Miracle-dz/UniFAR-FTUs huggingface dataset:
A Likelihood Model That Accounts for Censoring Due to Fetal Loss Can Accurately Test the Effects of Maternal and Fetal Genotype on the Probability of Miscarriage

Objective: Heritable maternal and fetal thrombophilia and/or hypofibrinolysis are important causes of miscarriage. Under the constraint that fetal genotype is observed only after a live birth, estimating risk is complicated. Censoring prevents use of published statistical methodology. We propose techniques to determine whether increases in miscarriage are due to the fetal genotype, maternal genotype, or both. Methods: We propose a study to estimate the risk of miscarriage contributed by an allele, expressed in either dominant or recessive fashion. Using a multinomial likelihood, we derive maximum likelihood estimates of risk for different genotype groups. We describe likelihood ratio tests and a planned hypothesis testing strategy. Results: Parameter estimation is accurate (bias <0.0011, root mean squared error <0.0780, n = 500). We used simulation to estimate power for studies of three gene mutations: the 4G hypofibrinolytic mutation in the plasminogen activator inhibitor gene (PAI-1), the prothrombin G20210A mutation, and the Factor V Leiden mutation. With 500 families, our methods have approximately 90% power to detect an increase in the miscarriage rate of 0.2, above a background rate of 0.2. Conclusion: Our statistical method can determine whether increases in miscarriage are due to fetal genotype, maternal genotype, or both despite censoring.
Securing SSL Certificate Verification through Dynamic Linking

Recent discoveries of widespread vulnerabilities in the SSL/TLS protocol stack, particular with regard to the verification of server certificates, has left the security of the Internet's communications in doubt. Newly proposed SSL trust enhancements address many of these vulnerabilities, but are slow to be deployed and do not solve the problem of securing existing software. In this work, we provide new mechanisms that offer immediate solutions to addressing vulnerabilities in legacy code. We introduce CertShim, a lightweight retrofit to SSL implementations that protects against SSL vulnerabilities, including those surveyed by Georgiev et. al., in a manner that is transparent to the application. We demonstrate CertShim's extensibility by adapting it to work with Convergence, DANE, and Client-Based Key Pinning. CertShim imposes just 20 ms overhead for an SSL verification call, and hooks the SSL dependencies of 94% of Ubuntu's most popular packages with no changes necessary to existing applications. This work significantly increases system-wide security of SSL communications in non-browser software, while simultaneously reducing the barriers to evaluating and adopting the myriad alternative proposals to the certificate authority system.
Image reconstruction using priors from deep learning

Tomosynthesis, i.e. reconstruction of 3D volumes using projections from a limited perspective is a classical inverse, ill-posed or under constrained problem. Data insufficiency leads to reconstruction artifacts that vary in severity depending on the particular problem, the reconstruction method and also on the object being imaged. Machine learning has been used successfully in tomographic problems where data is insufficient, but the challenge with machine learning is that it introduces bias from the learning dataset. A novel framework to improve the quality of the tomosynthesis reconstruction that limits the learning dataset bias by maintaining consistency with the observed data is proposed. Convolutional Neural Networks (CNN) are embedded as regularizers in the reconstruction process to introduce the expected features and characterstics of the likely imaged object. The minimization of the objective function keeps the solution consistent with the observations and limits the bias introduced by the machine learning regularizers, improving the quality of the reconstruction. The proposed method has been developed and studied in the specific problem of Cone Beam Tomosynthesis Flouroscopy (CBT-fluoroscopy)1 but it is a general framework that can be applied to any image reconstruction problem that is limited by data insufficiency.
Additional intraarticular tranexamic acid further reduced postoperative blood loss compared to intravenous and topical bathed tranexamic acid in total hip arthroplasty: a retrospective sequential series study

Topical tranexamic acid (TXA) administration has been described to be effective in decreasing blood loss in total hip arthroplasty (THA). The aim of this retrospective study was to evaluate whether topical intraarticular TXA administration in addition to intravenous (IV) and topical bathed TXA further reduces blood loss in THA patients.
Percutaneous Minimally Invasive (MIS) Guide Wire-less Self-Tapping Pedicle Screw Placement in the Thoracic and Lumbar Spine: Safety and Initial Clinical Experience Technical Note

