SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences.

Background: Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids.Addgene's repository alone offers around 150,000 plasmids.

Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics.

Unlabelled: Somatic mutational profiling is increasingly being used to identify potential targets for breast cancer. However, limited tumor-sequencing data from Hispanic/Latinas (H/L) are available to guide treatment. To address this gap, we performed whole-exome sequencing (WES) and RNA sequencing on 146 tumors and WES of matched germline DNA from 140 H/L women in California.

The Diabetes teleMonitoring of patients in insulin Therapy (DiaMonT) trial: study protocol for a randomized controlled trial.

Background: The effect of telemedicine solutions in diabetes remains inconclusive. However, telemedicine studies have shown a positive trend in regards to glycemic control. The telemedicine interventions that facilitate adjustment of medication seems to improve glycemic control more effectively.

Characterization of pig skin microbiome and appraisal as an in vivo subcutaneous injection model.

Pig skin is commonly used in the medical industry as an injection model due to its compelling physiological affinity to human skin. However, the pig neck skin microflora remains largely uncharacterized, which may have undesirable implications for the translatability of results to humans. This study aimed to characterize pig neck skin microbiome with direct comparison with human skin microflora at emblematic injection sites to appraise its suitability as an injection model.

Correlation in Dose-Response to Rapid- and Long-Acting Insulin for People with Type 1 Diabetes.

In diabetes, it can become necessary to switch between pump- and pen-based insulin treatment. This switch involves a translation between rapid- and long-acting insulin analogues. In standard-of-care translation algorithms, a unit-to-unit conversion is applied.

Injection site microflora in persons with diabetes: why needle reuse is not associated with increased infections?

Needle reuse is a common practice and primary cause of customer compliance issues such as pain, bruising, clogging, injection site reactions (ISR), and associated lipodystrophy. This study aimed to characterize skin microflora at injection sites and establish microbial contamination of used pen injectors and needles. The second objective was to evaluate the risk of infections during typical and repeated subcutaneous injections.

Short Term Blood Glucose Prediction based on Continuous Glucose Monitoring Data.

Continuous Glucose Monitoring (CGM) has enabled important opportunities for diabetes management. This study explores the use of CGM data as input for digital decision support tools. We investigate how Recurrent Neural Networks (RNNs) can be used for Short Term Blood Glucose (STBG) prediction and compare the RNNs to conventional time-series forecasting using Autoregressive Integrated Moving Average (ARIMA).

Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature.

The finding that transformed mouse B-1 and B-2 progenitors give rise to B-cell acute lymphoblastic leukemias (B-ALLs) with varied aggressiveness suggests that B-cell lineage might also be a factor in the initiation and progression of pediatric B-ALLs in humans. If this is the case, we hypothesized that human pediatric B-ALLs would share gene expression patterns with mouse B-1 or B-2 progenitors. We tested this premise by deriving a distinct 30-gene B-1 and B-2 progenitor signature that was applied to a microarray data set of human pediatric ALLs.

Machine Learning-Based Adherence Detection of Type 2 Diabetes Patients on Once-Daily Basal Insulin Injections.

Background: Lack of treatment adherence can lead to life-threatening health complications for people with type 2 diabetes (T2D). Recent improvements and availability in continuous glucose monitoring (CGM) technology have enabled various possibilities to monitor diabetes treatment. Detection of missed once-daily basal insulin injections can be used to provide feedback to patients, thus improving their diabetes management.

Fast Assessment of Glycemic Control based on Continuous Glucose Monitoring Data.

Diabetes has become a major public health problem in the world. In this context, early assessment of glycemic control is essential in order to avoid life-threatening health complications. A panel of diabetes experts have recently proposed a list of recommendations when using Continuous Glucose Monitoring (CGM) for glycemic control assessment including a minimum of two weeks of CGM data.

Feasibility of a New Approach to Initiate Insulin in Type 2 Diabetes.

Background: Treatment inertia and prescription complexity are among reasons that people with type 2 diabetes (T2D) do not reach glycemic targets. This study investigated feasibility of a new approach to basal insulin initiation, where the dose needed to reach a glycemic target is estimated from two weeks of insulin and continuous glucose monitoring (CGM) data.

