MaxSSmap: A GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes. We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the highest scoring fragment for exact alignment. We evaluate MaxSSmap's accuracy and runtime when mapping simulated Illumina E.coli and human chromosome one reads of different lengths and 10\% to 30\% mismatches with gaps to the E.coli genome and human chromosome one. We also demonstrate applications on real data by mapping ancient horse DNA reads to modern genomes and unmapped paired reads from NA12878 in 1000 genomes. We show that MaxSSmap attains comparable high accuracy and low error to fast Smith-Waterman programs yet has much lower runtimes. We show that MaxSSmap can map reads rejected by BWA and NextGenMap with high accuracy and low error much faster than if Smith-Waterman were used. On short read lengths of 36 and 51 both MaxSSmap and Smith-Waterman have lower accuracy compared to at higher lengths. On real data MaxSSmap produces many alignments with high score and mapping quality that are not given by NextGenMap and BWA. The MaxSSmap source code is freely available from http://www.cs.njit.edu/usman/MaxSSmap

Development and evaluation of machine learning algorithms for biomedical applications

Gene network inference and drug response prediction are two important problems in computational biomedicine. The former helps scientists better understand the functional elements and regulatory circuits of cells. The latter helps a physician gain full understanding of the effective treatment on patients. Both problems have been widely studied, though current solutions are far from perfect. More research is needed to improve the accuracy of existing approaches. This dissertation develops machine learning and data mining algorithms, and applies these algorithms to solve the two important biomedical problems. Specifically, to tackle the gene network inference problem, the dissertation proposes (i) new techniques for selecting topological features suitable for link prediction in gene networks; a graph sparsification method for network sampling; (iii) combined supervised and unsupervised methods to infer gene networks; and (iv) sampling and boosting techniques for reverse engineering gene networks. For drug sensitivity prediction problem, the dissertation presents (i) an instance selection technique and hybrid method for drug sensitivity prediction; (ii) a link prediction approach to drug sensitivity prediction; a noise-filtering method for drug sensitivity prediction; and (iv) transfer learning approaches for enhancing the performance of drug sensitivity prediction. Substantial experiments are conducted to evaluate the effectiveness and efficiency of the proposed algorithms. Experimental results demonstrate the feasibility of the algorithms and their superiority over the existing approaches

A Lagrangian for Hamiltonian vector fields on singular Poisson manifolds

On a manifold equipped with a bivector field, we introduce for every Hamiltonian a Lagrangian on paths valued in the cotangent space whose stationary points projects onto Hamiltonian vector fields. We show that the remaining components of those stationary points tell whether the bivector field is Poisson or at least defines an integrable distribution - a class of bivector fields generalizing twisted Poisson structures that we study in detail.Comment: 27 page

A re-examination of the Salicornias (Amaranthaceae) of Saudi Arabia and their polymorphs

During the period from 1964 to 1999 Saudi Arabian species of Salicornia were wrongly treated under the European species, S. europaea L. Recent explorations proved that there are two separate allopatric species of Salicornia in Saudi Arabia, one inhabiting the inland salt-marshes of the Najd (highlands) and the other inhabiting the Arabian Gulf Coast (lowlands). Morphological, ecological and exploratory studies confirm that they are two distinct species. The two species differ in features of bark, axillary spikes, basal vegetative segment(s) of spike, fertile segments, colour of senescent plants, and flowering, fruiting and germination phenology. As both the species have been described earlier from Iran, they are now new records for Saudi Arabia. The species are, S. persica ssp. iranica (Akhani) Kadereit & Piirainen and S. sinus-persica Akhani. S. sinus-persica, of which the status was thought doubtful has been confirmed. Both the species have been described and illustrated. Each species comprises a number of polymorphs. As leaves and flowers are rudimentary, confusing species circumscriptions, a proliferation of binomials has resulted in the taxonomy of Salicornia. To mitigate such confusion, the full range of variability of the Saudi Arabian species has been documented

Analisis semiotik pada kolom muhasabah dalam majalah Ar-Risalah edisi Juli 2005-Agustus 2006

