Analyzing Biomarker Discovery: Estimating the Reproducibility of Biomarker Sets

Many researchers try to understand a biological condition by identifying biomarkers. This is typically done using univariate hypothesis testing over a labeled dataset, declaring a feature to be a biomarker if there is a significant statistical difference between its values for the subjects with different outcomes. However, such sets of proposed biomarkers are often not reproducible - subsequent studies often fail to identify the same sets. Indeed, there is often a very small overlap between the biomarkers proposed in pairs of related studies that explore the same phenotypes over the same distribution of subjects. This paper first defines the Reproducibility Score for a labeled dataset as a measure (taking values between 0 and 1) of the reproducibility of the results produced by an arbitrary fixed biomarker discovery process for a given distribution of subjects. We then provide ways to reliably estimate this score by defining algorithms that produce an over-bound and an under-bound for this score for a given dataset and biomarker discovery process, for the case of univariate hypothesis testing on dichotomous groups. We confirm that these approximations are meaningful by providing empirical results on a large number of datasets and show that these predictions match known reproducibility results. We have also created a publicly available website, hosted at <a href="https://biomarker.shinyapps.io/BiomarkerReprod/">https://biomarker.shinyapps.io/BiomarkerReprod/</a>, that produces these Reproducibility Score approximations for any given dataset (with continuous or discrete features and binary class labels).

Download Full-text

Postoperative analgesia effects of sulfentanyl plus dexmedetomidine in patients received VATS

Pteridines ◽

10.1515/pteridines-2020-0007 ◽

2020 ◽

Vol 31 (1) ◽

pp. 55-60

Author(s):

Haoyu Jiang ◽

Ying Zheng ◽

Chang Liu ◽

Ying Bao

Keyword(s):

Statistical Difference ◽

Control Group ◽

Control Groups ◽

Significant Statistical Difference ◽

Post Surgery ◽

Intravenous Analgesia ◽

The Mean ◽

Nsclc Patients ◽

And Control ◽

Time Point

AbstractBackground To evaluate sulfentanyl combined with dexmedetomidine hydrochloride on postoperative analgesia in patients who received video-assisted thoracic surgery (VATS) and its effects on serum norepinephrine (NE), dopamine (DA), 5-hydroxytryptamine (5-HT), and prostaglandin (PGE2).Material and Methods Ninety-nine non-small cell lung cancer (NSCLC) patients who received VATS were included in the study. All the patients received intravenous inhalation compound anesthesia. Of the 99 cases, 49 subjects (control group) received sulfentanyl for patient controlled intravenous analgesia (PICA) and other 50 cases (experiment group) received sulfentanyl combined with dexmedetomidine hydrochloride for PICA after operation of VATS. The analgesic effects of the two groups were evaluated according to Visual Analogue Scales (VAS) and the Bruggrmann Comfort Scale (BCS). The serum pain mediator of NE, DA, 5-HT, and PGE2 were examined and compared between the two groups in the first 24 h post-surgery.Results The VAS scores for the experiment group were significant lower than that of control group on the time points of 8, 16, and 24 h post-surgery (pall<0.05), and the BCS scores of the experiment group in the time points of 8, 16, and 24 h were significantly higher than that of controls (p<0.05). However, the VAS and BCS scores were not statistical differently in the time point of 1, 2, and 4 h post-surgery (pall>0.05). The mean sulfentanyl dosage was 63.01 ± 5.14 μg and 67.12 ± 6.91 μg for the experiment and control groups respectively with significant statistical difference (p<0.05). The mean analgesic pump pressing times were 4.30 ± 1.31 and 5.31 ± 1.46 for experiment and control groups respectively with significant statistical difference (p<0.05). The serum NE, DA, 5-HT, and PGE2 levels were significantly lower in the experimental group compared to that of control group in the time point of 12 h post-surgery (pall<0.05). The side effects of nausea, vomiting, delirium, rash, and hypotension atrial fibrillation were not statistically different between the two groups (pall>0.05).Conclusion Patient controlled intravenous analgesia of sulfentanyl combined with dexmedetomidine hydrochloride was effective in reducing the VAS score and serum pain mediators in NSCLC patients who received VAST.