BACKGROUND: Multiple methods for minimally invasive (MIS) thoracic and lumbar pedicle screw placement exist. The guide wire is almost universally used for most insertion techniques; however, its use is not without complication and potentially prolongs surgical procedures. OBJECTIVE: To evaluate the safety of percutaneous MIS guide wire-less pedicle screw placement in the thoracic and lumbar spine at a single institution over a 3-year experience. METHODS: Forty-one patients who underwent posterior instrumentation with 110 transpedicular MIS thoracic and lumbar screws by a single surgeon from 2011 to 2014 were analyzed. The mean age was 63 years at the time of surgery. Etiological diagnoses were adult spinal deformity, trauma, spondylosis/spondylolisthesis, and other spinal diseases. Pedicle screws were inserted with the use of a guide wire-free technique in which anatomy-specific entry sites and fluoroscopic landmarks were used to guide the surgeon. A square, sharp-tipped pedicle screw was carefully advanced under biplanar fluoroscopic image (anteroposterior and lateral) down the pedicle into the body. No tapping or any type of electromonitoring was performed. An independent spine surgeon using medical records and thoracic/lumbar computed tomography taken during the postoperative period reviewed all patients. RESULTS: The number of the screws inserted at each level was as follows: total, 110; thoracic, 30; and lumbar, 80. All screws were evaluated by computed tomography to assess screw position. Seven screws (6.3%) were inserted with moderate cortical perforation, including 3 screws (2.7%) that violated the medial wall. There were no neurological, vascular, or visceral complications with up to 3 years of follow-up. CONCLUSION: The percutaneous MIS guide wire-less technique of lumbar and thoracic pedicle screw placement performed using a biplanar fluoroscopic guidance in a stepwise, consistent manner is an accurate, safe, and reproducible method of insertion to treat a variety of spinal disorders. ABBREVIATIONS: MIS, minimally invasive spine TP, transverse process
The effects of latent variables in the development of comorbidity among common mental disorders

Background: Although numerous studies have examined the role of latent predispositions to internalizing and externalizing disorders in the structure of comorbidity among common mental disorders, none examined latent predispositions in predicting development of comorbidity. Methods: A novel method was used to study the role of latent variables in the development of comorbidity among lifetime DSM‐IV disorders in the National Comorbidity Surveys. Broad preliminary findings are briefly presented to describe the method. The method used survival analysis to estimate time‐lagged associations among 18 lifetime DSM‐IV anxiety, mood, behavior, and substance disorders. A novel estimation approach examined the extent to which these predictive associations could be explained by latent canonical variables representing internalizing and externalizing disorders. Results: Consistently significant positive associations were found between temporally primary and secondary disorders. Within‐domain time‐lagged associations were generally stronger than between‐domain associations. The vast majority of associations were explained by a model that assumed mediating effects of latent internalizing and externalizing variables, although the complexity of this model differed across samples. A number of intriguing residual associations emerged that warrant further investigation. Conclusions: The good fit of the canonical model suggests that common causal pathways account for most comorbidity among the disorders considered. These common pathways should be the focus of future research on the development of comorbidity. However, the existence of several important residual associations shows that more is involved than simple mediation. The method developed to carry out these analyses provides a unique way to pinpoint these significant residual associations for subsequent focused study. Depression and Anxiety, 2011. © 2011 Wiley‐Liss, Inc.
Characteristics Associated With Decreased or Increased Mortality Risk From Glycemic Therapy Among Patients With Type 2 Diabetes and High Cardiovascular Risk: Machine Learning Analysis of the ACCORD Trial

