate the financial burden to the U.S. Army of suicide by enlisted Soldiers during their first year of service. METHODS: This analysis included new Army enlisted Soldiers who started initial entry training from October 2012 through September 2016 and subsequently died by suicide within their first year of service. Outpatient and inpatient direct medical, direct nonmedical, recruiting, and training costs to the Army were calculated. RESULTS: During the 48-month observational study period, 29 Soldiers died by suicide within their respective first year of service. The described financial costs accrued by the Army as a result of these deaths were $152,271-with an average of $6,091 per healthcare utilizer. Recruiting and training costs were $1,115,860 for all suicide cases. CONCLUSION: Average direct cost per healthcare utilizer increased during a Soldier's first year of service. This may be associated with the transition through different phases of training and to the first operational duty station. PUBLIC HEALTH IMPLICATIONS: Results obtained through this cost-of-illness analysis may serve as baseline metrics to inform future cost-effectiveness studies.

Mortality Among Male U.S. Army Soldiers Within 18 Months of Separation.

INTRODUCTION: Understanding how soldiers die after separation from military service, particularly those who die shortly after separating from service, may help to identify opportunities to ease transitions to civilian life. MATERIALS AND METHODS: Mortality data were analyzed for male U.S. Army soldiers who died within 18 months of their separation from service (from 1999 to 2011). Descriptive statistics were calculated for natural, accidental, suicidal, homicidal, undetermined, and legal/operation of war deaths and were stratified by age, component, time in service, and type of discharge. Crude and age-adjusted mortality rates, standardized for all years using the 2004 Regular Army population, were also calculated. The Public Health Review Board of the U.S. Army Public Health Center approved this study as Public Health Practice. RESULTS: Of the 1,884,653 male soldiers who separated from service during the study period, 3,819 died within 18 months of separation. A majority of all separations were Reserve or National Guard (58%), and 62% of decedents were in the Reserve or National Guard. Deaths from natural causes (38%) were the most common, followed by accident deaths (34%), suicides (20%), homicides (6%), undetermined deaths (2%), and legal/operation of war deaths (<1%). For overall mortality, age-adjusted rates were higher among the male U.S. population when compared to male soldiers who had separated from the Army. CONCLUSIONS: The time period immediately following separation from the Army presents a unique challenge for many soldiers. Developing more effective pre-separation prevention programs that target specific risks requires knowing the causes of death for natural deaths, suicides, and accidents. Over half of all deaths occurring shortly after separation from service are preventable. Continued surveillance of specific causes of preventable deaths following separation can improve pre-separation prevention programs and transitions to post-service care.

Successful response of primary sclerosing cholangitis and associated ulcerative colitis to oral vancomycin may depend on brand and personalized dose: report in an adolescent.

Primary sclerosing cholangitis (PSC) is a rare, progressive liver disease characterized by cholestasis and bile duct fibrosis that has no accepted therapy known to delay or arrest its progression. We report a 23-year-old female patient who at age 14 was diagnosed with moderate pancolonic ulcerative colitis (UC) and at age 15 with small-duct PSC unresponsive to conventional therapy. The patient began single drug therapy with the antibiotic oral vancomycin (OVT) and achieved normalization of liver enzymes and resolution of UC symptoms with colonic mucosal healing. These improvements have persisted over 8 years. There has been no colon dysplasia, liver fibrosis or failure, bile duct stricture, or cancer. Of note, the patient's response was dependent on the brand of oral vancomycin capsule, as well as dose. This raised the questions of possible differences in bioequivalence of different commercial versions of the drug and whether this factor might play into the variability of efficacy seen in published trials. Evidence suggests that oral vancomycin both alters the intestinal microbiome and has immunomodulatory effects. Its striking effectiveness in this and other patients supports further investigation in randomized trials, with careful attention to its bioavailability profile in the gut.

Open-label prospective therapeutic clinical trials: oral vancomycin in children and adults with primary sclerosing cholangitis.

