Alternative Approach to Fisher’s Exact Test with Application in Pedagogical Research

2018 ◽  
pp. 50-59
Author(s):  
Tomas Barot ◽  
Radek Krpec
Keyword(s):  
Exact Test ◽  
Fisher's Exact Test ◽  
Alternative Approach ◽  
Fisher’S Exact Test ◽  
Pedagogical Research

scholarly journals TERT promoter hotspot mutations and gene amplification in metaplastic breast cancer

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Edaise M. da Silva ◽  
Pier Selenica ◽  
Mahsa Vahdatinia ◽  
Fresia Pareja ◽  
Arnaud Da Cruz Paula ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Amplification ◽  
Genetic Alterations ◽  
Wild Type ◽  
Histologic Subtype ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Fisher’S Exact Test ◽  
Hotspot Mutations ◽  
Or Gene

AbstractMetaplastic breast cancers (MBCs) are characterized by complex genomes, which seem to vary according to their histologic subtype. TERT promoter hotspot mutations and gene amplification are rare in common forms of breast cancer, but present in a subset of phyllodes tumors. Here, we sought to determine the frequency of genetic alterations affecting TERT in a cohort of 60 MBCs with distinct predominant metaplastic components (squamous, 23%; spindle, 27%; osseous, 8%; chondroid, 42%), and to compare the repertoire of genetic alterations of MBCs according to the presence of TERT promoter hotspot mutations or gene amplification. Forty-four MBCs were subjected to: whole-exome sequencing (WES; n = 27) or targeted sequencing of 341-468 cancer-related genes (n = 17); 16 MBCs were subjected to Sanger sequencing of the TERT promoter, TP53 and selected exons of PIK3CA, HRAS, and BRAF. TERT promoter hotspot mutations (n = 9) and TERT gene amplification (n = 1) were found in 10 of the 60 MBCs analyzed, respectively. These TERT alterations were less frequently found in MBCs with predominant chondroid differentiation than in other MBC subtypes (p = 0.01, Fisher’s exact test) and were mutually exclusive with TP53 mutations (p < 0.001, CoMEt). In addition, a comparative analysis of the MBCs subjected to WES or targeted cancer gene sequencing (n = 44) revealed that MBCs harboring TERT promoter hotspot mutations or gene amplification (n = 6) more frequently harbored PIK3CA than TERT wild-type MBCs (n = 38; p = 0.001; Fisher’s exact test). In conclusion, TERT somatic genetic alterations are found in a subset of TP53 wild-type MBCs with squamous/spindle differentiation, highlighting the genetic diversity of these cancers.

scholarly journals Association of P10L Polymorphism in Melanopsin Gene with Chronic Insomnia in Mexicans

2021 ◽  
Vol 18 (2) ◽  
pp. 571
Author(s):  
Bianca Ethel Gutiérrez-Amavizca ◽  
Ernesto Prado Montes de Oca ◽  
Jaime Paul Gutiérrez-Amavizca ◽  
Oscar David Castro ◽  
Cesar Heriberto Ruíz-Marquez ◽  
...  
Keyword(s):  
Statistical Power ◽  
Medical Condition ◽  
Severity Index ◽  
Recessive Model ◽  
Chronic Insomnia ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Increased Risk ◽  
Fisher’S Exact Test ◽  
And Function