Skripsi ini berjudul “ANALISIS SEMIOTIK PADA KOLOM MUHASABAH DALAM MAJALAH AR-RISALAH EDISI JULI 2005-AGUSTUS 2006”. Skripsi ini bertujuan untuk mengetahuai tema/topik yang terdapat dalam kolom Muhasabah Majalah Ar Risalah Edisi Juli 2005 - Agustus 2006 dan mengetahui struktur penandaan pada kolom Muhasabah dalam Majalah Ar Risalah Edisi Juli 2005 - Agustus 2006. Adapun jenis penelitian yang digunakan dalam penelitian ini adalah kualitatif, dan untuk memahami materi-materi atau pesan dakwah dalam kolom “Muhasabah” majalah Ar Risalah Edisi Juli 2005 - Agustus 2006, penulis menggunakan pendekatan semiotika. Semiotik digunakan untuk menelisik atau menguak sistem tanda yang digunakan dalam kolom tersebut. Ada tiga tahap dalam kinerja semiotik, yaitu pemaknaan denotatif yang bertujuan mencari makna sesuai dengan tanda yang ada (penanda), sedangkan tahap kedua menggunakan pemaknaan konotatif, yang bertujuan untuk mencari makna dibalik tanda, sehingga lebih pada menekankan pada penelusuran faktor-faktor mengapa tanda tersebut dapat muncul, dan tahap ketiga adalah ekspansif, yang lebih mengedepankan peran dari pembaca (dalam hal ini penulis) untuk merekonstruksi makna dari sistem tanda tersebut. Hasil penelitian tersebut menunjukkan bahwa materi-materi Islam dalam kolom “Muhasabah” terbagi kedalam tiga kategori yaitu; Aqidah, Syari'ah, dan Akhlak. Tema-tema tersebut merupakan inti ajaran Islam, sehingga masyarakat luas dapat memetik pelajaran atau hikmah dari kolom muhasabah. Kolom Muhasabah didesain sebagai wahana introspeksi atau mawas diri, sehingga impact atau dampak dapat langsung dirasakan oleh masing-masing pembaca. Akhirnya setelah membaca kolom tersebut, diharapkan mampu mengaktualisasikan nilai-nilai (values) keisalaman dalam tataran praktis. Dengan demikian dunia Islam akan bersinar, yang diterangi oleh lentera kemuliaan akhlak dan kualitas kinerja (ibadah) yang didukung oleh ketahanan iman yang membaja dalam dada. Sedangkan sistem penandaan yang ada di kolom Muhasabah mengikuti alur semiotik komunikasi. Semiotik ini mempermudah pemahaman pembaca dalam menangkap pesan yang divisualisasikan melalui tanda yang berbentuk gambar maupun teks yang mengikutinya sebagai penanda, sehingga tanpa melakukan produksi teks, reader langsung dapat memahami pesan tersebut. Alur kedua adalah semiotik konotatif, semiotik ini lebih mengedepankan pada pemaknaan dari tanda tersebut, sehingga unsur petanda lebih dominan dari penandanya. Prinsip kedua ini digunakan dalam menjelaskan sistem tanda yang digunakan dalam kolom Muhasabah. Akhirnya dengan membaca uraian tersebut, pembaca dapat memahami tanda yang dimaksudkan lebih komprehenship, sehingga akan mengurangi resiko kesalahan dalam interpretasi makna atas tanda

Determination of Seed Viability of Eight Wild Saudi Arabian Species by Germination and X-Ray Tests

Our purpose was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of eight wild species (Salvia spinosa, Salvia aegyptiaca, Ochradenus baccatus, Ochradenus arabicus, Suaeda aegyptiaca, Suaeda vermiculata, Prosopisfarcta and Panicumturgidum) from Saudi Arabia. Several days were required to determine viability of all eight species via germination tests, while immediate results on filled/viable seeds were obtained with the X-ray test. Seeds of all the species, except Sa.aegyptiaca, showed high viability in both the germination (98–70% at 25/15 °C, 93–66% at 35/25 °C) and X-ray (100–75%) test. Furthermore, there was general agreement between the germination (10% at 25/15 °C and 8% at 35/25 °C) and X-ray (5%) tests that seed viability of Sa.aegyptiaca was very low, and X-ray analysis revealed that this was due to poor embryo development. Seeds of P.farcta have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min), and they exhibited high viability in both the germination (98% at 25/15 °C and 93% at 35/25 °C) and X-ray (98%) test. Most of the nongerminated seeds of the eight species except those of Sa.aegyptiaca were alive as judged by the tetrazolium test (TZ). Thus, for the eight species examined, the X-ray test was a good and rapid predictor of seed viability

