Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of pregnancies in healthcare data: A changing landscape

Key Points • Traditionally, in studies using healthcare utilization databases, investigators identify pregnancies starting from their outcome and calculate the first day of the last menstrual period (LMP) by subtracting the estimated gestational age from the date of delivery. • The relatively new ICD-10-CM Z3A codes, which indicate the gestational age at the time of the encounter, can be used for a potentially more precise LMP estimation than ICD-9-CM codes supported. • In an article recently published in PDS, Bertoia and colleagues put forward an algorithm that allows prospective identification of pregnancies in US claims by using ICD-10-CM Z3A codes. • Other research groups have developed related approaches that can identify ongoing pregnancies. • In addition to providing an up-to-date description of the basics of pregnancy-identification methods using existing healthcare data sources, we critically review advantages and challenges of these approaches.
Genetics and epigenetics of self‐injurious thoughts and behaviors: Systematic review of the suicide literature and methodological considerations

Suicide is a multifaceted and poorly understood clinical outcome, and there is an urgent need to advance research on its phenomenology and etiology. Epidemiological studies have demonstrated that suicidal behavior is heritable, suggesting that genetic and epigenetic information may serve as biomarkers for suicide risk. Here we systematically review the literature on genetic and epigenetic alterations observed in phenotypes across the full range of self‐injurious thoughts and behaviors (SITB). We included 577 studies focused on genome‐wide and epigenome‐wide associations, candidate genes (SNP and methylation), noncoding RNAs, and histones. Convergence of specific genes is limited across units of analysis, although pathway‐based analyses do indicate nervous system development and function and immunity/inflammation as potential underlying mechanisms of SITB. We provide suggestions for future work on the genetic and epigenetic correlates of SITB with a specific focus on measurement issues.
Experimental Investigations of Magnetohydrodynamic Plasma Jets

This thesis primarily focuses on understanding the plasma behavior during the helicity injection stage of a pulsed spheromak experiment. Spheromak formation consists of a series of dynamic steps whereby highly localized plasma near the electrodes evolves toward a Taylor state equilibrium. The dynamical evolution stage has been modeled as a series of equilibrium states in the past. However, the experiments at the Caltech spheromak facility have revealed that unbalanced J x B forces drive non equilibrium Alfvenic flows during these preliminary stages. The Caltech spheromak experiment uses coplanar electrodes to produce a collimated plasma jet flowing away from the electrodes. The jet formation stage precedes the spheromak formation and serves as a mechanism for feeding particles, magnetic helicity, energy, and toroidal flux into the system. Detailed density and flow velocity measurements of hydrogen and deuterium plasma jets have revealed that the jets are extremely dense with β [subscript thermal] ~1. Furthermore, the flow velocity was found to be Alfvenic with respect to the the toroidal magnetic field produced by the axial current within the plasma. An existing magnetohydrodynamics (MHD) model has been generalized to successfully predict the effect of plasma current on the jet's density and flow velocity. The behavior of these laboratory jets is in stark contrast to the often considered model for astrophysical jets describing them as equilibrium configurations with hollow density profiles. Other contributions of this thesis include the following. 1. The thesis presents an analytical proof that resistive MHD equilibrium with closed flux tubes is not feasible. This implies that sustained spheromak experiments cannot maintain helicity while being in a strict equilibrium. 2. The thesis describes measurements to characterize the circuit parameters of the high voltage discharge circuit used in the Caltech spheromak experiment. 3. The thesis also describes the setup of novel He-Ne laser interferometers used to measure the density of plasma jets. The ease of alignment of these interferometers was greatly enhanced by having unequal path lengths of the scene and reference beams. 4. Finally, the thesis details the setup for a soft X-ray (SXR)/Vacuum ultra violet (VUV) imaging system. Some preliminary images of reconnecting flux tubes captured by the imaging setup are also presented.
GeneHome – a Novel Model to Deliver Care to Individuals with Genetic Predisposition to Cancer

