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Risk factor profiles for gastric cancer prediction with respect to Helicobacter pylori:A study of a tertiary care hospital in Pakistan

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Artificial Intelligence in Gastroenterology 2023年第1期4卷 10-27页

作者： Shahid Aziz Simone König muhammad Umer tayyab Saeed Akhter Shafqat Iqbal Maryum Ibrar Tofeeq Ur-Rehman Tanvir Ahmad Alfizah Hanafiah Rabaab Zahra Faisal Rasheed Patients Diagnostic Lab Isotope Application DivisionPakistan Institute of Nuclear Science and TechnologyIslamabad 44000Pakistan Department of Microbiology Quaid-i-Azam UniversityIslamabad 45320Pakistan Interdisciplinary Center for Clinical Research Core Unit ProteomicsUniversity of MünsterMünster 48149Germany Management Information System Division Pakistan Institute of Nuclear Science and TechnologyIslamabad 44000Pakistan Centre for Liver and Digestive Diseases Holy Family HospitalRawalpindi 46300Pakistan Pakistan Scientific and Technological Information Centre Quaid-i-Azam UniversityIslamabad 45320Pakistan Department of Pharmacy Quaid-i-Azam UniversityIslamabad 45320Pakistan Faculty of Medicine Department of Medical Microbiology and ImmunologyUniversiti Kebangsan MalaysiaCherasKuala Lumpur 56000Malaysia

BACKGROUND Gastric cancer(GC)is the fourth leading cause of cancer-related deaths *** relies on histopathology and the number of endoscopies is *** pylori(***)infection is a major risk *** To develop an in-silico GC prediction model to reduce the number of diagnostic surgical *** meta-data of patients with gastroduodenal symptoms,risk factors associated with GC,and *** infection status from Holy Family Hospital Rawalpindi,Pakistan,were used with machine *** A cohort of 341 patients was divided into three groups[normal gastric mucosa(NGM),gastroduodenal diseases(GDD),and GC].Information associated with socioeconomic and demographic conditions and GC risk factors was collected using a *** infection status was determined based on urea breath *** association of these factors and histopathological grades was assessed statistically.K-Nearest Neighbors and Random Forest(RF)machine learning models were *** This study reported an overall frequency of 64.2%(219/341)of *** infection among enrolled *** was higher in GC(74.2%,23/31)as compared to NGM and GDD and higher in males(54.3%,119/219)as compared to *** abdominal pain(72.4%,247/341)was observed than other clinical symptoms including vomiting,bloating,acid reflux and *** majority of the GC patients experienced symptoms of vomiting(91%,20/22)with abdominal pain(100%,22/22).The multinomial logistic regression model was statistically significant and correctly classified 80%of the GDD/GC ***,income level,vomiting,bloating and medication had significant association with GDD and GC.A dynamic RF GC-predictive model was developed,which achieved>80%test *** GC risk factors were incorporated into a computer model to predict the likelihood of developing GC with high sensitivity and *** model is dynamic and will be further improved and validated by including n

关键词： Gastric cancer Gastritis Machine learning Prediction model Helicobacter pylori

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Application of Seismic Attributes for Delineation of Channel Geometries and Analysis of Various Aspects in Terms of Lithological and Structural Perspectives of Lower Goru Formation, Pakistan

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International Journal of Geosciences 2014年第12期5卷 1490-1502页

作者： tayyab muhammad Naseer Shazia Asim Mirza Naseer Ahmad Farrukh Hussain Shahid Nadeem Qureshi Department of Earth Sciences Quaid-I-Azam University Islamabad Pakistan China University of Geosciences Wuhan China School of Sciences Nusrat Jahan College Rabwah Pakistan Deewan Petroleum Limited Islamabad Pakistan COMSATS Institute of Information Technology (CIIT) Islamabad Pakistan