Download Full-text

The Effectiveness of Antibiotic-Coated Ventriculoperitoneal Shunts for Prevention of Shunt Infections in Patients with Myelomeningocele

Pediatric Neurosurgery ◽

10.1159/000516379 ◽

2021 ◽

pp. 1-4

Author(s):

Bilal Ertuğrul ◽

Metin Kaplan ◽

Ömer Batu Hergünsel ◽

Bekir Akgün ◽

Sait Öztürk ◽

...

Keyword(s):

Protective Effect ◽

Statistical Difference ◽

Shunt Infection ◽

Infection Rates ◽

Ventriculoperitoneal Shunts ◽

Significant Statistical Difference ◽

Shunt Infections

Purpose: Hydrocephalus is a common comorbidity among the newborns, with myelomeningocele (MMC) and ventriculoperitoneal (VP) shunts being frequently used for the treatment of such patients. In this study, we aimed to compare the effectiveness of antibiotic-free and antibiotic-coated shunts to reduce the rate of shunt infection in patients with hydrocephalus and accompanying MMC. Methods: 116 patients with hydrocephalus and MMC who were treated with VP shunts were included in the study. Shunt infection rates among antibiotic-free and antibiotic-coated shunts were compared. Results: Of the 116 patients included in the study, 39 had antibiotic-coated shunts and 77 had antibiotic-free shunts. Shunt infection developed in 4 of the 39 cases treated with antibiotic-coated shunts and in 5 of the 77 cases treated with shunts without antibiotics. No significant statistical difference was found between antibiotic-coated and antibiotic-free VP shunts in terms of shunt infection (p = 0.450, p > 0.05). Conclusion: In patients with MMC, using VP shunts containing antibiotics was found not to have a protective effect in preventing shunt infection. Whether the sac is intact or ruptured does not affect this result.

Download Full-text

The effect of Hyoscine Butylbromide on the rate of vaginal delivery in cases of secondary arrest of cervical dilatation: A rondomized controlled clinical trial

QJM ◽

10.1093/qjmed/hcab115.006 ◽

2021 ◽

Vol 114 (Supplement_1) ◽

Author(s):

Mohamed Ahmed Elkady ◽

Dina Yahia Mansour ◽

Alyaa Mostafa Elshamy

Keyword(s):

Vaginal Delivery ◽

Statistical Difference ◽

Saline Group ◽

Cervical Dilatation ◽

Control Group ◽

Controlled Clinical Trial ◽

Hyoscine Butylbromide ◽

Labor Time ◽

Significant Statistical Difference ◽

Significant Difference

Abstract Background For decades, health providers have worked to manage labor actively and safely, with the goal of shortening the duration of painful labor. Reduction of cesarean sections and maternal complication is also an important aspect of labor management. Antispasmodic are commonly administrating during labor in both developing and developed countries, although there is a paucity of scientific reports validating this. Hyoscine butylbromide is an effective antispasmodic drug. Therefore, We aim to assess efficacy of Hyoscine butylbromide on rate of vaginal delivery in cases of 2ry arrest of cervical dilatation. Objective To assess whether the intravenous injection of hyoscine butylbromide is effective in progress of labor in which cases with 2ry arrest of cervical dilatation. Patients and Methods The study included 100 pregnant women (PG, P1, P2, P3) conducted at Ain Shams University Maternity Hospital, the inclusion Criteria were: term uncomplicated singleton pregnancy in a spontaneous active labor, with cephalic presentation. The patient must be free from any medical disorder associated with pregnancy and free from any obstetric complication. Cases were subdivided into 2 groups: Study group: 50 patients received 40mg iv Hyoscine Butylbromide (as Buscopan 20mg\mrl) when the cervix >4cm dilated and was >50% effaced. Control group: 50 patients received 2ml saline as placebo. Results Significant increase in vaginal delivery rate (72%) in Hyoscine group; compared to Saline group (52%); with significant statistical difference (p = 0.04). Highly significant decrease in 1st and 2nd stage labor time in Hyoscine group; compared to Saline group; with highly significant statistical difference (p < 0.05 respectively). These results observed without significant difference as regards 3rd stage labor time and postpartum hemorrhage (p > 0.05), APGAR score and NICU admission (p > 0.05). Conclusion From the current study we can conclude that HBB 40 mg is safe and effective in increasing vaginal delivary rate in cases of 2ry arrest of 12 dilatation. It is effective in decreasing first and second stage of labor. It has no maternal or neonatal adverse effect. It is easy and available.

