943 research outputs found
Organizational Culture and Performance: An Empirical Study of SMEs in Pakistan. Journal of Management and Research,
No full textThis study aims to identify the prevailing type of culture and its relationship with performance in SMEs operating in Pakistan. Using competing value framework, the cultural profile and dominant characteristics of SMEs are identified and investigated to ascertain their implied relationship with organizational performance on the basis of certain self-assessment variables. For this purpose, primary data was collected form SME employees through a self-administered survey questionnaire. The results revealed that ‘hierarchy’ culture is the prevailing type of culture and a statistically significant relationship exists between organizational culture and performance among the sampled SMEs. The study concludes with certain important insinuations for theory and practice especially concerned with SMEs
Hydraulic simulations to evaluate and predict design and operation of the Chashma Right Bank Canal
No full textIrrigation systems / Irrigation canals / Flow control / Velocity / Canal regulation techniques / Hydraulics / Simulation models / Design / Operations / Crop-based irrigation / Distributary canals / Water delivery / Policy / Protective irrigation / Water allocation / Water requirements / Sedimentation / Water distribution / Equity / Water conveyance / Pakistan / Chashma Right Bank Canal
Precise motion descriptors extraction from stereoscopic footage using DaVinci DM6446
No full textA novel approach to extract target motion descriptors in multi-camera video surveillance systems is presented. Using two static surveillance cameras with partially overlapped field of view (FOV), control points (unique points from each camera) are identified in regions of interest (ROI) from both cameras footage. The control points within the ROI are matched for correspondence and a meshed Euclidean distance based signature is computed. A depth map is estimated using disparity of each control pair and the ROI is graded into number of regions with the help of relative depth information of the control points. The graded regions of different depths will help calculate accurately the pace of the moving target and also its 3D location. The advantage of estimating a depth map for background static control points over depth map of the target itself is its accuracy and robustness to outliers. The performance of the algorithm is evaluated in the paper using several test sequences. Implementation issues of the algorithm onto the TI DaVinci DM6446 platform are considered in the paper
Integration of Information Technology in Financial Services and its Adoption by the Financial Sector in Pakistan
No full textThe development of digital innovation is a clear indication of the expansion of financial technology (Fintech) businesses over the previous ten years. Fintech concepts have only lately begun to be accepted by established players in the financial sector. Despite recent bank purchases of Fintech firms, the majority of these businesses are self-funded and accessible to other banks. Because many banks, besides the well-known big ones, continue to provide outdated, outrageously expensive, and bureaucratic financial services, Fintech companies have the potential to replace many crucial tasks presently carried out by traditional banks. In other words, it\u27s expected that Fintech firms will have a replacement effect, forcing banks to abandon certain kinds of business. The incentives for a bank to take risks and increase its effectiveness and profitability may have altered as a result of Fintech advancements. This exemplifies how Fintech developments will affect bank risk, efficiency, and profitability because they offer a competitive source of credit to conventional banks. The purpose of this research is to look into the problems from a global standpoint.
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Clitopilus cretoalbus A. Izhar, Zaman, M. Asif, H. Bashir, Niazi & Khalid 2023, sp. nov