The aim of this pilot study was to determine the association of the P10L (rs2675703) polymorphism of the OPN4 gene with chronic insomnia in uncertain etiology in a Mexican population. A case control study was performed including 98 healthy subjects and 29 individuals with chronic insomnia not related to mental disorders, medical condition, medication or substance abuse. Samples were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Genetic analyses showed that the T allele of P10L increased risk to chronic insomnia in a dominant model (p = 1 ×10−4; odds ratio (OR) = 9.37, CI = 8.18–335.66, Kelsey statistical power (KSP) = 99.9%), and in a recessive model (p = 7.5 × 10−5, OR = 9.37, KSP = 99.3%, CI = 2.7–34.29). In the insomnia group, we did not find a correlation between genotypes and chronotype (p = 0.219 Fisher’s exact test), severity of chronic insomnia using ISI score (p = 0.082 Fisher’s exact test) and ESS score (p ˃ 0.999 Fisher’s exact test). However, evening chronotype was correlated to daytime sleepiness severity, individuals with an eveningness chronotype had more severe drowsiness according to their insomnia severity index (ISI) score (p = 0.021 Fisher’s exact test) and Epworth sleepiness scale (ESS) score (p = 0.015 Fisher’s exact test) than the morningness and intermediate chronotype. We demonstrated that the T allele of the P10L polymorphism in the OPN4 gene is associated with chronic insomnia in Mexicans. We suggest the need to conduct larger studies in different ethnic populations to test the probable association and function of P10L and other SNPs in the OPN4 gene and in the onset of chronic insomnia.

scholarly journals Detection of AZF microdeletions and reproductive hormonal profile analysis of infertile sudanese men pursuing assisted reproductive approaches

BMC Urology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hassan Osman Alhassan Elsaid ◽  
Tarteel Gadkareim ◽  
Tagwa Abobakr ◽  
Eiman Mubarak ◽  
Mehad A. Abdelrhem ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Klinefelter Syndrome ◽  
Semen Analysis ◽  
Control Group ◽  
Male Factor ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Infertile Men ◽  
Significant Difference ◽  
Fisher’S Exact Test

Abstract Background Male factor is the major contributor in roughly half of infertility cases. Genetic factors account for 10–15% of male infertility. Microdeletions of azoospermia factors (AZF) on the Yq region are the second most frequent spermatogenesis disorder among infertile men after Klinefelter syndrome. We detected in our previous study a frequency of 37.5% AZF microdeletions which investigated mainly the AZFb and AZFc. We attempted in this study for the first time to evaluate the frequencies of all AZF sub-regions microdeletions and to analyze reproductive hormonal profiles in idiopathic cases of azoospermic and oligozoospermic men from Sudan. Methods A group of 51 medically fit infertile men were subjected to semen analysis. Four couples have participated in this study as a control group. Semen analysis was performed according to WHO criteria by professionals at Elsir Abu-Elhassan Fertility Centre where samples have been collected. We detected 12 STSs markers of Y chromosome AZF microdeletions using a multiplex polymerase chain reaction. Analysis of reproductive hormone levels including Follicle Stimulating, Luteinizing, and Prolactin hormones was performed using ELISA. Comparisons between outcome groups were performed using Student’s t-test Chi-square test or Fisher’s exact test. Results AZF microdeletion was identified in 16 out of 25 Azoospermic and 14 out of 26 of the Oligozoospermic. Microdeletion in the AZFa region was the most frequent among the 30 patients (N = 11) followed by AZFc, AZFd (N = 4 for each) and AZFb (N = 3). Among the Oligozoospermic participants, the most frequent deletions detected were in the AZFa region (N = 10 out of 14) and was significantly associated with Oligozoospermic phenotype, Fisher's Exact Test (2-sided) p = 0.009. Among the Azoospermic patients, the deletion of the AZFc region was the most frequent (N = 9 out of 16) and was significantly associated with Azoospermia phenotype Fisher's Exact Test p = 0.026. There was a significant difference in Y chromosome microdeletion frequency between the two groups. The hormonal analysis showed that the mean levels of PRL, LH, and FSH in Azoospermic patients were slightly higher than those in oligozoospermic. A weak negative correlation between prolactin higher level and Azoospermic patients was detected. (AZFa r = 0.665 and 0.602, p = 0.000 and 0.0004, AZFb r = 0.636 and 0.409, p = 0.000 and 0.025, and AZFd r = 0.398 and 0.442, p = 0.029 and 0.015). The correlation was positive for AZFa and negative for AZFb and AZFd. Conclusions We concluded in this study that the incidences of microdeletions of the Y chromosome confined to AZF a, b, c and d regions is 58.8% in infertile subjects with 31.4% were Azoospermic and 27.5% were Oligozoospermic. This might provide a piece of evidence that these specified regions of the Y chromosome are essential for controlling spermatogenesis. These findings will be useful for genetic counseling within infertility clinics in Sudan and to adopt appropriate methods for assisted reproduction.