Miano area is one of the distinct major hydrocarbon producing fields of the Lower Indus basin. Lower Goru is the reservoir strait in this area. The aim of the present study is to exploit the channels reservoirs and other stratigraphic features in such a terrain where there is always a challenge for the geoscientist to search and exploit the channeled reservoirs. To resolve this issue we have utilized attribute analysis on high resolution 3D-seismic data for the detailed comparative studies for the channels. There are many astonishing features that are identified in the current study, which could not otherwise be easily enhanced with the help of 2D Seismic Data. Seismic attributes such as coherency, frequency (are also appropriate for lithological discrimination), which are sensitive to the channel edges are applied for the channel delineation and their geometrical analysis. Spectral decomposition techniques are also applied for the delineation of channels and to appropriately select the best band for channels identification. Three types of channel geometries are recognized: 1) highly sinuous channel;2) narrow-broad meandering belts;3) moderate to high sinuous channel. NW-SE, N-W trending faults can be helpful to compartmentalize the reservoir. Instantaneous and dominant frequency are more beneficial for further field development based on Gamma Ray logs from nearby drilled wells and dimensional perspectives analysis of the channel reservoir.

关键词： Seismic Attributes Spectral Decomposition Lower Goru Strait Miano Lower Indus Basin Channels

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Gene Action Studies in the Inheritance of Economic Traits in Diallel Cross of Lentil (Lens culinaris Medik)

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American Journal of Plant Sciences 2016年第6期7卷 756-768页

作者： Fahim Abbas Asim Riaz Tanzeela Zafar muhammad Hassan Hafiz muhammad Imran Umar Javed Hassan Waseem Alam Saleh muhammad Mudassir Mahmood Hamza Sohail Usman Ali Tiwana muhammad tayyab Iqbal muhammad Bilal Nanjing Agriculture University Nanjing China Department of Pharmacy Health and Well-Being University of Sunderland Sunderland UK Centre of Agricultural Biochemistry and Biotechnology Faculty of Agriculture University of Agriculture Faisalabad Pakistan Department of Plant Breeding & Genetics Bahauddin Zakariya University Multan Pakistan Department of Entomology Bahauddin Zakariya University Multan Pakistan Department of Horticulture Bahauddin Zakariya University Multan Pakistan Arid Zone Research Institute Bahawalpur Pakistan Department of Plant Breeding & Genetics PMAS-UAA Rawalpindi Pakistan

The present study was conducted in 4 × 4 half diallel cross fashion using the genotypes named as NL-2002, NL-2006, Punjab Masoor-2009 and Markaz-2009 for the evaluation of gene action in the inheritance of economic traits of lentil by following the Griffing (1956) Method of analysis. Minirap 13.1 Copyright© 2000, Minitab inc. Method II, Model I was used for the analysis and gene action was computed by variance component analysis using Mixed Model with GLM (general linear model) procedure. The F1 direct crosses along with the parental genotypes were then evaluated by framing the experiment in RCBD in 3 replications. The data were recorded for the characters which are under the study are, plant height (cm), number of primary branches, number of secondary branches, number of pods per plant, number of seed per pod, seed yield per plant, biomass (gram), 100 seeds weight (gram), harvest index (%), yield per plant. The simple ANOVA for all the characters revealed that difference among genotypes was highly significant. As significant differences were present between the genotypes, it permitted subsequent analysis of the data. The Combining Ability (CA) results showed that value of variance for GCA (General Combining Ability) was significantly higher than that of those of the values of variance of SCA (Specific Combining Ability). Hence current results clearly depicted the role of additive type of gene action governing the characters under study.

