Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.

BACKGROUND: Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples. METHODS: Using Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers. RESULTS: HPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1-93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392). CONCLUSIONS: Unbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.

Assessment of Language and Indexing Biases Among Chinese-Sponsored Randomized Clinical Trials.

Importance: Language and indexing biases may exist among Chinese-sponsored randomized clinical trials (CS-RCTs). Such biases may threaten the validity of systematic reviews. Objective: To evaluate the existence of language and indexing biases among CS-RCTs on drug interventions. Design, Setting, and Participants: In this retrospective cohort study, eligible CS-RCTs were retrieved from trial registries, and bibliographic databases were searched to determine their publication status. Eligible CS-RCTs were for drug interventions conducted from January 1, 2008, to December 31, 2014. The search and analysis were conducted from March 1 to August 31, 2019. Primary trial registries were recognized by the World Health Organization and the Drug Clinical Trial Registry Platform sponsored by the China Food and Drug Administration. Exposures: Individual CS-RCTs with positive vs negative results (positive vs negative CS-RCTs). Main Outcomes and Measures: For assessing language bias, the main outcome was the language of the journal in which CS-RCTs were published (English vs Chinese). For indexing bias, the main outcome was the language of the bibliographic database where the CS-RCTs were indexed (English vs Chinese). Results: The search identified 891 eligible CS-RCTs. Four hundred seventy CS-RCTs were published by August 31, 2019, of which 368 (78.3%) were published in English. Among CS-RCTs registered in the Chinese Clinical Trial Registry (ChiCTR), positive CS-RCTs were 3.92 (95% CI, 2.20-7.00) times more likely to be published in English than negative CS-RCTs; among CS-RCTs in English-language registries, positive CS-RCTs were 3.22 (95% CI, 1.34-7.78) times more likely to be published in English than negative CS-RCTs. These findings suggest the existence of language bias. Among CS-RCTs registered in ChiCTR, positive CS-RCTs were 2.89 (95% CI, 1.55-5.40) times more likely to be indexed in English bibliographic databases than negative CS-RCTs; among CS-RCTs in English-language registries, positive CS-RCTs were 2.19 (95% CI, 0.82-5.82) times more likely to be indexed in English bibliographic databases than negative CS-RCTs. These findings support the existence of indexing bias. Conclusions and Relevance: This study suggests the existence of language and indexing biases among registered CS-RCTs on drug interventions. These biases may distort evidence synthesis toward more positive results of drug interventions.

Adverse cardiac events after vascular surgery are prevalent despite negative results of preoperative stress testing.

OBJECTIVE: Cardiac risk assessment is a critical component of vascular disease management before surgical intervention. The predictive risk reduction of a negative cardiac stress test result remains poorly defined. The objective of this study was to compare the incidence of postoperative cardiac events among patients with negative stress test results vs those who did not undergo testing. METHODS: We reviewed all patients who underwent elective open abdominal aortic aneurysm repair, suprainguinal bypass, endovascular aneurysm repair (EVAR), carotid endarterectomy (CEA), and infrainguinal bypass within the Vascular Study Group of New England from 2003 to 2017. We excluded patients with positive stress test results (n = 3312) and studied two mutually exclusive groups: elective surgery patients with a negative stress test result and elective surgery patients with no stress test (total n = 26,910). The primary outcome was a composite of in-hospital postoperative cardiac events (dysrhythmia, heart attack, heart failure) or death. RESULTS: A preoperative stress test was obtained in 66.3% of open repairs, 42.8% of suprainguinal bypasses, 37.1% of EVARs, 36.0% of CEAs, and 31.2% of infrainguinal bypasses. The proportion of patients receiving a preoperative stress test varied widely across centers, from 37.1% to 80.0%. The crude odds ratio of in-hospital postoperative cardiac event or death was 1.37 (95% confidence interval [CI], 1.07-1.76) for open repair and 1.52 (CI, 1.13-2.03) for suprainguinal bypass, indicating that patients with negative stress test results before these procedures were 37% and 52% more likely to suffer a postoperative event or die compared with patients selected to proceed directly to surgery without testing. Conversely, the crude odds ratio was 0.92 (CI, 0.66-1.29) for EVAR, 0.92 (CI, 0.70-1.21) for CEA, and 1.13 (CI, 0.90-1.40) for infrainguinal bypass, indicating that patients undergoing these procedures had a similar likelihood of sustaining an event whether they had a negative stress test result or proceeded directly to surgery without a stress test. CONCLUSIONS: The use of cardiac stress testing before vascular surgery varies widely throughout New England. Whereas patients are often appropriately selected to proceed directly to surgery, a negative preoperative stress test result should not assuage the concern for an adverse outcome as these patients retain a substantial likelihood of cardiac events, especially after large-magnitude procedures.

