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Article ; Online: Global Expansion of Jeffrey's Insights: Jeffrey Modell Foundation's Genetic Sequencing Program for Primary Immunodeficiency.

Quinn, Jessica / Modell, Vicki / Johnson, Britt / Poll, Sarah / Aradhya, Swaroop / Orange, Jordan S / Modell, Fred

2022 Volume 13, Page(s) 906540

Abstract: ... of the diagnostic odyssey, but because of cost and barriers to access, it is regularly unobtainable. The Jeffrey ... in January 2019 for patients within the Jeffrey Modell Centers Network (JMCN) with an underlying PI, but no ... Modell Foundation (JMF) introduced "Jeffrey's Insights", a no-charge genetic sequencing pilot program ...

Abstract	Genetic disorders that impair the immune system, known as Primary Immunodeficiencies (PI), include over 450 single-gene inborn errors of immunity. Timely and appropriate diagnosis and treatment is vital to quality of life (QOL) and sometimes survival, as patients are susceptible to frequent, persistent, severe, and sometimes life-threatening infections or autoimmunity. Suspected PI patients that do not have a genetic diagnosis often endure a prolonged, onerous, inefficient, and expensive experience, known as a diagnostic odyssey. The resulting diagnostic delay prohibits proper disease management and treatment, causing unnecessary distress and diminished QOL. Next-generation sequencing (NGS) offers relief from the distress of the diagnostic odyssey, but because of cost and barriers to access, it is regularly unobtainable. The Jeffrey Modell Foundation (JMF) introduced "Jeffrey's Insights", a no-charge genetic sequencing pilot program, in January 2019 for patients within the Jeffrey Modell Centers Network (JMCN) with an underlying PI, but no genetic diagnosis. Building on the success of the pilot program, JMF expanded it globally to more than 400 Centers in the JMCN in early 2020. The most current version of Invitae's PI Panel available was used for this program. All participating clinicians were invited to complete a brief questionnaire assessing prior impediments to access and post-sequencing alterations in disease management and treatment. A total of 1,398 patients were tested, with 20.3% receiving a molecular diagnosis and many more receiving helpful diagnostic leads. Results obtained from genetic sequencing led to an alteration of clinical diagnosis, disease management, treatment, and genetic counseling in 39%, 38%, 35%, and 53% of patients, respectively. The global expansion of this program further underscores the crucial need for NGS for PI, along with its efficiency and potential cost savings. The results of this program to date further define rationale for the availability of comprehensive diagnostic NGS for patients with PI when requisitioned by an expert immunologist.
MeSH term(s)	Delayed Diagnosis ; High-Throughput Nucleotide Sequencing ; Humans ; Mutation ; Quality of Life
Language	English
Publishing date	2022-06-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.906540
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Jeffrey's insights: Jeffrey Modell Foundation's global genetic sequencing pilot program to identify specific primary immunodeficiency defects to optimize disease management and treatment.

Quinn, Jessica / Modell, Vicki / Holle, Jennifer / Truty, Rebecca / Aradhya, Swaroop / Johnson, Britt / Orange, Jordan / Modell, Fred

Immunologic research

2020 Volume 68, Issue 3, Page(s) 126–134

Abstract: ... often unavailable, mainly due to cost and inaccessibility. In January 2019, the Jeffrey Modell ... Foundation (JMF) launched a free genetic sequencing pilot program for Jeffrey Modell Centers Network (JMCN ...

Abstract	Primary immunodeficiencies (PI) are genetic defects of the immune system that result in chronic and often life-threatening infections and/or life-threatening autoimmunity if not diagnosed and treated. Patients with a suspected PI, but without a genetic diagnosis, commonly undergo a diagnostic odyssey that is costly, time-consuming, and arduous. This delay in diagnosis prevents appropriate disease management and treatment, contributing to prolonged suffering and decreased quality of life. Although next generation sequencing (NGS) can provide these patients with relief from such a diagnostic odyssey, it is often unavailable, mainly due to cost and inaccessibility. In January 2019, the Jeffrey Modell Foundation (JMF) launched a free genetic sequencing pilot program for Jeffrey Modell Centers Network (JMCN) patients clinically diagnosed with an underlying PI. A total of 21 sites within the JMCN were invited to participate. JMF collaborated with Invitae, and testing was comprised of Invitae's Primary Immunodeficiency Panel, which currently includes 207 genes. A questionnaire was disseminated to each participating physician to evaluate barriers to access to genetic sequencing and changes in disease management and treatment after testing. One hundred fifty-eight patients and 29 family members were tested in this pilot study. Twenty-one percent of patients with a suspected monogenic disorder received a molecular diagnosis, and others received potentially useful diagnostic leads. Based on the results of genetic sequencing, clinical diagnosis was altered in 45% of patients, disease management was altered in 40%, treatment was altered in 36%, and genetic counseling was altered in 62%. The results of this pilot program demonstrate the utility, cost-efficiency, and critical importance of NGS for PI and make the case for broad scale sequence-based diagnostics for PI patients when requested by expert immunologists.
MeSH term(s)	Adolescent ; Child ; Child, Preschool ; DNA Mutational Analysis/methods ; Female ; Foundations/economics ; Foundations/organization & administration ; Genetic Testing/economics ; Genetic Testing/methods ; Genetic Variation ; Health Services Accessibility/economics ; Health Services Accessibility/organization & administration ; High-Throughput Nucleotide Sequencing/economics ; Humans ; Immunologic Deficiency Syndromes/diagnosis ; Immunologic Deficiency Syndromes/genetics ; Male ; Pilot Projects ; Quality of Life ; Severity of Illness Index ; Young Adult
Language	English
Publishing date	2020-05-02
Publishing country	United States
Document type	Journal Article ; Observational Study
ZDB-ID	632857-x
ISSN	1559-0755 ; 0257-277X
ISSN (online)	1559-0755
ISSN	0257-277X
DOI	10.1007/s12026-020-09131-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Bark Beetle Demography in a Jeffrey Pine Stand as Influenced by Mechanized Thinning and Prescribed Fire

