A linear memory algorithm for Baum-Welch training

Background: Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. Methods and results: We introduce a linear space algorithm for Baum-Welch training. For a hidden Markov model with M states, T free transition and E free emission parameters, and an input sequence of length L, our new algorithm requires O(M) memory and O(L M T_max (T + E)) time for one Baum-Welch iteration, where T_max is the maximum number of states that any state is connected to. The most memory efficient algorithm until now was the checkpointing algorithm with O(log(L) M) memory and O(log(L) L M T_max) time requirement. Our novel algorithm thus renders the memory requirement completely independent of the length of the training sequences. More generally, for an n-hidden Markov model and n input sequences of length L, the memory requirement of O(log(L) L^(n-1) M) is reduced to O(L^(n-1) M) memory while the running time is changed from O(log(L) L^n M T_max + L^n (T + E)) to O(L^n M T_max (T + E)). Conclusions: For the large class of hidden Markov models used for example in gene prediction, whose number of states does not scale with the length of the input sequence, our novel algorithm can thus be both faster and more memory-efficient than any of the existing algorithms.Comment: 14 pages, 1 figure version 2: fixed some errors, final version of pape

Dense, irregular, yet always graphic 33-uniform hypergraph degree sequences

A $3$-uniform hypergraph is a generalization of simple graphs where each hyperedge is a subset of vertices of size $3$. The degree of a vertex in a hypergraph is the number of hyperedges incident with it. The degree sequence of a hypergraph is the sequence of the degrees of its vertices. The degree sequence problem for $3$-uniform hypergraphs is to decide if a $3$-uniform hypergraph exists with a prescribed degree sequence. Such a hypergraph is called a realization. Recently, Deza \emph{et al.} proved that the degree sequence problem for $3$-uniform hypergraphs is NP-complete. Some special cases are easy; however, polynomial algorithms have been known so far only for some very restricted degree sequences. The main result of our research is the following. If all degrees are between $\frac{2n^2}{63}+O(n)$ and $\frac{5n^2}{63}-O(n)$ in a degree sequence $D$, further, the number of vertices is at least $45$, and the degree sum can be divided by $3$, then $D$ has a $3$-uniform hypergraph realization. Our proof is constructive and in fact, it constructs a hypergraph realization in polynomial time for any degree sequence satisfying the properties mentioned above. To our knowledge, this is the first polynomial running time algorithm to construct a $3$-uniform hypergraph realization of a highly irregular and dense degree sequence

Effectiveness of different trap design in mass trapping of Bothynoderes punctiventris Germar

The discovery of an aggregation attractant for Bothynoderes punctiventris Germ. raised several questions for possible improvements of IPM of Bothynoderes punctiventris in sugar beet. First results on exploration of possibilities for its use for monitoring purposes as well as for mass trapping of adults of the pest are described in this paper. Trap design effectiveness was evaluated in the overwintering fields of sugar beet weevil for two years in localities in Serbia and Hungary. Among trap designs tested it was proved that baited CSALOMON® TAL trap design was optimal

Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

Background: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site.Results: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci.Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact.Conclusion: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect.This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species

Overview of Registered Clinical Trials on Manual Therapy: Possible Implications of Genetic Testing for Personalized Treatment

Background/aim: Manual therapy (MT) is a frequently applied intervention offering individualized treatment in the clinic. In addition to the traditional approaches of MT, measuring molecular response to MT may offer better understanding of MT outcomes in order to provide specific personalized treatment. The aim of this study was to summarize MT-related registered clinical trials, as well as to search for any evidence on MT and genetics.Patients and methods: A comprehensive search was conducted within the Clinical Trials database with predefined keywords mining for all types of MT-related clinical trials.Results: From the 47 trials, 20 had results and 27 had no results. MT alleviated pain and improved function almost in all trials. One registered clinical trial had investigated molecular outcomes of MT.Conclusion: MT is an effective and individualized treatment offering option in the management of several conditions. Interestingly, a clinical trial was found investigating molecular genetics and MT pinpointing an already existing link between genetics and MT. Therefore, further clinical trials may focus on genetics and MT for providing specific personalized treatment in future.</p

Association of symptoms of insomnia and sleep parameters among kidney transplant recipients

Objective: Insomnia complaints are frequent among kidney transplant (kTx) recipients and are associated with fatigue, depression, lower quality of life and increased morbidity. However, it is not known if subjective insomnia symptoms are associated with objective parameters of sleep architecture. Thus, we analyze the association between sleep macrostructure and EEG activity versus insomnia symptoms among kTx recipients. Methods: Participants (n1 = 100) were selected from prevalent adult transplant recipients (n0 = 1214) followed at a single institution. Insomnia symptoms were assessed by the Athens Insomnia Scale (AIS) and standard overnight polysomnography was performed. In a subgroup of patients (n2 = 56) sleep microstructure was also analyzed with power spectral analysis. Results: In univariable analysis AIS score was not associated with sleep macrostructure parameters (sleep latency, total sleep time, slow wave sleep, wake after sleep onset), nor with NREM and REM beta or delta activity in sleep microstructure. In multivariable analysis after controlling for covariables AIS score was independently associated with the proportion of slow wave sleep (β = 0.263; CI: 0.026–0.500) and REM beta activity (β = 0.323; CI = 0.041–0.606) (p < 0.05 for both associations). Conclusions: Among kTx recipients the severity of insomnia symptoms is independently associated with higher proportion of slow wave sleep and increased beta activity during REM sleep but not with other parameters sleep architecture. The results suggest a potential compensatory sleep protective mechanism and a sign of REM sleep instability associated with insomnia symptoms among this population