scholarly journals Fuzzy-FishNet: A highly precise distribution-free network approach for feature selection in clinical proteomics

2015 ◽  
Author(s):  
Wilson Wen Bin Goh
Keyword(s):  
Feature Selection ◽  
Small Sample Size ◽  
Small Sample ◽  
Clinical Proteomics ◽  
P Value ◽  
Fisher Exact Test ◽  
Proteomics Data ◽  
Exact Test ◽  
Genomics And Proteomics ◽  
T Distribution

Network-based analysis methods can help resolve coverage and inconsistency issues in proteomics data. Previously, it was demonstrated that a suite of rank-based network approaches (RBNAs) provides unparalleled consistency and reliable feature selection. However, reliance on the t-statistic/t-distribution and hypersensitivity (coupled to a relatively flat p-value distribution) makes feature prioritization for validation difficult. To address these concerns, a refinement based on the fuzzified Fisher exact test, Fuzzy-FishNet was developed. Fuzzy-FishNet is highly precise (providing probability values that allows exact ranking of features). Furthermore, feature ranks are stable, even in small sample size scenario. Comparison of features selected by genomics and proteomics data respectively revealed that in spite of relative feature stability, cross-platform overlaps are extremely limited, suggesting that networks may not be the answer towards bridging the proteomics-genomics divide.

An Integrated Feature Selection Algorithm for Cancer Classification using Gene Expression Data

2019 ◽  
Vol 21 (9) ◽  
pp. 631-645 ◽  
Author(s):  
Saeed Ahmed ◽  
Muhammad Kabir ◽  
Zakir Ali ◽  
Muhammad Arif ◽  
Farman Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Accuracy ◽  
Early Stage ◽  
Small Sample Size ◽  
Feature Selection Method ◽  
Small Sample ◽  
Expression Data ◽  
Base Function

Aim and Objective: Cancer is a dangerous disease worldwide, caused by somatic mutations in the genome. Diagnosis of this deadly disease at an early stage is exceptionally new clinical application of microarray data. In DNA microarray technology, gene expression data have a high dimension with small sample size. Therefore, the development of efficient and robust feature selection methods is indispensable that identify a small set of genes to achieve better classification performance. Materials and Methods: In this study, we developed a hybrid feature selection method that integrates correlation-based feature selection (CFS) and Multi-Objective Evolutionary Algorithm (MOEA) approaches which select the highly informative genes. The hybrid model with Redial base function neural network (RBFNN) classifier has been evaluated on 11 benchmark gene expression datasets by employing a 10-fold cross-validation test. Results: The experimental results are compared with seven conventional-based feature selection and other methods in the literature, which shows that our approach owned the obvious merits in the aspect of classification accuracy ratio and some genes selected by extensive comparing with other methods. Conclusion: Our proposed CFS-MOEA algorithm attained up to 100% classification accuracy for six out of eleven datasets with a minimal sized predictive gene subset.

scholarly journals Synergistic effect of genetic polymorphisms in TLR6 and TLR10 genes on the risk of pulmonary tuberculosis in a Moldavian population

2021 ◽  
pp. 175342592110299
Author(s):  
Alexander Varzari ◽  
Igor V. Deyneko ◽  
Elena Tudor ◽  
Harald Grallert ◽  
Thomas Illig
Keyword(s):  
Pulmonary Tuberculosis ◽  
Interaction Analysis ◽  
P Value ◽  
Fisher Exact Test ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exact Test ◽  
Pulmonary Tb ◽  
The Republic

