A systematic search for positive selection in higher plants (Embryophytes)

BACKGROUND: Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. RESULTS: Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >>1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (Magnoliophytes) without saturation of 4- fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta- sheets, but were less negative and more variant on the surface and away from the hydrophobic core. CONCLUSION: Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes

Modeling effects of crop production, energy development and conservation-grassland loss on avian habitat

Birds are essential components of most ecosystems and provide many services valued by society. However, many populations have undergone striking declines as their habitats have been lost or degraded by human activities. Terrestrial grasslands are vital habitat for birds in the North American Prairie Pothole Region (PPR), but grassland conversion and fragmentation from agriculture and energy-production activities have destroyed or degraded millions of hectares. Conservation grasslands can provide alternate habitat. In the United States, the Conservation Reserve Program (CRP) is the largest program maintaining conservation grasslands on agricultural lands, but conservation grasslands in the PPR have declined by over 1 million ha since the program’s zenith in 2007. We used an ecosystemservices model (InVEST) parameterized for the PPR to quantify grassland-bird habitat remaining in 2014 and to assess the degradation status of the remaining grassland-bird habitat as influenced by crop and energy (i.e., oil, natural gas, and wind) production. We compared our resultant habitat-quality ratings to grassland-bird abundance data from the North American Breeding Bird Survey to confirm that ratings were related to grassland-bird abundance. Of the grassland-bird habitat remaining in 2014, about 19% was degraded by crop production that occurred within 0.1 km of grassland habitats, whereas energy production degraded an additional 16%. We further quantified the changes in availability of grasslandbird habitat under various land-cover scenarios representing incremental losses (10%, 25%, 50%, 75%, and 100%) of CRP grasslands from 2014 levels. Our model identified 1 million ha (9%) of remaining grassland-bird habitat in the PPR that would be lost or degraded if all CRP conservation grasslands were returned to crop production. Grassland regions world-wide face similar challenges in maintaining avian habitat in the face of increasing commodity and energy production to sate the food and energy needs of a growing world population. Identifying ways to model the impacts of the tradeoff between food and energy production and wildlife production is an important step in creating solutions

Does colon cancer ever metastasize to bone first? a temporal analysis of colorectal cancer progression

<p>Abstract</p> <p>Background</p> <p>It is well recognized that colorectal cancer does not frequently metastasize to bone. The aim of this retrospective study was to establish whether colorectal cancer ever bypasses other organs and metastasizes directly to bone and whether the presence of lung lesions is superior to liver as a better predictor of the likelihood and timing of bone metastasis.</p> <p>Methods</p> <p>We performed a retrospective analysis on patients with a clinical diagnosis of colon cancer referred for staging using whole-body ¹⁸F-FDG PET and CT or PET/CT. We combined PET and CT reports from 252 individuals with information concerning patient history, other imaging modalities, and treatments to analyze disease progression.</p> <p>Results</p> <p>No patient had isolated osseous metastasis at the time of diagnosis, and none developed isolated bone metastasis without other organ involvement during our survey period. It took significantly longer for colorectal cancer patients to develop metastasis to the lungs (23.3 months) or to bone (21.2 months) than to the liver (9.8 months). Conclusion: Metastasis only to bone without other organ involvement in colorectal cancer patients is extremely rare, perhaps more rare than we previously thought. Our findings suggest that resistant metastasis to the lungs predicts potential disease progression to bone in the colorectal cancer population better than liver metastasis does.</p

Optical trapping with "on-demand" two-photon luminescence using Cr:LiSAF laser with optically addressed saturable Bragg reflector

We demonstrate a diode-pumped Cr:LiSAF laser with controllable and reliable fast switching between its continuous-wave and mode-locked states of operation using an optically-addressed semiconductor Bragg reflector, permitting dyed microspheres to be continuously trapped and monitored using a standard microscope imaging and on-demand two-photon-excited luminescence techniques

Effect of lisdexamfetamine dimesylate on sleep in adults with attention-deficit/hyperactivity disorder

