Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been ...trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.
The design and implementation of effective environmental policies need to be informed by a holistic understanding of the system processes (biophysical, social and economic), their complex ...interactions, and how they respond to various changes. Models, integrating different system processes into a unified framework, are seen as useful tools to help analyse alternatives with stakeholders, assess their outcomes, and communicate results in a transparent way. This paper reviews five common approaches or model types that have the capacity to integrate knowledge by developing models that can accommodate multiple issues, values, scales and uncertainty considerations, as well as facilitate stakeholder engagement. The approaches considered are: systems dynamics, Bayesian networks, coupled component models, agent-based models and knowledge-based models (also referred to as expert systems). We start by discussing several considerations in model development, such as the purpose of model building, the availability of qualitative versus quantitative data for model specification, the level of spatio-temporal detail required, and treatment of uncertainty. These considerations and a review of applications are then used to develop a framework that aims to assist modellers and model users in the choice of an appropriate modelling approach for their integrated assessment applications and that enables more effective learning in interdisciplinary settings.
•We review five common integrated modelling approaches.•Model choice considers purpose, data type, scale and uncertainty treatment.•We present a guiding framework for selecting the most appropriate approach.
Climate change is impacting the function and distribution of habitats used by marine, coastal, and diadromous species. These impacts often exacerbate the anthropogenic stressors that habitats face, ...particularly in the coastal environment. We conducted a climate vulnerability assessment of 52 marine, estuarine, and riverine habitats in the Northeast U.S. to develop an ecosystem-scale understanding of the impact of climate change on these habitats. The trait-based assessment considers the overall vulnerability of a habitat to climate change to be a function of two main components, sensitivity and exposure, and relies on a process of expert elicitation. The climate vulnerability ranks ranged from low to very high, with living habitats identified as the most vulnerable. Over half of the habitats examined in this study are expected to be impacted negatively by climate change, while four habitats are expected to have positive effects. Coastal habitats were also identified as highly vulnerable, in part due to the influence of non-climate anthropogenic stressors. The results of this assessment provide regional managers and scientists with a tool to inform habitat conservation, restoration, and research priorities, fisheries and protected species management, and coastal and ocean planning.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Current models of cell-cycle control, based on classic studies of fused cells, predict that nuclei in a shared cytoplasm respond to the same CDK activities to undergo synchronous cycling. However, ...synchrony is rarely observed in naturally occurring syncytia, such as the multinucleate fungus Ashbya gossypii. In this system, nuclei divide asynchronously, raising the question of how nuclear timing differences are maintained despite sharing a common milieu.
We observe that neighboring nuclei are highly variable in division-cycle duration and that neighbors repel one another to space apart and demarcate their own cytoplasmic territories. The size of these territories increases as a nucleus approaches mitosis and can influence cycling rates. This nonrandom nuclear spacing is regulated by microtubules and is required for nuclear asynchrony, as nuclei that transiently come in very close proximity will partially synchronize. Sister nuclei born of the same mitosis are generally not persistent neighbors over their lifetimes yet remarkably retain similar division cycle times. This indicates that nuclei carry a memory of their birth state that influences their division timing and supports that nuclei subdivide a common cytosol into functionally distinct yet mobile compartments.
These findings support that nuclei use cytoplasmic microtubules to establish “cells within cells.” Individual compartments appear to push against one another to compete for cytoplasmic territory and insulate the division cycle. This provides a mechanism by which syncytial nuclei can spatially organize cell-cycle signaling and suggests size control can act in a system without physical boundaries.
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•Nuclear division time is inherited despite lineages mixing in one cytoplasm•Nuclei repel neighbors to demarcate independent cytoplasmic territories•Nuclear territory size is sensed and controlled through the cell cycle•Nuclear spacing is controlled by microtubules and required for nuclear asynchrony
•The sequence template file published with 2016 ISFG STR sequence nomenclature guidelines is comprehensively revised.•Listed forensic STRs have been expanded to include loci less commonly used but in ...need of detailed sequence descriptions.•A wide range of sequence variation features in and around forensic STRs have been identified and their annotations added to the new guide.•The sequence guide is now available as an FTP download allowing dynamic revisions and includes a date-stamped change log to detail future changes.
The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide.
Background
Chronic anal fissure (CAF) is commonly treated by colorectal surgeons. Pharmacological treatment is considered first-line therapy. An alternative treatment modality is chemical ...sphincterotomy with injection of botulinum toxin (BT). However, there is a lack of a consensus on the BT administration procedure among colorectal surgeons.
Methods
A national survey approved by the American Society of Colon and Rectal Surgeons (ASCRS) Executive Council was sent to all members. An eight-question survey was sent via ASCRS email correspondence between December 2019 and February 2020. Questions were derived from available meta-analyses and expert opinions on BT use in CAF patients and included topics such as BT dose, injection technique, and concomitant therapies. The survey was voluntary and anonymous, and all ASCRS members were eligible to complete it. Responses were recorded and analyzed via an online survey platform.
Results
216 ASCRS members responded to the survey and 90% inject 50-100U of BT. Most procedures are performed under MAC anesthesia (56%). A majority of respondents (64%) inject into the internal sphincter and a majority (53%) inject into 4 quadrants in the anal canal circumference. Some respondents perform concomitant manual dilatation (34%) or fissurectomy (38%). Concomitant topical muscle relaxing agents are not used uniformly among respondents.
Discussion
Injection of BT for CAF is used commonly by colorectal surgeons. There is consensus on BT dosage, administration site, technique, and the use of monitored anesthesia care.
Background
Enhanced Recovery After Surgery (ERAS) programs aim to standardize perioperative care to reduce morbidity and cost. Our study examined an Active Post-Discharge Surveillance (APDS) program ...in reducing avoidable readmissions and emergency department (ED) visits in postoperative colorectal ERAS patients.
Methods
Colectomy (right, subtotal and total) and low anterior resection cases performed at a tertiary care hospital between 2015 and 2018 were reviewed. ED visits, 30-day readmissions, and patients’ APDS participation were assessed. Our APDS followed a modern text messaging paradigm offered to all patients free-of-charge.
Results
Of 236 patients that underwent colectomy, 123 utilized APDS and 113 did not. Overall, both non-surveillance (NS) and active surveillance (AS) groups had similar preoperative characteristics. Length of hospital stay at index surgery was longer in the NS compared to AS group, 4.7 ± 2.6 vs. 2.6 ± 2.8 days, respectively (
p
< 0.001). In the NS group, 16 patients visited the ED, of which 14 (14/16, 87.5%) were ultimately readmitted. One patient was directly readmitted from the surgeon’s office, resulting in a total of 15 (15/113, 13.3%) total patients readmitted by postoperative day (POD) 30. In the AS group, 9 patients visited the ED, of which 7 (7/9, 77.8%) were ultimately readmitted. One patient was directly readmitted, resulting in a total of 8 (8/123, 6.5%) total patients readmitted by POD 30. AS patients had significantly lower odds of visiting the ED when compared to NS patients (OR: 0.356; 95% CI: 0.138–0.919;
p
= 0.0328). Similarly, AS patients had significantly lower odds of readmission when compared to NS patients (OR: 0.343; 95% CI: 0.132–0.892;
p
= 0.0283).
Conclusions
APDS allows many postoperative issues to be resolved in outpatient settings without ER visits or readmission. This indicates APDS is a valuable ERAS adjunct by establishing a cost-effective and convenient communication line between patients and their surgical team.
Graphical abstract
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