Les comportements écologiques des dirigeants des entreprises tunisiennes

À la fin des années 1980, plusieurs entreprises tunisiennes, en réaction essentiellement à la législation environnementale, ont commencé à élaborer des initiatives environnementales en optant pour des niveaux d’engagements environnementaux différents. L’objectif de cette recherche est d’identifier les comportements écologiques des dirigeants des entreprises tunisiennes en se basant sur leur niveau d’engagement environnemental. Sur un échantillon de 55 entreprises, les résultats montrent l’existence de trois comportements : défensif, conformiste et citoyen. Les résultats montrent aussi que la taille joue un rôle dans l’adoption d’un comportement plus responsable. En revanche, aucune relation n’a été trouvée entre le comportement écologique et le secteur d’activité.In 1988, some Tunisian firms, essentially in reaction with the environmental regulation, have instituted environmental initiatives. The objective of this research is to classify the Tunisian managers based on their environmental commitment. In a sample of 55 firms, the results show the existence of three groups based on environmental commitment; reactive, conformist and citizen managers. Firm size had a major impact on the environmental commitment. But no relationship was found between environmental commitment and activity sector

American Options Based on Malliavin Calculus and Nonparametric Variance Reduction Methods

This paper is devoted to pricing American options using Monte Carlo and the Malliavin calculus. Unlike the majority of articles related to this topic, in this work we will not use localization fonctions to reduce the variance. Our method is based on expressing the conditional expectation E[f(St)/Ss] using the Malliavin calculus without localization. Then the variance of the estimator of E[f(St)/Ss] is reduced using closed formulas, techniques based on a conditioning and a judicious choice of the number of simulated paths. Finally, we perform the stopping times version of the dynamic programming algorithm to decrease the bias. On the one hand, we will develop the Malliavin calculus tools for exponential multi-dimensional diffusions that have deterministic and no constant coefficients. On the other hand, we will detail various nonparametric technics to reduce the variance. Moreover, we will test the numerical efficiency of our method on a heterogeneous CPU/GPU multi-core machine

Simple Subject-Verb Agreement: a Morphosyntactic Path to Arabic Variations

The analytic object of this dissertation is to formally model the Arabic subject-verb agreement aspects, more particularly, the verbal agreement with simple subject DPs. It aims to define how φ-agreement is formally manifested across the Arabic varieties, more specifically, Standard Arabic and the current dialects, and hopes to draw the latter varieties’ interrelation. In other words, this thesis hopes to advance the overall understanding of subject-verb agreement in Arabic and contribute to a clearer and simpler view of a number of specific syntactic phenomena. Most important of all, the subject DP relative order with respect to the verbal predicate influences the possible subject-verb-agreement choices attested in Standard Arabic (SA), whereby a subject-verb (SV) order shows full agreement in all φ-features, but a verb-subject (VS) order shows only partial agreement, typically, in Gender and Person. Nonetheless, full subject-verb agreement in VS order is robustly found in different dialects of the Arab world, in which the Number feature is obligatory. Remarkably, not only is the partial agreement attested in SA absent in the modern dialects, but also Gender and Number morphology distinctions may often be minimized. On the one hand, a masculine agreement is syncretic whenever the agreement relation is established between a verbal predicate and dual or plural subject DPs, whether they are masculine or feminine. On the other hand, plural and dual nouns trigger plural agreement on the agreeing verbal predicate; the plural number is syncretic whenever the subject DP is plural or dual. What’s more, the Arabic (traditional) texts have an abundance of examples that do not conform to the SA norm of agreement and whose well-formedness is unquestionable, suggesting that the agreement asymmetry may not be absolute. These observations urge an in-depth investigation, assuming that they may present profound paradoxes when analyzed via the standard Agree-based mechanism. Despite the dissimilarity between SA and the modern dialects in terms of subject-verb agreement, these varieties are mostly alike in other matters. For these reasons, I believe that any account to the subject-verb agreement must take these points into consideration. To my knowledge, there has been no detailed analysis devoted to the interrelation between the standard variety and the modern dialects in terms of subject-verb agreement. So, believing that any syntactic account to the subject-verb agreement in Arabic ought to be flexible to cover the various agreement phenomena, I argue that the various (often outwardly non-canonical) agreement patterns in Arabic are manifestations of the core syntactic Agree mechanism. Their agreement behavior is often attributed to a fundamental mismatch between the syntactic and morphological components, subject to variety/dialect-specific requirements. In simple terms, taking the core properties of the Agree-based system to feature valuation (Chomsky, 2000 et seq.), the assumptions in Distributed Morphology (Halle & Marantz, 1993; 1994; Halle, 1994, among others), and the feature geometry advocated by Harley & Ritter (2002), among others, I posit that these agreement patterns attest very general conditions on the agreement and φ-feature manifestations in Arabic, defined in terms of restrictions on T’s φ-Probe that agrees with the subject DP. Overall, given the formulation of the conditions advanced, the agreement facts across the Arabic varieties, I believe, arise naturally and predictably from the interaction of Agree, conditions on T’s φ-Probe, and postsyntactic requirements

