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Human Reproduction (Oxford, England) Oct 2023Can machine learning predict the number of oocytes retrieved from controlled ovarian hyperstimulation (COH)?
STUDY QUESTION
Can machine learning predict the number of oocytes retrieved from controlled ovarian hyperstimulation (COH)?
SUMMARY ANSWER
Three machine-learning models were successfully trained to predict the number of oocytes retrieved from COH.
WHAT IS KNOWN ALREADY
A number of previous studies have identified and built predictive models on factors that influence the number of oocytes retrieved during COH. Many of these studies are, however, limited in the fact that they only consider a small number of variables in isolation.
STUDY DESIGN, SIZE, DURATION
This study was a retrospective analysis of a dataset of 11,286 cycles performed at a single centre in France between 2009 and 2020 with the aim of building a predictive model for the number of oocytes retrieved from ovarian stimulation. The analysis was carried out by a data analysis team external to the centre using the Substra framework. The Substra framework enabled the data analysis team to send computer code to run securely on the centre's on-premises server. In this way, a high level of data security was achieved as the data analysis team did not have direct access to the data, nor did the data leave the centre at any point during the study.
PARTICIPANTS/MATERIALS, SETTING, METHODS
The Light Gradient Boosting Machine algorithm was used to produce three predictive models: one that directly predicted the number of oocytes retrieved and two that predicted which of a set of bins provided by two clinicians the number of oocytes retrieved fell into. The resulting models were evaluated on a held-out test set and compared to linear and logistic regression baselines. In addition, the models themselves were analysed to identify the parameters that had the biggest impact on their predictions.
MAIN RESULTS AND THE ROLE OF CHANCE
On average, the model that directly predicted the number of oocytes retrieved deviated from the ground truth by 4.21 oocytes. The model that predicted the first clinician's bins deviated by 0.73 bins whereas the model for the second clinician deviated by 0.62 bins. For all models, performance was best within the first and third quartiles of the target variable, with the model underpredicting extreme values of the target variable (no oocytes and large numbers of oocytes retrieved). Nevertheless, the erroneous predictions made for these extreme cases were still within the vicinity of the true value. Overall, all three models agreed on the importance of each feature which was estimated using Shapley Additive Explanation (SHAP) values. The feature with the highest mean absolute SHAP value (and thus the highest importance) was the antral follicle count, followed by basal AMH and FSH. Of the other hormonal features, basal TSH, LH, and testosterone levels were similarly important and baseline LH was the least important. The treatment characteristic with the highest SHAP value was the initial dose of gonadotropins.
LIMITATIONS, REASONS FOR CAUTION
The models produced in this study were trained on a cohort from a single centre. They should thus not be used in clinical practice until trained and evaluated on a larger cohort more representative of the general population.
WIDER IMPLICATIONS OF FINDINGS
These predictive models for the number of oocytes retrieved from COH may be useful in clinical practice, assisting clinicians in optimizing COH protocols for individual patients. Our work also demonstrates the promise of using the Substra framework for allowing external researchers to provide clinically relevant insights on sensitive fertility data in a fully secure, trustworthy manner and opens a number of exciting avenues for accelerating future research.
STUDY FUNDING/COMPETING INTEREST(S)
This study was funded by the French Public Bank of Investment as part of the Healthchain Consortium. T.Fe., C.He., J.C., C.J., C.-A.P., and C.Hi. are employed by Apricity. C.Hi. has received consulting fees and honoraria from Vitrolife, Merck Serono, Ferring, Cooper Surgical, Dibimed, Apricity, and Fairtility and travel support from Fairtility and Vitrolife, participates on an advisory board for Merck Serono, was the founder and organizer of the AI Fertility conference, has stock in Aria Fertility, TMRW, Fairtility, Apricity, and IVF Professionals, and received free equipment from Planar in exchange for first user feedback. C.J. has received a grant from BPI. J.C. has also received a grant from BPI, is a member of the Merck AI advisory board, and is a board member of Labelia Labs. C.He has a contract for medical writing of this manuscript by CHU Nantes and has received travel support from Apricity. A.R. haș received honoraria from Ferring and Organon. T.Fe. has received a grant from BPI.
TRIAL REGISTRATION NUMBER
N/A.
