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  1. Thesis ; Online: Algorithms for efficient sensitive search and sample comparison on petabase-scale genomics data

    Mustafa, Harun

    2022  

    Abstract: Ever-decreasing genome sequencing costs have led to an explosion in sequencing throughput, with the global sequencing capacity expected to exceed one exabyte per year in the next decade. This includes samples from clinical and human genome sequencing ... ...

    Abstract Ever-decreasing genome sequencing costs have led to an explosion in sequencing throughput, with the global sequencing capacity expected to exceed one exabyte per year in the next decade. This includes samples from clinical and human genome sequencing projects, model and non-model organisms, as well as metagenomes that pool sequences from communities of microorganisms. Much of these data are deposited in data banks in the form of short inexact sequence fragments which traditionally needed to be assembled into longer genome fragments before they could be analysed. Due to both the limited computational capacity to assemble genomes using established algorithms and the lack of established indexing practices for unassembled data, a majority of the raw data in these data banks is effectively inaccessible to a large portion of the scientific community. Tools that index unassembled sequencing data typically organise the data into an annotated sequence graph structure. Graph nodes represent words extracted from the indexed sequences, while annotations store metadata by associating nodes with different attributes or sample labels. Due to the heterogeneous nature of biological sequence data, many sequence graph tools optimise for either high compression of or efficient query to a database of a specific type of data, spawning many index formats with limited inter-compatibility. Striving to develop a more unified approach to sequence graph-based indexing that can accommodate many different sequence types, we have developed the MetaGraph framework for constructing, querying from, and assembling sequences from annotated De Bruijn graphs. MetaGraph further pushes the boundaries of sequence collection representation, providing highly compressed lossless succinct representations accompanied by scalable construction and optimised query procedures to ensure greater or comparable query performance to existing methods. We provide representations tailored towards a variety of data types, including sequences originating from reference ...
    Keywords succinct data structures ; metagenomics ; algorithms ; high-throughput sequencing ; genome graphs ; info:eu-repo/classification/ddc/004 ; info:eu-repo/classification/ddc/570 ; Data processing ; computer science ; Life sciences
    Subject code 006 ; 004
    Language English
    Publisher ETH Zurich
    Publishing country ch
    Document type Thesis ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Perfect adaptation in biology.

    Khammash, Mustafa H

    Cell systems

    2021  Volume 12, Issue 6, Page(s) 509–521

    Abstract: A distinctive feature of many biological systems is their ability to adapt to persistent stimuli or disturbances that would otherwise drive them away from a desirable steady state. The resulting stasis enables organisms to function reliably while being ... ...

    Abstract A distinctive feature of many biological systems is their ability to adapt to persistent stimuli or disturbances that would otherwise drive them away from a desirable steady state. The resulting stasis enables organisms to function reliably while being subjected to very different external environments. This perspective concerns a stringent type of biological adaptation, robust perfect adaptation (RPA), that is resilient to certain network and parameter perturbations. As in engineered control systems, RPA requires that the regulating network satisfy certain structural constraints that cannot be avoided. We elucidate these ideas using biological examples from systems and synthetic biology. We then argue that understanding the structural constraints underlying RPA allows us to look past implementation details and offers a compelling means to unravel regulatory biological complexity.
    MeSH term(s) Acclimatization ; Adaptation, Physiological ; Homeostasis ; Models, Biological ; Synthetic Biology
    Language English
    Publishing date 2021-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2021.05.020
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  3. Article: A Bibliometric Analysis and Review of Nudge Research Using VOSviewer.

    Jia, Chenjin / Mustafa, Hasrina

    Behavioral sciences (Basel, Switzerland)

    2022  Volume 13, Issue 1

    Abstract: With growing demands of decision making in the current era, the impact of the drivers behind individuals' preferences and institutional strategies becomes prominent. Coined in 2008, ...