No full textClitopilus cretoalbus A.Izhar, Zaman, M.Asif, H.Bashir, Niazi & Khalid sp. nov Mycobank: MB843564 Figs 3–4 Diagnosis Clitopilus cretoalbus sp. nov. is close to C. scyphoides but the latter differs by its hygrophanous pileus with smaller diameter (3–6 mm), short stipe (4–9 mm), small colourless basidiospores (5–7 × 3.5–4.5 µm), absence of cystidia and pale yellow pileipellis. Etymology The specific epithet ʻ cretoalbus ʼ refers to chalk white colour of basidiocarps. Type material Holotype PAKISTAN – Punjab Province • Sheikhupura; 31°42′40″ N, 73°59′16″ E; 236 m a.s.l.; 3 Aug. 2017; A. Izhar Skp 102; GenBank nos: ON117610 (nrITS), ON229505 (nrLSU); LAH[35709]. Additional material examined PAKISTAN – Punjab Province • Sheikhupura; 31°42′40″ N, 73°59′16″ E; 236 m a.s.l.; 20 Jul. 2018; A. Izhar Skp 106; GenBank no.: ON229117 (nrITS); LAH[37112] • same data as for preceding; 12 Aug. 2021; A. Izhar Skp 107; GenBank no.: ON229118 (nrITS); LAH[37113] • Lahore, Jhok Reserve Forest; 31°25ʹ36.01ʺ N, 74°7ʹ11.13ʺ E; 217 m a.s.l.; 23 Aug. 2020; A.N. Khalid MN16; GenBank nos: OM935685 (nrITS), OM934826 (nrLSU); LAH[37017] • Bahawalpur, Lal Suhanra National Park, under Bombax ceiba L.; 31°26′28″ N, 74°8′7″ E; 125–140 m a.s.l.; 5 Sep. 2020; M. Asif AG130; GenBank no.: ON241754 (nrITS); LAH[37111] • Khushab, Noorpur Thal, Peelowains; 32°20′ N, 72°20′ E; 185 m a.s.l.; 8 Aug. 2021; Z. Khan & J. Khan PW18; GenBank no.: OM935686 (nrITS); LAH[37016]. – Khyber Pakhtunkhwa Province • Swat, Tehsil Kabal, Village Deolai; 34°34′ N, 72°08′ E; 1000 m a.s.l.; 25 Jul. 2021; H. Bashir GHSS02; GenBank no.: ON326583 (nrITS); LAH[37126]. Description Basidiomata clitocyboid, infundibuliform, or omphaloid, usually very small in size. Pileus 25–30 mm, concave, infundibuliform or umbilicate, context very fragile, white (2.5YR9/2), later chalk white, pale yellow at the disc (5Y 8/3), small brown patches develop when touched or dried, umbo never found, surface smooth to finely fibrillose under the lens, margins inrolled, becoming relatively straight towards maturity, cracks or furcations develop at pyramidal portions. Lamellae adnate to deeply decurrent, very thin, membranous, somewhat distant to close, sometimes bifurcated, white (2.5YR9/2) concolorous to pileus, up to 1.8 mm in height, edges entire, lamellulae abundant, present in 1–3 tiers. Stipe 10–25 × 1–4 mm, almost central, slightly eccentric in a few specimens, sub-cylindrical, concolorous to pileus, surface smooth or minutely pubescent, white mycelium at the base. Odor farinaceous. Basidiospores [100/5/5] (4.5–)6.4–7.5(‒8.5) × (3.6‒)3.9–4.6(‒5.5) μm, avl × avw = 6.7 × 4.4 μm, Q = 1.2‒1.54, avQ = 1.5, oblong, broadly ellipsoid or amygdaliform, hyaline to pale in 5% KOH, thin-walled, smooth-walled, frequent lipidic guttules, apiculus prominent, mostly isolated, few in tetrads. Basidia 13‒25 × 6.3‒8 μm, avl × avw = 18.7 × 7.2 μm, clavate, hyaline in 5% KOH, 4-spored, rarely 2-spored, sterigmata up to 3–3.4 µm in length, no clamp connections at base. Cheilocystidia 17‒30 × 5.5‒8.8 μm, avl × avw = 23 × 7 μm, polymorphic, subcylindrical, lageniform, some filiform, septate, few with apical or lateral outgrowths, resembling end cells of pileipellis, hyaline to pale in 5% KOH, often present in clusters. Pleurocystidia not found. Sub-hymenium irregular in texture, composed of 2–3 layers of ellipsoid hyphal elements, 3–13 × 4–8 μm. Pileipellis consists of a cutis of hyaline to pale cylindrical thin-walled hyphae 4–8 μm wide, avw = 6.2 μm, few pigmented brownish, hyphae parallel, often interwoven, many isolated and clustered ascendingly, terminal elements 5–8 μm wide. Pileal trama consists of subregular, hyaline, thin-walled, relatively inflated hyphae 8–14 μm wide, few oleiferous hyphae present. Stipitipellis a cutis composed of hyaline, loosely arranged or interwoven hyphae 4–5.5 μm wide, thin-walled, many clustered ascendingly. Habitat Scattered or in small groups on nutrient-rich loamy soil and gregarious in grassy plots. Known distribution Currently only known from Pakistan.Published as part of Izhar, Aiman, Khan, Zaman, Asif, Muhammad, Bashir, Hira, Rani, Afifa Kainat, Niazi, Abdul Rehman & Khalid, Abdul Nasir, 2023, Clitopilus cretoalbus sp. nov. (Entolomataceae, Agaricales), a new species from Pakistan, pp. 168-184 in European Journal of Taxonomy 861 on pages 174-179, DOI: 10.5852/ejt.2023.861.2075, http://zenodo.org/record/774659
Continuous degradation of maltose: Improvement in stability and catalytic properties of maltase (α-glucosidase) through immobilization using agar-agar gel as a support
No full textMaltose degrading enzyme was immobilized
within agar-agar support via entrapment method due to its
industrial utilization. The maximum immobilization efficiency
(82.77 %) was achieved using 4.0 % agar-agar
keeping the diameter of bead up to 3.0 mm. The matrix
entrapment showed maximum catalytic activity at pH 7.0
and temperature 65 C. Substrate saturation kinetics
showed that the Km of immobilized enzyme increased from
1.717 to 2.117 mM ml-1 where as Vmax decreased from
8,411 to 7,450 U ml-1 min-1 as compared to free enzyme.