Topics: Female; Humans; Retrospective Studies; Birth Rate; Treatment Outcome; Ovarian Hyperstimulation Syndrome; Ovulation Induction; Oocytes; Fertilization in Vitro
PubMed: 37581894
DOI: 10.1093/humrep/dead163 -
Journal of Medical Internet Research Aug 2023Inconsistencies between a protocol and its umbrella review (UR) may mislead readers about the importance of findings or lead to false-positive results. Furthermore, not...
BACKGROUND
Inconsistencies between a protocol and its umbrella review (UR) may mislead readers about the importance of findings or lead to false-positive results. Furthermore, not documenting and explaining inconsistencies in the UR could reduce its transparency. To our knowledge, no study has examined the methodological consistency of the protocols with their URs and assessed the transparency of the URs when generating evidence.
OBJECTIVE
This study aimed to investigate the inconsistency of protocols with their URs in the methodology and assess the transparency of the URs.
METHODS
We searched medical-related electronic databases from their inception to January 1, 2022. We investigated inconsistencies between protocols and their publications and transparencies in the search strategy, inclusion criteria, methods of screening and data extraction, quality assessment, and statistical analysis.
RESULTS
We included 31 protocols and 35 publications. For the search strategy, 39 inconsistencies between the protocols and their publications were found in 26 of the 35 (74%) URs, and 16 of these inconsistencies were indicated and explained. There were 84 inconsistencies between the protocols and their URs regarding the inclusion criteria in 31 of the 35 (89%) URs, and 29 of the inconsistencies were indicated and explained. Deviations from their protocols were found in 12 of the 32 (38%) URs reporting the methods of screening, 14 of the 30 (47%) URs reporting the methods of data extraction, and 11 of the 32 (34%) URs reporting the methods for quality assessment. Of the 35 URs, 6 (17%) were inconsistent with their protocols in terms of the tools for quality assessment; one-half (3/6, 50%) of them indicated and explained the deviations. As for the statistical analysis, 31 of the 35 (89%) URs generated 61 inconsistencies between the publications and their protocols, and 16 inconsistencies were indicated and explained.
CONCLUSIONS
There was a high prevalence of inconsistencies between protocols and publications of URs, and more than one-half of the inconsistencies were not indicated and explained in the publications. Therefore, how to promote the transparency of URs will be a major part of future work.
Topics: Humans; Publications; Research Design; Databases, Factual; Review Literature as Topic
PubMed: 37531172
DOI: 10.2196/43299 -
Scientific Reports Feb 2024The involvement of the hand flexors in trigger finger is not clear. This study aimed to examine the rigidity of the flexor tendon in the first pulley territory in the...
The involvement of the hand flexors in trigger finger is not clear. This study aimed to examine the rigidity of the flexor tendon in the first pulley territory in the hand by using ultrasound in a healthy population, as well as to create a reference scale of rigidity for the flexor tendons to compare those values in trigger fingers. We tested 35 healthy volunteers using a linear ultrasound transducer and the color Doppler method. Rigidity levels below the first pulley were examined and compared between the different fingers of the hand and the relationship between rigidity and sex and the three different age groups was evaluated. In the healthy population, the rigidity of the flexor tendons of the hand in the territory of the first pulley varied between 233.1 and 962.8 kPa, with an average of 486.42 kPa and standard deviation of 114.85. We showed that the flexors in the dominant hand were more rigid, there was a difference between the rigidity of the flexor tendons of the thumb and the other fingers of the same hand, and the ring finger of the dominant hand had stiffer flexor tendons than the fingers of the other hand in the male population. We created a value scale for the rigidity of the flexor tendons of the fingers. This base scale can be compared between different pathologies, including trigger finger. The study and all experimental protocols were approved by the local ethical committee.
