A Practical Study of Longitudinal Reference Based Compressed Sensing for MRI

Compressed sensing (CS) is a new signal acquisition paradigm that enables the reconstruction of signals and images from a low number of samples. A particularly exciting application of CS is Magnetic Resonance Imaging (MRI), where CS significantly speeds up scan time by requiring far fewer measurements than standard MRI techniques. Such a reduction in sampling time leads to less power consumption, less need for patient sedation, and more accurate images. This accuracy increase is especially pronounced in pediatric MRI where patients have trouble being still for long scan periods. Although such gains are already significant, even further improvements can be made by utilizing past MRI scans of the same patient. Many patients require repeated scans over a period of time in order to track illnesses and the prior scans can be used as references for the current image. This allows samples to be taken adaptively, based on both the prior scan and the current measurements. Work by Weizman has shown that so-called reference based adaptive-weighted temporal Compressed Sensing MRI (LACS-MRI) requires far fewer samples than standard Compressed Sensing (CS) to achieve the same reconstruction signal-to-noise ratio (RSNR). The method uses a mixture of reference-based and adaptive-sampling. In this work, we test this methodology by using various adaptive sensing schemes, reconstruction methods, and image types. We create a thorough catalog of reconstruction behavior and success rates that is interesting from a mathematical point of view and is useful for practitioners. We also solve a grayscale compensation toy problem that supports the insensitivity of LACS-MRI to changes in MRI acquisition parameters and thus showcases the reliability of LACS-MRI in possible clinical situations

Estresores psicosociales asociados a preeclampsia en mujeres de Lima, Perú

Objetivo: Analizar la relación entre estresores psicosociales y preeclampsia en mujeres atendidas en el Hospital Vitarte 2017. Materiales y métodos: Estudio de casos y controles, realizado en el Hospital de Vitarte en Lima, Perú, en 40 puérperas, asignadas en dos grupos apareados por distrito de procedencia y fecha de ingreso, 20 casos con diagnóstico de preeclampsia durante la gestación y 20 controles sin preeclampsia, puérperas de parto normal. Se utilizaron cuatro instrumentos: el Inventario de Ansiedad Rasgo Estado (IDARE), el Inventario de Depresión Rasgo Estado (IDERE), el APGAR familiar y la ficha de tamizaje de violencia basada en género para la identificación de estresores psicosociales (ansiedad, depresión, disfunción familiar y violencia). Se consideraron las pruebas Chi cuadrado (significativo p<0.05) y Odds Ratio para hallar el riesgo de presentar preeclampsia con sus intervalos de confianza al 95%. Resultados: Los estresores psicológicos asociados significativamente con preeclampsia fueron: ansiedad estado (OR: 33.8; IC 95%: 1.80636.91), ansiedad rasgo (OR: 27.8; IC 95%: 1.48-526.14), ansiedad (OR: 41.0; IC 95%: 2.18-770.12), depresión estado (OR: 57.0; IC 95%: 6.00541.46), depresión rasgo (OR: 27.8; IC 95%: 1.48-526.14) y depresión (OR: 76.0; IC 95%: 7.69 750.49). Los estresores sociales asociados significativamente con preeclampsia fueron: violencia psicológica (OR: 10.2; IC 95%: 1.12-93.34) y violencia basada en género (OR: 10.2; IC 95%: 1.12-93.34). Los estresores psicológicos (OR: 107.6; IC 95%: 10.20-1135.58) y sociales (OR: 22.6; IC 95%: 4.37-117.46) se asociaron significativamente a preeclampsia. Conclusiones: Hubo relación estadísticamente significativa entre estresores psicosociales y preeclampsia

Perfil epidemiológico de pacientes tamizados reactivos para VIH y hepatitis B que acuden al Hospital Vitarte, 2018