BACKGROUND: Oral vancomycin (OV) in primary sclerosing cholangitis (PSC) has been evaluated as a potential therapeutic agent. We report the long-term biochemical course and outcomes of patients with PSC treated with OV. METHODS: Patients were enrolled in 2 open-label clinical trials (ClinicalTrials.gov Identifier: NCT01802073 and NCT01322386) and offered OV at 50 mg/kg/day in 3 divided doses if weight <30kg, and 500 mg 3 times/day if weight ≥30kg. Patients with biliary strictures requiring stenting or awaiting liver transplant were excluded. Liver biochemistry, MRCP and histology were documented at baseline and while on OV. The primary outcome was a decrease in elevated gamma glutamyl transferase (GGT), alkaline phosphatase (ALP), and/or alanine aminotransferase (ALT) from baseline. RESULTS: 30 subjects were enrolled, and 29 additional subjects who learned of the clinical trial requested OV (total n = 59; median age was 13.5 years [range, 1.5-44 years]; 64.4% were male; and 94.9% had inflammatory bowel disease [IBD]). The median treatment duration was 2.7 years (range, 0.2-14 years). Ninety-six percent (57/59), 81.3% (48/59), and 94.9% (56/59) experienced reduction of GGT, ALP, and ALT, respectively. Furthermore, 39% (23/59), 22% (13/59), and 55.9% (33/59) experienced normalization of GGT, ALP, and ALT, respectively, within the first 6 months of OV treatment. One patient underwent liver transplantation 8 years after beginning OV treatment, and one developed biliary strictures requiring endoscopic intervention. OV was well-tolerated by patients, and no patient developed treatment-related adverse events. CONCLUSION: In PSC, OV was well-tolerated and was associated with improvement in liver chemistry. A randomized placebo-controlled clinical trial is warranted.

Adjusting Suicide Rates in a Military Population: Methods to Determine the Appropriate Standard Population.

The choice of the standard population is important when calculating adjusted rates for a military population: results can influence policies and funding allocations for programs and initiatives for suicide prevention. We describe the methodological considerations and decision-making process used in choosing a standard population for adjusting rates to compare suicide among US Army soldiers and the general US population. We examined 5 different standard populations, using the direct method to adjust annual suicide rates for the Army and the US population, 2004 to 2015, for age and for age and sex. The pattern of the Army and US population age- and sex-adjusted rates remained consistent with crude rates when adjusted to any of the Army standard population distributions. Using an Army distribution as the standard population produces suicide rates consistent with routine messaging about suicide trends among Army soldiers.

Prenatal treatment of ornithine transcarbamylase deficiency.

PURPOSE OF STUDY: Patients with neonatal urea cycle defects (UCDs) typically experience severe hyperammonemia during the first days of life, which results in serious neurological injury or death. Long-term prognosis despite optimal pharmacological and dietary therapy is still poor. The combination of intravenous sodium phenylacetate and sodium benzoate (Ammonul®) can eliminate nitrogen waste independent of the urea cycle. We report attempts to improve outcomes for males with severe ornithine transcarbamylase deficiency (OTCD), a severe X-linked condition, via prenatal intravenous administration of Ammonul and arginine to heterozygous carrier females of OTCD during labor. METHODS USED: Two heterozygote OTCD mothers carrying male fetuses with a prenatal diagnosis of OTCD received intravenous Ammonul, arginine and dextrose-containing fluids shortly before birth. Maintenance Ammonul and arginine infusions and high-caloric enteral nutrition were started immediately after birth. Ammonul metabolites were measured in umbilical cord blood and the blood of the newborn immediately after delivery. Serial ammonia and biochemical analyses were performed following delivery. SUMMARY OF RESULTS: Therapeutic concentrations of Ammonul metabolites were detected in umbilical cord and neonatal blood samples. Plasma ammonia and glutamine levels in the postnatal period were within the normal range. Peak ammonia levels in the first 24-48h were 53mcmol/l and 62mcmol/l respectively. The boys did not experience neurological sequelae secondary to hyperammonemia and received liver transplantation at ages 3months and 5months. The patients show normal development at ages 7 and 3years. CONCLUSION: Prenatal treatment of mothers who harbor severe OTCD mutations and carry affected male fetuses with intravenous Ammonul and arginine, followed by immediate institution of maintenance infusions after delivery, results in therapeutic levels of benzoate and phenylacetate in the newborn at delivery and, in conjunction with high-caloric enteral nutrition, prevents acute hyperammonemia and neurological decompensation. Following initial medical management, early liver transplantation may improve developmental outcome.