Polymorphisms in genes that control immune function and regulation may influence susceptibility to pulmonary tuberculosis (TB). In this study, 14 polymorphisms in 12 key genes involved in the immune response ( VDR, MR1, TLR1, TLR2, TLR10, SLC11A1, IL1B, IL10, IFNG, TNF, IRAK1, and FOXP3) were tested for their association with pulmonary TB in 271 patients with TB and 251 community-matched controls from the Republic of Moldova. In addition, gene–gene interactions involved in TB susceptibility were analyzed for a total of 43 genetic loci. Single nucleotide polymorphism (SNP) analysis revealed a nominal association between TNF rs1800629 and pulmonary TB (Fisher exact test P = 0.01843). In the pairwise interaction analysis, the combination of the genotypes TLR6 rs5743810 GA and TLR10 rs11096957 GT was significantly associated with an increased genetic risk of pulmonary TB (OR = 2.48, 95% CI = 1.62–3.85; Fisher exact test P value = 1.5 × 10−5, significant after Bonferroni correction). In conclusion, the TLR6 rs5743810 and TLR10 rs11096957 two-locus interaction confers a significantly higher risk for pulmonary TB; due to its high frequency in the population, this SNP combination may serve as a novel biomarker for predicting TB susceptibility.

scholarly journals Analisis faktor kejadian wasting pada anak balita 12-59 bulan di Puskesmas Bulili Kota Palu: Studi cross sectional

2021 ◽  
Vol 6 (2) ◽  
pp. 111
Author(s):  
Hepti Muliyati ◽  
Menis Mbali ◽  
Hadidja Bando ◽  
Riana Pangestu Utami ◽  
Opyn Mananta
Keyword(s):  
Public Health ◽  
Birth Weight ◽  
Low Birth Weight ◽  
Public Health Problem ◽  
Sampling Technique ◽  
P Value ◽  
Fisher Exact Test ◽  
Important Public Health Problem ◽  
Cross Sectional ◽  
Exact Test

Wasting on children is an important public health problem because of its considerable impact on their health and growth. This problem could lead to iron deficiency which could induce infection disease and probably lower a child’s intelligence as a long-term effect. This study aimed to analyze factors related to wasting on 12-59 months children in Bulili Public Health Center (PHC), Palu City. The analytical descriptive study designed with a cross-sectional approach was applied in this study. One hundred and twenty-one subject was selected from 283 children with purposive sampling technique. Data were analyzed with chi-square and Fisher exact test with significant (p < 0,05). The result showed that most children with low birth weight experienced wasting with a p-value = 0,000. Most of the children from higher-income families did not experience wasting with a p-value = 0,004. Most children who didn’t receive breastfeeding milk did not experience wasting with a p-value = 0,958. This study concluded a correlation between low birth weight and income to wasting, but breastfeeding practice was not related.

scholarly journals Retrospective, observational study on usage of evogliptin in T2DM patients: A real-World experience in Indian patients

2021 ◽  
Vol 8 (3) ◽  
pp. 205-207
Author(s):  
Abhijit Trailokya ◽  
Amol Aiwale ◽  
Roshan Pawar ◽  
Suhas Erande
Keyword(s):  
Real World ◽  
Small Sample Size ◽  
Small Sample ◽  
Hypoglycemic Agents ◽  
P Value ◽  
Base Line ◽  
Oral Hypoglycemic Agents ◽  
Naive Patient ◽  
Indian Patients ◽  
Treatment Naïve

This study aimed to assess effectiveness and safety of Evogliptin 5 mg in patients with T2DM who were prescribed Evogliptin alone or with other oral hypoglycemic agents in real world scenario. Overall 20 patients who received Evogliptin as routine clinical practice in management of T2DM were analyzed retrospectively from single center. Data collected from past medical records. Primary endpoint was mean changes in HbA1c from baseline to weeks 24 and secondary endpoints were Change in HbA1c from baseline to weeks 12 Change from baseline in FPG & PPG at weeks 12 & 24.Significant reduction in HbA1c at the end of 12 and 24 weeks of Evogliptin therapy was - 0.9% and -1.45% respectively from the baseline of HbA1c 8.6% (p value &#60;0.001). At the end of 12 and 24 weeks of addition of Evogliptin, significant reduction in FBG were seen i.e -49.5 mg/dl and -90.7mg/dl respectively from base line of 182 mg/dl and reduction in PPG was -79.4mg/dl and -116.6mg/dl respectively from base line 277 mg/dl (p value &#60;0.001). Evogliptin was found to be effective when added to the patients who were uncontrolled on dual / triple oral anti-diabetic medications and even in treatment naïve patient. It effectively showed reduction in HbA1c, FBG and PPG and the end of 12 and 24 weeks when added to existing anti-diabetic medications & well tolerated in type 2 diabetes Indian patients.Small sample size and retrospective study

scholarly journals Discrepancy of Blast Percentage between the Bone Marrow Aspirate and Flow Cytometry and Its Impact on Survival Outcomes in Patients with Myelodysplastic Syndromes Excess Blast (MDS-EB)

