nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

<p>Abstract</p> <p>Background</p> <p>Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe.</p> <p>Results</p> <p>We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers.</p> <p>Reviewers</p> <p>This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman).</p

Children’s use of reasoning by exclusion to track identities of occluded objects

Reasoning by exclusion allows us to infer properties of unobserved objects from currently observed objects, formalized by P or Q, not P, therefore Q. Previous work suggested that, by age 3, children can use this kind of reasoning to infer the location of a hidden object after learning that another location is empty (e.g. Mody & Carey, 2016). In the current study, we asked whether children could use reasoning by exclusion to infer the identities of previously unobserved occluded objects in a task that required them to track the locations of multiple occluded objects. Forty-nine 4-7-yearolds viewed animated arrays of virtual “cards” depicting images which were then hidden by occluders. The occluders then swapped locations during the maintenance period. Children were asked to select which card was hidden in a probed location. During the encoding period, we manipulated whether children saw all the card faces (Face-up block) or all but one of the card faces (Exclusion block), for which children had to reason by exclusion to infer the target in half of the trials. We found that all children succeeded in the Face-up block, but only 6-year-olds succeed in the Exclusion block when they had to deploy logical reasoning to identify a previously-unseen hidden target. Our results suggest that children’s ability to reason by exclusion to infer the identity of a hidden target while tracking multiple objects and locations may undergo protracted development.Published versio

Associations of Weight Change With Changes in Calf Muscle Characteristics and Functional Decline in Peripheral Artery Disease.

Background Among people with lower extremity peripheral artery disease, obesity is associated with faster functional decline than normal weight. The association of weight loss with functional decline in peripheral artery disease is unknown. Methods and Results Adults with an ankle-brachial index &lt;0.90 were identified from Chicago-area hospitals in 2002-2004. Weight and 6-minute walk distance were measured annually. Weight change categories were weight loss or gain (≥5 pounds/year at ≥1 visit) or stable (weight change &lt;5 pounds at each visit). Participants reported whether weight loss was "intentional" or "unintentional." Calf muscle area was measured with computed tomography every 2 years. Associations of weight change with changes in calf muscle area and 6-minute walk distance were analyzed using mixed-effects models and adjusted for age, body mass index, ankle-brachial index, physical activity, and other confounders. Among 389 participants, mean ankle-brachial index was 0.63±0.16, mean age was 74.5±7.8, and mean body mass index was 28.1±5.1 kg/m2. Over 3.23±1.37 years, muscle area declined more in adults with intentional weight loss versus stable or gain (pair-wise comparisons, P&lt;0.001). Intentional weight loss was associated with less annual decline in 6-minute walk distance than weight gain (intentional loss, 3.7 m; stable, -14.0 m; gain, -28.5 m; unintentional loss, -20.8 m; pair-wise comparison intentional loss versus gain, P=0.003). Conclusions Despite a greater loss of calf muscle area, adults with peripheral artery disease who intentionally lost ≥5 pounds experienced less functional decline than those who gained weight. A randomized trial is needed to establish whether benefits of weight loss in peripheral artery disease outweigh potential adverse effects

Durability of Benefits From Supervised Treadmill Exercise in People With Peripheral Artery Disease.

Background It is currently unknown whether 6 months of supervised treadmill exercise has a durable benefit on 6-minute walk performance, even after exercise is completed, in people with peripheral artery disease. Methods and Results A total of 156 participants with peripheral artery disease were randomized to 1 of 3 groups: supervised treadmill exercise, supervised resistance training, or attention control. Participants received supervised sessions during months 1 to 6 and telephone contact during months 6 to 12. Primary outcomes were change in 6-minute walk distance and short physical performance battery at 6-month follow-up and have been reported previously. Secondary outcomes were change in 6-minute walk and short physical performance battery at 12-month follow-up and are reported here. A group of 134 participants (86%) completed the 12-month follow-up. At 6-month follow-up, compared with control, 6-minute walk distance improved in the treadmill exercise group (+36.1 m, 95% CI =13.9-58.3, P=0.001). Between 6- and 12-month follow-up, 6-minute walk distance significantly declined (-28.6 m, 95% CI=-52.6 to -4.5, P=0.020) and physical activity declined -272 activity units (95% CI =-546 to +2, P=0.052) in the treadmill exercise group compared with controls. At 12-month follow-up, 6 months after completing supervised treadmill exercise, change in 6-minute walk distance was not different between the treadmill exercise and control groups (+7.5, 95% CI =-17.5 to +32.6, P=0.56). There were no differences in short physical performance battery change between either exercise group and control at 6-month or 12-month follow-up. Conclusions A 6-month supervised treadmill exercise intervention that improved 6-minute walk distance at 6-month follow-up did not have persistent benefit at 12-month follow-up. These results do not support a durable benefit of supervised treadmill exercise in peripheral artery disease. Clinical Trial Registration URL : https://www.clinicaltrials.gov . Identifier: NCT 00106327

Racial Differences in the Effect of Granulocyte Macrophage Colony-Stimulating Factor on Improved Walking Distance in Peripheral Artery Disease: The PROPEL Randomized Clinical Trial.