Medical-encounter mental health diagnoses, non-fatal injury and polypharmacy indicators of risk for accident death in the US Army enlisted soldiers, 2004-2009.

Accidents are a leading cause of deaths in U.S. active duty personnel. Understanding accident deaths during wartime could facilitate future operational planning and inform risk prevention efforts. This study expands prior research, identifying health risk factors associated with U.S. Army accident deaths during the Afghanistan and Iraq war. Military records for 2004-2009 enlisted, active duty, Regular Army soldiers were analyzed using logistic regression modeling to identify mental health, injury, and polypharmacy (multiple narcotic and/or psychotropic medications) predictors of accident deaths for current, previously, and never deployed groups. Deployed soldiers with anxiety diagnoses showed higher risk for accident deaths. Over half had anxiety diagnoses prior to being deployed, suggesting anticipatory anxiety or symptom recurrence may contribute to high risk. For previously deployed soldiers, traumatic brain injury (TBI) indicated higher risk. Two-thirds of these soldiers had first TBI medical-encounter while non-deployed, but mild, combat-related TBIs may have been undetected during deployments. Post-Traumatic Stress Disorder (PTSD) predicted higher risk for never deployed soldiers, as did polypharmacy which may relate to reasons for deployment ineligibility. Health risk predictors for Army accident deaths are identified and potential practice and policy implications discussed. Further research could test for replicability and expand models to include unobserved factors or modifiable mechanisms related to high risk. PTSD predicted high risk among those never deployed, suggesting importance of identification, treatment, and prevention of non-combat traumatic events. Finally, risk predictors overlapped with those identified for suicides, suggesting effective intervention might reduce both types of deaths.

Thermodynamics of mixtures of patchy and spherical colloids of different sizes: A multi-body association theory with complete reference fluid information.

We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [A. Bansal et al., J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have the same size. The patchy, solvent particles have short-range directional interactions, while the solute particles have short-range isotropic interactions. The hard-sphere mixture without any association site forms the reference fluid. An important ingredient within the multi-body association theory is the description of clustering of the reference solvent around the reference solute. Here we account for the physical, multi-body clusters of the reference solvent around the reference solute in terms of occupancy statistics in a defined observation volume. These occupancy probabilities are obtained from enhanced sampling simulations, but we also present statistical mechanical models to estimate these probabilities with limited simulation data. Relative to an approach that describes only up to three-body correlations in the reference, incorporating the complete reference information better predicts the bonding state and thermodynamics of the physical solute for a wide range of system conditions. Importantly, analysis of the residual chemical potential of the infinitely dilute solute from molecular simulation and theory shows that whereas the chemical potential is somewhat insensitive to the description of the structure of the reference fluid, the energetic and entropic contributions are not, with the results from the complete reference approach being in better agreement with particle simulations.

Frequency of Improvised Explosive Devices and Suicide Attempts in the U.S. Army.

