Development of FPGA-based multi-sensor excitation low voltage (MSELV) chassis at Jefferson Lab.

The design and development of the sensor excitation and read back chassis was driven by the requirements for the monitoring and control of two conduction-cooled superconducting magnets in Hall B for the 12 GeV accelerator upgrade. The torus and solenoid superconducting magnets require extensive instrumentation. Sensor selection was accomplished by applying Jefferson Lab's (JLab) risk mitigation process, which employed a failure modes and effects analysis approach. The goal was to accommodate all sensor types for monitoring and control and to develop a generic multisensor excitation low voltage chassis that would be used across both magnet systems with a reduced set of functions. The chassis has been deployed in experimental Hall B at JLab and has been performing successfully since July 2016.

Mixed impact of Xpert(®) MTB/RIF on tuberculosis diagnosis in Cambodia.

SETTING: National Tuberculosis (TB) Program sites in northwest Cambodia. OBJECTIVE: To evaluate the impact of Xpert(®) MTB/RIF at point of care (POC) as compared to non-POC sites on the diagnostic evaluation of people living with the human immunodeficiency virus (PLHIV) with TB symptoms and patients with possible multidrug-resistant (MDR) TB. DESIGN: Observational cohort of patients undergoing routine diagnostic evaluation for TB following the rollout of Xpert. RESULTS: Between October 2011 and June 2013, 431 of 822 (52%) PLHIV with TB symptoms and 240/493 (49%) patients with possible MDR-TB underwent Xpert. Xpert was more likely to be performed when available as POC. A smaller proportion of PLHIV at POC sites were diagnosed with TB than at non-POC sites; however, at POC sites, a higher proportion of those diagnosed with TB were bacteriologically positive. There was poor agreement between Xpert and other tests such as smear microscopy and culture. Overall, the evaluation of patients with possible MDR-TB increased following Xpert rollout, yet for patients confirmed as having drug resistance on drug susceptibility testing, only 46% had rifampin resistance that would be identified with Xpert. CONCLUSION: Although utilization of Xpert was low, it may have contributed to an increase in evaluations for possible MDR-TB and a decline in empiric treatment for PLHIV when available as POC.

Contexte : Sites du Programme National contre la Tuberculose (TB) dans le nord-ouest du Cambodge.Objectif : Evaluer l'impact du Xpert® MTB/RIF dans des sites où il est réalisé sur place (POC) comparés aux autres sites sur le diagnostic des personnes vivant avec le VIH (PVVIH) et ayant des symptômes de TB ainsi que des patients présumées de TB multirésistante (MDR).Schéma : Cohorte d'observation de patients bénéficiant d'une évaluation diagnostique de routine pour la TB après le lancement de l'Xpert.Résultats : Entre octobre 2011 et juin 2013, 431/822 (52%) PVVIH ayant des symptômes de TB et 240/493 (49%) patients avec suspicion de TB-MDR ont eu un test Xpert. L'Xpert a été réalisé plus souvent lorsqu'il était disponible en POC. Une plus faible proportion de PVVIH a eu un diagnostic de TB dans les sites POC que dans les sites non-POC ; cependant, dans les sites POC, une proportion plus élevée des patients ayant eu un diagnostic de TB a eu une bactériologie positive. L'accord entre l'Xpert et les autres tests (par exemple la microscopie de frottis ou la culture) a été médiocre. Dans l'ensemble, l'évaluation des patients présumées de TB-MDR a augmenté après le lancement de l'Xpert, mais parmi les patients ayant eu une pharmacorésistance confirmée par test de pharmacosensibilité, seulement 46% ont eu une résistance à la rifampicine qui aurait été identifiée par Xpert.Conclusion : Même si l'utilisation de l'Xpert a été faible, l'Xpert pourrait avoir contribué à une augmentation de l'évaluation des suspicions de TB-MDR et à un déclin du traitement empirique des PVVIH quand il est disponible sur place.

Marco de referencia: Los centros del Programa Nacional contra la Tuberculosis en el noroeste de Camboya.Objetivo: Evaluar la repercusión de la práctica de la prueba Xpert® MTB/RIF en el lugar de la consulta, en comparación con la realización de la prueba en otro centro, sobre la evaluación diagnóstica de las personas aquejadas de infección por el virus de la inmunodeficiencia humana (PVVIH) que presentan síntomas de tuberculosis (TB) y de los pacientes con presunción de TB multidrogorresistente (TB-MDR).Método: Fue este un estudio observacional de cohortes de pacientes en curso de evaluación diagnóstica corriente de la TB, después de la introducción de la prueba Xpert.Resultados: De octubre del 2011 a junio del 2013 se practicó la prueba Xpert a 431 de los 822 PVVIH que presentaban síntomas de TB (52%) y a 240 de los 493 pacientes con presunción de TB-MDR (49%). La probabilidad de realizar la prueba Xpert fue mayor cuando esta se podía practicar en el lugar de la consulta. La proporción de PVVIH en quienes se diagnosticó TB en los centros que practicaban localmente la prueba Xpert fue menor que en los demás centros; sin embargo, en los centros que contaban con la prueba fue más alta la proporción de casos de TB confirmados bacteriológicamente. Se observó una baja concordancia entre los resultados de la prueba Xpert y las otras pruebas (la baciloscopia y el cultivo). En general, tras el despliegue de la prueba molecular se investigó un mayor número de pacientes con presunción de TB-MDR; sin embargo, de los pacientes en quienes se confirmó la farmacorresistencia mediante pruebas de sensibilidad solo un 46% presentaba resistencia a rifampicina, que podía detectar la prueba Xpert.Conclusión: Si bien la utilización de la prueba Xpert fue muy limitada, su disponibilidad contribuyó a la investigación de más casos con presunción de TB-MDR y a una disminución del tratamiento empírico de las PPVIH, cuando la prueba Xpert se practicaba en el lugar de la consulta.

Krüppel-like factor 1: hematologic phenotypes associated with KLF1 gene mutations.

Krüppel-like factor 1 (KLF1) is a pleiotropic erythroid transcription factor that is essential for hematopoiesis. KLF1 mutations have been associated with severe hematologic disorders, including congenital dyserythropoietic anemia type IV (CDAN4) due to a dominant-negative missense mutation (c.973G>A, p.Glu325Lys) and transfusion-dependent hemolytic anemia in compound heterozygotes for loss-of-function mutations. In addition, several benign hematologic conditions are due to KLF1 haploinsufficiency. Herein, we review the genotype-phenotype relationship associated with KLF1 mutations and discuss the utility of KLF1 gene testing in laboratory hematology.

Rollout of Xpert(®) MTB/RIF in Northwest Cambodia for the diagnosis of tuberculosis among PLHA.

OBJECTIVE: To describe the implementation and utilization of the Xpert (®) MTB/RIF (Xpert) assay to diagnose tuberculosis (TB) among people living with the human immunodeficiency virus/acquired immune-deficiency syndrome (HIV/AIDS, PLHA) in Cambodia. DESIGN: Following the rollout of Xpert, an evaluation was conducted in four provinces of Cambodia from March to December 2012 to determine the utilization, performance, and turnaround time (TAT) of Xpert among PLHA. Data were collected from paper-based patient registers. RESULTS: Of 497 PLHA with a positive TB symptom screen, 357 (72%) were tested with smear microscopy, and 250 (50%) with Xpert; 25 (10%) PLHA tested with Xpert were positive for TB and none were rifampicin-resistant. The utilization of Xpert increased from 23% to 75%, with a median TAT of 1 day. Across districts, utilization ranged from zero to 85%, while the TAT ranged from zero to 22 days. CONCLUSION: While early data show increasing utilization of Xpert for PLHA with a positive symptom screen, most patients underwent smear microscopy as an initial diagnostic test. Training delays and challenges associated with specimen referral may have contributed to variability in Xpert uptake and TAT, particularly for sites without onsite Xpert testing. Enhanced programmatic support, particularly for specimen referral and results reporting, may facilitate appropriate utilization.

Objectif : Décrire la mise en œuvre et l'utilisation du test Xpert(R) MTB/RIF afin de diagnostiquer la tuberculose (TB) parmi des personnes vivant avec le VIH/SIDA (virus de l'mmunodéficience humaine/syndrome de l'immunodéficience acquise ; PLHA) au Cambodge.Schéma : Après le déploiement du test Xpert, une évaluation a été réalisée dans quatre provinces du Cambodge entre mars et décembre 2012 afin de déterminer l'utilisation, la performance et le délai d'exécution du Xpert parmi les PLHA. Des données ont été recueillies à partir des dossiers papiers des patients.Résultats : Sur 497 PLHA ayant une grille de symptômes de TB positive, 357 (72%) ont bénéficié d'une microscopie de frottis et 250 (50%) ont eu un test Xpert ; 25 (10%) PLHA testés par Xpert étaient positifs pour la TB et aucun n'était résistant à la rifampicine. L'utilisation du Xpert est passée de 23% à 75% avec un délai d'exécution médian d'un jour. Dans les districts, l'utilisation allait de zéro à 85% et le délai de mise en œuvre allait de zéro à 22 jours.Conclusion : Si les données précoces montrent une utilisation croissante du Xpert chez les PLHA avec une grille de symptômes positive, la majorité des patients bénéficiait initialement d'un diagnostic par examen microscopique de frottis. Les délais de formation et les problèmes posés par l'envoi des spécimens peuvent avoir contribué à la variabilité du recours au Xpert et au délai de sa mise en œuvre, particulièrement dans les endroits dépourvus de possibilité de test Xpert sur place. Davantage de soutien aux programmes, notamment en termes d'envoi des spécimens et de retour des résultats, pourrait faciliter son utilisation appropriée.

Objetivo: Describir la introducción y la utilización de la prueba Xpert(R) MTB/RIF en el diagnóstico de la tuberculosis (TB) de las personas aquejadas de infección por el virus de la inmunodeficiencia humana (VIH) y sida (PLHA) en Camboya.Método: Tras el despliegue de Xpert, se llevó a cabo una evaluación en cuatro provincias de Camboya de marzo a diciembre del 2012 con el fin de determinar el tipo de utilización, el rendimiento diagnóstico y el tiempo de obtención de los resultados de la prueba Xpert en las PLHA. Se recogieron los datos de los pacientes a partir de los registros en soporte de papel.Resultados: De los 497 PLHA y una detección positiva de síntomas de la TB, en 357 casos se practicó una baciloscopia (72%) y en 250 la Xpert (50%); 25 de las personas examinadas con Xpert obtuvieron un resultado positivo (10%) y en ninguna se observó resistencia a rifampicina. La utilización de la prueba aumentó de 23% a 75% y la mediana del lapso hasta obtener el resultado fue un día. En los diferentes distritos, el uso de la prueba osciló entre 0% y 85% y el lapso hasta la notificación del resultado fue de cero a 22 días.Conclusión: Los datos iniciales indicaron un aumento de la utilización de la prueba Xpert en las PLHA que presentan una detección positiva de síntomas de la TB, pero en la mayoría de los pacientes se practicó la baciloscopia del esputo como prueba diagnóstica inicial. Es posible que los retrasos en la capacitación y las dificultades relacionadas con la remisión de las muestras hayan contribuido a la variabilidad en la aceptación de la Xpert y en el tiempo de obtención de los resultados, sobre todo en los centros donde no se practica la prueba en el lugar de atención. Se podría fomentar el uso apropiado de esta prueba mediante un apoyo programático, dirigido especialmente a la remisión de las muestras y la notificación de los resultados.

The utility of stool cultures for diagnosing tuberculosis in people living with the human immunodeficiency virus.

BACKGROUND: Delayed diagnosis of tuberculosis (TB) increases mortality. OBJECTIVE: To evaluate whether stool culture improves the diagnosis of TB in people living with the human immunodeficiency virus (PLHIV). DESIGN: We analysed cross-sectional data of TB diagnosis in PLHIV in Cambodia, Thailand and Viet Nam. Logistic regression was used to assess the association between positive stool culture and TB, and to calculate the incremental yield of stool culture. RESULTS: A total of 1693 PLHIV were enrolled with a stool culture result. Of 228 PLHIV with culture-confirmed TB from any site, 101 (44%) had a positive stool culture; of these, 91 (90%) had pulmonary TB (PTB). After adjusting for confounding factors, a positive stool culture was associated with smear-negative (odds ratio [OR] 26, 95% confidence interval [CI] 12-58), moderately smear-positive (OR 60, 95%CI 23-159) and highly smear-positive (OR 179, 95%CI 59-546) PTB compared with no PTB. No statistically significant association existed with extra-pulmonary TB compared with no extra-pulmonary TB (OR 2, 95%CI 1-5). The incremental yield of one stool culture above two sputum cultures (5%, 95%CI 3-8) was comparable to an additional sputum culture (7%, 95%CI 4-11). CONCLUSION: Nearly half of the PLHIV with TB had a positive stool culture that was strongly associated with PTB. Stool cultures may be used to diagnose TB in PLHIV.

Diagnostic testing for α-globin gene disorders in a heterogeneous North American population.

Adult hemoglobin is a heterotetramer composed of two α-globin chains and two ß-globin chains (α2 ß2 ), each of which contains a heme molecule capable of binding oxygen and facilitating oxygen transport. The α-globin chains are expressed from duplicated genes within a tandem gene cluster located on chromosome region 16p13.3. High-level expression of the α-globin genes commences early in fetal development and continues throughout life. The α-thalassemia syndromes are among the most single-gene disorders, resulting from decreased synthesis of α-globin chains or synthesis of functionally abnormal α-globin chains. These disorders are most common in South East Asia, but also occur in many other populations. The most common cause of α-thalassemia is gene deletions, of which more than seventy have been reported. In addition, a small but significant proportion of cases involve point mutations of the α-globin genes. Ideally, the diagnostic strategy should include allele-specific assays for commonly occurring deletions, as well as methods for detection of rare or novel deletions and point mutations. Here we provide an overview of the diagnostic methods available and our experience using these assays in a reference laboratory serving a heterogeneous at-risk population.

Association between distance to HIV testing site and uptake of HIV testing for tuberculosis patients in Cambodia.

SETTING: Banteay Meanchey Province, Cambodia. OBJECTIVE: Cambodia has the highest incidence of tuberculosis (TB) in Asia. Not all TB patients are tested for human immunodeficiency virus (HIV). We assessed the association between distance to HIV testing facility and HIV testing rates. METHODS: We analyzed data on TB patients from 11 clinics to determine the proportion tested for HIV infection. We categorized each TB clinic as having a voluntary confidential counseling and testing (VCCT) center onsite, or being at <15 min, 15-30 min or >30 min driving distance to the nearest VCCT. RESULTS: Of 1017 TB patients not previously tested for HIV, 708 (70%) were tested. Of 481 TB patients without onsite VCCT, 297 (62%) were tested, compared to 410 (77%) of 535 TB patients with onsite VCCT (RR 0.6, 95%CI 0.5-0.7). When the VCCT site was >15 min from the TB clinic, HIV testing occurred only half as frequently as when onsite VCCT was available. CONCLUSION: TB patients treated at clinics without onsite or nearby HIV testing are less commonly tested for HIV infection. Making HIV testing available to TB patients without the necessity of traveling to a distant HIV testing site is likely to increase HIV testing rates.

One-dimensional diffusion of colloids in polymer solutions.

For colloid-polymer systems confined in one-dimensional channels, the diffusion of the colloidal particles is obtained by tracking individual particles using enhanced video microscopy and digital image analysis. For short times, the diffusion is normal, of the Fickian type, with mean-squared displacement varying linearly with time. For long times, however, the mean-squared displacement is found to increase more slowly with time, being proportional to the square root of time, in agreement with the theoretical prediction for diffusion of hard rods in one dimension in which mutual crossing of the particles cannot take place. The crossover from short-time to long-time diffusion is observed and is found to depend on the colloid and polymer concentrations. Unexpectedly, for small polymer-to-colloid size ratios, it is the polymer rather than the colloid concentration which has a leading effect on the colloid diffusion.

Self-calibration of biplanar radiographs for a retrospective comparative study of the 3D correction of adolescent idiopathic scoliosis.

A novel technique for the 3D reconstruction of the spine from X-ray images is presented. The algorithm is based on the self-calibration of biplanar radiographs. It allows the 3D reconstruction of spines from old uncalibrated preoperative and postoperative radiographs. The reliability of the new self-calibration technique was investigated by validating its results against those of the Direct Linear Transform (DLT) on real images. An accuracy experiment was also performed using a dry spine specimen under controlled conditions. The results indicate that self-calibration is a viable technique, accurate enough to extract meaningful 3D clinical data for retrospective studies.

Hb H hydrops foetalis syndrome: a case report and review of literature.

Haemoglobin H (Hb H) disease is caused by deletion or inactivation of three alpha-globin genes, leaving only one intact and active alpha-globin gene. People with Hb H disease usually have moderate anaemia, but are generally thought to be asymptomatic. Some Hb H disease patients require transfusions, and there are reports of fetuses with Hb H disease who have severe anaemia in utero resulting in fatal hydrops foetalis syndrome. We now report a case of Hb H hydrops foetalis syndrome, caused by the inheritance of a hitherto novel alpha-globin gene point mutation (codon 35 TCC-->CCC or Serine-->Proline) and an alpha-thalassaemia deletion of the Filipino type removing all zeta-alpha-globin genes on the other chromosome 16. The infant was delivered prematurely because of pericardial effusion and fetal distress, and was found to have severe anaemia and congenital anomalies. A review of the relevant literature on this syndrome is presented, and serves to underscore the phenotypic variations of Hb H disease and the need for surveillance for this condition among newborns and genetic counselling in communities with a high proportion of at-risk populations.

Hemoglobin H (Hb H) disease in Canada: molecular diagnosis and review of 116 cases.