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5441-5441
Author(s):  
Meera Yogarajah ◽  
Phuong L. Nguyen ◽  
Rong He ◽  
Hassan B. Alkhateeb ◽  
Mithun Vinod Shah ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Flow Cytometry ◽  
Small Sample Size ◽  
Scoring Systems ◽  
Standard Of Care ◽  
Risk Groups ◽  
Small Sample ◽  
International Prognostic Scoring System ◽  
P Value ◽  
Number Of Patients

Background MDS is a heterogeneous disease and the revised International Prognostic Scoring System (IPSS-R) is utilized in prognostication. The percentage (%) of blasts in the bone marrow is determined in the aspirate morphologically. Though the former is the standard of care the blast percentage is also reported by flow cytometry and biopsy which can many times be inconsistent. We previously presented the utilization of biopsy based blast percentage which showed meaningful prognostic groups compared to aspirate. In this study we compare the blasts as reported by the aspirate and flow cytometry in MDS-EB in calculating IPSS-R. Methods The MDS database was reviewed for cases of MDS-EB after due IRB approval at the Mayo clinic. We calculated IPSS-R scores based on the aspirate blast % (IPSS-RAsp) and flow blast% (IPSS-Rfl). The aspirate blast percentage was reported morphologically. Suboptimal aspirates were excluded from the study. The flow blast percentage was determined by immunophenotyping. The overall survival (OS) was determined by IPSS-RAsp and IPSS-RFl. OS estimates were calculated by Kaplan-Meier curves and log-rank testing using JMP v.13. Uno's concordance statistic was used to compare the 2 risk scoring systems. Results Of 1322 patients, 431 (33%) cases were identified with MDS-EB out of which 120 (29%) cases had blasts reported in the aspirate and flow. Based on aspirate MDS EB1: 54% (n=65), MDS EB2 46% (n=55). The hematological, cytogenetic and R-IPSS categories were compared between MDS-EB1 and MDS- EB 2. The blast percentage and hemoglobin levels was significantly different between MDS-EB1 and EB2 as seen in table 1, however the IPSS-R risk groups were not significantly different. The flow cytometry was concordant with aspirate in 66/120 (55%) cases. Out of the dis-concordant cases only 20% (11/54) was upstaged by flow cytometry with most of the patients being down staged as expected by the techniques used in processing the blood and hence not reliable when reported low (Figure 1). The OS outcomes based on the IPSS- R asp, IPSS-Rfl areshown in figure 2A,2B .The p value with aspirate based R-IPSS was more significant than flow cytometry based R-IPSS (p= 0.0007 vs 0.0174). We compared the two models for observed OS differences using the Uno model which was not statistically significant. (p= 0.6) Conclusions Both models did not show a difference which is likely due to the very small sample size. However flow cytometry did down stage more patients when disconcordant and may have less value in that setting. It would be ideal to compare all 3 models aspirate, biopsy and flow cytometry however we did not have enough number of patients to do the comparison. Disclosures Patnaik: Stem Line Pharmaceuticals.: Membership on an entity's Board of Directors or advisory committees. Al-Kali:Astex Pharmaceuticals, Inc.: Research Funding.

scholarly journals An Ensemble Classification Method for High-Dimensional Data Using Neighborhood Rough Set

Complexity ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Jing Zhang ◽  
Guang Lu ◽  
Jiaquan Li ◽  
Chuanwen Li
Keyword(s):  
Feature Selection ◽  
Rough Set ◽  
Small Sample Size ◽  
High Dimensional Data ◽  
Classification Performance ◽  
Small Sample ◽  
Ensemble Classification ◽  
High Dimensional ◽  
Sample Classification ◽  
Neighborhood Rough Set