Implementation of rapid rule out of myocardial infarction using high-sensitivity troponin: cross-sectional survey of English hospitals.

OBJECTIVES: Recent guidance recommended use of high-sensitivity troponin for rapid rule out of myocardial infarction (MI) in the English health service. We aimed to determine the extent of implementation of this guidance across English hospitals. METHODS: This study conducted a cross-sectional questionnaire survey of 131 English acute hospitals with over 10 000 admissions per year. RESULTS: We received 125/131 responses (95%), with 110/125 (88%) reporting use of a high-sensitivity troponin assay and responses showing progressive implementation over the last 10 years. High-sensitivity troponin was reported to be used for rapid rule out of MI in 92/110 Trusts (84%). Review of guidelines received from 95/110 Trusts identified that 71/95 (75%) provided guidance for rapid MI rule out with high-sensitivity troponin: 57 recommended testing at 0 and 3 hours, 4 recommended testing at 0 and 2 hours, and 9 recommended testing at 0 and 1 hour, and timing was unclear at one Trust. CONCLUSIONS: English acute hospital Trusts report widespread implementation of high-sensitivity troponin for rapid rule out of MI, with most recommending testing at 0 and 3 hours.

Null hypothesis significance testing and effect sizes: can we 'effect' everything or anything?

The Null Hypothesis Significance Testing (NHST) paradigm is increasingly criticized. Estimation approaches such as point estimates and confidence intervals, while having limitations, provide better descriptions of results than P-values and statements about significance levels. Their use is supported by many statisticians. The effect size approach is an important part of power and sample size calculations at the experimental design stage and in meta-analysis and in the interpretation of the biological importance of study results. Care is needed, however, to ensure that such effect sizes are relevant for the endpoint. Effect sizes should not be used to interpret results without accompanying limits, such as confidence intervals. New methods, especially Bayesian approaches, are being developed; however, no single method provides a simple answer. Rather there is a need to improve researchers understanding of the complex issues underlying experimental design, statistical analysis and interpretation of results.

A non-parametric statistical test of null treatment effect in sub-populations.

Randomized clinical trials are designed to estimate the average treatment effect (ATE). If heterogeneity of treatment effect exists, then it is possible that there may be subjects who derive a treatment effect different from the ATE. We propose a method to test the hypothesis that there exist subjects who derive benefit (or harm) against the null hypothesis that the treatment has no benefit (or harm) on each of the smallest sub-populations defined by discrete baseline covariates. Our approach is nonparametric, which generates the null distribution of the test statistic by the permutation principle. A key innovation of our method is that stochastic simulation is built into the test statistic to detect signals that may not be linearly related to the multiple covariates. This is important because, in many real clinical problems, the treatment effect is not linearly correlated with relevant baseline characteristics. We applied the method to a real randomized study that compared the Implantable Cardioverter Defibrillator (ICD) with conventional medical therapy in reducing total mortality in a low ejection fraction population. Simulations and power calculations were performed to compare the proposed test with existing methods.

Will more sensitive diagnostics identify tuberculosis missed by clinicians? Evaluating Xpert MTB/RIF testing in Guatemala.

OBJECTIVE: To assess the impact of introducing Xpert as a follow-on test after smear microscopy on the total number pulmonary TB notifications. METHOD: Genexpert systems were installed in six departments across Guatemala, and Xpert was indicated as a follow-on test for people with smear-negative results. We analyzed notifications to national tuberculosis (TB) programmes (NTP) and the project's laboratory data to assess coverage of the intervention and case detection yield. Changes in quarterly TB notifications were analyzed using a simple pre/post comparison and a regression model controlling for secular notification trends. Using a mix of project and NTP data we estimated the theoretical yield of the intervention if testing coverage achieved 100%. RESULTS: Over 18,000 smear-negative individuals were eligible for Xpert testing during the intervention period. Seven thousand, one hundred and ninety-three people (39.6% of those eligible) were tested on Xpert resulting in the detection of 199 people with smear-negative, Xpert positive results (2.8% positivity rate). In the year before testing began 1098 people with smear positive and 195 people with smear negative results were notified in the six intervention departments. During the intervention, smear-positive notification remained roughly stable (1090 individuals, 0.7%), but smear-negative notifications increased by 167 individuals (85.6%) to an all-time high of 362. After controlling for secular notifications trends over an eight-quarter pre-intervention period, combined pulmonary TB notifications (both smear positive and negative) were 19% higher than trend predictions. If Xpert testing coverage approached 100% of those eligible, we estimate there would have been a+41% increase in TB notifications. CONCLUSIONS: We measured a large gain in pulmonary notifications through the introduction of Xpert testing alone. This indicates a large number of people with TB in Guatemala are seeking health care and being tested, yet are not diagnosed or treated because they lack bacteriological confirmation. Wider use of more sensitive TB diagnostics and/or improvements in the number of people clinically diagnosed with TB have the potential to significantly increase TB notifications in this setting, and potentially in other settings where a low proportion of pulmonary notifications are clinically diagnosed.