OBJECTIVE Identifying patients who may experience decreased or increased mortality risk from intensive glycemic therapy for type 2 diabetes remains an important clinical challenge. We sought to identify characteristics of patients at high cardiovascular risk with decreased or increased mortality risk from glycemic therapy for type 2 diabetes using new methods to identify complex combinations of treatment effect modifiers. RESEARCH DESIGN AND METHODS The machine learning method of gradient forest analysis was applied to understand the variation in all-cause mortality within the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial (N = 10,251), whose participants were 40–79 years old with type 2 diabetes, hemoglobin A1c (HbA1c) ≥7.5% (58 mmol/mol), cardiovascular disease (CVD) or multiple CVD risk factors, and randomized to target HbA1c <6.0% (42 mmol/mol; intensive) or 7.0–7.9% (53–63 mmol/mol; standard). Covariates included demographics, BMI, hemoglobin glycosylation index (HGI; observed minus expected HbA1c derived from prerandomization fasting plasma glucose), other biomarkers, history, and medications. RESULTS The analysis identified four groups defined by age, BMI, and HGI with varied risk for mortality under intensive glycemic therapy. The lowest risk group (HGI <0.44, BMI <30 kg/m2, age <61 years) had an absolute mortality risk decrease of 2.3% attributable to intensive therapy (95% CI 0.2 to 4.5, P = 0.038; number needed to treat: 43), whereas the highest risk group (HGI ≥0.44) had an absolute mortality risk increase of 3.7% attributable to intensive therapy (95% CI 1.5 to 6.0; P < 0.001; number needed to harm: 27). CONCLUSIONS Age, BMI, and HGI may help individualize prediction of the benefit and harm from intensive glycemic therapy.
A Contribution to the Morphology and Phylogeny of Chlamydodon, with Three New Species from China (Ciliophora, Cyrtophoria)

Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne‐like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer somatic kineties, and/or an elongated body shape. Chlamydodon crassidens sp. n. is characterized mainly by an inverted triangular body shape, a posteriorly interrupted cross‐striated band (5–6 μm wide), and a large cytostome. Moreover, we provided small‐subunit (SSU) rDNA sequences of C. similis sp. n. and C. oligochaetus sp. n. Maximum likelihood (ML) and Bayesian inference (BI) consistently placed C. similis sp. n. as a sister to C. paramnemosyne, but showed different branching position of C. oligochaetus sp. n. , which may be due to a low taxon sampling in the Chlamydodontidae and/or an insufficient resolution of the marker gene at species level.
Design and Implementation of a Cordless Power Supply System for Pervasive Medical Devices

Pervasive medical devices are able to provide diagnostic information inside intangible in vivo organs. For better inspection, additional power besides cell batteries is required by doctors to enable locomotion and active control of devices such as capsule endoscope. We present the design and implementation of a cordless power supply system based on 900MHz RF signals. It consists of an antenna, an impedance matching network circuit, a rectifier circuit cum voltage multiplier, and a LDO (low drop out voltage regulator). After matching analytical results and simulation ones, we further implement the power supply system in a PCB and measure it with Agilent spectrum analyzer and Tektronix oscilloscope. It is also interesting that wireless signals from any 900M GSM mobile phone talking nearby can be absorbed and converted into enough power by the system. It is believed to enable the external control and the locomotion of active endoscopes as well as other power hunger pervasive medical devices.
Lower extremity function and subsequent disability: consistency across studies, predictive models, and value of gait speed alone compared with the short physical performance battery.

BACKGROUND Although it has been demonstrated that physical performance measures predict incident disability in previously nondisabled older persons, the available data have not been fully developed to create usable methods for determining risk profiles in community-dwelling populations. Using several populations and different follow-up periods, this study replicates previous findings by using the Established Populations for the Epidemiologic Study of the Elderly (EPESE) performance battery and provides equations for the prediction of disability risk according to age, sex, and level of performance. METHODS Tests of balance, time to walk 8 ft, and time to rise from a chair 5 times were administered to 4,588 initially nondisabled persons in the four sites of the EPESE and to 1,946 initially nondisabled persons in the Hispanic EPESE. Follow-up assessment for activity of daily living (ADL) and mobility-related disability occurred from 1 to 6 years later. RESULTS In the EPESE, compared with those with the best performance (EPESE summary performance score of 10-12), the relative risks of mobility-related disability for those with scores of 4-6 ranged from 2.9 to 4.9 and the relative risk of disability for those with scores of 7-9 ranged from 1.5 to 2.1, with similar consistent results for ADL disability. The observed rates of incident disability according to performance level in the Hispanic EPESE agreed closely with rates predicted from models developed from the EPESE sites. Receiver operating characteristic curves showed that gait speed alone performed almost as well as the full battery in predicting incident disability. CONCLUSIONS Performance tests of lower extremity function accurately predict disability across diverse populations. Equations derived from models using both the summary score and the gait speed alone allow for the estimation of risk of disability in community-dwelling populations and provide valuable information for estimating sample size for clinical trials of disability prevention.
Evaluating grade of tone mapped high dynamic range images