Mining useful knowledge from high-dimensional data is a hot research topic. Efficient and effective sample classification and feature selection are challenging tasks due to high dimensionality and small sample size of microarray data. Feature selection is necessary in the process of constructing the model to reduce time and space consumption. Therefore, a feature selection model based on prior knowledge and rough set is proposed. Pathway knowledge is used to select feature subsets, and rough set based on intersection neighborhood is then used to select important feature in each subset, since it can select features without redundancy and deals with numerical features directly. In order to improve the diversity among base classifiers and the efficiency of classification, it is necessary to select part of base classifiers. Classifiers are grouped into several clusters by k-means clustering using the proposed combination distance of Kappa-based diversity and accuracy. The base classifier with the best classification performance in each cluster will be selected to generate the final ensemble model. Experimental results on three Arabidopsis thaliana stress response datasets showed that the proposed method achieved better classification performance than existing ensemble models.

scholarly journals Analisis Perbedaan Posisi Meneran Miring Kiri dan Setengah Duduk Pada Ibu Bersalin Dengan Lama Kala II Di RSUD Dr. H. Moch Anshari Saleh Banjarmasin

2019 ◽  
pp. 39-46
Author(s):  
Dewi Pusparani Sinambela ◽  
St. Hateriah
Keyword(s):  
Univariate Analysis ◽  
Data Retrieval ◽  
Bivariate Analysis ◽  
P Value ◽  
Fisher Exact Test ◽  
Exact Test ◽  
Second Stage Of Labor ◽  
Second Stage ◽  
Long Time ◽  
Second Stage Labor

Latar Belakang: Lama Kala II dalam persalinan yaitu jangka waktu mulai dari serviks berdilatasi penuh sampai dengan kelahiran bayi tidak boleh melebihi 2 jam pada primigravidan dan 1 jam pada multigravida. Pemilihan posisi melahirkan sangat dianjurkan untuk memberikan rasa nyaman pada ibu, posisi dapat membantu penurunan janin ke dasar panggul dan mempercepat proses persalinan. Dari data yang diperoleh bulan Januari 2018 jumlah persalinan kala II lama sebanyak 0,30% dari 240 persalinan normal.Tujuan: Menganalisis Perbedaan Posisi Meneran Miring Kiri dan Setengah Duduk Pada Ibu Bersalin Dengan Lama Kala II.Metode: Jenis penelitian ini adalah Analisis kuantitatif. Rancangan penelitian menggunakan quasi eksperiment. Populasi penelitian semua ibu bersalin di RSUD Dr. H. Moch Anshari Saleh Banjarmasin. Pengambilan sebanyak 30 responden. Pengambilan data dilakukan dengan menggunakan ceklist. Analisa data yang dilakukan adalah Analisa Univariat dan Analisa Bivariat dengan uji Fisher Exact Test.Hasil: Responden yang menggunakan posisi meneran miring kiri 15 orang (50%) dan setengah duduk sebanyak 15 orang (50%). Jumlah responden primipara yang mengalami persalinan kala II 60 menit sebanyak 12 orang (40,0%), primipara yang mengalami kala II 60 menit sebanyak 2 orang (6,7%) dan responden multipara yang mengalami kala II 30 menit sebanyak 16 orang (53,3%), multipara yang mengalami kala II 30 menit sebanyak 0 orang (0%) dari hasil uji Fisher Exact Test dengan nilai p sebesar 0,483.Simpulan: Tidak ada perbedaan posisi miring kiri dengan posisi setengah duduk terhadap kemajuan persalinan kala II di RSUD Dr. H. Moch. Anshari Saleh Banjarmasin. Kata Kunci: Lama Kala II, Persalinan, Posisi Meneran.   Analysis of Different Left and Half Posisition Straining on Mother with Second Duration of Labour In RSUD Dr. H. Moch Anshari Saleh BanjarmasinABSTRACT Background: The duration of second stage of labor is the period from the full dilated cervix to the birth of the baby should not exceed 2 hours in primigravida and 1 hour in multigravida. Position selection is very beneficial for giving comfort to the mother, the position can help lower the fetus to the pelvic floor and improve labor. From the data obtained in January 2018 the number of prolonged second stage deliveries was 0.30% of 240 normal deliveries.Objective: Analyze the Differences in Position Meniring Left and Half Seated at the Maternity with Long Time II.Method: This type of research is quantitative analysis. The study design used quasi experiment. The study population of all mothers giving birth at Dr. RSUD H. Moch Anshari Saleh Banjarmasin. Taking as many as 30 respondents. Data retrieval is done using a checklist. Data analysis performed was Univariate Analysis and Bivariate Analysis with Fisher Exact Test.Results: Respondents who used the left oblique piercing position were 15 people (50%) and half sat as many as 15 people (50%). The number of primiparous respondents who increased labor at second time 60 minutes was 12 people (40.0%), primipara who added second stage 60 minutes as many as 2 people (6.7%) and multiparous respondents who used second time 30 minutes as many as 16 people (53.3%), multiparas who replaced time II 30 minutes as many as 0 people (0%) from the results of the Fisher Exact Test with a p value of 0.483.Conclusion: There was no difference in left oblique position with sitting position towards the progress of second stage labor in Dr. Hospital. H. Moch. Ansari Saleh Banjarmasin.  Keywords : Second Duration, Labour, Straining Position 