BACKGROUND: Improvised explosive devices (IEDs) were a prominent and initially new threat in the Iraq and Afghanistan war which raised concerns and anticipatory fear in and out of theater. This study examined the association of monthly IED rates with risk of soldier suicide attempt among those deployed and nondeployed. METHODS: Person-month records for all active duty Regular Army suicide attempters from 2004 through 2009 (n = 9,791) and an equal-probability sample of control person-months (n = 183,826) were identified. Logistic regression analyses examined soldiers' risk of attempting suicide as a function of monthly IED frequency, controlling for sociodemographics, service-related characteristics, rate of deployment/redeployment, and combat deaths and injuries. The association of IED frequency with suicide attempt was examined overall and by time in service and deployment status. FINDINGS: Soldiers' risk of suicide attempt increased with increasing numbers of IEDs. Suicide attempt was 26% more likely for each 1,000 IED increase in monthly frequency (odds ratio [OR] = 1.26, 95% confidence interval [CI] = 1.22-1.30). The association of IED frequency with suicide attempt was greater for soldiers in their first 2 years of service (OR = 1.30, 95% CI = 1.25-1.36) than for those with 3 or more years of service (OR = 1.18, 95% CI = 1.12-1.24). Among soldiers in their first 2 years of service, the association was constant, regardless of deployment status (χ22 = 3.89, p = 0.14). Among soldiers with 3 or more years of service, the association was higher for those never deployed (OR = 1.12, 95% CI = 1.01-1.24) and currently deployed (OR = 1.14, 95% CI = 1.05-1.23) than for those previously deployed. DISCUSSION: To our knowledge, this is the first study to examine and demonstrate an association between the aggregate frequency of IEDs and risk of suicide attempts among U.S. Army soldiers. This association was observed across deployment status and time in service, and for early-career soldiers in particular. The findings suggest that the threat of new weapons may increase stress burden among soldiers. Targeting risk perception and perceived preparedness, particularly early in a soldier's career, may improve psychological resilience and reduce suicide risk.

An Examination of Potential Misclassification of Army Suicides: Results from the Army Study to Assess Risk and Resilience in Servicemembers.

Debate continues about the accuracy of military suicide reporting due to concerns that some suicides may be classified as accidents to minimize stigma and ensure survivor benefits. We systematically reviewed records for 998 active duty Army deaths (510 suicides; 488 accident, homicide, and undetermined deaths; 2005-2009) and, using research criteria, reclassified 8.2% of the nonsuicide cases to definite suicide (1), suicide probable (4), or suicide possible (35). The reclassification rate to definite suicide was only 0.2% (1/488). This low rate suggests that flagrant misclassification of Army deaths is uncommon and surveillance reports likely reflect the "true" population of Army suicides.

Medically Documented Suicide Ideation Among U.S. Army Soldiers.

We used administrative data to examine predictors of medically documented suicide ideation (SI) among Regular Army soldiers from 2006 through 2009 (N = 10,466 ideators, 124,959 control person-months). Enlisted ideators (97.8% of all cases) were more likely than controls to be female, younger, older when entering service, less educated, never or previously deployed, and have a recent mental health diagnosis. Officer ideators were more likely than controls to be female, younger, younger when entering service, never married, and have a recent mental health diagnosis. Risk among enlisted soldiers peaked in the second month of service and declined steadily, whereas risk among officers remained relatively stable over time. Risk of SI is highest among enlisted soldiers early in Army service, females, and those with a recent mental health diagnosis.

Structure and thermodynamics of a mixture of patchy and spherical colloids: A multi-body association theory with complete reference fluid information.

A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures. Because of multi-body correlations, predicting the structure and thermodynamics of such systems remains a challenge. Earlier Marshall and Chapman [J. Chem. Phys. 139, 104904 (2013)] developed a theory wherein association effects due to interactions multiply the partition function for clustering of particles in a reference hard-sphere system. The multi-body effects are incorporated in the clustering process, which in their work was obtained in the absence of the bulk medium. The bulk solvent effects were then modeled approximately within a second order perturbation approach. However, their approach is inadequate at high densities and for large association strengths. Based on the idea that the clustering of solvent in a defined coordination volume around the solute is related to occupancy statistics in that defined coordination volume, we develop an approach to incorporate the complete information about hard-sphere clustering in a bulk solvent at the density of interest. The occupancy probabilities are obtained from enhanced sampling simulations but we also develop a concise parametric form to model these probabilities using the quasichemical theory of solutions. We show that incorporating the complete reference information results in an approach that can predict the bonding state and thermodynamics of the colloidal solute for a wide range of system conditions.

Risk Factors, Methods, and Timing of Suicide Attempts Among US Army Soldiers.

