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Article ; Online: Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes.

Ryan, Louise / Lawless, Colleen / Hughes, Graham M

2024 Volume 40, Issue 1

Abstract: Summary: Sensory receptor gene families have undergone extensive expansion and loss across vertebrate evolution, leading to significant variation in receptor counts between species. However, due to their species-specific nature, conventional reference- ... ...

Abstract	Summary: Sensory receptor gene families have undergone extensive expansion and loss across vertebrate evolution, leading to significant variation in receptor counts between species. However, due to their species-specific nature, conventional reference-based annotation tools often underestimate the true number of sensory receptors in a given species. While there has been an exponential increase in the taxonomic diversity of publicly available genome assemblies in recent years, only ∼30% of vertebrate species on the NCBI database are currently annotated. To overcome these limitations, we developed 'Sensommatic', an automated and accessible sensory receptor annotation pipeline. Sensommatic implements BLAST and AUGUSTUS to mine and predict sensory receptor genes from whole genome assemblies, adopting a one-to-many gene mapping approach. While designed for vertebrates, Sensommatic can be extended to run on non-vertebrate species by generating customized reference files, making it a scalable and generalizable tool. Availability and implementation: Source code and associated files are available at: https://github.com/GMHughes/Sensommatic.
MeSH term(s)	Animals ; Genome ; Chromosome Mapping ; Software ; Vertebrates/genetics ; Molecular Sequence Annotation
Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae040
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Zs.A 2374: Show issues

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Article ; Online: Maxillary mass in a 1-year-old feline.

Groff, Allison M / Welsh, Peter J / Lynch, Colleen M / Oliveira, Ryan / Fransson, Boel

Journal of the American Veterinary Medical Association

2024 Volume 262, Issue 5, Page(s) 708–711

Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	390811-2
ISSN	1943-569X ; 0003-1488
ISSN (online)	1943-569X
ISSN	0003-1488
DOI	10.2460/javma.24.01.0031
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Zs.A 423: Show issues

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Article ; Online: Vaccine Passports Done Equitably.

Tanner, Ryan / Flood, Colleen M

JAMA health forum

2021 Volume 2, Issue 4, Page(s) e210972

Language	English
Publishing date	2021-04-01
Publishing country	United States
Document type	Journal Article
ISSN	2689-0186
ISSN (online)	2689-0186
DOI	10.1001/jamahealthforum.2021.0972
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Article ; Online: Burn Surge Capacity: Recognizing the Catastrophe Phase in Crisis Standards of Care.

Kearns, Randy D / Bettencourt, Amanda P / Hickerson, William L / Palmieri, Tina L / Biddinger, Paul D / Ryan, Colleen M / Jeng, James C

Journal of burn care & research : official publication of the American Burn Association

2024

Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2224246-6
ISSN	1559-0488 ; 1559-047X
ISSN (online)	1559-0488
ISSN	1559-047X
DOI	10.1093/jbcr/irae010
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Zs.A 6223: Show issues

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Article ; Online: Risk factors for failure after rotational muscle flap coverage for prosthetic knee infections.

Kim, Billy I / Wixted, Colleen M / Schwartz, Andrew M / Jiranek, William A / Ryan, Sean P / Seyler, Thorsten M

Journal of orthopaedic surgery (Hong Kong)

2024 Volume 32, Issue 1, Page(s) 10225536241230349

Abstract: Introduction: Soft tissue defects are a devastating complication of prosthetic joint infections (PJI) after total knee arthroplasty (TKA). Rotational flaps are commonly utilized to address these defects with variable reports of success. This study aimed ...