Download Full-text

Qualitative and quantitative aspects of pain in lateral posterior thoracotomy patients

Revista Latino-Americana de Enfermagem ◽

10.1590/s0104-11692006000500011 ◽

2006 ◽

Vol 14 (5) ◽

pp. 708-712 ◽

Cited By ~ 3

Author(s):

Thaiza Teixeira Xavier ◽

Gilson de Vasconcelos Torres ◽

Vera Maria da Rocha

Keyword(s):

Pain Intensity ◽

Statistical Difference ◽

Descriptive Study ◽

Pain Scale ◽

Study Group ◽

Men And Women ◽

Evaluation Form ◽

Qualitative And Quantitative ◽

Significant Statistical Difference ◽

Lateral Posterior

Descriptive study that proposed to compare the qualitative and quantitative behavior of the pain in lateral posterior thoracotomy patients. The sample was consisted of 18 individuals with an average age of 44 years. The instruments used were physiotherapy evaluation form, numerical pain scale and McGill questionnaire for pain. The pain on the numerical pain scale was considered moderate(5) for both sexes. The descriptors of the McGill questionnaire choosen by the patients with higher frequency were: in the sensorial component, beat4, pointed1, shock2, final and pull2; in the afetive component, tired1, bored1, punishald1 and miserable1 and in the evaluative component was flat. The characteristics of pain in the sensorial group were more evidents on male group. No significant statistical difeferences were observed between quantitative answers concerning pain between the men and women. On the qualitative aspects , was observed an predominancy of the same descriptors of pain in afetive component for both sexes. Pain intensity was categorized as moderate. No significant statistical difference were observed between the pain on the post-operatory lateral posterior thoracotomy. These data demonstrate a necessity for an analysis with a larger study group.

Download Full-text

Standard CHOP immuno-chemotherapy of primary mediastinal lymphomas

Orvosi Hetilap ◽

10.1556/oh.2011.29091 ◽

2011 ◽

Vol 152 (19) ◽

pp. 735-742

Author(s):

Tamás Schneider ◽

Erika Tóth ◽

József Lővey ◽

Zsuzsanna Molnár ◽

Beáta Deák ◽

...

Keyword(s):