关键词： Lentil Diallel Gene Action Studies

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Growth, Physiological and Molecular Responses of Cotton (Gossypium arboreum L.) under NaCl Stress

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American Journal of Plant Sciences 2014年第5期5卷 605-614页

作者： Sameera Hassan muhammad Bilal Sarwar Sajjad Sadique Bushra Rashid Beenish Aftab Bahaeldeen Babiker Mohamed tayyab Husnain Center of Excellence in Molecular Biology University of the Punjab Lahore Pakistan

Salinity is one of the most serious growth limiting factor, therefore, no longer being ignored. Although, cotton is fairly salt tolerant;its sensitivity at crop stand and yield is affected. This study is planned to identify the growth, physiological and molecular parameters in local cotton varieties FDH 171 and FDH 786 under NaCl stress. There was 100% seed germination but hypocotyl length was reduced at increasing level of NaCl. Plant height, fresh and dry biomass were reduced as the plants were subjected to increased stress of NaCl. Stomatal conductance, transpiration and photosynthetic rate and ionic imbalance were found to be reduced under the gradual increase in NaCl stress and affected the plant’s overall physiological processes. PCR product of AtNHX3 has been identified in stressed and non-stressed plants. Thus, the genotypes FDH 171 & FDH 786 were found tolerant to adoption of salt stress and could be used as a source in crop improvement.

关键词： Salt Stress Gossypium arboretum Cotton Gas Exchange Parameters Growth Analysis

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Economic and Social Impact Assessment of Chronic Diseases Among the Low-Income Population in Southern Punjab,Pakistan

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Proceedings of Anticancer Research 2024年第4期8卷 67-74页

作者： Mehran Khan muhammad Arbab Nasir muhammad Umar Asadullah Faiz Mirza muhammad Abdul Bari Ayesha Saeed Fiza Nazeer Khan Saliha Mehboob Malik Akashah Usama tayyab Bahawalpur College of Pharmacy BMDC Complex63100BahawalpurPunjabPakistan

Introduction:Chronic diseases are becoming more prevalent *** effects of chronic illnesses are disastrous not only for the diagnosed person but also for their entire *** study explores chronic diseases’social and economic impact on low-income *** study aims to determine the economic and social implications of various chronic diseases and the loss of income due to these conditions among low-income individuals in Southern Punjab,***:A sample of 424 patients was selected from different areas of Southern *** were collected using a questionnaire that included questions about economic status,self-reported health status,social status,management strategies,and health insurance,among other ***:The mean monthly income of the respondents was found to be 57,097.6 Pakistani rupee(PKR),and the mean monthly expenses for treatment were 8,256.1 *** loss of income was calculated at 15%.Additionally,62%of patients spent more than 10%of their monthly income on managing their *** 85%of the respondents reported that chronic diseases affected their social ***,80%of patients lacked health ***:Chronic diseases impose significant economic and social burdens on patients and their families in Southern *** reduce the burden of chronic diseases,the government should enhance healthcare services in this region and provide health insurance to low-income families.

关键词： Chronic diseases Low-income families Economic impact Punjab Pakistan

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Dosimetric Impact of Tumor Position and Lung Density Variations in Lung Stereotactic Body Radiotherapy

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2014年第1期3卷 43-48页

作者： Hideharu Miura Norihisa Masai Ryoong-Jin Oh Hiroya Shiomi Kouichi Yamada muhammad Nauman usmani Toshihiko Inoue Department of Medical Physics & Engineering Osaka University Graduate School of Medicine Osaka Japan Miyakojima IGRT Clinic Osaka Japan