Abstract	Introduction: Soft tissue defects are a devastating complication of prosthetic joint infections (PJI) after total knee arthroplasty (TKA). Rotational flaps are commonly utilized to address these defects with variable reports of success. This study aimed to identify predictors of poor outcomes in rotational muscle flap placement after prosthetic knee infections. The authors hypothesized that outcomes may vary based on infecting pathogen and treatment characteristics. Methods: 44 cases of rotational muscle flaps for prosthetic knee infection were retrospectively evaluated at a tertiary referral hospital from 2007 to 2020. Muscle flap types included 39 medial and four lateral gastrocnemius, and one anterior tibialis. Minimum follow-up was 1 year (median: 3.4 years). Primary outcome was flap-related complications. Secondary outcomes included recurrent infection requiring additional surgery, final joint outcomes, and mortality. Results: One-year complication-free flap survivorship was 83.9%, recurrent infection-free survivorship was 65.7%, and amputation-free survivorship was 79%. Multivariable cox regression revealed that rheumatoid arthritis diagnosis (HR: 3.4; Conclusion: Rotational muscle flaps for soft tissue coverage of the knee are often performed in limb salvage situations with poor survivorship from flap complications, reinfections, and amputation. When considering surgical options for limb salvage, patients should be counseled on these risks.
MeSH term(s)	Humans ; Retrospective Studies ; Methicillin-Resistant Staphylococcus aureus ; Treatment Outcome ; Knee Prosthesis/adverse effects ; Muscle, Skeletal/surgery ; Risk Factors ; Prosthesis-Related Infections/surgery ; Prosthesis-Related Infections/etiology
Language	English
Publishing date	2024-01-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1493368-8
ISSN	2309-4990 ; 1022-5536
ISSN (online)	2309-4990
ISSN	1022-5536
DOI	10.1177/10225536241230349
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Zs.A 5104: Show issues

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Article ; Online: Auditory masking in odobenid and otariid carnivoresa).

Jones, Ryan A / Sills, Jillian M / Synnott, Mitzi / Mulsow, Jason / Williams, Rob / Reichmuth, Colleen

The Journal of the Acoustical Society of America

2023 Volume 154, Issue 3, Page(s) 1746–1756

Abstract: As the only living species within the odobenid lineage of carnivores, walruses (Odobenus rosmarus) have no close relatives from which auditory information can be extrapolated. Sea lions and fur seals in the otariid lineage are the nearest evolutionary ... ...

Abstract	As the only living species within the odobenid lineage of carnivores, walruses (Odobenus rosmarus) have no close relatives from which auditory information can be extrapolated. Sea lions and fur seals in the otariid lineage are the nearest evolutionary outgroup. To advance understanding of odobenid and otariid hearing, we conducted behavioral testing with two walruses and one California sea lion (Zalophus californianus). Detection thresholds for airborne sounds were measured from 0.08 to at least 16 kHz in ambient noise conditions and then re-measured in the presence of octave-band white masking noise. Walruses were more sensitive than the sea lion at lower frequencies and less sensitive at higher frequencies. Critical ratios for the walruses ranged from 20 dB at 0.2 kHz to 32 dB at 10 kHz, while critical ratios for the sea lion ranged from 16 dB at 0.2 kHz to 35 dB at 32 kHz. The masking values for these species are comparable to one another and to those of terrestrial carnivores, increasing by about 3 dB per octave with increasing frequency. Despite apparent differences in hearing range and sensitivity, odobenids and otariids have a similar ability to hear signals in noisy conditions.
MeSH term(s)	Animals ; Sea Lions ; Walruses ; Hearing ; Biological Evolution ; Sound
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0020911
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Zs.B 591: Show issues

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Article ; Online: The Posterior Approach is Associated With Lower Total Encounter and 90-Day Costs When Compared to the Direct Anterior Approach.

Cochrane, Niall H / Wixted, Colleen M / Kim, Billy I / Holland, Christopher T / Ryan, Sean P / Bolognesi, Michael P / Wellman, Samuel S

The Journal of arthroplasty

2024

Abstract: Background: The clinical impact of the surgical approach in total hip arthroplasty (THA) has been widely reviewed. This study evaluated the total encounter and 90-day costs of THA for 2 surgical approaches (posterior [P] and direct anterior [DA]) in 1 ... ...

