Reconstructing phylogenies from nucleotide pattern probabilities : a survey and some new result

The variations between homologous nucleotide sequences representative of various species are, in part, a consequence of the evolutionary history of these species. Determining the evolutionary tree from patterns in the sequences depends on inverting the stochastic processes governing the substitutions from their ancestral sequence. We present a nl.J.mber of recent (and some new) results which allow for a tree to be reconstructed from the expected frequencies of patterns in its leaf colorations generated under various Markov models. We summarise recent work using Hadamard conjugation, which provides an analytic relation between the parameters of Kimura's 3ST model on a phylogenetic tree and the sequence patterns produced. We give two applications of the theory by describing new properties of the popular "maximum parsimony" method for tree reconstruction

Ipsilateral M1 transcranial direct current stimulation increases excitability of the contralateral M1 during an active motor task: Implications for stroke rehabilitation

IntroductionAnodal transcranial direct current stimulation (a-tDCS) of the primary motor cortex (M1) elicits an increase in cortical excitability that outlasts the period of stimulation. However, little is known about effects of a-tDCS on the contralateral M1 during and after ipsilateral M1 stimulation. Therefore, we investigated the changes in corticospinal excitability and inhibition of the left M1 during and after 20min of a-tDCS to the right M1.Material and methodsEight healthy participants received real (2mA) and SHAM a-tDCS to the right M1 randomized across 2 testing sessions. Single- and paired-pulse transcranial magnetic stimulation (TMS) was applied to the left M1 to measure changes motor-evoked potential (MEP) amplitude from the right extensor carpi radialis (ECR) at 130% of resting and active motor threshold, cortical silent period (CSP) and short-interval cortical inhibition (SICI). Active motor threshold was measured during a wrist extension contraction that was less than 5% of maximal electromyographic activation of the ECR. TMS measurements were recorded at baseline, every 5min for 20min during and 10min after a-tDCS.ResultsThe results showed a significant (P<0.05) increase in left M1 MEP amplitude and reduction in CSP duration during (10 and 15min) and after (immediately and 10min post) a-tDCS to the right M1, only during the active motor task. A significant reduction (P<0.05) in SICI during the active task was also found immediately and 10min post a-tDCS. No significant changes in MEP amplitude, CSP and SICI were observed in the resting or active task during SHAM tDCS.DiscussionThe increase in left M1 MEP amplitude and reduction in CSP and SICI during and after 20min of right M1 a-tDCS is most likely to be attributed to a reduction in interhemispheric inhibition that is modulated by a-tDCS during the performance of an active task. Our findings may have significant implications for stroke rehabilitation whereby the application of a-tDCS on the contralesional M1 during neurorehabilitation of the paretic limb may be beneficial for inducing neuroplasticity of the ipsilesional M1 to improve motor function

Distant echoes: evoking the soundscapes of the past in the radio documentary series Noise: a human history

This article asks whether radio can ever successfully evoke an accurate sense of the sound of the past. It does so through a reflective critical analysis of the 2013 BBC Radio 4 documentary series, Noise: A Human History, by its own writer and presenter. It explores how the ‘sound design’ of the series met the challenge of providing a longue durée history of sound without having recourse to authentic sound archive recordings for most of the period being covered. Through an analysis of key sequences, and by highlighting the significance of the broader context of production, it argues that it is possible for epistemologically valuable history to emerge, even via a medium that treats sound more as a device for evoking the imagination than as something possessing evidential status in itself. The article does this by invoking the series as a practical example of ‘historical acoustemology’, and by suggesting that in radio notions of subjectivity and perceptual mimesis are key to understanding the medium's success. In doing so, the article calls for a redefinition of the notion of the radiogenic – arguing for a move away from seeing ‘raw’ sound as the key ingredient of sound design, and towards greater attention to the influence of radio's other characteristics as a time-based, institutionally-produced mass medium

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Surface-reconstructed Icosahedral Structures for Lead Clusters

We describe a new family of icosahedral structures for lead clusters. In general, structures in this family contain a Mackay icosahedral core with a reconstructed two-shell outer-layer. This family includes the anti-Mackay icosahedra, which have have a Mackay icosahedral core but with most of the surface atoms in hexagonal close-packed positions. Using a many-body glue potential for lead, we identify two icosahedral structures in this family which have the lowest energies of any known structure in the size range from 900 to 15000 lead atoms. We show that these structures are stabilized by a feature of the many-body glue part of the interatomic potential.Comment: 9 pages, 8 figure

Concurrent transcranial direct current stimulation and progressive resistance training in Parkinson's disease: Study protocol for a randomised controlled trial