Genetic testing for hereditary cancer predisposition is more widely available, resulting in more patients being identified as carriers of pathogenic variants (PV) of cancer susceptibility genes. PV carriers may be at high risk for multiple cancers of different organ systems. Traditional high-risk cancer screening is often organ specific and conducted separately by specialists. However, with many genes associated with 3 or more types of cancer risks, coordination of such cancer screening can be overwhelming for patients and providers. At Moffitt Cancer Center (MCC), GeneHome clinic functions as a “home” to conduct and coordinate prevention, screening, counseling, and education for individuals carrying germline genetic PVs across the entire spectrum of cancer genes. The screening includes, but is not limited to, history review, physical examination, image studies, blood tests, urine tests, and endoscopy. GeneHome is a novel model for genetic high-risk cancer surveillance and has grown in 4 years since establishment. We sought to study various characteristics of the patient population it serves, common themes in referral patterns and evolution of the clinic since its inception. A total of 821 patients were seen over 42 months, encompassing PV carriers of 46 genes. Patients were 84.9% female and 13.3% male. Most PVs were of BRCA1 and BRCA2. Most patients had private insurance, and most were from Florida. Annual increase in patient visits was over 74.7% over the last year. Overall, GeneHome has been well accepted by providers and patients and is a valuable service for patients with a genetic predisposition to cancer.
CPT1 Mediated Ionizing Radiation-Induced Intestinal Injury Proliferation via Shifting FAO Metabolism Pathway and Activating the ERK1/2 and JNK Pathway

The intestinal compensatory proliferative potential is a key influencing factor for susceptibility to radiation-induced intestinal injury. Studies indicated that the carnitine palmitoyltransferase 1 (CPT1) mediated fatty acid β-oxidation (FAO) plays a crucial role in promoting the survival and proliferation of tumor cells. Here, we aimed to explore the effect of 60Co gamma rays on CPT1 mediated FAO in the radiation-induced intestinal injury models, and investigate the role of CPT1 mediated FAO in the survival and proliferation of intestinal cells after irradiation. We detected the changed of FAO in the plasma and small intestine of Sprague Dawley (SD) rats at 24 h after 60Co gamma irradiation (0, 5 and 10 Gy), using target metabolomics, qRT-PCR, immunohistochemistry (IHC), western blot (WB) and related enzymatic activity kits. We then analyzed the FAO changes in radiation-induced intestinal injury models regardless of ex vivo (mice enteroids), or in vitro (normal human intestinal epithelial cell lines, HIEC-6). HIEC-6 cells were transduced with lentivirus vector GV392 and treated with puromycin for obtaining CPT1 stable knockout cell lines, named CPT1 KO. CPT1 enzymatic activities of HIEC-6 cells and mice enteroids were also inhibited by pharmaceutical inhibitor ST1326 and Etomoxir (ETO), to study the function of CPT1 in the survival and proliferation of HIEC-6 cells after 60Co gamma irradiation. We found that CPT1 mediated FAO was altered in the small intestine of the SD rats after irradiation, especially, the expression level and enzymatic activity of CPT1 were significantly increased. Similarly, the expression levels of CPT1 were also remarkably enhanced in mice enteroids and HIEC-6 cells after irradiation. CPT1 inhibition decreased the proliferation of the HIEC-6 cells and mice enteroids after irradiation partially by reducing the extracellular signal-regulated kinase (ERK1/2) and c-Jun N-terminal kinase (JNK) pathways activation, CPT1 inhibition also reduced the proliferation of mice enteroids after irradiation partially by down-regulating the Wnt/β-catenin signaling activity. In conclusion, our study indicated that CPT1 plays a crucial role in promoting intestinal epithelial cell proliferation after irradiation.
Vitamin D intakes and health outcomes in infants and preschool children: Summary of an evidence report