Introducción: Las infecciones por VIH y hepatitis B son un problema de salud mundial, debido a la morbi-mortalidad y el impacto socioeconómico que generan. Frente a ello, la comunidad internacional propuso un plan de acción para evitar su propagación y erradicar el SIDA al 2030. Objetivo: Describir el perfil epidemiológico de pacientes tamizados reactivos para VIH y hepatitis B que acuden al Hospital Vitarte durante el 2018. Material y métodos: Estudio observacional, descriptivo, retrospectivo, transversal, realizado en el Hospital Vitarte mediante observación documental de 62 historias clínicas de pacientes tamizados con prueba rápida de VIH y hepatitis B reactiva, atendidos en el Consultorio de Consejería. Se evaluaron características sociodemográficas, comportamiento sexual y antecedentes personales. Para el análisis se empleó estadística descriptiva. Resultados: El 53.2% eran mujeres, su edad promedio fue 31 años y en varones 37 años, predominó la educación secundaria completa en ambos grupos con 42.4% y 55.2% respectivamente, el 57.6% de mujeres eran convivientes y el 62.1% de varones solteros. La edad promedio de inicio de relaciones sexuales fue 17 años, el promedio de parejas sexuales en mujeres fue 2.4 y en varones 8.4, el 32.5% no usaron preservativo, 6.9% de varones era homosexual y 13.8% bisexual. El 19.4% eran gestantes, 8.1% puérperas, 6.5% postaborto. El 33.9% tenía antecedentes quirúrgicos, 40.3% bebía alcohol, 19.4% tenía tatuajes, 3.2% piercing, 11.3% consumió drogas o tuvo tuberculosis, 6.5% recibió transfusión sanguínea. El 61.3% dio reactivo a la prueba rápida de VIH y el 41.9 % reactivo para hepatitis B. Conclusiones: Los pacientes tamizados reactivos para VIH y hepatitis B tienen entre 30 a 59 años, con educación secundaria, estado civil conviviente, su primera relación sexual fue a los 17 años, con un promedio de 5 parejas sexuales, más del 30% no usaba preservativo, 9.7% era homosexual o bisexual, con antecedentes de consumo de alcohol, cirugías y tatuajes

A Practical Study of Longitudinal Reference Based Compressed Sensing for MRI

Compressed sensing (CS) is a new signal acquisition paradigm that enables the reconstruction of signals and images from a low number of samples. A particularly exciting application of CS is Magnetic Resonance Imaging (MRI), where CS significantly speeds up scan time by requiring far fewer measurements than standard MRI techniques. Such a reduction in sampling time leads to less power consumption, less need for patient sedation, and more accurate images. This accuracy increase is especially pronounced in pediatric MRI where patients have trouble being still for long scan periods. Although such gains are already significant, even further improvements can be made by utilizing past MRI scans of the same patient. Many patients require repeated scans over a period of time in order to track illnesses and the prior scans can be used as references for the current image. This allows samples to be taken adaptively, based on both the prior scan and the current measurements. Work by Weizman [20] has shown that so-called reference based adaptive-weighted temporal Compressed Sensing MRI (LACS-MRI) requires far fewer samples than standard Compressed Sensing (CS) to achieve the same reconstruction signal-to-noise ratio (RSNR). The method uses a mixture of reference-based and adaptive-sampling. In this work, we test this methodology by using various adaptive sensing schemes, reconstruction methods, and image types. We create a thorough catalog of reconstruction behavior and success rates that is interesting from a mathematical point of view and is useful for practitioners. We also solve a grayscale compensation toy problem that supports the insensitivity of LACS-MRI to changes in MRI acquisition parameters and thus showcases the reliability of LACS-MRI in possible clinical situations

A Quantitative Assay for Insulin-expressing Colony-forming Progenitors

The field of pancreatic stem and progenitor cell biology has been hampered by a lack of in vitro functional and quantitative assays that allow for the analysis of the single cell. Analyses of single progenitors are of critical importance because they provide definitive ways to unequivocally demonstrate the lineage potential of individual progenitors. Although methods have been devised to generate "pancreatospheres" in suspension culture from single cells, several limitations exist. First, it is time-consuming to perform single cell deposition for a large number of cells, which in turn commands large volumes of culture media and space. Second, numeration of the resulting pancreatospheres is labor-intensive, especially when the frequency of the pancreatosphere-initiating progenitors is low. Third, the pancreatosphere assay is not an efficient method to allow both the proliferation and differentiation of pancreatic progenitors in the same culture well, restricting the usefulness of the assay

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer

Glucocorticoid signaling enhances expression of glucose-sensing molecules in immature pancreatic beta-like cells derived from murine embryonic stem cells in vitro