Purpose of this study was to evaluate the variation of the dose to gross tumor volume (GTV) related to tumor position and lung density for lung stereotactic body radiotherapy (SBRT) using a virtual phantom. The density of the equivalent lung surrounding the GTV (10 mm diameter) was defined as 0.10, 0.15, 0.25, 0.35, and 0.45 g/cm3. A planning target volume (PTV) was generated by adding a uniform 8 mm margin to the internal target volume (ITV). We defined that the 99% of the GTV should be covered by 100% of the prescribed dose using Monte Carlo (MC) calculation. The GTV structure was replicated from ITV to the PTV periphery at 1 mm intervals. Planned dose to the GTV was defined as the predicted dose in the replicated GTV structure. Simulated dose to the GTV was defined as the calculated dose in the replicated GTV structure taking into account the tumor position error. D99 of the planned dose to the GTV at the 8 mm shift position was 78.1%, 81.6%, 87.3%, 91.4% and 94.4% at equivalent lung densities of 0.10, 0.15, 0.25, 0.35, and 0.45 g/cm3, respectively. D99 of the simulated dose to the GTV at the 8 mm shift position was 96.9%, 95.3%, 94.2%, 95.1 % and 96.3% at equivalent lung densities of 0.10, 0.15, 0.25, 0.35, and 0.45 g/cm3, respectively. Planned dose to GTV is strongly dependent on lung density and tumor position errors, while simulated dose to GTV does not show any significant dependence.

关键词： Lung Cancer Stereotactic Body Radiotherapy Tumor Position Error Lung Density Monte Carlo

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Evaluation of Various Mango Varieties against the Infection Dynamics of Powdery Mildew (<i>Oidium mangiferae</i>Bert.)

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American Journal of Plant Sciences 2014年第15期5卷 2372-2377页

作者： Syed Atif Hasan Naqvi Rashida Perveen Syed Amir Manzoor Hafiz muhammad Imran Umar muhammad tayyab Iqbal Fatima Liaquat Taha Majid Ahsan Irshad Department of Forestry FAST Bahauddin Zakariya University Multan Pakistan Department of Plant Breeding & Genetics FAST Bahauddin Zakariya University Multan Pakistan Department of Plant Pathology FAST Bahauddin Zakariya University Multan Pakistan Department of Soil Science FAST Bahauddin Zakariya University Multan Pakistan

Mango (Mangifera indica L: Anacardiaceae) is regarded as the most liked fruit in tropical and sub-tropical regions of the world. Powdery mildew of mango caused by Oidium mangiferae Bert. is one of the major plant pathological constraints in growing healthy mango orchards. The apparent symptoms of the disease occurred on young tissues of all parts of flowers, leaves and fruits. Severe blossom infection could result in complete damage to fruit;flower failed to open and drop off from the inflorescence. The inflorescence revealed a pattern of disease from tip to downward and showed itself by the emergence of wefts of white mycelium on the affected parts. Twenty-five mango varieties i.e. Langra, Dusehri, Ratole No.12, Fajri, Sindhri, Chaunsa Samar Bahisht, Anwar ratole, Neelam, Yakta, Tota Pari, Sensation, Saroli, Malda, Ghulab e Khas, Chaunsa Black, Chaunsa white, Anmol, Almas, Shan e Ali, Shan e Mustafa, Mahmood Khan, Armughan, Zafaran, Malda Late and Early Gold were evaluated through the observation of symptoms on young inflorescence to determine the disease incidence, disease severity index and average yield of fruit. The study was carried out in a randomized compete block design with twenty-five treatments and three replications. The mango varieties presented different performance in relation to powdery mildew incidence and could be categorized into eight groups. Maximum disease incidence was observed (33.33%, 26.66% and 26.66%, 26.66%) on Dusehri, Chaunsa Samar Bahisht, Malda and Ratole No.12 respectively and minimum disease incidence was (3.66% and 3.66%) noted on Almas and Sensation. These two varieties showed to be tolerant against the disease. It might be concluded that the presence or absence of symptoms caused by the powdery mildew had no such effect on the fruit yield of the mango cultivars.