Επίδραση αναλόγου της προστακυκλίνης στην επούλωση αναστομώσεων του παχέος εντέρου επίμυων σε συνθήκες αποφρακτικού ειλεού

2012 ◽  
Author(s):  
Γεώργιος Γαλανόπουλος
Keyword(s):  
Analysis Of Variance ◽  
Anova Analysis ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Significant Difference ◽  
Fisher’S Exact Test

Στόχος της παρούσας διδακτορικής διατριβής ήταν η πειραματική μελέτη της επίδρασης της ιλοπρόστης (ανάλογο της προστακυκλίνης) στην επούλωση αναστομώσεων του παχέος εντέρου επίμυων σε συνθήκες αποφρακτικού ειλεού. Για τη μελέτη χρησιμοποιήθηκαν 80 άρρενες επίμυες, οι οποίοι χωρίστηκαν τυχαιοποιημένα σε 4 (1, 2, 3, 4) ομάδες, με 2 (α, β) ισοδύναμες υποομάδες έκαστη. Στην ομάδα 1 (ελέγχου) και 3 (ιλοπρόστη) διενεργήθηκε τμηματική εντερεκτομή και τελικοτελική αναστόμωση. Στην ομάδα 2 (ειλεός) και 4 (ειλεός και ιλοπρόστη) επιτεύχθηκαν αρχικά συνθήκες αποφρακτικού ειλεού και 24 ώρες μετά διενεργήθηκε τμηματική εντερεκτομή και τελικοτελική αναστόμωση. Η ιλοπρόστη χορηγήθηκε στις ομάδες 3 και 4 σε δόση 2μg/kg Β.Σ. σε 3ml διαλύματος NaCl 0,9% ενδοπεριτοναϊκά, διεγχειρητικά και κάθε ημέρα μέχρι τη θυσία, ενώ αντίστοιχα στις ομάδες 1 και 2 στα πειραματόζωα χορηγούνταν 3ml διαλύματος NaCl 0,9%. Σε κάθε ομάδα τα μισά πειραματόζωα (υποομάδα 1α, 2α, 3α, 4α) θυσιάστηκαν την 4η μετεγχειρητική ημέρα και τα υπόλοιπα (υποομάδα 1β, 2β, 3β, 4β) την 8η. Κατά τη νεκροτομή γινόταν μακροσκοπικός έλεγχος για ρήξη της αναστόμωσης, ύπαρξη περιτονίτιδος ή περιαναστομωτικού αποστήματος καθώς και ποσοτική αξιολόγηση των συμφύσεων σύμφωνα με την κλίμακα Van der Hamm. Ακολουθούσε μέτρηση της πίεσης διάσπασης και στη συνέχεια τμήμα της αναστόμωσης αποστέλλονταν για ιστολογική εξέταση κατά την οποία αξιολογούνταν η φλεγμονώδης αντίδραση (διήθηση από ουδετερόφιλα), η νεοαγγειογένεση, ο αριθμός των ινοβλαστών και η εναπόθεση νεοκολλαγόνου. Η ταξινόμηση των μικροσκοπικών ευρημάτων έγινε σύμφωνα με την κλίμακα Ehrlich και Hunt με τις τροποποιήσεις κατά Phillips. Επιπλέον, προσδιορίστηκε βιοχημικά η συγκέντρωση υδροξυπρολίνης και κολλαγενάσης I επί της αναστόμωσης. Για την συνοπτική παρουσίαση των αποτελεσμάτων υπολογίστηκαν απόλυτες και σχετικές συχνότητες (ποσοστά %), δείκτες κεντρικής τάσης (μέσοι όροι, διάμεσες τιμές) και δείκτες διασποράς (ελάχιστες τιμές, μέγιστες τιμές, τυπικές αποκλίσεις). Για τη σύγκριση των μέσων όρων χρησιμοποιήθηκε το κριτήριο της Ελάχιστης Σημαντικής Διαφοράς (Least Significant Difference-LSD), μετά από την εφαρμογή της μεθόδου ANOVA (Analysis of Variance). Για τις συγκρίσεις των ποσοστών, εφαρμόστηκε ο ακριβής έλεγχος του Fisher (Fisher’s Exact Test). Από την ανάλυση των πειραματικών δεδομένων προέκυψε ότι η ενδοπεριτοναϊκή χορήγηση ιλοπρόστης σε συνθήκες αποφρακτικού ειλεού, έχει ως αποτέλεσμα τον περιορισμό της αρνητικής δράσης του ειλεού στην επούλωση των αναστομώσεων του παχέος εντέρου. Συγκεκριμένα, την 4η και 8η μετεγχειρητική ημέρα ελαττώνει σημαντικά την απώλεια σωματικού βάρους. Επίσης, προάγει τη νεοαγγειογένεση, ενώ συγχρόνως αυξάνει τον πολλαπλασιασμό των ινοβλαστών και τη συγκέντρωση υδροξυπρολίνης. Επιπλέον, την 4η μετεγχειρητική ημέρα ελαττώνει τη φλεγμονώδη αντίδραση και μειώνει τη συγκέντρωση κολλαγενάσης Ι. Σταδιακά, την 8η μετεγχειρητική ημέρα αυξάνει τη σύνθεση νεοκολλαγόνου στην περιοχή της αναστόμωσης. Οι παραπάνω δράσεις έχουν ως αποτέλεσμα την αύξηση της μηχανικής ισχύος των αναστομώσεων, κατά την 4η και 8η μετεγχειρητική ημέρα, όπως αυτή προκύπτει από τη μέτρηση των πιέσεων διάσπασης. Συμπερασματικά, η άμεση μετεγχειρητική ενδοπεριτοναϊκή χορήγηση ιλοπρόστης ενισχύει τους μηχανισμούς επούλωσης και αντισταθμίζει την αρνητική δράση του ειλεού στην επούλωση των αναστομώσεων του παχέος εντέρου.

