A method for construction of long randomized open reading frames and polypeptides

A method is presented for construction of randomized open readingframe sequences (ORFs) and gene libraries containing them. Thebuilding blocks for the ORFs were 75 bp long DNA fragments generatedby cloning sequences from a single synthetic oligonucleotidepreparation by bridge mutagenesis. The fragments had the propertythat, regardless of their orientation in the ligated product,the ORF of the construct was maintained. The heterogeneity ofthe ORFs resulted from the random ligation of 2000 differentDNA fragments. The randomized ORFs were cloned downstream fromthe lac promoter in a multicopy plasmid in Escherichia coli.To test the method, a library of 10⁶ clones was constructed.     

On the capacity of binary and Gaussian channels withrun-length-limited inputs

Bounds on the capacity of binary symmetric channels and additive Gaussian channels with run-length-limited two-level (binary, bipolar) inputs are presented, and their tightness is demonstrated for some cases. Stationary input sequences, which do not degrade capacity, are considered when deriving the bounds. Lower bounds on the magnetic recording density for a simple continuous-time recording model incorporating a minimal intertransition constraint are evaluated for soft and hard decisions. A superiority of about 1.5 dB in signal-to-noise ratio is observed for the soft-decision scheme     

On the efficiency of quantization-based integration methods for building simulation

Models describing energy consumption, heating, and cooling of buildings usually impose difficulties to the numerical integration algorithms used to simulate them. Stiffness and the presence of frequent discontinuities are among the main causes of those difficulties, that become critical when the models grow in size. Quantized State Systems (QSS) methods are a family of numerical integration algorithms that can efficiently handle discontinuities and stiffness in large models. For this reason, they are promising candidates for overcoming the mentioned problems. Based on this observation, this article studies the performance of QSS methods in some systems that are relevant to the field of building simulation. The study includes a performance comparison of different QSS algorithms against state-of-the-art classic numerical solvers, showing that the former can be more than one order of magnitude faster.     

Elevated Circulating and Placental SPINT2 Is Associated with Placental Dysfunction

Biomarkers for placental dysfunction are currently lacking. We recently identified SPINT1 as a novel biomarker; SPINT2 is a functionally related placental protease inhibitor. This study aimed to characterise SPINT2 expression in placental insufficiency. Circulating SPINT2 was assessed in three prospective cohorts, collected at the following: (1) term delivery (n = 227), (2) 36 weeks (n = 364), and (3) 24–34 weeks’ (n = 294) gestation. SPINT2 was also measured in the plasma and placentas of women with established placental disease at preterm (<34 weeks) delivery. Using first-trimester human trophoblast stem cells, SPINT2 expression was assessed in hypoxia/normoxia (1% vs. 8% O2), and following inflammatory cytokine treatment (TNFα, IL-6). Placental SPINT2 mRNA was measured in a rat model of late-gestational foetal growth restriction. At 36 weeks, circulating SPINT2 was elevated in patients who later developed preeclampsia (p = 0.028; median = 2233 pg/mL vs. controls, median = 1644 pg/mL), or delivered a small-for-gestational-age infant (p = 0.002; median = 2109 pg/mL vs. controls, median = 1614 pg/mL). SPINT2 was elevated in the placentas of patients who required delivery for preterm preeclampsia (p = 0.025). Though inflammatory cytokines had no effect, hypoxia increased SPINT2 in cytotrophoblast stem cells, and its expression was elevated in the placental labyrinth of growth-restricted rats. These findings suggest elevated SPINT2 is associated with placental insufficiency.     

Discriminatory processor sharing queues with stationary ergodic service times and the performance of TCP in overload

In a recent paper, Bonald and Roberts (2001) [6] studied non-persistent TCP connections in transient overload conditions, under the assumption that all connections have the same round-trip times. In this paper our goal is to develop theoretical tools that will enable us to relax this assumption and obtain explicit expressions for the rate of growth of the number of connections at the system, the rate at which TCP connections leave the system, as well as the time needed for the completion of a connection. To that end, we model the system as a discriminatory processor sharing (DPS) system which we analyze under very mild assumptions on the probability distributions related to different classes of arrivals: we only assume that the arrival rates of connections exist, and that the amount of information transmitted during a connection of a given type forms a stationary ergodic sequence. We then proceed to obtain explicit expressions for the growth rate of the number of connections at the DPS system for several specific probability distributions. We check through simulations the applicability of our queueing results for modeling TCP connections sharing a bottleneck.     

Capacitance-conductance investigation on the phase transitions in Ga nanoparticles

We have reported on coupled capacitance-conductance measurements on Ga nanoparticles embedded in vitreous matrices. The melting of nanoparticles was clearly detected as an abrupt increase in the capacitance vs. temperature scans. The influence of the embedding matrix and of the frequency of the applied field on the dielectric response was checked. The presence of a hysteresis cycle between melting and solidification has been detected. The technique allows the identification of the various solid phases of confined Ga.     

Correlation of omega-3 levels in serum phospholipid from 2053 human blood samples with key fatty acid ratios

Background  

This research was conducted to explore the relationships between the levels of omega-3 fatty acids in serum phospholipid and key fatty acid ratios including potential cut-offs for risk factor assessment with respect to coronary heart disease and fatal ischemic heart disease.     

Computational mereology: A study of part-of relations for multimedia indexing

How to index or retrieve multimedia objects is by no means obvious, because the computer can retrieve right multimedia material only if it reasons about its contents. We show that it is possible to write formal specifications of this reasoning process using set theory and mereology. We discuss the theoretical consequences of trying to use mereology and set theory for multimedia indexing and retrieval. We re-examine the roles of mereology and set theory in knowledge representation. We conclude that both commonsense set theories and mereologies should play the role of constraining databases of arbitrary multimedia objects, e.g. video clips. But although both should be viewed as database constraints, we argue that part-of hierarchies should be used to encode relatively permanent background knowledge, elsewhere names thereferential level, while member-of hierarchies should describe arbitrary multimedia records. We also propose a language and a set of axioms, SetNM, for natural mereologies with sets. A multimedia indexing system can then be viewed as a particular SetNM theory.