The immobilization significantly increased the stability of
maltase against various temperatures and immobilized
maltase retain 100 % of its original activity after 2 h at
50 C, whereas the free maltase only showed 60 % residual
activity under same condition. The reusability of entrapped
maltase showed activity up to 12 cycles and retained 50 %
of activity even after 5th cycle. Storage stability of agar
entrapped maltase retain 73 % of its initial activity even
after 2 months when stored at 30 C while free enzyme
showed only 37 % activity at same storage conditions
A role for gene-environment interactions in Autism Spectrum Disorder is suggested by an excess of potentially pathogenic variants in genes regulating exposure to toxicants
No full textObjective: Identify potentially pathogenic CNVs and SNVs targeting genes involved in regulation of
toxins exposure, namely in detoxification processes and physiological permeability
barriers (blood-brain barrier and placenta), in individuals with ASD.João Xavier Santos, Ana Rita Marques, Muhammad Asif and Joana Vilela are fellows of the BioSys-PhD programme and awardees of scholarships funded by Fundação para a Ciência e Tecnologia (FCT).
Autism Genome Project (AGP), Simons Foundation Autism Research Initiative (SFARI) and ARRA Autism Sequencing Consortium.N/
Inference dynamics in transcriptional regulation
No full textComputational systems biology is an emerging area of research that focuses on understanding
the holistic view of complex biological systems with the help of statistical, mathematical and
computational techniques. The regulation of gene expression in gene regulatory network is
a fundamental task performed by all known forms of life. In this subsystem, modelling the
behaviour of the components and their interactions can provide useful biological insights. Statistical
approaches for understanding biological phenomena such as gene regulation are proving
to be useful for understanding the biological processes that are otherwise not comprehensible
due to multitude of information and experimental difficulties. A combination of both the experimental
and computational biology can potentially lead to system level understanding of
biological systems.
This thesis focuses on the problem of inferring the dynamics of gene regulation from the
observed output of gene expression. Understanding of the dynamics of regulatory proteins in
regulating the gene expression is a fundamental task in elucidating the hidden regulatory mechanisms.
For this task, an initial fixed structure of the network is obtained using experimental
biology techniques. Given this network structure, the proposed inference algorithms make use
of the expression data to predict the latent dynamics of transcription factor proteins.
The thesis starts with an introductory chapter that familiarises the reader with the physical
entities in biological systems; then we present the basic framework for inference in transcriptional
regulation and highlight the main features of our approach. Then we introduce the
methods and techniques that we use for inference in biological networks in chapter 2; it sets
the foundation for the remaining chapters of the thesis. Chapter 3 describes four well-known
methods for inference in transcriptional regulation with pros and cons of each method.
Main contributions of the thesis are presented in the following three chapters. Chapter 4 describes
a model for inference in transcriptional regulation using state space models. We extend
this method to cope with the expression data obtained from multiple independent experiments
where time dynamics are not present. We believe that the time has arrived to package methods
like these into customised software packages tailored for biologists for analysing the expression
data. So, we developed an open-sources, platform independent implementation of this method
(TFInfer) that can process expression measurements with biological replicates to predict the
activities of proteins and their influence on gene expression in gene regulatory network.
The proteins in the regulatory network are known to interact with one another in regulating
the expression of their downstream target genes. To take this into account, we propose a novel
method to infer combinatorial effect of the proteins on gene expression using a variant of factorial hidden Markov model. We describe the inference mechanism in combinatorial factorial
hidden model (cFHMM) using an efficient variational Bayesian expectation maximisation algorithm.
We study the performance of the proposed model using simulated data analysis and
identify its limitation in different noise conditions; then we use three real expression datasets
to find the extent of combinatorial transcriptional regulation present in these datasets. This
constitutes chapter 5 of the thesis.