scholarly journals Efficiency of small mammal trapping in an Atlantic Forest fragmented landscape: the effects of trap type and position, seasonality and habitat

2014 ◽  
Vol 74 (3) ◽  
pp. 538-544 ◽  
Author(s):  
ALM Vieira ◽  
AS Pires ◽  
AF Nunes-Freitas ◽  
NM Oliveira ◽  
AS Resende ◽  
...  
Keyword(s):  
Ground Level ◽  
Fragmented Landscape ◽  
Pitfall Traps ◽  
Exact Test ◽  
Future Studies ◽  
Fisher's Exact Test ◽  
Fisher’S Exact Test ◽  
Trapping Methods ◽  
Mammal Communities ◽  
Total Effort

Trapping methods can strongly influence the sampling of mammal communities. This study compared the efficiency of the capture of small mammals in Sherman traps in two positions (at ground level and in trees) and pitfall traps in a fragmented landscape. Trapping sessions were carried out between October 2008 and October 2009 at two fragments (8 and 17 ha), an agroforest corridor between them, and the adjacent pasture. A total effort of 4622 trap-nights resulted in 155 captures of 137 individuals from six species. Pitfalls had greater success (4.03%), followed by Shermans on the ground (2.98%) and on trees (2.37%; χ2= 6.50, p = 0.04). Five species were caught in Sherman ground traps, four in pitfalls and just two on trees. There was no difference among trap types for marsupials (χ2 = 4.75; p = 0.09), while for rodents, pitfalls were more efficient than Shermans on the ground (Fisher's exact test, p = 0.02). As a result, the efficiency of each trap type differed among habitats, due to differences in their species composition. Pitfalls were more efficient in the rainy season (Fisher's exact test, p <0.0001) while Shermans on trees were more efficient in the dry season (Fisher's exact test, p = 0.009). There was no difference between seasons for Shermans on the ground (Fisher's exact test, p = 0.76). Considering the results found, we recommend that future studies of forest mammal communities, particularly those designed to test the effects of forest fragmentation, include combinations of different trap types.