Walker, Roger F / Swim, Shannon L / Johnson, Dale W / Miller, Watkins W / Fecko, Robert M

Journal of sustainable forestry. 2014 Oct. 3, v. 33, no. 7

2014

Abstract: ... by underburning were evaluated for their effects on bark beetle prevalence in pure, uneven-aged Jeffrey pine ... component, the Jeffrey pine beetle (Dendroctonus jeffreyi Hopkins) generally preferred larger trees ... on white fir far exceeded that on Jeffrey pine, and the greatest influence on the fir engraver ...

Abstract	Forest thinnings implemented with cut-to-length and whole-tree harvesting systems followed by underburning were evaluated for their effects on bark beetle prevalence in pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) interspersed with isolated California white fir (Abies concolor var. lowiana [Gord.] Lemm.). Based on pitch tube counts in a stand with a moderate bark beetle population in its pine component, the Jeffrey pine beetle (Dendroctonus jeffreyi Hopkins) generally preferred larger trees before treatment implementation, but after exhibiting mixed pretreatment tendencies concerning stand density demonstrated a posttreatment proclivity toward higher density. Cut-to-length thinning followed by underburning increased the pine beetle population while whole-tree thinning unaccompanied by burning reduced it. Tree mortality was induced by the bark beetle infestation but was not its sole cause. Pitch tube abundance on white fir far exceeded that on Jeffrey pine, and the greatest influence on the fir engraver (Scolytus ventralis LeConte) population was the prevalence of its host tree. The responses presented herein to these thinning and burning practices, which are being increasingly utilized in forest restoration efforts in the western USA, provide natural resource managers insight into potential forest health outcomes when implemented in Jeffrey pine and similar dry site forest types.
Keywords	Abies concolor ; Dendroctonus jeffreyi ; Pinus jeffreyi ; Scolytus ventralis ; bark beetles ; demography ; forest health ; forest restoration ; forest types ; managers ; mechanization ; prescribed burning ; stand density ; sustainable forestry ; tree mortality ; trees ; whole tree harvesting ; California
Language	English
Dates of publication	2014-1003
Size	p. 627-676.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2014.925401
Database	NAL-Catalogue (AGRICOLA)

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Article: Influences of Thinning and Underburning Restoration Practices on Red Turpentine Beetle Demography in Jeffrey Pine

Walker, Roger F / Swim, Shannon L / Fecko, Robert M / Johnson, Dale W / Miller, Watkins W

Journal of sustainable forestry. 2014 Oct. 3, v. 33, no. 7

2014

Abstract: ... LeConte) colonization in pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.). Based on pitch ... over the intermediate term when implemented in Jeffrey pine and similar dry site forest types. ...

Abstract	Forest thinnings implemented with cut-to-length and whole-tree harvesting systems followed by prescribed underburning were evaluated for their effects on red turpentine beetle (Dendroctonus valens LeConte) colonization in pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.). Based on pitch tube abundance expressed as bole surface area-based counts, this beetle was significantly more prevalent where thinnings were implemented regardless of harvesting approach than in the unthinned treatment, but the population increases were confined to the burned stand portions. Substantial evidence indicated that fire-induced crown and bole damage culminating in compromised defense mechanisms elevated turpentine beetle colonization, and some evidence suggested a proclivity of this beetle to attack stems exhibiting general characteristics of low vigor, specifically smaller trees with weak crowns. Tree mortality was likely induced by the turpentine beetle infestation but was probably not its sole cause. The responses presented herein to these thinning and burning practices, which are being increasingly relied upon in forest restoration efforts in the western USA, provide natural resource managers insight into potentially compromised forest health outcomes over the intermediate term when implemented in Jeffrey pine and similar dry site forest types.
Keywords	Dendroctonus valens ; Pinus jeffreyi ; burning ; defense mechanisms ; demography ; forest health ; forest restoration ; forest types ; harvesting ; managers ; population growth ; stems ; sustainable forestry ; tree mortality ; tree trunk ; trees ; turpentine ; vigor ; whole tree harvesting ; Western United States
Language	English
Dates of publication	2014-1003
Size	p. 677-727.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2014.925403
Database	NAL-Catalogue (AGRICOLA)