Topics: Humans; Male; Trigger Finger Disorder; Fingers; Tendons; Hand; Ultrasonography
PubMed: 38316861
DOI: 10.1038/s41598-024-52971-y -
The Lancet. Oncology Mar 2024Quality assurance remains a neglected component of many trials, particularly for technical interventions, such as surgery and radiotherapy, for which quality of... (Review)
Review
Quality assurance remains a neglected component of many trials, particularly for technical interventions, such as surgery and radiotherapy, for which quality of treatment is an important component in defining outcomes. We aimed to evaluate evidence for the processes used in radiotherapy quality assurance of clinical trials. A systematic review was undertaken focusing on use of a pre-trial outlining benchmark case and subsequent on-trial individual case reviews of outlining for recruited patients. These pre-trial and on-trial checks are used to ensure consistency and standardisation of treatment for each patient recruited to the trial by confirming protocol compliance. Non-adherence to the trial protocol has been shown to have a negative effect on trial outcomes. 29 studies published between January, 2000, and December, 2022, were identified that reported on either outlining benchmark case results or outlining individual case review results, or both. The trials identified varied in their use of radiotherapy quality assurance practices and reporting of outcomes was inconsistent. Deviations from trial protocols were frequent, particularly regarding outlining. Studies correlating benchmark case results with on-trial individual case reviews provided mixed results, meaning firm conclusions could not be drawn regarding the influence of the pre-trial benchmark case on subsequent on-trial performance. The optimal radiotherapy quality assurance processes were unclear, and there was little evidence available. Improved reporting of outcomes from radiotherapy quality assurance programmes is needed to develop an evidence base for the optimal approach to radiotherapy quality assurance in trials.
Topics: Humans; Radiation Oncology; Benchmarking; Quality Assurance, Health Care
PubMed: 38423056
DOI: 10.1016/S1470-2045(23)00625-3 -
Frontiers in Psychology 2023This study explores the attributions and coping strategies of athletes who experienced psychological impact from sport injuries or illness from a qualitative methodology.
INTRODUCTION
This study explores the attributions and coping strategies of athletes who experienced psychological impact from sport injuries or illness from a qualitative methodology.
PURPOSE
To understand athletes' unique perspectives on injury and recovery, framed in the Global Model of Sport Injuries, and contribute to the development of effective interventions and support programs for athletes.
METHODS
A qualitative research approach was employed, conducting semi-structured interviews with an sample of 16 athletes, representing diverse backgrounds and competitive levels. Interviews were transcribed and analyzed using NVivo software, identifying themes and codes related to attributions and coping strategies.
RESULTS
Athletes attributed their sport injury mostly to bad luck, routine deviations, and negative mental states, while coping strategies used included cognitive restructuring, emotional calming, seeking social support, mental withdrawal, and behavioral risk. Factors such as training deviations, social support, psychological responses, and injury diagnosis seems to have influenced the coping strategies employed.
CONCLUSIONS
Sport injuries and illnesses significantly impact athletes' careers and wellbeing. Support and effective communication from coaching staff and healthcare professionals were identified as crucial for athletes' wellbeing. These findings contribute to understanding the psychological processes and experiences involved in sport injury recovery and highlight key elements for prevention and intervention protocols. Future research should explore communication patterns in sports contexts and assess attributions and coping strategies at different stages of injury recovery.
PubMed: 37965668
DOI: 10.3389/fpsyg.2023.1287951 -
Reproductive Biology and Endocrinology... Jul 2023The number of oocytes retrieved does not always coincide with the number of follicles aspirated in in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI)...
BACKGROUND
The number of oocytes retrieved does not always coincide with the number of follicles aspirated in in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) treatment. Patients with high expectation of retrieval sometimes obtain few oocytes, which may be induced by improper operation or therapeutic factors. The purpose of this study was to evaluate the distribution data of oocyte retrieval rate (ORR) and to explore the risk factors for low ORR in patients with polycystic ovary syndrome (PCOS) undergoing IVF/ICSI.
METHODS
A total of 2478 patients with PCOS undergoing IVF/ICSI were involved in this retrospective case-control study from March 2016 to October 2021. The oocyte retrieval rate was calculated as the ratio of the number of obtained oocytes to the number of follicles (≥ 12 mm) on the trigger day. Patients were divided into a low ORR and a normal ORR group with the boundary of one standard deviation from the mean value of ORR. The patient characteristics, treatment protocols, serum hormone levels, and embryonic and pregnancy outcomes were analyzed.
RESULTS
The ORR exhibited a non-normal distribution, with a median of 0.818. The incidence of complete empty follicle syndrome was 0.12% (3/2478). The proportion of patients in the low ORR group who received the progestin-primed protocol was significantly higher than that in the normal ORR group (30.30% vs. 17.69%). A logistic regression analysis showed that the serum estradiol level/follicle (≥ 12 mm) ratio (OR: 0.600 (0.545-0.661)) and progesterone level (OR: 0.783 (0.720-0.853)) on the trigger day were significant factors in the development of a low ORR, with optimal cutoff values of 172.85 pg/ml and 0.83 ng/ml, respectively, as determined by receiver operating curve. Fewer high-quality embryos (2 vs. 5) and more cycles with no available embryos (5.42% vs. 0.43%) were found in the low ORR group.