scholarly journals The yield of colorectal cancer among fast track patients with normocytic and microcytic anaemia

2014 ◽  
Vol 96 (4) ◽  
pp. 289-293 ◽  
Author(s):  
IG Panagiotopoulou ◽  
D Fitzrol ◽  
RA Parker ◽  
J Kuzhively ◽  
N Luscombe ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Logistic Regression ◽  
Odds Ratio ◽  
Fast Track ◽  
Microcytic Anaemia ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Significant Difference ◽  
Fisher’S Exact Test ◽  
Normocytic Anaemia

Introduction We receive fast track referrals on the basis of iron deficiency anaemia (IDA) for patients with normocytic anaemia or for patients with no iron studies. This study examined the yield of colorectal cancer (CRC) among fast track patients to ascertain whether awaiting confirmation of IDA is necessary prior to performing bowel investigations. Methods A review was undertaken of 321 and 930 consecutive fast track referrals from Centre A and Centre B respectively. Contingency tables were analysed using Fisher’s exact test. Logistic regression analyses were performed to investigate significant predictors of CRC. Results Overall, 229 patients were included from Centre A and 689 from Centre B. The odds ratio for microcytic anaemia versus normocytic anaemia in the outcome of CRC was 1.3 (95% confidence interval [CI]: 0.5–3.9) for Centre A and 1.6 (95% CI: 0.8–3.3) for Centre B. In a logistic regression analysis (Centre B only), no significant difference in CRC rates was seen between microcytic and normocytic anaemia (adjusted odds ratio: 1.9, 95% CI: 0.9–3.9). There was no statistically significant difference in the yield of CRC between microcytic and normocytic anaemia (p=0.515, Fisher’s exact test) in patients with anaemia only and no colorectal symptoms. Finally, CRC cases were seen in both microcytic and normocytic groups with or without low ferritin. Conclusions There is no significant difference in the yield of CRC between fast track patients with microcytic and normocytic anaemia. This study provides insufficient evidence to support awaiting confirmation of IDA in fast track patients with normocytic anaemia prior to requesting bowel investigations.

scholarly journals Assessment of speech nasality in children with Robin Sequence

CoDAS ◽  
2015 ◽  
Vol 27 (1) ◽  
pp. 51-57 ◽  
Author(s):  
Rosana Prado-Oliveira ◽  
Ilza Lazarini Marques ◽  
Luiz de Souza ◽  
Telma Vidoto de Souza-Brosco ◽  
Jeniffer de Cássia Rillo Dutka
Keyword(s):  
Group Identification ◽  
Surgical Techniques ◽  
Point Scale ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Percentage Occurrence ◽  
Robin Sequence ◽  
Age At Surgery ◽  
Fisher’S Exact Test ◽  
The Relationship