Diagnostic performance of mycologic and serologic methods in a cohort of patients with suspected sporotrichosis / Resultados diagnósticos de los métodos micológicos y serológicos en una cohorte de pacientes con sospecha de esporotricosis

Background: The gold standard for the sporotrichosis diagnosis is culture; however, serologic approaches have been recently implemented to aid in the sporotrichosis diagnosis. Nevertheless, the clinical consequences of the introduction of serologic tests are poorly addressed. Aims: To correlate the results of culture and serology of patients with suspected sporotrichosis. Methods: A retrospective study of 198 patients with suspected sporotrichosis was conducted. Information about culture isolation of Sporothrix from clinical samples and antibody detection by an enzyme-linked immunosorbent assay (ELISA) were obtained from the medical records of the patients. Results: Positive culture and antibody detection was observed in the samples of 84 patients (42.4%). Forty-one samples (20.7%) showed negative results with both techniques and divergent results were obtained in the samples of 73 patients (36.9%). False negative results in the ELISA were observed with 23 patients (31.5%), 78.3% of them with less than 30 days of infection (p = 0.0045). Among the initial false positive ELISA in the sera of 50 patients, four samples in culture yielded the growth of Sporothrix, and 27 improved with itraconazole. At the end of follow-up, a diagnosis of proven or probable sporotrichosis was established in 139 patients, and possible sporotrichosis in 11 patients. The treatment of the patients with probable sporotrichosis with antifungal drugs resulted in clinical cure for these individuals. Conclusions: These two techniques are complementary in the diagnosis of sporotrichosis, making diagnosis and clinical decision more precise

Antecedentes: El método de referencia en el diagnóstico de la esporotricosis es el cultivo, aunque las técnicas serológicas pueden complementar el diagnóstico. Sin embargo, la interpretación de las pruebas serológicas en la práctica clínica y en el diagnóstico de la enfermedad necesitan un abordaje más eficiente. Objetivos: Correlacionar los resultados del cultivo y la serología en pacientes con posibles síntomas de esporotricosis. Métodos: Se realizó un estudio retrospectivo de 198 pacientes con posibles síntomas de esporotricosis. Para establecer el diagnóstico se tuvieron en cuenta el aislamiento de Sporothrix a partir de las muestras clínicas y la detección de anticuerpos anti-Sporothrix realizados por un análisis de inmunoabsorción enzimática (ELISA), datos todos ellos registrados en las respectivas historias clínicas. Resultados: Los cultivos y la detección de anticuerpos fueron positivos en 84 pacientes (42,4%). Las muestras de 41 pacientes (20,7%) resultaron negativas con ambas técnicas y en 73 pacientes (36,9%) los resultados fueron divergentes. Se obtuvieron resultados falsos negativos en el ELISA en 23 pacientes (31,5%), el 78,3% de ellos con menos de 30días de infección (p = 0,0045). De los 50 pacientes con un resultado falso positivo en el ELISA, en 4 de ellos se obtuvo cultivo positivo de Sporothrix y 27 mejoraron con itraconazol. Al finalizar el estudio se estableció un diagnóstico de esporotricosis, que fue probada o probable en 139 pacientes y posible en 11 pacientes. El tratamiento de pacientes con esporotricosis probable con fármacos antifúngicos produjo la cura clínica de estos individuos. Conclusiones: Estos dos métodos son complementarios en el diagnóstico de la esporotricosis y ayudan a la toma de las decisiones clínicas más acertadas

Diagnostic performance of mycologic and serologic methods in a cohort of patients with suspected sporotrichosis.

BACKGROUND: The gold standard for the sporotrichosis diagnosis is culture; however, serologic approaches have been recently implemented to aid in the sporotrichosis diagnosis. Nevertheless, the clinical consequences of the introduction of serologic tests are poorly addressed. AIMS: To correlate the results of culture and serology of patients with suspected sporotrichosis. METHODS: A retrospective study of 198 patients with suspected sporotrichosis was conducted. Information about culture isolation of Sporothrix from clinical samples and antibody detection by an enzyme-linked immunosorbent assay (ELISA) were obtained from the medical records of the patients. RESULTS: Positive culture and antibody detection was observed in the samples of 84 patients (42.4%). Forty-one samples (20.7%) showed negative results with both techniques and divergent results were obtained in the samples of 73 patients (36.9%). False negative results in the ELISA were observed with 23 patients (31.5%), 78.3% of them with less than 30 days of infection (p=0.0045). Among the initial false positive ELISA in the sera of 50 patients, four samples in culture yielded the growth of Sporothrix, and 27 improved with itraconazole. At the end of follow-up, a diagnosis of proven or probable sporotrichosis was established in 139 patients, and possible sporotrichosis in 11 patients. The treatment of the patients with probable sporotrichosis with antifungal drugs resulted in clinical cure for these individuals. CONCLUSIONS: These two techniques are complementary in the diagnosis of sporotrichosis, making diagnosis and clinical decision more precise.