Methods: This was an exploratory single arm study with a maximum length of 84 days.

Modelling of fasting glucose-insulin dynamics from sparse data.

With the fast growth of diabetes prevalence, the disease is now considered an epidemic. Diabetes is characterized by elevated glucose levels, that may be treated with insulin. Tight control of glucose is essential for prevention of complications and patients' well-being.

Improved accuracy assessment for 3D genome reconstructions.

Background: Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome conformation had been difficult to elucidate but the advent chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin architecture and yielded numerous biological insights. Although most of these findings have flowed from analysis of proximity data produced by these assays, added value in generating 3D reconstructions has been demonstrated, deriving, in part, from superposing genomic features on the reconstruction.

Replication confers β cell immaturity.

Pancreatic β cells are highly specialized to regulate systemic glucose levels by secreting insulin. In adults, increase in β-cell mass is limited due to brakes on cell replication. In contrast, proliferation is robust in neonatal β cells that are functionally immature as defined by a lower set point for glucose-stimulated insulin secretion.

Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas.

Background: Rare multicentric lower-grade gliomas (LGGs) represent a unique opportunity to study the heterogeneity among distinct tumor foci in a single patient and to infer their origins and parallel patterns of evolution.

Methods: In this study, we integrate clinical features, histology, and immunohistochemistry for 4 patients with multicentric LGG, arising both synchronously and metachronously. For 3 patients we analyze the phylogeny of the lesions using exome sequencing, including one case with a total of 8 samples from the 2 lesions.

A deep learning approach to adherence detection for type 2 diabetics.

Diabetes has become one of the biggest health problems in the world. In this context, adherence to insulin treatment is essential in order to avoid life-threatening complications. In this pilot study, a novel adherence detection algorithm using Deep Learning (DL) approaches was developed for type 2 diabetes (T2D) patients, based on simulated Continuous Glucose Monitoring (CGM) signals.

Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy.

Purpose: We aimed to validate GEMCaP (Genomic Evaluators of Metastatic Cancer of the Prostate) as a novel copy number signature predictive of prostate cancer recurrence.

Materials And Methods: We randomly selected patients who underwent radical prostatectomy at Cleveland Clinic or University of Rochester from 2000 to 2005. DNA isolated from the cancer region was extracted and subjected to high resolution array comparative genomic hybridization.

Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant .

mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 mutant LGGs.

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.

The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g.

Pollutant Concentrations and Toxic Effects on the Red Alga Ceramium tenuicorne of Sediments from Natural Harbors and Small Boat Harbors on the West Coast of Sweden.

This investigation set out to analyze the toxicity of surface sediments in a number of natural harbors and small boat harbors on the west coast of Sweden. This was done with the growth inhibition method with Ceramium tenuicorne. Also, concentrations of copper (Cu), lead (Pb), zinc (Zn), irgarol, organotin compounds, and polycyclic aromatic hydrocarbons (PAHs) in the sediments were analyzed.

Reconstruction of 3D genome architecture via a two-stage algorithm.

Background: The three-dimensional (3D) configuration of chromosomes within the eukaryote nucleus is an important factor for several cellular functions, including gene expression regulation, and has also been linked with cancer-causing translocation events. While visualization of such architecture remains limited to low resolutions, the ability to infer structures at increasing resolutions has been enabled by recently-devised chromosome conformation capture techniques. In particular, when coupled with next generation sequencing, such methods yield an inventory of genome-wide chromatin contacts or interactions.

Validating the Use of Google Trends to Enhance Pertussis Surveillance in California.

Introduction And Methods: Pertussis has recently re-emerged in the United States. Timely surveillance is vital to estimate the burden of this disease accurately and to guide public health response. However, the surveillance of pertussis is limited by delays in reporting, consolidation and dissemination of data to relevant stakeholders.

Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma.

Glioblastoma (GBM) is the most common and aggressive human brain tumor. Human cytomegalovirus (HCMV) immediate-early (IE) proteins that are endogenously expressed in GBM cells are strong viral transactivators with oncogenic properties. Here, we show how HCMV IEs are preferentially expressed in glioma stem-like cells (GSC), where they colocalize with the other GBM stemness markers, CD133, Nestin, and Sox2.