PURPOSE: To report the outcomes of primary palatoplasty in Robin Sequence (RS); to verify the relationship between modalities of assessment of nasality; to compare nasality between techniques at palatoplasty. METHODS: This study involved the identification of hypernasality in four modalities: live assessment with 4-point scale; live assessment with cul-de-sac test; multiple listeners' ratings of recorded phrase; nasometric assessment. Live ratings of speech nasality and nasalance scores were retrieved from charts, while a recorded phrase was rated by listeners for occurrence of hypernasality. Agreement between the modalities was established as well as association between nasality, nasal turbulence and age at surgery and at assessment. Fisher's exact test was used to compare findings between surgical techniques. RESULTS: Agreement between nasalance, live assessment with 4-point scale, live assessment with cul-de-sac, and multiple listeners' ratings of recorded samples ranged between reasonable (0.32) and perfect (1.00). Percentage occurrence of hypernasality varied largely between assessment modalities. Mean occurrence of hypernasality was lower for the group submitted to Furlow technique (26%) than the group that received von Langenbeck technique (53%). Only findings obtained live were statistically significant (scale: p=0.012; cul-de-sac: p<0.001). Listeners identified nasal turbulence for 22 (32%) samples out of the 69 recordings, and an association was found between hypernasality and nasal turbulence. CONCLUSION: Lower occurrence of hypernasality was identified for patients with RS in Furlow group. Identification of hypernasality varied largely among the four assessment modalities.

Patterns of opioid use in patients with trigeminal neuralgia undergoing neurosurgery

2019 ◽  
Vol 131 (6) ◽  
pp. 1805-1811
Author(s):  
Andrew I. Yang ◽  
Brendan J. McShane ◽  
Frederick L. Hitti ◽  
Sukhmeet K. Sandhu ◽  
H. Isaac Chen ◽  
...  
Keyword(s):  
Trigeminal Neuralgia ◽  
Facial Pain ◽  
Opioid Use ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Fisher’S Exact Test ◽  
Long Term Follow Up ◽  
Neurosurgical Intervention

OBJECTIVEFirst-line treatment for trigeminal neuralgia (TN) is pharmacological management using antiepileptic drugs (AEDs), e.g., carbamazepine (CBZ) and oxcarbazepine (OCBZ). Surgical intervention has been shown to be an effective and durable treatment for TN that is refractory to medical therapy. Despite the lack of evidence for efficacy in patients with TN, the authors hypothesized that patients with neuropathic facial pain are prescribed opioids at high rates, and that neurosurgical intervention may lead to a reduction in opioid use.METHODSThis is a retrospective study of patients with facial pain seen by a single neurosurgeon. All patients completed a survey on pain medications, medical comorbidities, prior interventions for facial pain, and a validated pain outcome tool (the Penn Facial Pain Scale). Patients subsequently undergoing neurosurgical intervention completed a survey at the 1-month follow-up in the office, in addition to telephone interviews using a standardized script between 1 and 6 years after intervention. Univariate and multivariate logistic regression were used to predict opioid use.RESULTSThe study cohort consisted of 309 patients (70% Burchiel type 1 TN [TN1], 18% Burchiel type 2 [TN2], 6% atypical facial pain [AFP], and 6% TN secondary to multiple sclerosis [TN-MS]). At initial presentation, 20% of patients were taking opioids. Of these patients, 55% were receiving concurrent opioid therapy with CBZ/OCBZ, and 84% were receiving concurrent therapy with at least one type of AED. Facial pain diagnosis (for diagnoses other than TN1, odds ratio [OR] 2.5, p = 0.01) and facial pain intensity at its worst (for each unit increase, OR 1.4, p = 0.005) were predictors of opioid use at baseline. Neurosurgical intervention led to a reduction in opioid use to 8% at long-term follow-up (p < 0.01, Fisher’s exact test; n = 154). Diagnosis (for diagnoses other than TN1, OR 4.7, p = 0.002) and postintervention reduction in pain at its worst (for each unit reduction, OR 0.8, p < 10−3) were predictors of opioid use at long-term follow-up. On subgroup analysis, patients with TN1 demonstrated a decrease in opioid use to 5% at long-term follow-up (p < 0.05, Fisher’s exact test), whereas patients with non-TN1 facial pain did not. In the nonsurgical group, there was no statistically significant decrease in opioid use at long-term follow-up (n = 81).CONCLUSIONSIn spite of its high potential for abuse, opioid use, mostly as an adjunct to AEDs, is prevalent in patients with facial pain. Opportunities to curb opioid use in TN1 include earlier neurosurgical intervention.

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