    Abstract With growing demands of decision making in the current era, the impact of the drivers behind individuals' preferences and institutional strategies becomes prominent. Coined in 2008,
    Language English
    Publishing date 2022-12-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2651997-5
    ISSN 2076-328X
    ISSN 2076-328X
    DOI 10.3390/bs13010019
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  4. Article: Caveolae-Mediated Extracellular Vesicle (CMEV) Signaling of Polyvalent Polysaccharide Vaccination: A Host-Pathogen Interface Hypothesis.

    Li, Shengwen Calvin / Kabeer, Mustafa H

    Pharmaceutics

    2022  Volume 14, Issue 12

    Abstract: We published a study showing that improvement in response to splenectomy associated defective, in regards to the antibody response to ... ...

    Abstract We published a study showing that improvement in response to splenectomy associated defective, in regards to the antibody response to Pneumovax
    Language English
    Publishing date 2022-11-30
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics14122653
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  5. Article ; Online: Design and analysis of management platform based on financial big data.

    Chen, Yuhua / Mustafa, Hasri / Zhang, Xuandong / Liu, Jing

    PeerJ. Computer science

    2023  Volume 9, Page(s) e1231

    Abstract: Traditional financial accounting will become limited by new technologies which are unable to meet the market development. In order to make financial big data generate business value and improve the information application level of financial management, ... ...

    Abstract Traditional financial accounting will become limited by new technologies which are unable to meet the market development. In order to make financial big data generate business value and improve the information application level of financial management, aiming at the high error rate of current financial data classification system, this article adopts the fuzzy clustering algorithm to classify financial data automatically, and adopts the local outlier factor algorithm with neighborhood relation (NLOF) to detect abnormal data. In addition, a financial data management platform based on distributed Hadoop architecture is designed, which combines MapReduce framework with the fuzzy clustering algorithm and the local outlier factor (LOF) algorithm, and uses MapReduce to operate in parallel with the two algorithms, thus improving the performance of the algorithm and the accuracy of the algorithm, and helping to improve the operational efficiency of enterprise financial data processing. The comparative experimental results show that the proposed platform can achieve the best the running efficiency and the accuracy of financial data classification compared with other methods, which illustrate the effectiveness and superiority of the proposed platform.
    Language English
    Publishing date 2023-03-07
    Publishing country United States
    Document type Journal Article
    ISSN 2376-5992
    ISSN (online) 2376-5992
    DOI 10.7717/peerj-cs.1231
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  6. Article ; Online: The Implementations Special Third-Order Ordinary Differential Equations (ODE) for 5th-order 3rd-stage Diagonally Implicit Type Runge-Kutta Method (DITRKM)

    Firas A. Fawzi / Mustafa H. Jumaa

    Ibn Al-Haitham Journal for Pure and Applied Sciences, Vol 35, Iss 1, Pp 92-

    2022  Volume 101

    Abstract: The derivation of 5th order diagonal implicit type Runge Kutta methods (DITRKM5) for solving 3rd special order ordinary differential equations (ODEs) is introduced in the present study. The DITRKM5 techniques are the name of the approach. This approach ... ...

    Abstract The derivation of 5th order diagonal implicit type Runge Kutta methods (DITRKM5) for solving 3rd special order ordinary differential equations (ODEs) is introduced in the present study. The DITRKM5 techniques are the name of the approach. This approach has three equivalent non-zero diagonal elements. To investigate the current study, a variety of tests for five various initial value problems (IVPs) with different step sizes h were implemented. Then, a comparison was made with the methods indicated in the other literature of the implicit RK techniques. The numerical techniques are elucidated as the qualification regarding the efficiency and number of function evaluations compared with another literature of the implicit RK approaches from the result of the computations. In addition, the stability polynomial for DITRK method is derived and analyzed.
    Keywords numerical methods ; ordinary differential equations ; diagonal implicit type runge kutta methods ; initial value problems ; stability polynomial analysis ; Science ; Q
    Subject code 518
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher University of Baghdad
    Document type Article ; Online
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  7. Article ; Online: The effects of negative social media connotations on subjective wellbeing of an ageing population: A stressor-strain-outcome perspective.