Abstract Background A systematic review was commissioned to support an international expert group charged to update the Food and Agriculture Organisation of the United Nations (FAO)/World Health Organisation (WHO)’s vitamin D intake recommendations for children aged 0–4 years. Materials and methods Multiple electronic databases were searched to capture studies published from database inception to the 2nd week of June 2020 according to key questions formulated by the FAO/WHO. Relevant studies were summarised and synthesised by key questions and by health outcomes using the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) approach. Results The 146 included studies examined the effects of different vitamin D intake levels on a variety of health outcomes (e.g. infectious disease, growth, neurodevelopment, rickets, and bone mineral density), and on outcomes for setting vitamin D upper limits (e.g. hypercalcemia, hypercalciuria, and nephrocalcinosis). For most outcomes, the strength of evidence was low or very low. Evidence was rated moderate for the effect of daily vitamin D supplementation on raising serum 25(OH)D concentrations, and a random-effects meta-regression analysis of 28 randomised controlled trials (mostly in infants 0–12 months) showed that each 100 IU/d increase in vitamin D supplementation was associated with an average of 1.92 (95% CI 0.28, 3.56) nmol/L increase in achieved 25-hydroxy-vitaminn D (25[OH]D) concentration (n = 53 intervention arms; p = .022) with large residual heterogeneity (I2 = 99.39%). Evidence was very low on two of the upper limit outcomes – hypercalcemia and hypercalciuria. Conclusions The evidence report provided the expert group with a foundation and core set of data to begin their work to set vitamin D nutrient reference values. To move the field forward, future studies should use standardised 25(OH)D assay measurements and should examine the relationship between long-term vitamin D status and health outcomes. Key Messages Results of a large complex systematic review suggest the current totality of evidence from trials and prospective observational studies do not reach sufficient certainty level to support a causal relationship between vitamin D intake and asthma, wheeze, eczema, infectious diseases, or rickets (most trials reported no rickets) in generally healthy infants and young children. In this systematic review, the only body of evidence that reached a moderate level of certainty was regarding the effect of daily vitamin D supplementation (vitamin D3 or D2 supplements to infants/children) on increasing serum 25(OH)D concentrations. However, currently there is no consensus on the definitions of vitamin D status, e.g. deficiency, insufficiency, sufficiency and toxicity, based on serum 25(OH)D concentrations. This systematic review provided an international expert group a foundation and core set of data through intake-response modelling to help set vitamin D nutrient reference values for infants and children up to 4 years of age.
The immune cell infiltrate in the tumour microenvironment of phaeochromocytomas and paragangliomas

Emerging evidence suggests the composition of the tumour microenvironment (TME) correlates with clinical outcome and that each tumour type has a unique TME including a variable population of inflammatory cells. We performed immunohistochemistry on 65 phaeochromocytoma and paraganglioma (PPGL) tumour samples with 20 normal adrenal medulla samples for comparison. The immune cells assessed were macrophages, lymphocytes and neutrophils, and we compared the proportion of infiltration of these immune cells with clinical and histopathological factors. There was a higher proportion of immune cells in tumour tissue compared to non-neoplastic adrenal medulla tissue, with a predominance of macrophages. There was a higher proportion of M2:M1 macrophages and T-helper lymphocytes in aggressive tumours compared to indolent ones. For SDHB-associated tumours, there was a higher proportion of M2 macrophage infiltration, with higher M2:M1 in aggressive SDHB PPGLs compared to indolent tumours. These data demonstrate that immune cells do infiltrate the TME of PPGLs, confirming that PPGLs are immunologically active tumours. Differences in the TME of PPGLs were observed between aggressive and indolent tumours. These differences could potentially be exploited as an aid in predicting tumour behaviour.
Image-Guided Cochlear Implant Programming: A Systematic Review and Meta-analysis

