archivist: An R Package for Managing, Recording and Restoring Data Analysis Results

Everything that exists in R is an object [Chambers2016]. This article examines what would be possible if we kept copies of all R objects that have ever been created. Not only objects but also their properties, meta-data, relations with other objects and information about context in which they were created. We introduce archivist, an R package designed to improve the management of results of data analysis. Key functionalities of this package include: (i) management of local and remote repositories which contain R objects and their meta-data (objects' properties and relations between them); (ii) archiving R objects to repositories; (iii) sharing and retrieving objects (and it's pedigree) by their unique hooks; (iv) searching for objects with specific properties or relations to other objects; (v) verification of object's identity and context of it's creation. The presented archivist package extends, in a combination with packages such as knitr and Sweave, the reproducible research paradigm by creating new ways to retrieve and validate previously calculated objects. These new features give a variety of opportunities such as: sharing R objects within reports or articles; adding hooks to R objects in table or figure captions; interactive exploration of object repositories; caching function calls with their results; retrieving object's pedigree (information about how the object was created); automated tracking of the performance of considered models, restoring R libraries to the state in which object was archived.Comment: Submitted to JSS in 2015, conditionally accepte

Saliva, hair, tears, and other biological materials obtained non-invasively for diagnosis in pregnancy: a literature review

As medical technology evolves, clinicians are increasingly choosing relatively painless non-invasive methods of patient diagnosis and treatment. There are two principles behind this: greater patient comfort and lower cost. Tears, hair, saliva, urine, and faeces can replace blood for diagnosis. The varied constituents in these biological materials can serve as biomarkers for the detection of both local and systemic diseases. In this paper, we review a range of diagnostic techniques — all using biological material obtained via non-invasive procedure — for detecting medical conditions in pregnant women. PubMed, Medline, Embase, and the Cochrane Library were searched from January 1996 until December 2018. Forty seven studies were included: thirty-five original articles, nine reviews and three meta-analysis. Analysis showed that saliva, hair, tears, and other biological material — obtained via non-invasive methods — may serve as clinically informative biomarkers. These biomarkers may be used for: toxicology, psychological studies, disease detection, biomonitoring, and drug abuse. The analysis of tears, hair, saliva, urine, and faeces is a safe, noninvasive and useful diagnostic tool within groups of pregnant women, but further investigation is necessary to fully realize the promise of these novel diagnostic tools

Is there a future for cell-free fetal dna tests in screening for preeclampsia?

CffDNA screening is a powerful diagnostic tool in the prenatal diagnosis algorithm for chromosomal abnormalities. With detailed ultrasound examination as the mainstay of first-trimester risk assessment, cffDNA has been shown to be superior to first-trimester combined screening (FTCS) in false-positive rates for trisomy 21 detection. In light of the growing interest in cffDNA testing and the possibility of it replacing first-trimester biochemistry, we decided to investigate the usefulness of cffDNA tests in early-pregnancy risk assessment for preeclampsia (PE). The aim of this review paper was to evaluate clinical application of first-trimester cfDNA in predicting PE, as well as to investigate its possible use in first-trimester PE screening enhancement, also in cases where biochemistry is not performed.

The practical use of acetylsalicylic acid in the era of the ASPRE trial. Update and literature review

It is now well established that acetylsalicylic acid — one of the most widely prescribed drugs today — has brought a new era in maternal-fetal medicine. The History of medicine mentions several antecedents. Extracts made from willow contained in clay tablets are reported in both ancient Sumer and Egypt. In 400 BC, Hippocrates referred to the use of salicylic tea to reduce fevers. In the 1950s, acetylsalicylic acid entered the Guinness Book of Records as the highest selling painkiller. There is little doubt that acetylsalicylic acid — one of the first drugs to enter common usage — remains one of the most researched drugs in the world

Contemporary management of prenatally diagnosed spina bifida aperta — an update

Spina bifida aperta is a relatively common congenital defect that occurs in the general population. Once the disorder hasbeen diagnosed, a discussion, that can be emotionally-charged, ensues about whether to treat it prenatally or to only offer surgery postnatally. Given that there are good arguments for and against both options, it is of paramount importance to gain a good understanding of the major advantages and disadvantages of the various surgical approaches. The aim of our paper is to summarize current knowledge about spina bifida and the potential benefits of prenatal surgery

Long-term outcomes of prenatally diagnosed ventriculomegaly — 10 years of Polish tertiary centre experience

Objectives: To estimate the prevalence, associated anomalies, and postnatal outcomes in infants prenatally diagnosed with ventriculomegaly.  Material and methods: All cases of ventriculomegaly that were examined and treated by the 1st Department of Obstet- rics and Gynecology, at the Medical University of Warsaw, from August 2007 until November 2017 were included in this study. Ultrasound data, and information on perinatal outcomes and long-term postnatal follow up were retrospectively collected by a standardised telephone survey. Ventriculomegaly was diagnosed when the atrial width of the lateral ventri- cles was ≥ 10 mm. The cases analyzed were divided into two subgroups: isolated ventriculomegaly (IVM) and non-isolated ventriculomegaly (NIVM). Neurodevelopmental complications were differentiated as either moderate or severe and were compared within each group and between groups.  Results: There were 118 cases of prenatally diagnosed ventriculomegaly. Complete follow up records were collected for 54 cases (45.8%). IVM was diagnosed in 29/54 (53.7%) cases, while NIVM was diagnosed in the remaining 25 (46.3%). The mean ventricular width for IVM was 16.93 mm (range 10.0 mm–73.0 mm) and 14.08 mm (range 9.0 mm–27.1 mm) for NIVM (p = 0.28). The mean gestational age at delivery for the IVM cases was 36 + 4 weeks and in the NIVM group 33 + 4 weeks (p = 0.022). Mild VM (10–12 mm) was diagnosed in 22/54 cases (40.7%), moderate VM (13–15 mm) in 12/54 (22.3%) and severe (≥ 15 mm) in 20/54 (37%). Among the infants with IVM the rate of severe medical complications was 29.6% (8/28) and for NIVM 667% (8/12) (p = 0.041). Less severe medical conditions affected 6/28 of the infants with IVM (21.4%) vs 9/12 NIVM cases (75%) (p = 0.012).  Conclusions: In terms of prenatal diagnosis, treatment of ventriculomegaly remains challenging due to a lack of specific prognostic factors and the significant risk of neurodevelopmental disorders. Nevertheless, isolated ventriculomegaly has significantly better long-term outcomes compared with non-isolated ventriculomegaly. In our material, the rate of severe neurodevelopmental disorders in the non-isolated ventriculomegaly cases was associated with a 52% rate of adverse perinatal outcomes. On the other hand, less severe medical conditions occurred in 21.4% of the infants with IVM and in 75% of the NIVM cases. Furthermore, obstetrical data suggest that the risks of premature delivery and caesarean section are significantly higher in cases of non-isolated ventriculomegaly.

Preferences and expectations among Polish women regarding prenatal screening

Objectives: Patients’ attitudes and expectations of prenatal screening for genetic abnormalities throughout pregnancy are rarely analyzed by researchers as emotions and fears are both important and challenging factors. Prenatal counselling has never been so difficult as we live in the era of detailed ultrasound scans, cell-free fetal DNA and detailed microarray testing. The aim of this study was to investigate Polish women’s attitudes towards screening for chromosomal abnormalities and fetal defects.  Material and methods: The study was a prospective survey conducted among a population of Polish women. An electronic questionnaire regarding prenatal diagnostics was distributed to a total number of 1072 female volunteers.  Results: 1044 patients (97.30%) stated that they were motivated to undergo prenatal diagnostics and would want to be informed about fetal abnormalities. Over 90% of the respondents would want to be informed about serious defects with a high mortality rate (including trisomy 13 or 18). More than half the Polish women (54.83%) stated they were willing to consider terminating pregnancy in the case of a severe abnormality.  Conclusions: Polish women expect prenatal screening. Almost all Polish women would want to be informed about both genetic and anatomical abnormalities and over half of them would consider terminating pregnancy in the case of a severe abnormality. Willingness to learn about a defect increased with average household income, and the statement of a will to terminate pregnancy depended mostly on maternal age and type of fetal abnormality

Polish Society of Gynecology and Obstetrics statement on safety measures and performance of ultrasound examinations in obstetrics and gynecology during the SARS-CoV-2 pandemic

We present recommendations on performance and safety measures of ultrasound examinations in obstetrics and gynecologyduring the SARS COV-2 pandemic. The statement was prepared based on the current knowledge on the coronavirusby the Ultrasound Section of the Polish Society of Obstetrics and Gynecology. It has to be noted that the presented guidanceis based on limited evidence and is primarily based on experiences published by authors from areas most affected bythe virus thus far, such as China, Singapore, Hong Kong, and Italy. We realize that the pandemic situation is very dynamic.New data is published every day. Despite the imposed limitations related to the necessity of social distancing, it is crucialto remember that providing optimal care in safe conditions should remain the primary goal of healthcare providers. Weplan to update the current guidelines as the situation develops