Abstract	Background: The clinical impact of the surgical approach in total hip arthroplasty (THA) has been widely reviewed. This study evaluated the total encounter and 90-day costs of THA for 2 surgical approaches (posterior [P] and direct anterior [DA]) in 1 tertiary health system. Methods: This is a retrospective review of 2,101 THAs (1,092 P and 1,009 DA) by 4 surgeons (2 with the highest volume of DA and P, respectively) from 2017 to 2022 at 1 academic center. Demographics, comorbidities, operative time, length of hospital stay, 90-day hospital returns, and complications were compared. The total encounter cost and 90-day postoperative cost were itemized. Multivariable regression analyses evaluated associations with increased cost at each time point. Results: The DA cohort had a higher median encounter cost ($8,348.66 versus 7,332.42, P < .01), resulting from higher intraoperative (P < .01) and radiology (P < .01) expenses. Regression analyses demonstrated the DA was independently associated with increased encounter costs (odds ratio 1.1; 95% confidence interval 1.1 to 1.1; P < .01). There was a higher incidence of 90-day emergency department visits in the DA cohort (16 versus 12%, P = .02), with a trend toward increased readmissions. There was no difference in 90-day reoperations. Median 90-day cost was higher in the DA cohort ($126.99 versus 0.00, P < .01), and regression analyses demonstrated the DA had an association with increased 90-day cost (odds ratio 2.2; 95% confidence interval 1.5 to 3.0; P < .01). Conclusions: Despite a younger patient population, the DA was independently associated with increased encounter and 90-day costs in a single academic hospital system. This study may underestimate the cost difference, as capital costs such as specialized tables were not analyzed.
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	632770-9
ISSN	1532-8406 ; 0883-5403
ISSN (online)	1532-8406
ISSN	0883-5403
DOI	10.1016/j.arth.2024.03.024
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Zs.A 2134: Show issues

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Article ; Online: Physical and psychosocial outcomes among burn-injured people with heterotopic ossification: A burn model system study.

Won, Paul / Pickering, Trevor A / Schneider, Jeffrey C / Kowalske, Karen / Ryan, Colleen M / Carrougher, Gretchen J / Stewart, Barclay T / Yenikomshian, Haig A

Burns : journal of the International Society for Burn Injuries

2024 Volume 50, Issue 4, Page(s) 957–965

Abstract: Introduction: Heterotopic ossification (HO), or ectopic bone formation in soft tissue, is a not so rare and poorly understood debilitating sequela of burn injury. Individuals developing HO following burn injuries to their hands often experience ... ...

Abstract	Introduction: Heterotopic ossification (HO), or ectopic bone formation in soft tissue, is a not so rare and poorly understood debilitating sequela of burn injury. Individuals developing HO following burn injuries to their hands often experience reductions in mobility, significant contractures, and joint pain. This study identifies demographic characteristics of individuals who develop HO and compares their physical and psychosocial outcomes to the general burn population. Methods: Participant demographics, injury characteristics, and PROMIS-29 scores across three time points (discharge, six- and 12- months after injury) were extracted from the Burn Model System National Longitudinal Database representing participants from 2015-2022. Mixed-effects linear regression models were used to compare PROMIS scores across all three longitudinal measurements. Models were adjusted for age, sex, race/ethnicity, HO status, and burn size. Results: Of the 861 participants with data concerning HO, 33 were diagnosed with HO (3.8% of participants). Most participants with HO were male (n = 24, 73%) and had an average age of 40 + /- 13 years. Participants with HO had significantly larger burn size (49 +/-23% Total Body Surface Area (TBSA)) than those without HO (16 +/-17%). Participants with HO reported significantly worse physical function, depression, pain interference and social integration scores than those without HO. After adjusting for covariables, participants with HO continued to report statistically significantly worse physical function than those without HO. Although physical functioning was consistently lower, the two populations did not differ significantly among psychosocial outcome measures. Conclusions: While HO can result in physical limitations, the translation to psychosocial impairments was not evident. Targeted treatment of HO with the goal of maximizing physical function should be a focus of their rehabilitation. Level of evidence: 2b TYPE OF STUDY: Symptom Prevalence Study.
MeSH term(s)	Humans ; Ossification, Heterotopic/psychology ; Ossification, Heterotopic/etiology ; Burns/psychology ; Burns/complications ; Male ; Female ; Adult ; Middle Aged ; Quality of Life ; Linear Models ; Longitudinal Studies
Language	English
Publishing date	2024-01-19
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	197308-3
ISSN	1879-1409 ; 0305-4179
ISSN (online)	1879-1409
ISSN	0305-4179
DOI	10.1016/j.burns.2024.01.017
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Article: Juvenile Probation Officer Perception of Contingency Management to Target Caregiver Engagement and Training Outcomes.