In chapter 6, we focus on problem of inferring the groups of proteins that are under the
influence of same external signals and thus have similar effects on their downstream targets.
Main objectives for this work are two fold: firstly, identifying the clusters of proteins with
similar dynamics indicate their role is specific biological mechanisms and therefore potentially
useful for novel biological insights; secondly, clustering naturally leads to better estimation of
the transition rates of activity profiles of the regulatory proteins. The method we propose uses
Dirichlet process mixtures to cluster the latent activity profiles of regulatory proteins that are
modelled as latent Markov chain of a factorial hidden Markov model; we refer to this method
as DPM-FHMM. We extensively test our methods using simulated and real datasets and show
that our model shows better results for inference in transcriptional regulation compared to a
standard factorial hidden Markov model.
In the last chapter, we present conclusions about the work presented in this thesis and
propose future directions for extending this work
Case Studies in Cryptol - A study of domain specific languages for DSP algorithms
No full textDigital Signal Processing (DSP) has become part of many electronic applications these days; confluent to this, Domain Specific Languages (DSLs) are prevailing among practitioners of many engineering domains. Cryptol is a domain specific language for cryptography, it was designed by Galois and it has been used by NSA from the start. Cryptol is designed for cryptographic specifications; however, this project aims at evaluating Cryptol as a domain specific language for digital signal processing algorithms. The report also includes a proposal for extensions to Cryptol to make it applicable to DSP algorithms. This thesis derives its motivation from the DSL for DSP research that the Functional Programming group has started with Ericsson. This project involved implementing a set of DSP algorithms in Cryptol and analyzing applicability of Cryptol from the experiences in this new domain. This study shows that Cryptol is too specialised to cryptographic algorithms and that it is not possible to specify, run or verify many DSP algorithms in Cryptol. However there is a special class of DSP algorithms that are far easier to code in Cryptol than in C or Java. Small overlap with DSP algorithms was expected since DSLs are customized for a certain problem area. The evaluation of Cryptol in the DSP domain revealed that some enhancements are necessary to make it applicable to DSP algorithms. The outcome of this study is a set of extensions to Cryptol which are discussed towards the end of this report
A computational pipeline to identify phenotypic manifestations related to genes
No full textTese de Mestrado, Bioinformática e Biologia computacional, 2022, Universidade de Lisboa, Faculdade de CiênciasUma proporção de pacientes com doenças de neuro desenvolvimento, tem uma mutação
genética diretamente ligada à sua doença. A Perturbação do Espectro do Autismo (PEA) é uma
patologia de neuro desenvolvimento com apresentação clínica muito heterogênea (Cummings et
al., 2005). PEA é caracterizada por ter padrões de ações ou interesses repetitivos,
dificuldades/limitações em interações sociais e comunicação que se manifestam desde a infância.
Estes sintomas afetam mais homens que mulheres e podem variar em severidade. Talvez o maior
avanço em perceber a fisiopatologia do PEA é ter sido reconhecido a contribuição genética para
a etiologia do PEA com a ajuda do aparecimento de métodos NGS e WES (Daniel H. Geschwind,
2011; Asif et al., 2018). Há vários genes e mutações associados com o PEA o que aponta a uma
origem heterogenia da doença. A combinação de uma arquitetura genética complexa e pouco
compreendida, heterogeneidade fenotípica e o envolvimento de múltiplos loci que interagem entre
si dificulta a descoberta dos genes com mutações específicas que levam ao PEA.
Consequentemente, a etiologia genética dos distúrbios relacionados ao PEA permanece em
grande parte desconhecida (Gupta et al., 2006). Vários estudos demonstraram que duplicações ou
deleções de segmentos do genoma denominados de Variantes de Número de Cópias (CNVs),
polimorfismos de nucleotídeo único (SNPs) e variantes de nucleotídeo único (SNVs)
provavelmente têm um papel causal na PEA (Chang et al., 2014; Soler et al., 2018). O
estabelecimento da relação entre os diferentes genes com as variantes do fenótipo do PEA pode
facilitar o diagnóstico dos pacientes e, assim, possibilitar que os pacientes obtenham o tratamento
mais eficiente e específico numa idade mais jovem.