关键词： Powdery Mildew Oidium mangiferae Bert. Infection Varieties RCBD

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Dosimetric Comparison of Different Prescription Modes in Lung Stereotactic Body Radiation Therapy

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2014年第1期3卷 14-19页

作者： Hideharu Miura Norihisa Masai Ryoong-Jin Oh Hiroya Shiomi Kouichi Yamada Junichi Sasaki muhammad Nauman usmani Toshihiko Inoue Department of Medical Physics & Engineering Osaka University Graduate School of Medicine Osaka Japan Miyakojima IGRT Clinic Osaka Japan

The purpose of this study was to compare the dose-volume statistics of stereotactic body radiotherapy (SBRT) for lung cancer between planning target volume (PTV): D95 and gross tumor volume (GTV): D99 dose prescriptions using Monte Carlo (MC) calculation. Plans for 183 patients treated between October 2010 and April 2013 were generated based on four-dimensional (4D) computed tomography (CT) under free breathing. A uniform margin of 8 mm was added to the internal target volume (ITV) to generate PTV. A leaf margin of 2 mm was added to the PTV. The plans were calculated with two different dose prescription methods: 40 Gy to cover 95% of the PTV (PTV prescription) and 44 Gy to cover 99% of the GTV (GTV prescription). A 6-MV photon beam was used. A dose-volume histogram (DVH) analysis was performed for dose to the GTV using PTV and GTV dose prescriptions. For each treatment plan, we evaluated the minimum dose to 99% of the GTV (D99). The D99 of GTV was 44.5 ± 1.9 Gy and 44.0 ± 0.0 Gy for PTV and GTV prescriptions, respectively. The dose to the GTV had wide variations with PTV prescription. We recommend that GTV based dose prescription should be used to standardize dose to the tumor and to achieve highly conformal dose distributions in SBRT for lung cancer.

关键词： Dose Prescription Monte Carlo Calculation Stereotactic Body Radiation Therapy Lung Cancer

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甘蔗秸秆及有机质对土壤养分转化及细菌群落结构特征的影响

甘蔗秸秆及有机质对土壤养分转化及细菌群落结构特征的影响

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作者：穆罕默德塔亚布（muhammad tayyab）福建农林大学

学位级别：硕士

中国农作物生产中过施偏施化肥现象严重。甘蔗作为单位面积生物产量最高的大田作物,生育期长,需肥量大。中国主产蔗区多为丘陵红壤,受灾害性气候影响频繁,甘蔗耕层浅薄、易流失;地力瘠薄,酸化普遍;土壤团粒结构匮乏,易板结。持续改善和... 详细信息

中国农作物生产中过施偏施化肥现象严重。甘蔗作为单位面积生物产量最高的大田作物,生育期长,需肥量大。中国主产蔗区多为丘陵红壤,受灾害性气候影响频繁,甘蔗耕层浅薄、易流失;地力瘠薄,酸化普遍;土壤团粒结构匮乏,易板结。持续改善和提升蔗作土壤生产力,是减少肥料投入,降低生产成本,实现产业绿色发展的重大关键技术之一。在原料蔗茎收获进厂压榨的同时,约有占甘蔗田间生物量20%左右的未成茎蔗株、蔗梢、蔗叶、叶鞘等弃置于田间,这些秸秆中含有大量的碳、氮、磷、钾及其他微量元素,具有巨大的养分转化利用潜力。传统的甘蔗秸秆处理方法多为焚烧,不仅污染环境,也造成养分的浪费。近年来,作物秸秆还田及高效利用受到广泛重视,秸秆废弃物及动物粪便因在提高土壤肥力（SF）方面作用显著而被作为土壤改良剂。这一应用的主要优点取决于土壤微生物的活性。本研究以甘蔗收获后的田间秸秆和有机质（羊粪）为土壤改良物料,对蔗田土壤在M,MS和S三种不同处理下的2个时期（第50天和第100天）,对各处理的土壤养分参数、主要指标酶活性、微生物群落结构组成及其与土壤养分参数参数的关联度进行研究。结果表明,无论甘蔗秸秆、有机质单独或混合掺入土壤中,对土壤养分指标均有显著的改良效果。MS处理在改良土壤pH、AP、TP方面具有显著优势,且见效迅速。M处理对TN、AN、NO3-改良的效果显著优于其他处理;M处理对pH、AP、TP的改良具有明显的时间效应,处理时间100天的M处理对AP、TP以及AK、TC的改良效果显著优于其他处理。土壤NH4+对MS、M改良的响应迅速,处理50天效果显著优于100天。M处理50天的UE、β-GC优势显著;除处理100天的S处理NP显著高于对照外,其他处理NP均显著小于对照;处理100天后,MS、M、S的CL方显示出比对照的显著优势。研究分析了各处理下的土壤细菌优势种群构成。结果表明,各处理的T优势属种类、丰度及同对照的差异性均表现显著。影响程度较大的细菌种类包括:处理50天的M处理中的Gammaproteobacteria,Flavobacteria,Sphingobacteria 与 Cytophagia,S 中的Deltaproteobacteria,Betaproteobacteria 与 Alphaproteobacteria,以及 CK中的Acidobacteria,Solibacteres与OPB35;处理100天的M处理中的Gammaproteobacteria 与 Cytophagia,MS 中的 Betaproteobacteria,S中的Alphaproteobacteria,Deltaproteobacteria 与 Solibacteres,以及CK中的 unidentified Acidobacteria。总体上,处理50天时含有机质的处理（M与MS）菌群丰度、多样性低于CK与S,但至100天时,M、MS处理的菌群丰度、多样性显著增加。研究还反映了 CK、S与M、MS之间存在明显的细菌群落构成差异。基于距离的功能冗余分析（dbRDA）表明,土壤总氮（TN）、总碳（TC）、速效氮（AN）、总磷（TP）、速效磷（AP）、速效钾（AK）和铵态氮（NH4+）是影响各处理细菌种群变异的主要因素。