CONCLUSIONS
For patients with PCOS, low estradiol levels/follicles (≥ 12 mm) and progesterone levels on the trigger day and the use of the progestin-primed protocol could be risk factors for low ORR, which leads to a limited number of embryos and more cycle cancellations.
Topics: Male; Pregnancy; Female; Humans; Polycystic Ovary Syndrome; Progestins; Progesterone; Oocyte Retrieval; Retrospective Studies; Case-Control Studies; Semen; Fertilization in Vitro; Risk Factors; Estradiol; Pregnancy Rate; Ovulation Induction
PubMed: 37468927
DOI: 10.1186/s12958-023-01118-1 -
Ophthalmic & Physiological Optics : the... Mar 2024Despite the well-known reproducibility issues of subjective refraction, most studies evaluating autorefractors compared differences between the device and subjective...
INTRODUCTION
Despite the well-known reproducibility issues of subjective refraction, most studies evaluating autorefractors compared differences between the device and subjective refraction. This work evaluated the performance of a novel handheld Hartmann-Shack-based autorefractor using an alternative protocol, which considered the inherent variability of subjective refraction.
METHODS
Participants underwent an initial measurement with a desktop autorefractor, two subjective refractions (SR1 and SR2) and a final measurement with the QuickSee Free (QSFree) portable autorefractor. Autorefractor performance was evaluated by comparing the differences between the QSFree and each of the subjective refractions with the difference between the subjective refractions (SR1 vs. SR2) using Bland-Altman analysis and percentage of agreement.
RESULTS
A total of 75 subjects (53 ± 14 years) were enrolled in the study. The average difference in the absolute spherical equivalent (M) between the QSFree and the SR1 and SR2 was ±0.24 and ±0.02 D, respectively, that is, very similar or smaller than the SR1 versus SR2 difference (±0.26 D). Average differences in astigmatic components were found to be negligible. The results demonstrate that differences between QSFree and both subjective refractions in J and J were within ±0.50 D for at least 96% of the measurements. The limits of agreement (LOAs) of the differences between QSFree and SR1, as well as QSFree and SR2, were higher than those observed between SR1 and SR2 for M, J and J .
CONCLUSIONS
A protocol was designed and validated for the evaluation of a refractive device to account for the variability of subjective refraction. This protocol was used to evaluate a novel portable autorefractor and observed a smaller difference between the device and subjective refractions than the difference between the two subjective refraction measurements in terms of mean bias error, although the standard deviation was higher.
Topics: Humans; Reproducibility of Results; Refractive Errors; Refraction, Ocular; Vision Tests; Optometry
PubMed: 38084770
DOI: 10.1111/opo.13263 -
MethodsX Dec 2023Soil organic carbon (SOC) plays an important role in agricultural soils, as it contributes to overall soil health as well as climate change mitigation and adaptation. By... (Review)
Review
Soil organic carbon (SOC) plays an important role in agricultural soils, as it contributes to overall soil health as well as climate change mitigation and adaptation. By conducting a meta-analysis, we aim to quantitatively summarize research studying the effects of cover crops (CC) on SOC pools throughout soil depths in arable cropland. We included global studies located in the climatic zones present in Europe. The pools chosen for this analysis are the particulate organic carbon (POC) and the mineral associated organic carbon (MAOC) and the microbial biomass carbon (MBC). Alongside, we will study the effects of a broad range of moderators, such as pedo-climatic factors, other agricultural management practices and CC characteristics e.g., type. We identified 71 relevant studies from 61 articles, of which mean values for SOC pools, standard deviations and sample sizes for treatments (CC) and controls (no CC) were extracted. To perform the meta-analysis, an effect size will be calculated for each study, which will then be summarized across studies by using weighing procedure. Consequently, this meta-analysis will provide valuable information on the state of knowledge on SOC pool change influenced by CC, corresponding quantitative summary results and the sources of heterogeneity influencing these results.
PubMed: 37817979
DOI: 10.1016/j.mex.2023.102411 -
The Lancet. Infectious Diseases May 2024Ad26.RSV.preF-RSV preF protein showed 80·0% vaccine efficacy against respiratory syncytial virus (RSV) lower respiratory tract disease (LRTD) in older adults during one...