    Zolkepli, Izzal Asnira / Tariq, Rehan / Isawasan, Pradeep / Shamugam, Lalitha / Mustafa, Hasrina

    PloS one

    2024  Volume 19, Issue 1, Page(s) e0296973

    Abstract: In recent years, users' privacy concerns and reluctance to use have posed a challenge for the social media and wellbeing of its users. There is a paucity of research on elderly users' negative connotations of social media and the way these connotations ... ...

    Abstract In recent years, users' privacy concerns and reluctance to use have posed a challenge for the social media and wellbeing of its users. There is a paucity of research on elderly users' negative connotations of social media and the way these connotations contribute to developing passive behaviour towards social media use, which, in turn, affects subjective wellbeing. To address this research vacuum we employed the stressor-strain-outcome (SSO) approach to describe the evolution of passive social media use behaviour from the perspective of communication overload, complexity, and privacy. We conceptualized subjective wellbeing as a combination of three components-negative feelings, positive feelings, and life satisfaction. Negative and positive feelings were used to derive an overall affect balance score that fluctuates between 'unhappiest possible' and 'happiest possible'. The proposed research framework was empirically validated through 399 valid responses from elderly social media users. Our findings reveal that communication overload and complexity raise privacy concerns among social media users, which leads to passive usage of social media. This passive social media use improved the subjective wellbeing favourably by lowering negative feelings and raising positive feelings and life satisfaction. The findings also revealed that respondents' overall affect balance leans towards positive feelings as a consequence of passive social media use. This study contributes to the field of technostress by illuminating how the SSO perspective aid the comprehension of the way passive social media use influences the subjective wellbeing of its users.
    MeSH term(s) Humans ; Aged ; Social Media ; Emotions ; Communication ; Mental Processes ; Aging
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0296973
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  8. Article ; Online: Subtuberositäre anterior schließende Osteotomie zur Korrektur der erhöhten posterioren Reklination des Tibiaplateaus.

    Petersen, Wolf / Al Mustafa, Hassan / Häner, Martin / Harrer, Jörg / Braun, Karl

    Operative Orthopadie und Traumatologie

    2024  Volume 36, Issue 2, Page(s) 117–124

    Abstract: Objective: Reduction of increased reclination of the tibial plateau (posterior slope) to improve the anterior stability of the knee joint.: Indications: Increased posterior reclination of the tibial plateau greater than 12° in combination with ... ...

    Title translation Subtuberosity anterior closing wedge osteotomy to correct the increased posterior slope of the tibial plateau.
    Abstract Objective: Reduction of increased reclination of the tibial plateau (posterior slope) to improve the anterior stability of the knee joint.
    Indications: Increased posterior reclination of the tibial plateau greater than 12° in combination with recurrent instability after anterior cruciate ligament (ACL) reconstruction.
    Contraindications: Hyperextension of more than 15° (relative).
    Surgical technique: Anterior skin incision approximately 8-10 cm above the tibial tuberosity. Insertion of two converging guidewires directly below the patellar tendon ending obliquely in the area of the posterior cruciate ligament (PCL) insertion. Control of the wire position with the image intensifier core. Oscillating saw osteotomy. Removal of the wedge and closure of the osteotomy. Osteosynthesis with interfragmentary screw and medial angle-stable plate.
    Postoperative management: Partial load with 10-20 kg for 2 weeks, then step by step increase in load. Mobility: free.
    Results: To date we have operated on 36 patients with recurrent instability after ACL reconstruction (20 men, 16 women, average age 34.4 years) in the manner described in this article. In 25 cases, enlarged bone tunnels were filled with allogeneic bone at the same time. The posterior slope of the tibial plateau could be reduced from an average of 14.5° to 8.8°. In 28 cases another ACL reconstruction was performed after an interval of 4-12 months. The Lysholm score significantly increased from 76.3 points to 89.2 points.
    MeSH term(s) Male ; Humans ; Female ; Adult ; Anterior Cruciate Ligament/surgery ; Anterior Cruciate Ligament Injuries/surgery ; Treatment Outcome ; Knee Joint/diagnostic imaging ; Knee Joint/surgery ; Tibia/diagnostic imaging ; Tibia/surgery ; Osteotomy/methods
    Language German
    Publishing date 2024-04-08
    Publishing country Germany
    Document type English Abstract ; Journal Article ; Review
    ZDB-ID 1007514-8
    ISSN 1439-0981 ; 0934-6694
    ISSN (online) 1439-0981
    ISSN 0934-6694
    DOI 10.1007/s00064-024-00845-x
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    Zs.A 2846: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  9. Article ; Online: Using Martial Arts Training as Exercise Therapy Can Benefit All Ages.