BACKGROUND: Parkinson\u27s disease (PD) results from a loss of dopamine in the brain, leading to movement dysfunctions such as bradykinesia, postural instability, resting tremor and muscle rigidity. Furthermore, dopamine deficiency in PD has been shown to result in maladaptive plasticity of the primary motor cortex (M1). Progressive resistance training (PRT) is a popular intervention in PD that improves muscular strength and results in clinically significant improvements on the Unified Parkinson\u27s Disease Rating Scale (UPDRS). In separate studies, the application of anodal transcranial direct current stimulation (a-tDCS) to the M1 has been shown to improve motor function in PD; however, the combined use of tDCS and PRT has not been investigated. METHODS/DESIGN: We propose a 6-week, double-blind randomised controlled trial combining M1 tDCS and PRT of the lower body in participants (n&thinsp;=&thinsp;42) with moderate PD (Hoehn and Yahr scale score 2-4). Supervised lower body PRT combined with functional balance tasks will be performed three times per week with concurrent a-tDCS delivered at 2 mA for 20 minutes (a-tDCS group) or with sham tDCS (sham group). Control participants will receive standard care (control group). Outcome measures will include functional strength, gait speed and variability, balance, neurophysiological function at rest and during movement execution, and the UPDRS motor subscale, measured at baseline, 3 weeks (during), 6 weeks (post), and 9 weeks (retention). Ethical approval has been granted by the Deakin University Human Research Ethics Committee (project number 2015-014), and the trial has been registered with the Australian New Zealand Clinical Trials Registry (ACTRN12615001241527). DISCUSSION: This will be the first randomised controlled trial to combine PRT and a-tDCS targeting balance and gait in people with PD. The study will elucidate the functional, clinical and neurophysiological outcomes of combined PRT and a-tDCS. It is hypothesised that combined PRT and a-tDCS will significantly improve lower limb strength, postural sway, gait speed and stride variability compared with PRT with sham tDCS. Further, we hypothesise that pre-frontal cortex activation during dual-task cognitive and gait/balance activities will be reduced, and that M1 excitability and inhibition will be augmented, following the combined PRT and a-tDCS intervention. <br /

Expression of kit ligand and amount of follicles as features of folliculogenesis disorder on rat (rattus novergicus) strain wistar with cisplatin

Kit Ligand (KL), one of the first growth factors in ovarian follicle, plays a key role in mammalian oogenesis and folliculogenesis. KL protein and mRNA expression is detected in the granulosa cells of follicles at all stages of development. Cisplatin is one of the first generation platinium compounds and is commonly used for treatment of ovarian, breast, testicular, and bladder cancers.The objective of this study was to prove the lower expression of kit ligand and amount of follicles, and the association between the expression of kit ligand and the amount of follicles, on rat (Rattus novergicus) strain wistar with cisplatin. This study was conducted at Laboratory of Experimental Animal and Veterinary Patology, Faculty of Veterinary, Airlangga University, Surabaya, May-July 2011. The research was performed by randomized post test only control group design. The research samples were Rat (Rattus novergicus) strain wistar which was admitted into inclusion criteria. At the diestrus period, the control group was injected by NaCl 0.9% IP, and the cisplatin group was injected by cisplatin 5 mg/kg w IP. The rat were slaughtered at the 7th day of estrus period on the control group, and at the diestrus period on the cisplatin group. Oophorectomy was performed, continued with immuno-histochemistry staining and hematoxylin eosin for examination on expression of kit ligand and amount of follicles. We achieved no association among the expression of kit ligand and the amounts of primordial, primary, secondary, and tertiary follicles (p=0.945, p=0.180, p=0.590, p=0.753) on the rat with cisplatin. In conclusion, In rat with cisplatin, the expresssion of kit ligand, the amount of primordial, primary, secondary, and tertiary follicles are low. (MOG 2011;19:102-108

Pengaruh tingkat stres dan kadar kortisol dengan jumlah folikel dominan pada penderita infertilitas yang menjalani fertilisasi invitro

Tujuan: Mempelajari hubungan antara tingkat stres dan kadarkortisol darah dengan jumlah folikel dominan pada pasien infertilitas yang menjalani prosedur fertilisasi in vitro Bahan dan Metode: Studi ini merupakan penelitian analitik crosssectional di dua klinik infertilitas di Surabaya selama 4 bulan.Didapatkan 30 subyek penelitian yang diambil data mengenai tingkat stres dengan menggunakan 2 kuisioner yaitu Percieved Stres Scale-10 (PSS-10) dan Infertility Reaction Scale (IRS) dankadar kortisol darah sewaktu pagi. Subyek penelitian kemudian menjalani prosedur stimulasi ovarium dan dilakukan penghitungan jumlah folikel dominan sebelum dilakukan tindakan ovum pickup Hasil: Dengan menggunakan hasil analisa statistik korelasi Spearman didapatkan hasil hubungan negatif antara tingkat stres menggunakan skoring PSS-10 (r=0,64; p<0,01) dan juga IRS(r=0,83; p<0,01) dengan jumlah folikel dominan. Didapatkan pula hubungan negatif antara kadar kortisol darah dengan jumlahfolikel dominan (r=0,80 p<0,01).Simpulan: Tingkat stres dapat berdampak pada jumlah folikeldominan. Kadar kortisol yang tinggi dapat menyebabkan jumlah folikel dominan semakin menurun

NTRFinder: a software tool to find nested tandem repeats

We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/