A Knowledge Gradient Policy for Sequencing Experiments to Identify the Structure of RNA Molecules Using a Sparse Additive Belief Model

We present a sparse knowledge gradient (SpKG) algorithm for adaptively selecting the targeted regions within a large RNA molecule to identify which regions are most amenable to interactions with other molecules. Experimentally, such regions can be inferred from fluorescence measurements obtained by binding a complementary probe with fluorescence markers to the targeted regions. We use a biophysical model which shows that the fluorescence ratio under the log scale has a sparse linear relationship with the coefficients describing the accessibility of each nucleotide, since not all sites are accessible (due to the folding of the molecule). The SpKG algorithm uniquely combines the Bayesian ranking and selection problem with the frequentist $\ell_1$ regularized regression approach Lasso. We use this algorithm to identify the sparsity pattern of the linear model as well as sequentially decide the best regions to test before experimental budget is exhausted. Besides, we also develop two other new algorithms: batch SpKG algorithm, which generates more suggestions sequentially to run parallel experiments; and batch SpKG with a procedure which we call length mutagenesis. It dynamically adds in new alternatives, in the form of types of probes, are created by inserting, deleting or mutating nucleotides within existing probes. In simulation, we demonstrate these algorithms on the Group I intron (a mid-size RNA molecule), showing that they efficiently learn the correct sparsity pattern, identify the most accessible region, and outperform several other policies

Crop Fertilization on Texas Alluvial Soils.

4 p

Religion, Warrior Elites, and Property Rights

In 1119 King Baldwin II of Jerusalem granted nine French knights space on the Temple Mount over the ruins of Solomon’s Temple to create the headquarters of a new monastic order: The Poor Fellow-Soldiers of Christ and of the Temple of Solomon, or the Knights Templar. They grew in wealth and power and became an influential and pervasive organization throughout Western Europe until King Philip of France suppressed them in 1307. The Templars were only one of a number of Christian holy orders of “warrior monks” founded after the First Crusade, with more than two-dozen others founded in Syria, Central and Eastern Europe, and Iberia. More importantly for this paper, the Templars are one example of what we label “warrior elites.” Our definition of warrior elites is not precise but includes pre-industrial full-time specialized soldiers that represent a relatively small part of a region’s military forces but possess disproportionate military strength. In addition, warrior elites often possess significant political and social power. This paper explores the extent to which warrior elites have two characteristics: they adopt a special religion, either different from the mainstream religion or a unique adaptation of the mainstream religion, and the special religion has provisions that enforce property rights. To the extent warrior elites have these two characteristics, we hypothesize they are an example of a social institution that evolves as a low-cost alternative to government and to ordinary religion as a method of property rights enforcement.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137777/1/Hull_&_Anderson_2017_Warrior_Elites_IJRR.pdfDescription of Hull_&_Anderson_2017_Warrior_Elites_IJRR.pdf : Paper published in peer-reviewed scholarly journal

Prevalence, underlying causes, and preventability of sepsis-associated mortality in US acute care hospitals

Importance: Sepsis is present in many hospitalizations that culminate in death. The contribution of sepsis to these deaths, and the extent to which they are preventable, is unknown. Objective: To estimate the prevalence, underlying causes, and preventability of sepsis-associated mortality in acute care hospitals. Design, Setting, and Participants: Cohort study in which a retrospective medical record review was conducted of 568 randomly selected adults admitted to 6 US academic and community hospitals from January 1, 2014, to December 31, 2015, who died in the hospital or were discharged to hospice and not readmitted. Medical records were reviewed from January 1, 2017, to March 31, 2018. Main Outcomes and Measures: Clinicians reviewed cases for sepsis during hospitalization using Sepsis-3 criteria, hospice-qualifying criteria on admission, immediate and underlying causes of death, and suboptimal sepsis-related care such as inappropriate or delayed antibiotics, inadequate source control, or other medical errors. The preventability of each sepsis-associated death was rated on a 6-point Likert scale. Results: The study cohort included 568 patients (289 [50.9%] men; mean [SD] age, 70.5 [16.1] years) who died in the hospital or were discharged to hospice. Sepsis was present in 300 hospitalizations (52.8%; 95% CI, 48.6%-57.0%) and was the immediate cause of death in 198 cases (34.9%; 95% CI, 30.9%-38.9%). The next most common immediate causes of death were progressive cancer (92 [16.2%]) and heart failure (39 [6.9%]). The most common underlying causes of death in patients with sepsis were solid cancer (63 of 300 [21.0%]), chronic heart disease (46 of 300 [15.3%]), hematologic cancer (31 of 300 [10.3%]), dementia (29 of 300 [9.7%]), and chronic lung disease (27 of 300 [9.0%]). Hospice-qualifying conditions were present on admission in 121 of 300 sepsis-associated deaths (40.3%; 95% CI 34.7%-46.1%), most commonly end-stage cancer. Suboptimal care, most commonly delays in antibiotics, was identified in 68 of 300 sepsis-associated deaths (22.7%). However, only 11 sepsis-associated deaths (3.7%) were judged definitely or moderately likely preventable; another 25 sepsis-associated deaths (8.3%) were considered possibly preventable. Conclusions and Relevance: In this cohort from 6 US hospitals, sepsis was the most common immediate cause of death. However, most underlying causes of death were related to severe chronic comorbidities and most sepsis-associated deaths were unlikely to be preventable through better hospital-based care. Further innovations in the prevention and care of underlying conditions may be necessary before a major reduction in sepsis-associated deaths can be achieved

Progress on stochastic background search codes for LIGO

One of the types of signals for which the LIGO interferometric gravitational wave detectors will search is a stochastic background of gravitational radiation. We review the technique of searching for a background using the optimally-filtered cross-correlation statistic, and describe the state of plans to perform such cross-correlations between the two LIGO interferometers as well as between LIGO and other gravitational-wave detectors, in particular the preparation of software to perform such data analysis.Comment: 7 pages, 1 encapsulated PostScript figure, uses IOP class files, submitted to the proceedings of the 4th Amaldi meeting (which will be published in Classical and Quantum Gravity

Zinc Deficiency and Fertilization.

2 p

Crop Fertilization on Texas Alluvial Soils.

4 p

Emotional Intelligence in Agenesis of the Corpus Callosum

People with agenesis of the corpus callosum (AgCC) with normal general intelligence have deficits in complex cognitive processing, as well as in social cognition. It is uncertain the extent to which impoverished processing of emotions may contribute to social processing deficiencies. We used the Mayer–Salovey–Caruso Emotional Intelligence Test to clarify the nature of emotional intelligence in 16 adults with AgCC. As hypothesized, persons with AgCC exhibited greater disparities from norms on tests involving more socially complex aspects of emotions. The AgCC group did not differ from norms on the Experiential subscale, but they were significantly below norms on the Strategic subscale. These findings suggest that the corpus callosum is not essential for experiencing and thinking about basic emotions in a “normal” way, but is necessary for more complex processes involving emotions in the context of social interactions