    Sun, Yao / Tabeshian, Roza / Mustafa, Hajer / Zehr, E Paul

    Exercise and sport sciences reviews

    2023  Volume 52, Issue 1, Page(s) 23–30

    Abstract: Martial arts training focuses on whole-body movement patterning, philosophy, interpersonal interactions, and functional self-defense. Such training has positive impacts on physical, psychological, and cognitive well-being in older adults and children ... ...

    Abstract Martial arts training focuses on whole-body movement patterning, philosophy, interpersonal interactions, and functional self-defense. Such training has positive impacts on physical, psychological, and cognitive well-being in older adults and children with and without clinical conditions. We hypothesize that martial arts training can be delivered as a form of exercise therapy for people at all ages to enhance overall health.
    MeSH term(s) Child ; Humans ; Aged ; Exercise Therapy ; Martial Arts/psychology
    Language English
    Publishing date 2023-09-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187040-3
    ISSN 1538-3008 ; 0091-6331
    ISSN (online) 1538-3008
    ISSN 0091-6331
    DOI 10.1249/JES.0000000000000326
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    In stock of ZB MED Cologne/Königswinter

    Se 318: Show issues Location:
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  10. Article: Rectus Sheath Hematoma as a Complication in Patients With COVID-19: Clinical and Imaging Findings.

    Emekli, Emre / Yıldırım, Mesut / Türkkanı, Mustafa H / Ödemiş Başpınar, Emel

    Cureus

    2023  Volume 15, Issue 5, Page(s) e38943

    Abstract: Objectives This study aims to investigate the frequency of rectus sheath hematoma (RSH), clinical findings, imaging findings, and prognosis in patients admitted to the hospital due to COVID-19. Methods In this retrospective study, the patient's ... ...

    Abstract Objectives This study aims to investigate the frequency of rectus sheath hematoma (RSH), clinical findings, imaging findings, and prognosis in patients admitted to the hospital due to COVID-19. Methods In this retrospective study, the patient's demographic characteristics, known diseases, laboratory values, RSH-related symptoms, the treatment they received, imaging modality used to diagnose RSH, and side and size of RSH were recorded. In addition, the inpatient ward to which the patients were admitted, length of hospital stay, time from the beginning of anticoagulant use to the diagnosis of RSH, and prognosis were noted. Results A total of 9,876 patients were admitted to the hospital due to COVID-19 and started anticoagulant treatment. Of these patients, 12 (0.12%) were determined to have RSH (female/male ratio: 5). The prothrombin time, activated partial thromboplastin time, international normalized ratio, hemoglobin, and hematocrit values ​​of 11 patients were within the reference ranges. The mean length of hospital stay was 12 (4.25-22.5) days, and the duration of anticoagulant use was 5.5 (4-10.75) days. RSH was diagnosed using USG in 10 patients and CT in two patients. Conclusion There has been an increase in the use of anticoagulants due to COVID-19, and accordingly, RSH is now more frequently diagnosed and has a more fatal course. Female gender, advanced age, severe COVID-19 disease, and elevated d-dimer at the time of presentation can be considered risk factors for the development of RSH. All physicians who treat and follow up on patients with COVID-19 should consider the possibility of RSH in the differential diagnosis of patients with acute abdominal pain and palpable masses. USG should be undertaken as the first-line imaging modality for the diagnosis of patients, but CT may also be necessary to detect RSH in some cases.
    Language English
    Publishing date 2023-05-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.38943
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