Over the past decade, we have characterized at the DNA level a total of 116 hemoglobin H (Hb H) disease patients living in Canada. The majority of patients were of southeast Asian descent (Chinese, Filipino, Laotian, Vietnamese), with a small number being of Mediterranean, Middle Eastern or East Indian background. A total of 15 distinct genotypes were detected, all but one being compound heterozygotes for a two-gene cis deletion and a single-gene deletion (-alpha/-) or a non-deletion mutation of the alpha2-globin gene (alpha(T) alpha/-). Seven different two-gene cis deletions were encountered, along with nine single-gene deletions and point mutations. The wide range of mutations associated with Hb H disease in Canada is a reflection of the population heterogeneity. The diagnosis of Hb H disease at the molecular level is important with respect to genetic counseling and the identification of families at risk for having pregnancies affected with Hb Bart's hydrops fetalis syndrome and/or Hb H disease. Six of the Hb H disease patients in our cohort had spouses who carried single-gene deletions, making these couples at risk for having children with Hb H disease. More important, seven patients had partners who carried two-gene cis deletions. These couples are at reproductive risk for both Hb Bart's hydrops fetalis syndrome and Hb H disease.

Frequency and ethnic distribution of the common DHCR7 mutation in Smith-Lemli-Opitz syndrome.

Smith-Lemli-Opitz syndrome (SLOS) is an inherited multiple malformation syndrome caused by enzymatic deficiency of 3beta-hydroxysterol-Delta(7)-reductase (DHCR7). SLOS is thought to be most common among European Caucasians, with an incidence of 1 in 20,000 to 1 in 30,000 births. To define the carrier rate and ethnic distribution of SLOS, we screened DNA samples from 2,978 unrelated individuals for the most common SLOS mutation (IVS8-1G-->C). Twenty-four heterozygotes of the IVS8-1G-->C mutation were detected in 2,978 individuals of European Caucasian and Black backgrounds. For European Caucasians, the carrier rate for SLOS may be as high as 1 in 30, suggesting an incidence of 1 in 1,700 to 1 in 13,400. This high number is supported by the recent observation of newborn and prenatal incidence of 1 in 22,000 in the Caucasian population. Ours is the first report of the IVS8-1G-->C mutation in persons of African ancestry. Published 2001 Wiley-Liss, Inc.

Late-onset metachromatic leukodystrophy clinically presenting as isolated peripheral neuropathy: compound heterozygosity for the IVS2+1G-->A mutation and a newly identified missense mutation (Thr408Ile) in a Spanish family.

We report the case of a 50-year-old woman and her 32-year-old daughter, both of whom are affected with adult-onset metachromatic leukodystrophy (MLD) clinically presenting as peripheral neuropathy. Arylsulfatase A (ARSA) activities were markedly reduced, and electrophysiology showed a severe demyelinating neuropathy with features of chronic acquired demyelinating polyneuropathy. Molecular genetic studies of the family revealed that the proband and her affected daughter are compound heterozygotes for the common IVS2+ 1G-->A mutation and a newly identified missense mutation, Thr408Ile. This case indicates that adult metachromatic leukodystrophy should be considered in adult patients with demyelinating peripheral neuropathy of unknown etiology.

DHCR7 genotypes of cousins with Smith-Lemli-Opitz syndrome.

Smith-Lemli-Opitz syndrome (SLOS) is an autosomal recessive disorder of cholesterol biosynthesis caused by mutations of the 7-dehydrocholesterol reductase gene (DHCR7). We report on three cousins with SLOS, all of whom were found to be compound heterozygotes for the common splice site mutation IVS8-1G-->C and the missense mutation T289I. DNA analysis of one set of parents demonstrated that the father carried the missense mutation and the mother carried the IVS8-1G-->C mutation. By extension, the two unrelated mothers were both heterozygous for IVS8-1G-->C. This finding supports the notion of a high carrier frequency of the IVS8-1G-->C null mutation in Northern European Caucasians.

Detection of severe nondeletional alpha-thalassemia mutations using a single-tube multiplex ARMS assay.

Alpha-thalassemia is a common hereditary anemia due to decreased or absent synthesis of alpha-globin chains. The most common causes of alpha-thalassemia are deletions that remove one or both functional alpha-globin genes, with a small proportion of cases involving nondeletional mutations of the alpha2- or alpha1-globin genes. Herein, we describe a single-tube multiplex amplification refractory mutation system (ARMS) assay for rapid detection of six of the most common and severe nondeletional alpha-thalassemia mutations. These alleles are found predominantly among southeast Asian populations, and are associated with the most severe forms of hemoglobin (Hb) H disease or Hb H hydrops fetalis.