BACKGROUND
Ad26.RSV.preF-RSV preF protein showed 80·0% vaccine efficacy against respiratory syncytial virus (RSV) lower respiratory tract disease (LRTD) in older adults during one RSV season. No RSV vaccines have shown three-season efficacy. We aimed to evaluate efficacy of Ad26.RSV.preF-RSV preF protein over three RSV seasons.
METHODS
CYPRESS was a randomised, double-blind, placebo-controlled, phase 2b study done at 40 US clinical research centres wherein adults aged 65 years or older were centrally randomly assigned 1:1 by computer algorithm to receive Ad26.RSV.preF-RSV preF protein or placebo (one intramuscular injection) on day 1. Investigators, participants, site personnel, and the sponsor were masked to vaccine allocation, except for individuals involved in preparation of study vaccinations. The primary endpoint (first occurrence of RSV-mediated LRTD meeting one of three case definitions) was previously reported. Here, the predefined exploratory endpoint of vaccine efficacy against RSV-positive LRTD was assessed in the per-protocol efficacy set (all participants randomly assigned and vaccinated without protocol deviations affecting efficacy) through season 1 and from day 365 until the end of season 3. Humoral and cellular immunogenicity was assessed in a subset of randomly assigned and vaccinated participants. The secondary endpoint of safety through the first RSV season was previously reported; follow-up for selected safety outcomes (fatal adverse events, adverse events leading to study discontinuation, serious adverse events, and vaccine-related serious adverse events) until study completion is reported here in all randomly assigned and vaccinated participants. This trial is registered with ClinicalTrials.gov, NCT03982199 and is complete.
FINDINGS
Of 6672 adults screened, 5782 participants (2891 each receiving vaccine or placebo) were enrolled and vaccinated between Aug 5 and Nov 13, 2019. The season 2 per-protocol efficacy set included 2124 vaccine recipients and 2126 placebo recipients (season 3: 864 and 881; across three seasons: 2795 and 2803, respectively). Vaccine efficacy against RSV LRTD was 76·1% (95% CI 26·9-94·2) over seasons 2 and 3 and 78·7% (57·3-90·4) across three seasons. For those in the immunogenicity subset (vaccine n=97; placebo n=98), immune responses remained above baseline for at least 1 year. Serious adverse events occurred in 47 (2·1%) and 12 (1·3%) vaccine recipients and 45 (2·1%) and 10 (1·1%) placebo recipients during seasons 2 and 3, respectively. No treatment-related serious or fatal adverse events were reported.
INTERPRETATION
Ad26.RSV.preF-RSV preF protein maintained high efficacy against RSV LRTD in older adults across three RSV seasons.
FUNDING
Janssen Vaccines & Prevention.
PubMed: 38801826
DOI: 10.1016/S1473-3099(24)00226-3 -
Journal of Molecular Modeling Jul 2023As a result of the diversity of microstructures encountered in cis-1,4-polybutadiene and the variety of measurement methods used, experimental values of variation of...
CONTEXT
As a result of the diversity of microstructures encountered in cis-1,4-polybutadiene and the variety of measurement methods used, experimental values of variation of glass transition temperature (Tg) with pressure are relatively dispersed. However, atomistic simulations enable access to valuable information for very well-controlled chemistry and structures with a well-defined and systematic acquisition protocol. By varying the temperature and pressure, the specific volume of the melt was computed, yielding results that deviated by only 2% from experimental data. A linear relationship between Tg and pressure was observed, with Tg predicted to be 162 K at zero pressure and a rate of change of Tg with respect to pressure (dTg/dP) of 0.24 K/MPa.
METHOD
The atomistic dilatometry experiments were conducted on a model of amorphous cis-1,4 polybutadiene with an approximate molecular weight of 5400 g/mol using the LAMMPS code and the all-atom forcefield pcff + . The dilatometry process involved cooling and heating at a rate of 9 × 10 K/min. The specific volume was calculated by averaging over seven independent configurations for each temperature. The Tait equation was employed to fit the specific volume evolution within the temperature range of 10 to 700 K under different pressures of 0, 60, and 100 MPa.
Topics: Transition Temperature; Temperature; Elastomers; Phase Transition
PubMed: 37452231
DOI: 10.1007/s00894-023-05658-6