Statistical Difference ◽

Clinical Symptoms ◽

Survival Rates ◽

Disease Free Survival ◽

B Cell Lymphoma ◽

Third Generation ◽

Chop Regimen ◽

Free Survival ◽

Significant Statistical Difference ◽

Mediastinal Lymphoma

Introduction: Primary mediastinal lymphoma (PMBCL) is an aggressive diffuse large B-cell lymphoma entity. It is a rare disease with specific clinical symptoms. The tumor is predominantly localized in the mediastinum but grows rapidly and infiltrates the surrounding tissues and organs. Two thirds of the patients are young females. Previous studies showed that third generation treatments are more effective than former standard cyclophosphamide-doxorubicin-vincristine-prednisolone (CHOP) regimens. Aim: Authors’ goal was to assess whether adding the anti-CD20 monoclonal antibody, rituximab to the standard CHOP regimen improves the efficacy of the treatment compared to their previous results with CHOP and third generation chemotherapy regimens. Methods: Between October, 2002 and December, 2004 they have started the rituximab-CHOP (R-CHOP) treatment of 20 newly diagnosed, previously untreated PMBCL patients. Results were compared to the data of 24 patients receiving CHOP (n = 9) or procarbazin-prednisolone-doxorubicin-cyclophosphamide-etoposide-cytosin-arabinoside-bleomycin-vincristin-methotrexate (ProMACE-CytaBOM) (n = 15) treatment in the past. Results: During an average follow-up of 64.6 months, the 5-year overall survival (OS) rate was significantly higher in the R-CHOP group compared to the CHOP treatment (79.4% vs. 33.3%; p = 0.026). However, due to the low number of cases, significant statistical difference could not be demonstrated in the 5-year event-free survival (EFS: 70.0% vs. 33.3%; p>0.05), disease-free survival (DFS: 70.0% vs. 33.3%; p>0.05) and relapse-free survival rate (RFS: 93.0% vs. 100%; p> 0.05), despite of the remarkable numeric difference. When comparing the 5-year survival rates of R-CHOP and ProMACE-CytaBOM treatments, the results were very similar without any significant statistical difference between the two types of treatment (OS: 79.4% vs. 80%; EFS: 70.0% vs. 60.0%; DFS: 70.0% vs. 60.0%; RFS: 93.0% vs. 82.0%; p> 0.05 in all cases). With adding rituximab to CHOP treatment, which was previously considered an insufficient treatment on its own, authors have obtained as good results in treating PMBCL as with third generation regimens. Patients have received the R-CHOP treatments without major side effects and mainly as out-patients. Conclusions: Standard R-CHOP treatment could therefore replace the more toxic third generation regimens in PMBCL as well. The data are comparable with those reported in the international literature. Orv. Hetil., 2011, 152, 735–742.

Download Full-text

Effects of sulphur on the yield, yield component characters and oil content of oilseed rape

Journal of Agricultural Sciences Belgrade ◽

10.2298/jas2101017r ◽

2021 ◽

Vol 66 (1) ◽

pp. 17-25

Author(s):

Valiollah Rameeh ◽

Maryam Niakan ◽

Mohammad Mohammadi

Keyword(s):

Brassica Napus ◽

Plant Height ◽

Oilseed Rape ◽

Seed Yield ◽

Oil Content ◽

Statistical Difference ◽

Mean Value ◽

Yield Component ◽

Brassica Napus L ◽

Significant Statistical Difference

The effects of four sulphur levels: S0, S1, S2 and S3, including 0, 12, 24 and 36 kg S ha-1, respectively, along with 115 kg N ha-1 were studied on yield-related traits of oilseed rape (Brassica napus L.). The significant variance of treatments was determined for plant height, yield component characters, seed yield and oil content. The sulphur application significantly increased most of the traits compared to the S0 level. The S3 (36 kg S ha-1) treatment led to the highest mean value of plant height (132 cm) which was classified with S2 (24 kg S ha-1) in the same statistical group. Sulphur had an increasing effect on pods per plant, and it ranged from 92 to 196 for S0 and S3 applications, respectively. S0 and S1 with 92 and 121 pods per plant were grouped in the same statistical group. In addition, S2, and S3 with 165 and 196 pods per plant showed no significant statistical difference. The sulphur application significantly increased seed yield compared to control (S0 level), and it ranged from 2744 to 3215 kg ha-1 in S0 and S3, respectively. The average oil contents of 45.69, 46.96, 47.46 and 49.53 % were detected for 0, 12, 24 and 36 kg S ha-1, respectively.