scholarly journals Hubungan Tingkat Pengetahuan Ibu Tentang Pemberian MP-ASI dengan Kejadian Diare pada Anak Usia 6-24 Bulan

2020 ◽  
Vol 9 (1) ◽  
pp. 34-42
Author(s):  
Alvian Merza Radi Putra ◽  
Melania Wahyuningsih ◽  
Fajarina Lathu
Keyword(s):  
P Value ◽  
Fisher Exact Test ◽  
Cross Sectional ◽  
Exact Test

Diare lebih dominan menyerang anak-anak karena daya tahan tubuh anak-anak yang masih lemah. Faktor penyebab diare pada anak salah satunya pemberian MP-ASI oleh ibu. Dalam praktiknya pengetahuan ibu tentang pemberian MP-ASI masih minim. Tujuan dari penelitian ini adalah untuk mengetahui hubungan tingkat pengetahuan ibu tentang pemberian MP-ASI dengan kejadian diare pada anak usia 6-24 bulan Di Posyandu Padukuhan Pugeran Maguwoharjo Depok Sleman Yogyakarta. Jenis penelitian yaitu kuantitatif observasional analitik dengan rancangan penelitian Cross Sectional. Populasi penelitian ini ibu yang memiliki anak usia 6-24 bulan berjumlah 41 bulan Juli 2019 di Padukuhan Pugeran Maguwoharjo Depok Sleman Yogyakarta. Teknik Sampling menggunakan total sampling. Instrumen pengambilan data berupa kuisioner. Analisa data menggunakan Fisher Exact Test. Hasil menunjukkan ibu yang memiliki pengetahuan baik 28 orang (68,3%) sedangkan yang berpengetahuan cukup sebanyak 13 orang (31,7%). Anak yang tidak pernah mengalami diare dalam kurun waktu 3 bulan terakhir sebanyak 29 anak (70,7%) dan yang pernah mengalami diare dalam kurun waktu 3 bulan terakhir sebanyak 12 anak (29,3%). Didapatkan hasil nilai p value sebesar 0,419. Tidak ada hubungan antara tingkat pengetahuan ibu tentang MP- ASI dengan kejadian diare pada anak usia 6-24 bulan di Padukuhan Pugeran Maguwoharjo Depok Sleman Yogyakarta.