To display high dynamic range (HDR) pictures by traditional displays, Tone mapping operators (TMOs) intent to compact HDR pictures to low dynamic range (LDR) pictures. Conventional image similarity assessment like MSE, structural similarity (SSIM) and PSNR cannot be directly applied to analyze the alteration between pair of images with distinct dynamic ranges. This paper calculates the grade of tone mapped images by using structural fidelity along with statistical naturalness. Determining the image grade has essential significance for many image processing tools and applications. The algorithm should automatically assess the grade of images and it should perform closely with the quality of human perception. Subjective evaluation is the straight and genuine way to assess tone mapped pictures however it is costly and highly time absorbing, making them difficult to be set into automatic optimization algorithms.
Phase imaging with multiple phase‐cycled balanced steady‐state free precession at 9.4 T

While phase imaging with a gradient echo (GRE) sequence is popular, phase imaging with balanced steady‐state free precession (bSSFP) has been underexplored. The purpose of this study was to investigate anatomical and functional phase imaging with multiple phase‐cycled bSSFP, in expectation of increasing spatial coverage of steep phase‐change regions of bSSFP. Eight different dynamic 2D pass‐band bSSFP studies at four phase‐cycling (PC) angles and two TE/TR values were performed on rat brains at 9.4 T with electrical forepaw stimulation, in comparison with dynamic 2D GRE. Anatomical and functional phase images were obtained by averaging the dynamic phase images and mapping correlation between the dynamic images and the stimulation paradigm, and were compared with their corresponding magnitude images. Phase imaging with 3D pass‐band and 3D transition‐band bSSFP was also performed for comparison with 3D GRE phase imaging. Two strategies of combining the multiple phase‐cycled bSSFP phase images were also proposed. Contrast between white matter and gray matter in bSSFP phase images significantly varied with PC angle and became twice as high as that of GRE phase images at a specific PC angle. With the same total scan time, the combined bSSFP phase images provided stronger phase contrast and visualized neuronal fiber‐like structures more clearly than the GRE phase images. The combined phase images of both 3D pass‐band and 3D transition‐band bSSFP showed phase contrasts stronger than those of the GRE phase images in overall brain regions, even at a longer TE of 20 ms. In contrast, phase functional MRI (fMRI) signals were weak overall and mostly located in draining veins for both bSSFP and GRE. Multiple phase‐cycled bSSFP phase imaging is a promising anatomical imaging technique, while its usage as fMRI does not seem desirable with the current approach.
Automated Analysis of Multi-View Software Architectures

Software architectures usually are comprised of different views for capturing static, runtime, and deployment aspects. What is currently missing, however, are formal validation and verification techniques ofmulti-view architecture in very early phases of the software development lifecycle. The main contribution of this paper therefore is the construction of a single formal model (in Promela) for certain stylized, and widely used, multi-view architectures by suitably interpreting and fusing sub-models from different UML diagrams. Possible counter-examples produced by model checking are fed back as test scenarios for debugging the multi-view architectural model. We have implemented this algorithm as a plug-in for the Enterprise Architect development tool, and successfully used SPIN model checking for debugging some industrial architectural multi-view models by identifying a number of undesirable corner cases.
Manuscript : “ Oxygen and indicators of stress for marine life in multi-model global warming projections ”