Objective To review studies evaluating clinically implemented image-guided cochlear implant programing (IGCIP) and to determine its effect on cochlear implant (CI) performance. Data Sources PubMed, EMBASE, and Google Scholar were searched for English language publications from inception to August 1, 2021. Study Selection Included studies prospectively compared intraindividual CI performance between an image-guided experimental map and a patient's preferred traditional map. Non-English studies, cadaveric studies, and studies where imaging did not directly inform programming were excluded. Data Extraction Seven studies were identified for review, and five reported comparable components of audiological testing and follow-up times appropriate for meta-analysis. Demographic, speech, spectral modulation, pitch accuracy, and quality-of-life survey data were collected. Aggregate data were used when individual data were unavailable. Data Synthesis Audiological test outcomes were evaluated as standardized mean change (95% confidence interval) using random-effects meta-analysis with raw score standardization. Improvements in speech and quality-of-life measures using the IGCIP map demonstrated nominal effect sizes: consonant–nucleus–consonant words, 0.15 (−0.12 to 0.42); AzBio quiet, 0.09 (−0.05 to 0.22); AzBio +10 dB signal-noise ratio, 0.14 (−0.01 to 0.30); Bamford–Kowel–Bench sentence in noise, −0.11 (−0.35 to 0.12); Abbreviated Profile of Hearing Aid Benefit, −0.14 (−0.28 to 0.00); and Speech Spatial and Qualities of Hearing Scale, 0.13 (−0.02 to 0.28). Nevertheless, 79% of patients allowed to keep their IGCIP map opted for continued use after the investigational period. Conclusion IGCIP has potential to precisely guide CI programming. Nominal effect sizes for objective outcome measures fail to reflect subjective benefits fully given discordance with the percentage of patients who prefer to maintain their IGCIP map.
The Impact of Public Cloud Price Schemes on Multi-Tenancy

—Multi-tenancy is one key element to make Software-as-a-Service profitable. Multi-tenancy refers to an architecture model where one software instance serves a set of multiple clients of different organizations, i.e., tenants. This reduces the number of application instances and consequently saves operational costs. This paper focuses on using relational databases in multi-tenant architectures, thereby stressing the cost aspect in public cloud environments. Investigating the various price schemes of cloud providers, it illustrates the difficulties to achieve cost-efficient multi-tenancy. As a result, the broad variety of price factors and schemes lead to certain, very different strategies and require adapting multi-tenant architectures to fit the respective cloud providers’ specifics.
The effect of submarine CO 2 vents on seawater: Implications for detection of subsea carbon sequestration leakage LIMNOLOGY and OCEANOGRAPHY

The effect of submarine carbon dioxide (CO 2 ) vents on seawater carbonate chemistry have been determined using hydrographical and marine carbonate data obtained from two submarine hydrothermal vent ﬁelds, as well as a reference station, all near the Jan Mayen Island in the Norwegian-Greenland Sea. We have shown that one can successfully determine the excess carbon that enters the seawater from the vents by applying a modiﬁed version of a back-calculation technique, which is traditionally used to study the invasion of excess atmospheric CO 2 in the surface ocean. As a result of this excess carbon, total dissolved inorganic carbon ( C T ) in the seawater surrounding the vents was on average 12 l mol kg 2 1 (1-30 l mol kg 2 1 ) higher compared to samples obtained from a reference station outside the venting areas. The observed excess C T was most signiﬁcant between 100 m and 200 m but was noticeable in all depths with the exception of the upper 10-20 m. The absence of a venting CO 2 signal in the surface water and the realism of the results are discussed. We believe the present method is promising for monitoring (detection and quantiﬁcation) of CO 2 leakage into the water column due to its high sensitivity and readiness for automation. The global carbon dioxide (CO 2 ) annual emissions due to fossil fuel burning and cement production are currently esti-mated to be at 9.7 gigatonnes carbon (Gt C 5 10 15 gC) (Peters et al. 2013), which is a record high since preindustrial era. The continuation and acceleration of these emissions is of global concern because they are the main drivers of anthropogenic global
Vortex Driven Acoustic Flow Instability