<p>Abstract</p> <p>Background</p> <p>Sleep problems are common in adults with attention-deficit/hyperactivity disorder (ADHD). This analysis aimed to evaluate the impact of lisdexamfetamine dimesylate (LDX) on sleep quality in adults with ADHD.</p> <p>Methods</p> <p>This 4-week, phase 3, double-blind, forced-dose escalation study of adults aged 18 to 55 years with ADHD randomized participants to receive placebo (n = 62), or 30 (n = 119), 50 (n = 117), or 70 (n = 122) mg/d LDX, taken once a day in the morning. The self-rated Pittsburgh Sleep Quality Index (PSQI) was administered at baseline and at week 4 to assess sleep quality. The PSQI global score assesses 7 sleep components (subjective sleep quality, sleep latency, sleep duration, habitual sleep efficiency, sleep disturbances, use of sleeping medications, and daytime dysfunction) each scored from 0 (no difficulty) to 3 (severe difficulty).</p> <p>Results</p> <p>The mean baseline PSQI global score was 5.8 for LDX and 6.3 for placebo (<it>P </it>= .19) indicating poor overall sleep quality. At endpoint, least squares (LS) mean change from baseline was -0.8 for LDX vs -0.5 for placebo (<it>P </it>= .33). The daytime functioning component showed significant improvement in LS mean change at endpoint for LDX compared with placebo (LDX -0.4 vs placebo 0.0, <it>P </it>= .0001). LS mean changes for the other 6 PSQI components did not significantly differ from placebo. Sleep-related treatment-emergent adverse events with an incidence ≥2% in the active treatment and placebo groups, respectively, were insomnia (19.3% and 4.8%), initial insomnia (5.0% and 3.2%), middle insomnia (3.6% and 0%), sleep disorder (0.6% and 3.2%), somnolence (0.3% and 3.2%), and fatigue (4.7% and 4.8%), and were generally mild or moderate in severity.</p> <p>Conclusion</p> <p>For most subjects, LDX was not associated with an overall worsening of sleep quality and significantly improved daytime functioning in adults with ADHD.</p> <p>Trial Registration</p> <p>clinicaltrials.gov Identifier: NCT00334880</p

Irradiation-Mediated Rescue of T Cell–Specific V(D)j Recombination and Thymocyte Differentiation in Severe Combined Immunodeficient Mice by Bone Marrow Cells

In SCID (severe combined immunodeficient) mice, proper assembly of immunoglobulin and T cell receptor (TCR) genes is blocked by defective V(D)J recombination so that B and T lymphocyte differentiation is arrested at an early precursor stage. Treating the mice with gamma irradiation rescues V(D)J rearrangement at multiple TCR loci, promotes limited thymocyte differentiation, and induces thymic lymphomas. These effects are not observed in the B cell lineage. Current models postulate that irradiation affects intrathymic T cell precursors. Surprisingly, we found that transfer of irradiated SCID bone marrow cells to unirradiated host animals rescues both TCR rearrangements and thymocyte differentiation. These data indicate that irradiation affects precursor cells at an earlier stage of differentiation than was previously thought and suggest new models for the mechanism of irradiation rescue

sQUlearn \unicode{x2013} A Python Library for Quantum Machine Learning

sQUlearn introduces a user-friendly, NISQ-ready Python library for quantum machine learning (QML), designed for seamless integration with classical machine learning tools like scikit-learn. The library's dual-layer architecture serves both QML researchers and practitioners, enabling efficient prototyping, experimentation, and pipelining. sQUlearn provides a comprehensive toolset that includes both quantum kernel methods and quantum neural networks, along with features like customizable data encoding strategies, automated execution handling, and specialized kernel regularization techniques. By focusing on NISQ-compatibility and end-to-end automation, sQUlearn aims to bridge the gap between current quantum computing capabilities and practical machine learning applications.Comment: 10+5 pages, 5+3 figure

Enrollment of adolescents and young adults onto SWOG cancer research network clinical trials: A comparative analysis by treatment site and era.

BackgroundFew adolescents and young adults (AYAs, 15-39 years old) enroll onto cancer clinical trials, which hinders research otherwise having the potential to improve outcomes in this unique population. Prior studies have reported that AYAs are more likely to receive cancer care in community settings. The National Cancer Institute (NCI) has led efforts to increase trial enrollment through its network of NCI-designated cancer centers (NCICC) combined with community outreach through its Community Clinical Oncology Program (CCOP; replaced by the NCI Community Oncology Research Program in 2014).MethodsUsing AYA proportional enrollment (the proportion of total enrollments who were AYAs) as the primary outcome, we examined enrollment of AYAs onto SWOG therapeutic trials at NCICC, CCOP, and non-NCICC/non-CCOP sites from 2004 to 2013 by type of site, study period (2004-08 vs 2009-13), and patient demographics.ResultsOverall, AYA proportional enrollment was 10.1%. AYA proportional enrollment decreased between 2004-2008 and 2009-2013 (13.1% vs 8.5%, P &lt; .001), and was higher at NCICCs than at CCOPs and non-NCICC/non-CCOPs (14.1% vs 8.3% and 9.2%, respectively; P &lt; .001). AYA proportional enrollment declined significantly at all three site types. Proportional enrollment of AYAs who were Black or Hispanic was significantly higher at NCICCs compared with CCOPs or non-NCICC/non-CCOPs (11.5% vs 8.8, P = .048 and 11.5% vs 8.6%, P = .03, respectively).ConclusionNot only did community sites enroll a lower proportion of AYAs onto cancer clinical trials, but AYA enrollment decreased in all study settings. Initiatives aimed at increasing AYA enrollment, particularly in the community setting with attention to minority status, are needed