Ryan-Pettes, Stacy R / Morrison, Meghan / Randall, Jeff / Halliday, Colleen / Ledgerwood, David M / Cunningham, Phillippe B

Journal of offender rehabilitation

2023 Volume 62, Issue 5, Page(s) 315–335

Abstract: Few community-based substance use treatment programs are available or skilled in treating justice-involved youth, highlighting the need to equip juvenile probation officers with the skills to deliver evidence-based substance use treatment. Contingency ... ...

Abstract	Few community-based substance use treatment programs are available or skilled in treating justice-involved youth, highlighting the need to equip juvenile probation officers with the skills to deliver evidence-based substance use treatment. Contingency management (CM) is evidence-based for treating substance use and shows promise for juvenile probation officers' successful uptake (positive opinions and trainability). However, research has not examined whether probation officers' positive beliefs and trainability generalize to target behaviors beyond those displayed by youth, but that nevertheless affect youth outcomes. This study examined probation officers' perceptions of using CM to engage caregivers and assessed probation officers' CM knowledge and CM delivery after training in a protocol-specific CM program for caregivers of substance-using youth on probation. Results showed probation officers were ambivalent about CM for caregivers. Results also showed that age, training format and how competency is assessed may be essential to consider. Implications for the dissemination of CM and future research are discussed.
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1061172-1
ISSN	1050-9674
ISSN	1050-9674
DOI	10.1080/10509674.2023.2213692
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Article ; Online: Introducing APEXMOD - A QGIS plugin for developing coupled surface-subsurface hydrologic modeling framework of APEX, MODFLOW, and RT3D-Salt

Park, Seonggyu / Jeong, Jaehak / Motter, Elizabeth / Bailey, Ryan T. / Green, Colleen H.M.

Environmental Modelling and Software. 2023 July, v. 165 p.105723-

2023

Abstract: This article presents APEXMOD, an open-source QGIS plugin that helps add a MODFLOW grid to the APEX watershed model. The APEX model integrates MODFLOW, a physically based groundwater model and RT3D-Salt, a groundwater nutrient and salt transport model, ... ...

Abstract	This article presents APEXMOD, an open-source QGIS plugin that helps add a MODFLOW grid to the APEX watershed model. The APEX model integrates MODFLOW, a physically based groundwater model and RT3D-Salt, a groundwater nutrient and salt transport model, for basin-scale application as a coupled surface-subsurface hydrologic modeling system. APEXMOD is developed as a tool that enables the dynamic linkage between APEX, MODFLOW, and RT3D-Salt. APEXMOD is written in Python and integrates QGIS geoprocessors and spatial packages. The APEXMOD interface is constructed with three modules: (i) a pre-processor that prepares inputs for MODFLOW and RT3D-Salt and performs spatial linkage between APEX subareas and MODFLOW grid cells, (ii) a model configurator that controls simulation options and scenario setting, and (iii) a post-processor for visualizing and analyzing model outputs. A case study was conducted in the Animas River watershed to demonstrate the core capabilities of APEXMOD.
Keywords	case studies ; computer software ; groundwater ; hydrologic models ; rivers ; watersheds ; APEX ; MODFLOW ; RT3D-salt ; QGIS plugin ; Groundwater-surface water interactions
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ISSN	1364-8152
DOI	10.1016/j.envsoft.2023.105723
Database	NAL-Catalogue (AGRICOLA)

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