关键词：甘蔗秸秆有机质土壤养分细菌群落组成

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Comparison of Absorbed Dose to Medium and Absorbed Dose to Water for Spine IMRT Plans Using a Commercial Monte Carlo Treatment Planning System

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2014年第1期3卷 60-66页

作者： muhammad Nauman usmani Norihisa Masai Ryoong-Jin Oh Hiroya Shiomi Daisaku Tatsumi Hideharu Miura Toshihiko Inoue Masahiko Koizumi Department of Medical Physics & Engineering Osaka University Graduate School of Medicine Osaka Japan Miyakojima IGRT Clinic Osaka Japan

Dose in radiation therapy has been reported as the water-equivalent dose using conventional dose calculation algorithms. The Monte Carlo (MC) algorithm employs characterization of human tissues by elemental composition and mass density. It enables more accurate dose calculation for radiation therapy treatment planning and typically reports absorbed dose to medium. Whether one should use dose to medium or tissue (Dm) in place of dose to water (Dw) for MC treatment planning remains the subject of debate. The aim of the current study is to evaluate the differences between dose-volume indices for Dm and Dw MC-calculated IMRT plans. Thirty-seven spine patients were selected for this study. The IMRT optimization and MC calculations were performed using the iPlan RT DoseTM ver 4.1.2 (Brainlab, Munich, Germany) treatment planning system (TPS) with an X-ray Voxel Monte Carlo (XVMC) dose calculation engine. Dw and Dm results for target and critical structures were evaluated using the dose-volume-based indices. Systematic differences between dose-volume indices computed with Dw and Dm were up to 5.2%, 4.2%, and 4.5% for D2, D50 and D98 indices of the clinical target volume (CTV), respectively and up to 1% for the critical structure dose indices. Our study demonstrates that employing Dm in place of Dw in MC-calculated IMRT treatment plans introduces a significant systematic difference in target DVHs. We recommend that for diffused target structures (such as spine tumors), dose to water is a better quantity for dose prescription in photon beam treatment planning using existing MC TPS. While for critical structures, it would be reasonable to report Dm always. However in future with the availability of finer spatial resolution, Dm will be the most suitable variable for both target and critical structures’ dose prescription and reporting in MC treatment planning.

关键词： Dose to Medium Dose to Water Monte Carlo IMRT

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