Kontribusi Karakteristik Ibu Terhadap kejadian Stunting Pada Anak Usia 24-36 Bulan Di Sleman Yogyakarta

2019 ◽  
Vol 12 (02) ◽  
Author(s):  
Prastiwi Putri Basuki ◽  
Triana Uminingsih
Keyword(s):  
P Value ◽  
Fisher Exact Test ◽  
Chi Square ◽  
Cross Sectional ◽  
Exact Test ◽  
Purposive Sampling

Stunting pada masa balita perlu mendapat perhatian khusus termasuk pada anak usia 24-36 bulan. Usia 24-36 bulan merupakan usia anak yang mengalami perkembangan pesat dalam kemampuan kognitif dan motorik. Banyak faktor yang mempengaruhi terjadinya kejadian stunting pada anak, antara lain karakteristik ibu. Tujuan dari penelitian ini adalah mengetahui kontribusi karakteristik ibu terhadap kejadian stunting pada anak usia 24-36 bulan. Penelitian ini merupakan penelitian observasional analitik dengan pendekatan cross sectional yang dilakukan di Desa Sendang Mulyo Minggir Sleman Yogyakarta. Sampel yang diambil sebanyak 75 anak usia 24-36 bulan dengan teknik purposive sampling. Analisis data  bivariat menggunakan Chi Square dan Fisher Exact Test dan analisis multivariat menggunakan regresi linier. Hasil penelitian menunjukkan bahwa pendidikan ibu (p value=0,000), pengetahuan ibu (p value=0,022) dan pemberian ASI Ekslusif (p value=0,011) yang artinya terdapat hubungan dengan kejadian stunting. Sedangkan status pekerjaan ibu (p value=0,217) tidak signifikan berhubungan dengan kejadian stunting. Berdasarkan analisis multivariat regresi linier menunjukkan hasil bahwa pendidikan ibu, status  pekerjaan ibu, pengetahuan ibu tentang gizi, dan pemberian ASI Ekslusif bersama-sama mempunyai kontribusi terhadap kejadian stunting sebesar 88,2%. Perlu peningkatan program multisektoral dengan melibatkan semua lapisan masyarakat untuk mengurangi kejadian stunting.

scholarly journals A profile and treatment outcome of seasonal hyper-acute panuveitis

1970 ◽  
Vol 2 (1) ◽  
pp. 35-38 ◽  
Author(s):  
E Shrestha
Keyword(s):  
Visual Acuity ◽  
Medical Treatment ◽  
Visual Outcome ◽  
P Value ◽  
Fisher Exact Test ◽  
Mean Values ◽  
Exact Test ◽  
Pediatric Age Group ◽  
Significant Difference ◽  
The Mean

Introduction: Seasonal hyper-acute panuveitis (SHAPU) is a sight-threatening disease and its management is challenging. Objective: To study the profile and evaluate the visual outcome of the patients of clinicallydiagnosed cases of SHAPU after treatment. Subjects and methods: A retrospective interventional hospital-based study was carried out involving 21 subjects with clinically-diagnosed SHAPU. The data were retrieved from the record section of the hospital and analyzed. The variables studied were demographic pattern, clinical condition, duration of presentation and visual acuity before and after the treatment. Statistics: The data were analyzed using Epi Info version 2000. Percentage prevalence, mean values with standard deviation, relative risk, 95% CI and p value were calculated. P value of < 0.05 was considered to be significant. Results: Among the 21 cases, the numbers of male and female were 11 (52.4 %) and 10 (46.7 %) respectively. A comparative analysis of gender in children and adults did not show any significant difference (RR=0.47, 95% CI = 0.22 - 1.01, Fisher exact test: p = 0.14). The mean for all ages was 7 ± 12.68 years, while the mean age in pediatric cases was 4.5 ± 3.91 years. Thirteen (61.9%) cases occurred in children below fifteen years. Fifteen (71.4 %) cases reported during September and October. Presenting visual acuity of all cases was less than 3/60. All of them received medical treatment. By the end of the 4th week, seven (33.3 %) patients regained vision to 6/18. Conclusion: SHAPU is more prevalent in pediatric age group. It is equally prevalent among males and females. The visual acuity can improve with early medical treatment. Keywords: SHAPU; panuveitis; steroid; phthisis bulbi DOI: 10.3126/nepjoph.v2i1.3702 Nep J Oph 2010;2(1) 35-38

Sign in / Sign up

Export Citation Format

Share Document