Download Full-text

Izometric effort in the balance stance of handball throw

Timisoara Physical Education and Rehabilitation Journal ◽

10.1515/tperj-2017-0024 ◽

2017 ◽

Vol 10 (19) ◽

pp. 97-102

Author(s):

Alexandru Andrei Gherman ◽

Leon Gomboș ◽

Adrian Pătrașcu ◽

Sergiu Pop

Keyword(s):

Postural Balance ◽

High Performance ◽

Statistical Difference ◽

Small Scale ◽

Balance Test ◽

Male And Female ◽

Significant Statistical Difference ◽

Isometric Effort ◽

Before And After ◽

Strong Relation

Abstract Postural balance plays an important role in high performance sports. The line between success and failure may be decided at such a small scale. In handball, postural balance may affect the accuracy of every technique that a played use, especially the throwing of the ball towards the goal. Our study aimed to identify the degree of influence that izometric effort has over the balance stance during a handball throw. Subjects: 210 1st year students from the Faculty of Physical Education and Sport, Babeș-Bolyai University from Cluj-Napoca, were involved in this study. The subjects were both male and female, with the ages between 18 and 21 years old, with and without former performance athlete background. Materials: We’ve conducted the balance test using the AMTI NETforce BP 400600 force platform and the actual isometric exercises were completed in the same laboratory. Two types of planks and a half-squat were used as the isometric exercises. Results: There was no significant statistical difference between the balance variables before and after isometric exercises while holding the ball in hand. There was a significant statistical difference between the displacement before and after for the position without the ball. Conclusion: There is no impact of the isometric effort over the balance stance while holding the handball ball in the throwing position. We’ve identified a strong relation between the isometric effort and the balance stance without the ball in hand.

Download Full-text

Categorization of Data Clustering Techniques

Handbook of Research on Public Information Technology ◽

10.4018/978-1-59904-857-4.ch052 ◽

2008 ◽

pp. 568-577

Author(s):

Baoying Wang ◽

Imad Rahal ◽

Richard Leipold

Keyword(s):

Unsupervised Learning ◽

Supervised Learning ◽

Data Clustering ◽

Analysis Data ◽

Discovery Process ◽

Data Set ◽

Market Basket ◽

Clustering Techniques ◽

Data Points ◽

Class Labels

Data clustering is a discovery process that partitions a data set into groups (clusters) such that data points within the same group have high similarity while being very dissimilar to points in other groups (Han & Kamber, 2001). The ultimate goal of data clustering is to discover natural groupings in a set of patterns, points, or objects without prior knowledge of any class labels. In fact, in the machine-learning literature, data clustering is typically regarded as a form of unsupervised learning as opposed to supervised learning. In unsupervised learning or clustering, there is no training function as in supervised learning. There are many applications for data clustering including, but not limited to, pattern recognition, data analysis, data compression, image processing, understanding genomic data, and market-basket research.

Download Full-text

Blood Pyruvate in Malignant Neoplastic Disorders

Clinical Chemistry ◽

10.1093/clinchem/12.3.158 ◽

1966 ◽

Vol 12 (3) ◽

pp. 158-164 ◽

Cited By ~ 3

Author(s):

H C Maneche

Keyword(s):

Statistical Difference ◽

Malignant Disease ◽

Hepatic Metastases ◽

Metastatic Carcinoma ◽

Enzymatic Method ◽

Significant Elevation ◽

Liver Disorders ◽

Significant Statistical Difference ◽

Blood Pyruvate ◽

Neoplastic Disorders

Abstract A moderate and statistically significant elevation of blood pyruvate levels, determined by an enzymatic method, was found in 60 patients with various malignant neoplastic disorders as compared with 20 control subjects. Studied were 42 cases of metastatic carcinoma, including 14 in which there were hepatic metastases and 18 cases of leukemia and lymphoma. No significant statistical difference was found when the values for the patients with malignant disease were compared with those found for a group of patients with non-neoplastic liver disorders.

Download Full-text