An omnibus test for the global null hypothesis.

Global hypothesis tests are a useful tool in the context of clinical trials, genetic studies, or meta-analyses, when researchers are not interested in testing individual hypotheses, but in testing whether none of the hypotheses is false. There are several possibilities how to test the global null hypothesis when the individual null hypotheses are independent. If it is assumed that many of the individual null hypotheses are false, combination tests have been recommended to maximize power. If, however, it is assumed that only one or a few null hypotheses are false, global tests based on individual test statistics are more powerful (e.g. Bonferroni or Simes test). However, usually there is no a priori knowledge on the number of false individual null hypotheses. We therefore propose an omnibus test based on cumulative sums of the transformed p-values. We show that this test yields an impressive overall performance. The proposed method is implemented in an R-package called omnibus.

"Stoneless" or Negative Ureteroscopy: A Reality in the Endourologic Routine or Avoidable Source of Frustration? Estimating the Risk Factors for a Negative Ureteroscopy.

INTRODUCTION: A "Negative" ureteroscopy (URS) is defined as a URS in which no stone is found during the procedure. It may occur when the stone has already been passed spontaneously or when it is located outside the collecting system. The aim of the study was to outline risk factors for Negative-URS. MATERIALS AND METHODS: We retrospectively analyzed the possible risk factors for Negative-URS from a database of 341 URS cases. In every case where presumptive ureteral stone was not found, a formal nephroscopy as well as a whole collecting system revision was completed. The Negative-URS group was compared with the non-Negative-URS group, in terms of patient and stone characteristics. RESULTS: The database of 341 URS cases included 448 different stone instances, of which 17 (3.8%) were negative and 431 (96.2%) were therapeutic. There was no statistical significant difference between the two groups concerning age, body mass index, stone location in the ureter, stone laterality, and whether the patient was prestented. The stepwise multiple logistic regression revealed three important risk factors, namely CT stone surface area (p < 0.0001), radiopacity of the stone at kidney, ureter, and bladder radiograph (KUB; p = 0.0004), and gender (p = 0.0011) with an area under the curve of 0.91. Women were found to have more possibilities to have a negative procedure by four- to sevenfold than men depending on the model. A nonradio-opaque stone at KUB is more likely to be correlated with a Negative-URS by 9.5- to 11-fold more than a radiopaque stone at KUB. For each increase of 1 U in CT stone surface area, there is an increase of 10%-12% to be non-negative. CONCLUSIONS: Female gender, a nonradio-opaque stone at KUB, and a smaller stone surface were statistically significantly different in the Negative-URS population.

Relationship Between Pelvic Organ Prolapse and Non-Human Papillomavirus Pap Smear Abnormalities.

OBJECTIVE: The aim of this study was to determine the association between pelvic organ prolapse (POP) and non-human papillomavirus (HPV) Papanicolaou (Pap) smear abnormalities. METHODS: This was a retrospective cohort study of women aged 40 to 70 years who presented for consultation at our institution between 2010 and 2015 and had results of a Pap smear and HPV test available within 5 years of their visit. We extracted demographic information, medical and social history, Pap smear, and HPV results from the electronic medical record. Associations between the presence of POP and non-HPV Pap smear abnormalities were estimated using univariable and multivariable analyses. RESULTS: We reviewed 1590 charts and excluded 980 women, leaving 610 women in the study: 183 with POP and 427 without POP. Women with POP were significantly older (58.2 ± 7.2 vs 55.6 ± 6.6, P < 0.01) and more likely to have a remote (>10 year) history of abnormal Pap smear (24.0% vs 14.8%, P < 0.01). The rate of non-HPV-associated abnormal Pap smears was higher in the POP group than in the non-POP group (12/183 [6.6%] vs 12/427 [2.8%], P = 0.029). In the POP group, the rate of non-HPV Pap smear abnormality was significantly associated with increasing prolapse stage (stage 1: 0/16 [0%], stage 2: 5/77 [6.5%], stage 3: 3/73 [4.1%], stage 4: 4/17 [23.5%]; P = 0.02). After controlling for age and remote history of abnormal Pap smear, the odds ratio for non-HPV Pap smear abnormalities in the POP group remained significant (2.49; 95% confidence interval, 1.08-5.79). CONCLUSIONS: Human papillomavirus-negative Pap smear abnormalities may be related to POP. Our findings have important implications for surgeons seeking to leave the cervix in situ in women with POP.