CO2 and O2 replace the fugacities. RI not mentioned anymore. Pag. 10788, from line 2: The goals of this study are to provide multi-model estimates of decadal-to-century scale trends in O2, and CO2 (together with fO2, fCO2, and other biologically relevant variables), as well as to identify underlying mechanisms using global warming simulations from six fully coupled atmosphere-ocean general circulation models and one model of intermediate complexity. [. ] Pag. 10789 line 2: The concentrations of dissolved inorganic carbon (DIC, i.e. the sum of CO2, HCO3^− and CO3^2concentrations) Pag. 10789 line 2: Higher dissolved CO2 concentrations (i.e. the sum of the CO2(aq) and H2CO3 concentrations) Pag 10796 lines 13-22: Similarly to the observation-based O2 frequency distribution, the modeled O2 frequencies range between 0 and 400 mmol m^-3, indicating the ability of the models to reproduce the correct range of variability of O2 in the upper pelagic layer. The highest peak in the observations is at ~300 mmol m^-3. Most models tend to overestimate the magnitude of this peak and/or exhibit it between 200 and 240 mmol m^-3. The observation-based and modeled CO2 values lie mostly between 0.01 and 0.06 mol m^-3, with the highest peak at ~0.02 mol m^-3. The magnitude of this peak is largely overestimated by CSM1.4, MPIM and, to a smaller extend, CCSM3 and GFDL. From Pag. 10797, line 9 to Pag. 10798 line 10: replaced fCO2 (fO2) with CO2 (O2). Pag 10814 line 20 – 10815 line 25: Section in the appendix replaced with “Projected changes in RI additional figure” The largest reductions are projected by BCM-C in the Southern Ocean, the North Atlantic and Pacific. Most of the decrease is related to the increase in fCO2 in many areas. RI is projected to increase in the Eastern South Atlantic in most models. This is consistent with the projected changes in fO2 in this region. The increase in fO2 dominates over the projected increase in fCO2 in this low oxygen region. The projected changes in RI in the eastern tropical and Southern Pacific and in the Bay of Bengal and the Arabian Sea are not consistent across the range of models, similarly as found for projected changes in fO2 in these low-O2 regions. (text previously at Pag. 10804 line 17-25) 2. Length: The paper is on the long side with a rather large number of figures. In my opinion, the paper has a substantial potential for a careful editorial pruning in order to make the manuscript easier to digest and follow. The introduction is a good example as it introduces many findings and concepts that are interesting but not relevant for this paper. We agree and deleted these paragraphs: Pag. 10789 lines 10-16 Pag. 10790 lines 13-19 Pag.10800: deleted line 23 (subsection: Attribution to mechanisms) Pag. 10790, line 2: deleted “and indicates increased stratification as the main driver of this decline. ” Fig. 6 and 10 are not presented anymore. Fig. 14 is now in the appendix (as Figs. B3)
Improving site selection in clinical studies: a standardised, objective, multistep method and first experience results

Introduction A considerable number of clinical studies experience delays, which result in increased duration and costs. In multicentre studies, patient recruitment is among the leading causes of delays. Poor site selection can result in low recruitment and bad data quality. Site selection is therefore crucial for study quality and completion, but currently no specific guidelines are available. Material and methods Selection of sites adequate to participate in a prospective multicentre cohort study was performed through an open call using a newly developed objective multistep approach. The method is based on use of a network, definition of objective criteria and a systematic screening process. Illustrative example of the method at work Out of 266 interested sites, 24 were shortlisted and finally 12 sites were selected to participate in the study. The steps in the process included an open call through a network, use of selection questionnaires tailored to the study, evaluation of responses using objective criteria and scripted telephone interviews. At each step, the number of candidate sites was quickly reduced leaving only the most promising candidates. Recruitment and quality of data went according to expectations in spite of the contracting problems faced with some sites. Conclusion The results of our first experience with a standardised and objective method of site selection are encouraging. The site selection method described here can serve as a guideline for other researchers performing multicentre studies. Trial registration number ClinicalTrials.gov: NCT02297581.