Devido aos recentes avanços nas tecnologias genómicas, os estudos genéticos em larga escala
estão a revelar um grande número de variantes genéticas que potencialmente contribuem para o
risco de doenças. O objetivo global deste trabalho foi propor um pipeline para identificar a
manifestação fenotípica de variantes genéticas putativas causadoras de doenças. Para isso, foram
estabelecidos dois objetivos específicos:
• Identificação de clusters de genes funcionalmente semelhantes;
• Inferir o fenótipo da doença para cada cluster separadamente.
Para alcançar estes objetivos, neste estudo foi usado um dataset que contem 3707 genes de
pacientes diagnosticados com PEA. A este dataset são aplicadas ferramenta como o DishIn e
GoSemSim para calcular o valor da semelhança semântica em pares de genes, obtendo no fim
uma matriz quadrada de semelhança semântica. Este valor é obtido pelas ferramentas ao
quantificar a informação partilhada entre dois termos GO, associados a cada gene, como o
conteúdo de informação do ancestral comum mais informativo de dois termos. As medidas para
calcular a semelhança semântica do conteúdo de informação usadas neste trabalho são Lin, Jiang
& Conrath e Rel. Através da matriz de semelhança semântica é calculada a matriz de distâncias à
qual são aplicados os algoritmos de clustering DBSCAN, Kmeans e hierárquico, de modo a obter
grupos de genes que sejam funcionalmente semelhantes.
Após a análise dos resultados, foi possível concluir que variantes genéticas podem ser
agrupados usando cálculos de semelhança semântica. Demonstrou-se que os genes que foram
agrupados são funcionalmente semelhantes, estavam inseridos em redes de interação genética e
podem levar a diferentes grupos de fenótipos de PEA. Os genes agrupados foram enriquecidos
para diferentes pathways e sub fenótipos relacionados ao PEA.In most neurodevelopmental diseases, a proportion of patients carries a known gene mutation
directly linked to their illness. Autism Spectrum Disorder (ASD) is a neurodevelopmental
pathology with very heterogeneous clinical presentation (Cummings et al., 2005). ASD is
characterized by symptoms of repetitive patterns of actions or interests, difficulties/limitations in
social interactions and communication that appear since childhood. These symptoms affect more
men than women and can vary in severity.
Perhaps the greatest advance in understanding the pathophysiology of ASD is the recognition
of the genetic contribution to the etiology of ASD with the help of the emergence of NGS and
WES methods (Daniel H. Geschwind, 2011; Asif et al., 2018). There are several genes and
mutations associated with ASD which point to a heterogeneous origin of the disease. A
combination of a complex and poorly understood genetic architecture, phenotypic heterogeneity
and the involvement of multiple loci interacting with one another hinder efforts to discover the
genes with specific mutations that lead to ASD. Consequently, the genetic etiology of disorders
related to ASD remains largely unknown (Gupta et al., 2006). Several studies demonstrated that
duplications or deletions of genome segments called Copy Number Variants (CNVs), single
nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) are likely to have a
causal role in ASD (Chang et al., 2014; Soler et al., 2018). The establishment of the relationship
between different genes to the ASD phenotype variants may facilitate the diagnosis of patients
and thus enable patients to obtain the correct treatment at a younger age.
Due to recent advances in genomic technologies, the large-scale genetic studies are
unraveling large numbers of genetic variants potentially contributing to disease risk. The global
objective of this work was to propose a pipeline to identify the phenotypic manifestation of
putative disease-causing genetic variants. For this purpose, two specific objectives were pursued:
• Identification of clusters of functionally similar genes;
• Inferring the disease phenotype for each cluster separately.
To achieve these goals in this study, a dataset containing 3707 genes from patients diagnosed
with ASD was used. Tools such as DishIn and GoSemSim are applied to this dataset to calculate
the value of semantic similarity in pairs of genes, obtaining in the end a square matrix of semantic
similarity. This value is obtained by the tools by quantifying the pairwise GO term semantic
similarity through the amount of information shared between two terms, such as the information
content of the most informative common ancestor of two terms. The measures to calculate the
similarity of information content used in this work are Lin, Jiang & Conrath and Rel. Through the
matrix of the semantic similarity matrix, the distance matrix is calculated to which the DBSCAN,
Kmeans and hierarchical clustering algorithms are applied, to obtain functionally similar clusters
of genes.
After analyzing the results, it was possible to conclude that genes that were disrupted by
genetic variants in patients can be clustered using semantic similarity measures. Clustered genes
were functionally similar, also indicated by gene interaction networks and can lead to different
ASD sub-phenotype. Genes clusters were enriched for different pathways and phenotype that
were related to ASD subtypes
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