A Loosely-Coupled Passive Dynamics and Finite Element based Model for Minimising Biomechanically Driven Unhealthy Joint Loads during Walking in Transtibial Amputees

The primary objective of a prosthetic foot is to improve the quality of life for amputees by enabling them to walk in a similar way to healthy individuals. Amputees su˙er from health risks including joint pain, back pain and joint inflammation. The aim of this thesis is to develop a new computational approach to reduce the likelihood of biomechanically driven joint pain in transtibial amputees resulting from sustained exposure to Unhealthy Loads (ULs) during walking. This is achieved by developing a computational methodology to achieve a customisable sti˙ness design solution for prosthetic feet so that the occurrence of unhealthy joint loads during walking is minimised.It is assumed that the healthy population is able to spend energy most optimally during walking at all walking speeds. During walking, the force exerted by the body on the ground is measured by the ground reaction force (GRF). The GRF value is normalised with the body weight defining a dimensionless parameter . The values are similar for both legs in healthy populations but are di˙erent for the sound and a˙ected leg for amputees. A new hypothesis has been proposed in this thesis that walking is comfortable for an amputee when the di˙erence between values is minimal between the amputee and an equivalent healthy population. The values for healthy adults, as well as amputees, follow a finite number of patterns. The pattern of the values (or the GRF curve) depends on the walking speed of an individual, categorised as slow, fast or free walking. However, it is observed in the literature that free walking speed (FWS) varies over a wide range for healthy individuals (e.g. 1.1 m/s to 1.5 m/s). As a result, it was diÿcult to establish a relationship between walking speed and GRF pattern. A novel parametrised description of GRF curves for a healthy population and amputees is proposed so that a new dimensionless velocity ratio parameter and the corresponding value of the FWS can be predicted by observing the GRF pattern of a healthy adult or an amputee. A new classification approach based on the parametrised description of GRF curves, along with the dimensionless velocity ratio parameter, has been recommended for categorising very slow, slow, free, fast and very fast walking. The GRF result predictions are validated on healthy adults in an experiment conducted in a gait lab. A group of candidates who walk a lot in their daily life were specially selected for this experiment. This classification approach is used to develop a new measure of ULs based on the parametrised GRF description for healthy population and amputees. An innovative computational methodology is proposed to design an optimal sti˙ness response of a prosthetic foot that minimises the occurrence of ULs. This is achieved by transferring the roll-over shape (ROS) information of the prosthetic foot and the corresponding information for a given velocity ratio across a passive walking dynamic (PWD) and a finite element model via a newly defined form of loose coupling. A theoretical case study is presented in which an amputee walks in a gait lab with a representative C-shaped prosthetic foot. The thesis explains how the proposed novel computational methodology is able to redesign the prosthetic foot in a way that is better suited to minimising ULs. The redesign process of the prosthetic foot has led to the development of an innovative 3D printable double keel and double heel design. With the advancement of carbon reinforced polymers and additive manufacturing technology, the sti˙ness customisation methodology proposed in this thesis has the potential to create a new generation of energy-eÿcient prosthetic feet