Most combustion machines feature internal flows with very high energy densities. If a small fraction of the total energy contained in the flow is diverted into oscillations, large mechanical or thermal loads on the structure can be the result, which are potentially devastating if not predicted correctly. This is particularly the case for lightweight high performing devices like rockets. The problem is commonly known as ”Combustion Instability”. Several mechanisms have been identified in the past that link the flow field to the acoustics inside a combustion chamber and thereby drive or dampen oscillations, one of them being vortex shedding. The interaction between the highly sheared flow behind an obstacle and longitudinal acoustic oscillations inside a solid rocket booster is investigated both analytically and experimentally. The analytical approach is developed based on modeling of the second order acoustic energy. The energy model is applied to the specific flow conditions just downstream of a single baffle protruding into the flow. The mean flow profile is assumed to be of the form of a hyperbolic tangent, the unsteady acoustic velocities are assumed to be sinusoidally oscillating. Solutions for the unsteady rotational velocities and the unsteady vorticity are derived. The resulting flow field is utilized in stability calculations for a simplified two-dimensional axial-symmetric geometry. This yields to linear growth rates of the (longitudinal) oscillation modes. The growth rates are functions of the chamber geometry, the mean flow properties and the properties of the shear layer created by the flow restriction. A cold flow experiment is designed, tested and performed in order to validate the analytical findings. Flow is injected radially into a tube with acoustic closed-closed end conditions. A
Health Risk Assessment by Consumption of Heavy Metal Contaminated Apples of Salooni, District Chamba, Himachal Pradesh

- In the present study, the atomic absorption spectroscopy (AAS) was employed for the determination of heavy metal concentration in three (Red, Royal and Golden) verities of apples growing in Salooni, District Chamba, Himachal Pradesh, India. An assessment of risk involved due to consumption of contaminated food also calculated. Accumulation of heavy metals especially Pb was found higher than the permissible limits of WHO/FAO standards in all varities of apples. As calculated, THQ was found >1 for Pb and Cd in all the studies samples. The overall study suggests that apples in the area were contaminated by the assayed metals and its consumption can cause potential health risks to consumers. Correlation analysis between heavy metals of soil and apples was also done and result showed that these heavy metals in fruits are not accumulated through soil.
Risk Management Technologies within the System of State Financial Control

The paper analyses international risk management models and identifies possibilities of their application within Russian state financial control. The legislative acts regulating the organisation and implementation of state financial control will need to be changed. Based upon the studies and analysis, a conclusion was drawn as to the application of risk management technology in the system of state financial control. The results can be used for improving risk management technologies within the state financial control in the conditions of digitization of economy.
Integrative Analysis Identiﬁes Multi-Omics Signatures That Drive Molecular Classiﬁcation of Uveal Melanoma

Simple Summary: Uveal melanoma (UM) is a heterogeneous disease driven by accumulative alterations at multi-omics levels including genomics, epigenomics and transcriptomics. It is of great clinical interest to identify UM molecular subtypes and subtype-speciﬁc biomarkers that could be used for prognosis and targeted therapy. Integrative clustering (iCluster) analysis is a new approach designed to identify cancer integrative subtypes (iSubtypes) and multi-omics signatures that drive molecular classiﬁcation of cancer. In this study, we performed an iCluster analysis of uveal melanoma (UM) multi-omics data and identiﬁed four UM iSubtypes, which formed two major iSubtypes (de-noted by M3 and D3) with distinct multi-omics landscapes. We showed that the integrative molecular classiﬁcation of UM was determined by concordant alterations at multi-omics levels including DNA copy number, DNA methylation, gene expression and somatic mutation. We further derived a gene panel that can be used to classify UM into high- or low-risk groups for metastasis. Abstract: By iCluster analysis, we found that the integrative molecular classiﬁcation of the UM was primarily driven by DNA copy number variation on chromosomes 3, 6 and 8, differential methylation and expression of genes involved in the immune system, cell morphogenesis, movement and migration, and differential mutation of genes including GNA11 , BAP1 , EIF1AX , SF3B1 and GNAQ . Integrative analysis revealed that pathways including IL6/JAK/STAT3 signaling, angiogenesis, allograft rejection, inﬂammatory response and interferon gamma response were hypomethylated and up-regulated in the M3 iSubtype, which was associated with a worse overall survival, compared to the D3 iSubtype. Using two independent gene expression datasets, we demonstrated that the subtype-driving genes had an excellent prognostic power in classifying UM into high- or low-risk groups for metastasis. Integrative analysis of UM multi-omics data provided a comprehensive view of UM biology for understanding the underlying mechanism leading to UM metastasis. The concordant molecular alterations at multi-omics levels revealed by our integrative analysis could be used for patient stratiﬁcation towards personalized management and surveillance.