Cochranmayo4838

Both high energy density and fast eating rates contribute to excess energy intakes. The energy intake rate (EIR; kcal/min) combines both the energy density (kcal/g) and eating rate (g/min) of a food to quantify the typical rate at which calories of different foods are ingested.

We describe the EIRs of diets in a multi-ethnic Asian population, and examine relationships between the consumption of high-EIR foods and total energy intake, body composition, and cardio-metabolic risk factors.

Diet and lifestyle data from the Singapore Multi-Ethnic Cohort 2 (n=7011; 21-75 y), were collected through interviewer-administrated questionnaires. The EIR for each of the 269 foods was calculated as the product of its eating rate and energy density. Multivariable models were used to examine associations between the relative consumption of foods with higher and lower EIRs and energy intake, body composition, and cardio-metabolic risks, after adjusting for age, sex, ethnicity, education level, physical activity, smoking sted cardiovascular disease risk in an Asian population.

Comparing foods by their EIRs summarizes the combined impact of energy density and eating rate, and may identify foods and dietary patterns that are associated with obesogenic eating styles and higher diet-related cardiovascular disease risk in an Asian population.

Current methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or in early amplifications are likely responsible for these deviations. Commonly used 4- and 5-parameter sigmoidal models appear to be particularly susceptible to this issue, often displaying patterns of autocorrelation in the residuals. The presence of this phenomenon, even for technical replicates, suggests that these parametric models may be misspecified. Specifically, they do not account for the sequential dependent nature of the amplification process that underlies qPCR fluorescence measurements.

We demonstrate that a Smooth Transition Autoregressive (STAR) model addresses this limitation by explicitly modeling the dependence between cycles and the gradual transition between amplification regimes. In summary, application of a STAR model to qPCR amplification data improves model fit and reduces autocorrelation in the residuals.

R scripts to reproduce all the analyses and results described in this manuscript can be found at https//github.com/bhsu4/GAPDH.SO.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

An important task in the analysis of single-cell RNA-Seq data is the estimation of differentiation potency, as this can help identify stem-or-multipotent cells in non-temporal studies or in tissues where differentiation hierarchies are not well established. A key challenge in the estimation of single-cell potency is the need for a fast and accurate algorithm, scalable to large scRNA-Seq studies profiling millions of cells.

Here we present a single-cell potency measure, called CCAT (Correlation of Connectome and Transcriptome), which can return accurate single-cell potency estimates of a million cells in minutes, a 100 fold improvement over current state-of-the-art methods. We benchmark CCAT against 8 other single-cell potency models and across 28 scRNA-Seq studies, encompassing over 2 million cells, demonstrating comparable accuracy than the current state-of-the-art, at a significantly reduced computational cost, and with increased robustness to dropouts.

CCAT is part of the SCENT R-package, freely available from https//github.com/aet21/SCENT.

CCAT is part of the SCENT R-package, freely available from https//github.com/aet21/SCENT.

Identification of small molecules in a biological sample remains a major bottleneck in molecular biology, despite a decade of rapid development of computational approaches for predicting molecular structures using mass spectrometry (MS) data. Recently, there has been increasing interest in utilizing other information sources, such as liquid chromatography (LC) retention time (RT), to improve identifications solely based on MS information, such as precursor mass-per-charge and tandem mass spectra (MS2).

We put forward a probabilistic modelling framework to integrate MS and RT data of multiple features in an LC-MS experiment. We model the MS measurements and all pairwise retention order information as a Markov random field and use efficient approximate inference for scoring and ranking potential molecular structures. Our experiments show improved identification accuracy by combining MS2 data and retention orders using our approach, thereby outperforming state-of-the-art methods. Furthermore, we demonstrate the benefit of our model when only a subset of LC-MS features have MS2 measurements available besides MS1.

Software and data is freely available at https//github.com/aalto-ics-kepaco/msms_rt_score_integration.

Software and data is freely available at https//github.com/aalto-ics-kepaco/msms_rt_score_integration.

Fludarabine, cyclophosphamide and rituximab (FCR) is the standard regimen for fit patients with untreated CD20-positive chronic lymphocytic leukemia (CLL). However, this combination is unavailable in Japan because rituximab is not approved for CLL. We investigated the efficacy and safety of FCR in this single-arm, multicenter study designed as a bridging study to the CLL8 study by the German CLL Study Group.

The study enrolled previously untreated patients with CLL of Binet stage B or C with active disease. Patients with a Cumulative Illness Rating Scale score of ≤6 and creatinine clearance of ≥70ml/min were eligible. Patients received 6cycles of FCR every 28days and were followed for up to 1year.

Seven patients were enrolled. this website The best overall response rate according to the 1996 NCI-WG Guidelines, the primary endpoint of the study, was 71.4% (95% confidence interval, 29.0-96.3%), with one patient achieving complete response. No deaths or progression occurred during follow-up. The main adverse event was hematotoxicity. CD4-positive T-cell count decreased in all patients; most patients showed no reduction in serum immunoglobulin G.

Although the number of patients was limited, FCR appears to be effective with manageable toxicity for treatment-naïve fit Japanese patients with CD20-positive CLL.

JapicCTI-132285.

JapicCTI-132285.

The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease 2019. This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored.

We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection.

https//github.com/sinc-lab/sarscov2-mirna-discovery.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

A study was conducted to compare the accuracy of medication histories compiled by pharmacy technicians with histories obtained through the usual multidisciplinary process.

A retrospective cohort study was conducted at a community teaching hospital from January 2017 through February 2018. Inclusion criteria included patient age of at least 18 years, use of 1 or more medications at the time of admission, and hospital admission through the emergency department. Each electronically documented medication history was assessed for accuracy. The objective was to compare the accuracy of pharmacy technician-collected medication histories to those obtained through the usual multidisciplinary process.

Of 215 patients screened, 183 were included in the study 91 patients whose medication histories were obtained through the usual multidisciplinary process and 92 whose medication histories were collected by pharmacy technicians. Overall, documentation for 1,773 medications listed in medication histories was reviewed. The primary outcome of medication history accuracy occurred 38% of the time with the usual multidisciplinary process and 70% of the time with pharmacy technician collection of medication histories (P < 0.001).

The study showed that the accuracy of medication histories was improved when histories were obtained by pharmacy technicians instead of via the usual multidisciplinary process.

The study showed that the accuracy of medication histories was improved when histories were obtained by pharmacy technicians instead of via the usual multidisciplinary process.Recent cancer immunotherapy development with immune checkpoint inhibitors has shown durable clinical responses in a wide variety of tumor types. These drugs targeting programmed cell death 1, its ligand programmed death ligand 1 and cytotoxic T cell lymphocyte-associated antigen 4 have revolutionized the field of cancer treatment. It is of significant interest in optimizing the immunotherapy for cancer patients beyond the conventional treatments such as surgery, chemotherapy and radiation. Many clinical trials evaluating the safety and efficacy of various combined regimens with immune checkpoint inhibitors have been reported and are in progress. Among gynecologic malignancy, endometrial cancers have distinct subtypes with microsatellite instability-high status and polymerase ɛ mutation. These types have been shown to immunogenic tumors and appropriated candidate for immune checkpoint inhibitors. Also, recurrent cervical cancer showed a promising objective response with single anti-PD1 Ab treatment. Despite their definite outcome and considerable potential of immunotherapy, not all patients received a survival benefit and further understanding of human tumor immunology is essential to improve this type of therapy. In this review, we have summarized the updated results of clinical trials of cancer immunotherapy for gynecologic malignancies and discussed the future perspectives.