Background The effects of race on response to medical therapy in people with peripheral artery disease ( PAD ) are unknown. Methods and Results In the PROPEL (Progenitor Cell Release Plus Exercise to Improve Functional Performance in PAD) Trial, PAD participants were randomized to 1 of 4 groups for 6 months: supervised treadmill exercise+granulocyte-macrophage colony-stimulating factor ( GM - CSF ) (Group 1), exercise+placebo (Group 2), attention control+ GM - CSF (Group 3), or attention control+placebo (Group 4). Change in 6-minute walk distance was measured at 12- and 26-week follow-up. In these exploratory analyses, groups receiving GM - CSF (Groups 1 and 3), placebo (Groups 2 and 4), exercise (Groups 1 and 2), and attention control (Groups 2 and 4) were combined, maximizing statistical power for studying the effects of race on response to interventions. Of 210 PAD participants, 141 (67%) were black and 64 (30%) were white. Among whites, GM - CSF improved 6-minute walk distance by +22.0 m (95% CI : -4.5, +48.5, P=0.103) at 12 weeks and +44.4 m (95% CI : +6.9, +82.0, P=0.020) at 26 weeks, compared with placebo. Among black participants, there was no effect of GM - CSF on 6-minute walk distance at 12-week ( P=0.26) or 26-week (-5.0 m [-27.5, +17.5, P=0.66]) follow-up, compared with placebo. There was an interaction of race on the effect of GM - CSF on 6-minute walk change at 26-week follow-up ( P=0.018). Exercise improved 6-minute walk distance in black ( P=0.006) and white ( P=0.034) participants without interaction. Conclusions GM - CSF improved 6-minute walk distance in whites with PAD but had no effect in black participants. Further study is needed to confirm racial differences in GM - CSF efficacy in PAD . Clinical Trial Registration URL : http://www.clinicaltrials.gov . Unique identifier: NCT 01408901

Two-year-olds use past memories to accomplish novel goals

Memory-guided planning involves retrieving relevant memories and applying that information in service of a goal. Previous studies have shown substantial development in this ability from 3 to 4 years of age. We investigated the emergence of memory-guided planning by asking whether 2-year-olds could draw on episodic memories of past experiences to generate and execute plans. In Experiments 1 and 2 (N = 32, ds > .7), 2-year-olds successfully did so, and this ability developed significantly across the third year of life. Furthermore, in Experiment 3 (N = 19, d = 0.63), 2-year-olds successfully applied episodic memories to guide plans in a novel problem context, suggesting flexibility in this ability. Together, these results suggest that some form of memory-guided planning emerges during the third year of life and may form the cognitive basis for episodic prospection later in development.F32 HD094554 - NICHD NIH HHSAccepted manuscrip

Corridor-based functional performance measures correlate better with physical activity during daily life than treadmill measures in persons with peripheral arterial disease

ObjectiveTo compare associations of physical activity during daily life with treadmill walking performance and corridor-based functional performance measures in persons with lower extremity peripheral arterial disease (PAD).Study DesignCross-sectional.SubjectsOne hundred fifty-six men and women with PAD who completed baseline measurements and were randomized into the study to improve leg circulation (SILC) exercise clinical trial.Main Outcome MeasuresParticipants completed a Gardner-Skinner treadmill protocol. Corridor-based functional performance measures were the 6-minute walk, walking velocity over four meters at usual and fastest pace, and the short physical performance battery (SPPB) (0-12 scale, 12 = best). Physical activity during daily life was measured continuously over 7 days with a Caltrac (Muscle Dynamics Fitness Network, Inc, Torrence, Calif) accelerometer.ResultsAdjusting for age, gender, and race, higher levels of physical activity during daily life were associated with greater distance achieved in the 6-minute walk (P trend = .001), faster fast-paced four-meter walking velocity (P trend < .001), faster usual-paced four-meter walking speed (P trend = .027) and a higher SPPB (P trend = .005). The association of physical activity level with maximum treadmill walking distance did not reach statistical significance (P trend = .083). There were no associations of physical activity with treadmill distance to onset of leg symptoms (P trend = .795).ConclusionFunctional performance measures are more strongly associated with physical activity levels during daily life than treadmill walking measures

Recruiting participants with peripheral arterial disease for clinical trials: Experience from the Study to Improve Leg Circulation (SILC)

ObjectiveTo describe the success of diverse recruitment methods in a randomized controlled clinical trial of exercise in persons with peripheral arterial disease (PAD).MethodsAn analysis of recruitment sources conducted for the 746 men and women completing a baseline visit for the study to improve leg circulation (SILC), a randomized controlled trial of exercise for patients with PAD. For each recruitment source, we determined the number of randomized participants, the rate of randomization among those completing a baseline visit, and cost per randomized participant.ResultsOf the 746 individuals who completed a baseline visit, 156 were eligible and randomized. The most frequent sources of randomized participants were newspaper advertising (n = 67), mailed recruitment letters to patients with PAD identified at the study medical center (n = 25), and radio advertising (n = 18). Costs per randomized participant were $2750 for television advertising,$2167 for Life Line Screening, $2369 for newspaper advertising,$3931 for mailed postcards to older community dwelling men and women, and $5691 for radio advertising. Among those completing a baseline visit, randomization rates ranged from 10% for those identified from radio advertising to 32% for those identified from the Chicago Veterans Administration and 33% for those identified from posted flyers.ConclusionMost participants in a randomized controlled trial of exercise were recruited from newspaper advertising and mailed recruitment letters to patients with known PAD. The highest randomization rates after a baseline visit occurred among participants identified from posted flyers and mailed recruitment letters to PAD patients