Pluripotent stem cells may serve as an alternative source of beta-like cells for replacement therapy of type 1 diabetes; however, the beta-like cells generated in many differentiation protocols are immature. The maturation of endogenous beta cells involves an increase in insulin expression starting in late gestation and a gradual acquisition of the abilities to sense glucose and secrete insulin by week 2 after birth in mice; however, what molecules regulate these maturation processes are incompletely known. Here, we aim to identify small molecules that affect immature beta cells. A cell-based assay, employing pancreatic beta-like cells derived from murine embryonic stem (ES) cells harboring a transgene containing an Insulin 1-promoter driven enhanced green fluorescent protein reporter, was used to screen a compound library (NIH Clinical Collection-003). Cortisone, a glucocorticoid, was among five positive hit compounds. Quantitative RT-PCR analysis revealed that glucocorticoids enhance the gene expression of not only insulin 1 but also glucose transporter-2 (Glut2; Slc2a2) and glucokinase (Gck), two molecules important for glucose sensing. Mifepristone, a pharmacological inhibitor of glucocorticoid receptor (GR) signaling, reduced the effects of glucocorticoids on Glut2 and Gck expression. The effects of glucocorticoids on ES-derived cells were further validated in immature primary islets. Isolated islets from 1-week-old mice had an increased Glut2 and Gck expression in response to a 4-day treatment of exogenous hydrocortisone in vitro. Gene deletion of GR in beta cells using rat insulin 2 promoter-driven Cre crossed with GRflox/flox mice resulted in a reduced gene expression of Glut2, but not Gck, and an abrogation of insulin secretion when islets were incubated in 0.5 mM D-glucose and stimulated by 17 mM D-glucose in vitro. These results demonstrate that glucocorticoids positively regulate glucose sensors in immature murine beta-like cells

Methane mitigation potential of foliage of fodder trees mixed at two levels with a tropical grass

Enteric methane (CH4) emitted by ruminant species is known as one of the main greenhouse gases produced by the agricultural sector. The objective of this study was to assess the potential the potential for CH4 mitigation and additionally the chemical composition, in vitro gas production, dry matter degradation (DMD), digestibility and CO2 production of five tropical tree species with novel forage potential including: Spondias mombin, Acacia pennatula, Parmentiera aculeata, Brosimum alicastrum and Bursera simaruba mixed at two levels of inclusion (15 and 30%) with a tropical grass (Pennisetum purpureum). The forage samples were incubated for 48 h, and a randomized complete block design was used. Crude protein content was similar across treatments (135 ± 42 g kg−1 DM), while P. purpureum was characterized by a high content of acid detergent fiber (335.9 g kg−1 DM) and B. simaruba by a high concentration of condensed tannins (20 g kg−1 DM). Likewise, A. pennatula and P. aculeata were characterized by a high content of cyanogenic glycosides and alkaloids respectively. Treatments SM30-PP70 (30% S. mombin + 70% P. purpureum) and BA30-PP70 (30% B. alicastrum + 70% P. purpureum) resulted in superior degradability at 48h than P. purpureum, while in the AP30-PP70 (30% A. pennatula + 70% P. purpureum) was lower than the control treatment (p ≤ 0.05). At 24 and 48 h, treatments that contained P. aculeata and B. alicastrum yield higher CH4 mL g−1 DOM than P. purpureum (p ≤ 0.05). The inclusion of these forage species had no statistical effect on the reduction of CH4 emissions per unit of DM incubated or degraded at 24 and 48 h with respect to P. purpureum although reductions were observed. The use of fodders locally available is an economic and viable strategy for the mitigation of the environmental impact generated from tropical livestock systems

Cells with surface expression of CD133^(high)CD71^(low) are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas

Progenitor cells in the adult pancreas are potential sources of endocrine beta cells for treating type 1 diabetes. Previously, we identified tri-potent progenitor cells in the adult (2–4 month-old) murine pancreas that were capable of self-renewal and differentiation into duct, acinar, and endocrine cells in vitro. These progenitor cells were named pancreatic colony-forming units (PCFUs). However, because PCFUs are a minor population in the pancreas (~ 1%) they are difficult to study. To enrich PCFUs, strategies using cell-surface marker analyses and fluorescence-activated cell sorting were developed. We found that CD133^(high)CD71^(low) cells, but not other cell populations, enriched PCFUs by up to 30 fold compared to the unsorted cells. CD133^(high)CD71^(low) cells generated primary, secondary, and subsequent colonies when serially re-plated in Matrigel-containing cultures, suggesting self-renewal abilities. In the presence of a laminin hydrogel, CD133^(high)CD71^(low) cells gave rise to colonies that contained duct, acinar, and Insulin+ Glucagon+ double-hormonal endocrine cells. Colonies from the laminin hydrogel culture were implanted into diabetic mice, and five weeks later duct, acinar, and Insulin+ Glucagon− cells were detected in the grafts, demonstrating tri-lineage differentiation potential of CD133^(high)CD71^(low) cells. These CD133^(high)CD71^(low) cells will enable future studies of putative adult pancreas stem cells in vivo

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery