The Cochrane Handbook for Systematic Reviews of Interventions is the official document that describes in detail the process of preparing and maintaining Cochrane systematic reviews on the effects of healthcare interventions.

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Cochrane Handbook for Systematic Reviews of Interventions

Statistical Analysis with Missing Data

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

An elevated level of total homocysteine (tHcy) in blood, denoted hyperhomocysteinemia, is emerging as a prevalent and strong risk factor for atherosclerotic vascular disease in the coronary, cerebral, and peripheral vessels, and for arterial and venous thromboembolism. The basis for these conclusions is data from about 80 clinical and epidemiological studies including more than 10,000 patients. Elevated tHcy confers a graded risk with no threshold, is independent of but may enhance the effect of the conventional risk factors, and seems to be a particularly strong predictor of cardiovascular mortality. Hyperhomocysteinemia is attributed to commonly occurring genetic and acquired factors including deficiencies of folate and vitamin B12. Supplementation with B-vitamins, in particular with folic acid, is an efficient, safe, and inexpensive means to reduce an elevated tHcy level. Studies are now in progress to establish whether such therapy will reduce cardiovascular risk.

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Homocysteine and Cardiovascular Disease

These guidelines for the treatment of persons who have or are at risk for sexually transmitted diseases (STDs) were updated by CDC after consultation with a group of professionals knowledgeable in the field of STDs who met in Atlanta on April 18-30, 2009. The information in this report updates the 2006 Guidelines for Treatment of Sexually Transmitted Diseases (MMWR 2006;55[No. RR-11]). Included in these updated guidelines is new information regarding 1) the expanded diagnostic evaluation for cervicitis and trichomoniasis; 2) new treatment recommendations for bacterial vaginosis and genital warts; 3) the clinical efficacy of azithromycin for chlamydial infections in pregnancy; 4) the role of Mycoplasma genitalium and trichomoniasis in urethritis/cervicitis and treatment-related implications; 5) lymphogranuloma venereum proctocolitis among men who have sex with men; 6) the criteria for spinal fluid examination to evaluate for neurosyphilis; 7) the emergence of azithromycin-resistant Treponema pallidum; 8) the increasing prevalence of antimicrobial-resistant Neisseria gonorrhoeae; 9) the sexual transmission of hepatitis C; 10) diagnostic evaluation after sexual assault; and 11) STD prevention approaches.

Sexually transmitted diseases treatment guidelines, 2010.

Objective. To examine trends in multiple births conceived using assisted reproductive technology (ART) in the United States between 1997 and 2000 and to estimate the proportion of all US multiple births attributable to ART use. Methods. We analyzed population-based data of 109 519 live-born infants who were conceived in the United States using ART and born between 1997 and 2000 and population-based data of 15 856 809 live-born infants who were delivered in the United States between 1997 and 2000. Multiple birth rates (the number of live-born infants delivered in multiple gestation pregnancies per 1000 live births) and the proportion of all US multiple births attributable to ART were evaluated. Results. The twin rate for ART patients increased between 1997 and 2000, reaching 444.7 per 1000 live births in 2000, whereas the triplet/+ rate declined substantially from 134.3 to 98.7 per 1000 live births from 1997–2000. From 1997–2000, the proportion of multiple births in the United States attributable to ART increased from 11.2% to 13.6%, whereas the proportion attributable to natural conception decreased from 69.9% to 64.5%. In 2000, the proportion of triplet/+ births attributable to ART and to natural conception was 42.5% and 17.7%, respectively. The contribution of ART to multiple births increased substantially with maternal age, from 11.6% for triplet/+ infants born to women aged 20 to 24 to 92.8% for women aged 45 to 49 years. Conclusions. The contribution of ART to twin birth rates continues to increase, but the contribution of ART to triplet/+ birth rates has declined.

https://pediatrics.aappublications.org/content/pediatrics/111/Supplement_1/1159.full.pdf

Trends in Multiple Births Conceived Using Assisted Reproductive Technology, United States, 1997–2000

Research evidence synthesis involves the aggregation of available information using well-defined and transparent methods to search, summarize, and interpret a body of literature, frequently following a systematic review approach. A scoping review is a relatively new approach to evidence synthesis and differs from systematic reviews in its purpose and aims.1 The purpose of a scoping review is to provide an overview of the available research evidence without producing a summary answer to a discrete research question.2 Scoping reviews can be useful for answering broad questions, such as “What information has been presented on this topic in the literature?” and for gathering and assessing information prior to conducting a systematic review.1 In this issue of the Journal of Hospital Medicine, Fan et al. used a scoping review to identify information available in the literature on contributors to loss and theft of controlled drugs in hospitals and the safeguards that have been suggested to address these diversions.3 The authors followed Arksey and O’Malley’s framework for scoping reviews and the PRISMA-ScR (Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews) checklist in reporting findings.2,4

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Methods for Research Evidence Synthesis: The Scoping Review Approach

Perinatal outcome among singleton infants conceived through assisted reproductive technology in the United States.

Local and systemic effects of cigarette smoking on folate and vitamin B-12.

Background The advent of fertility treatments has led to an increase in the rate of multiple births in the United States. However, the trends in and magnitude of the contribution of fertility treatments to the increase are uncertain. Methods We derived the rates of multiple births after natural conception from data on distributions of all births from 1962 through 1966 (before fertility treatments were available). Publicly available data on births from 1971 through 2011 were used to determine national multiple birth rates, and data on in vitro fertilization (IVF) from 1997 through 2011 were used to estimate the annual proportion of multiple births that were attributable to IVF and to non-IVF fertility treatments, after adjustment for maternal age. Trends in multiple births were examined starting from 1998, the year when clinical practice guidelines for IVF were developed with an aim toward reducing the incidence of multiple births. Results We estimated that by 2011, a total of 36% of twin births and 77% of triplet and higher-order births resulted from conception assisted by fertility treatments. The observed incidence of twin births increased by a factor of 1.9 from 1971 to 2009. The incidence of triplet and higher-order births increased by a factor of 6.7 from 1971 to 1998 and decreased by 29% from 1998 to 2011. This decrease coincided with a 70% reduction in the transfer of three or more embryos during IVF (P<0.001) and a 33% decrease in the proportion of triplet and higher-order births attributable to IVF (P<0.001). Conclusions Over the past four decades, the increased use of fertility treatments in the United States has been associated with a substantial rise in the rate of multiple births. The rate of triplet and higher-order births has declined over the past decade in the context of a reduction in the transfer of three or more embryos during IVF. (Funded by the Centers for Disease Control and Prevention.)

https://www.nejm.org/doi/pdf/10.1056/NEJMoa1301467

Maurizio Macaluso

Papers

Trends in Multiple Births Conceived Using Assisted Reproductive Technology, United States, 1997–2000

Methods for Research Evidence Synthesis: The Scoping Review Approach

Perinatal outcome among singleton infants conceived through assisted reproductive technology in the United States.

Local and systemic effects of cigarette smoking on folate and vitamin B-12.

Fertility treatments and multiple births in the United States.