IMPORTANCE: Suicide attempts in the US Army have risen in the past decade. Understanding the association between suicide attempts and deployment, as well as method and timing of suicide attempts, can assist in developing interventions. OBJECTIVE: To examine suicide attempt risk factors, methods, and timing among soldiers currently deployed, previously deployed, and never deployed at the time this study was conducted. DESIGN, SETTING, AND PARTICIPANTS: This longitudinal, retrospective cohort study of Regular Army-enlisted soldiers on active duty from 2004 through 2009 used individual-level person-month records to examine risk factors (sociodemographic, service related, and mental health), method, and time of suicide attempt by deployment status (never, currently, and previously deployed). Administrative data for the month before each of 9650 incident suicide attempts and an equal-probability sample of 153 528 control person-months for other soldiers were analyzed using a discrete-time survival framework. MAIN OUTCOMES AND MEASURES: Suicide attempts and career, mental health, and demographic predictors were obtained from administrative and medical records. RESULTS: Of the 9650 enlisted soldiers who attempted suicide, 86.3% were male, 68.4% were younger than 30 years, 59.8% were non-Hispanic white, 76.5% were high school educated, and 54.7% were currently married. The 40.4% of enlisted soldiers who had never been deployed (n = 12 421 294 person-months) accounted for 61.1% of enlisted soldiers who attempted suicide (n = 5894 cases). Risk among those never deployed was highest in the second month of service (103 per 100 000 person-months). Risk among soldiers on their first deployment was highest in the sixth month of deployment (25 per 100 000 person-months). For those previously deployed, risk was highest at 5 months after return (40 per 100 000 person-months). Currently and previously deployed soldiers were more likely to attempt suicide with a firearm than those never deployed (currently deployed: OR, 4.0; 95% CI, 2.9-5.6; previously deployed: OR, 2.7; 95% CI, 1.8-3.9). Across deployment status, suicide attempts were more likely among soldiers who were women (currently deployed: OR, 3.4; 95% CI, 3.0-4.0; previously deployed: OR, 1.5; 95% CI, 1.4-1.7; and never deployed: OR, 2.4; 95% CI, 2.3-2.6), in their first 2 years of service (currently deployed: OR, 1.9; 95% CI, 1.5-2.3; previously deployed: OR, 2.2; 95% CI, 1.9-2.7; and never deployed: OR, 3.1; 95% CI, 2.7-3.6), and had a recently received a mental health diagnosis in the previous month (currently deployed: OR, 29.8; 95% CI, 25.0-35.5; previously deployed: OR, 22.2; 95% CI, 20.1-24.4; and never deployed: OR, 15.0; 95% CI, 14.2-16.0). Among soldiers with 1 previous deployment, odds of a suicide attempt were higher for those who screened positive for depression or posttraumatic stress disorder after return from deployment and particularly at follow-up screening, about 4 to 6 months after deployment (depression: OR, 1.4; 95% CI, 1.1-1.9; posttraumatic stress disorder: OR, 2.4; 95% CI, 2.1-2.8). CONCLUSIONS AND RELEVANCE: Identifying the timing and risk factors for suicide attempt in soldiers requires consideration of environmental context, individual characteristics, and mental health. These factors can inform prevention efforts.

Response to strict and liberalized specific carbohydrate diet in pediatric Crohn's disease.

AIM: To investigate the specific carbohydrate diet (SCD) as nutritional therapy for maintenance of remission in pediatric Crohn's disease (CD). METHODS: Retrospective chart review was conducted in 11 pediatric patients with CD who initiated the SCD as therapy at time of diagnosis or flare. Two groups defined as SCD simple (diet alone, antibiotics or 5-ASA) or SCD with immunomodulators (corticosteroids and/or stable thiopurine dosing) were followed for one year and compared on disease characteristics, laboratory values and anthropometrics. RESULTS: The mean age at start of the SCD was 11.8 ± 3.0 years (range 6.6-17.6 years) with five patients starting the SCD within 5 wk of diagnosis. Three patients maintained a strict SCD diet for the study period and the mean time for liberalization was 7.7 ± 4.0 mo (range 1-12) for the remaining patients. In both groups, hematocrit, albumin and ESR values improved while on strict SCD and appeared stable after liberalization (P-value 0.006, 0.002, 0.002 respectively). The majority of children gained in weight and height percentile while on strict SCD, with small loss in weight percentile documented with liberalization. CONCLUSION: Disease control may be attainable with the SCD in pediatric CD. Further studies are needed to assess adherence, impact on mucosal healing and growth.