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Article: Evaluation of Mechanized Thinning and Prescribed Fire Effects on Long-Term Fuels Accumulations in Uneven-Aged Jeffrey Pine

Swim, Shannon L / Walker, Roger F / Johnson, Dale W / Fecko, Robert M / Miller, Watkins W

Journal of sustainable forestry. 2014 Nov. 17, v. 33, no. 8

2014

Abstract: ... aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) accompanied by isolated California white fir ...

Abstract	Forest thinnings implemented through cut-to-length and whole-tree harvesting followed by underburning were evaluated for their effects on long-term downed and dead fuels accumulations in pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) accompanied by isolated California white fir (Abies concolor var. lowiana [Gord.] Lemm.). Based on an initial inventory consisting of dry weight and fuel bed depth measurements conducted posttreatment, accumulations in the cut-to-length treatment were elevated according to most measures. Burned stand portions exhibited smaller quantities of fuels initially in individual timelag categories and in total as well as reduced fuel bed depths compared to their unburned counterparts except for the 1,000-hr fuels in the whole-tree treatment where postburn mortality of small stems nullified this effect. A linkage between initial mortality resulting from prescribed fire and final 1,000-hr fuels, as measured 8 yr later, was established but was probably attributable to combined thinning and burning effects. Over the course of the study, either greater accruals or diminished reductions in loading were apparent within burned stand portions compared to unburned portions, most notably in the whole-tree treatment. Results presented here provide insight into potentially compromised fuels reduction outcomes when implemented in uneven-aged stands on dry forest sites.
Keywords	Abies concolor ; Pinus jeffreyi ; forests ; fuels ; inventories ; long term effects ; mechanization ; mortality ; prescribed burning ; stems ; sustainable forestry ; uneven-aged stands ; whole tree harvesting ; California
Language	English
Dates of publication	2014-1117
Size	p. 827-859.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2014.966919
Database	NAL-Catalogue (AGRICOLA)

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Article: Long-Term Growth Responses of a Jeffrey Pine Stand to Mechanized Thinning and Prescribed Fire

Swim, Shannon L / Walker, Roger F / Johnson, Dale W / Fecko, Robert M / Miller, Watkins W

Journal of sustainable forestry. 2013 Nov. 17, v. 32, no. 8

2013

Abstract: ... uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) accompanied by isolated California white fir ... when implemented in Jeffrey pine and similar dry site forest types. ...

Abstract	Forest thinnings implemented with cut-to-length and whole-tree harvesting systems followed by underburning were evaluated for their effects on individual tree and stand level growth responses in pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) accompanied by isolated California white fir (Abies concolor var. lowiana [Gord.] Lemm.). Based on both dimension and volume measures, trees of the unburned whole-tree treatment combination exhibited the greatest individual growth responses. At the stand level, a diminished volume growth response in the whole-tree treatment was especially pronounced in the burned portion, mostly attributable to exaggerated stocking losses, while a superior response in the unburned cut-to-length combination likely reflected not only the absence of detrimental fire impacts but also benefits of on-site slash retention. For stand level biomass, diminished growth in the whole-tree treatment was again evident, with that in the burned portion again most pronounced, while biomass accrual in the unburned cut-to-length treatment combination was generally comparable to that in the unthinned control. Increasingly utilized in forest restoration efforts in the western USA, the responses presented herein to these thinning and burning practices provide natural resource managers insight into potential compromised outcomes when implemented in Jeffrey pine and similar dry site forest types.
Keywords	Abies concolor ; Pinus jeffreyi ; biomass ; forest restoration ; forest types ; harvesting ; mechanization ; prescribed burning ; slash ; trees ; whole tree harvesting ; United States
Language	English
Dates of publication	2013-1117
Size	p. 745-782.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2013.791232
Database	NAL-Catalogue (AGRICOLA)

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Article: Influences of mechanized thinning and prescribed underburning on radial growth of Jeffrey pine

Fecko, R.M / Walker, R.F / Frederick, W.B / Johnson, D.W / Miller, W.W

Journal of sustainable forestry. 2008, v. 26, no. 1

2008

Keywords	Pinus jeffreyi ; tree growth ; forest thinning ; prescribed burning ; growth rings ; stand density ; stand management ; forest yields ; dry environmental conditions ; forest trees ; tree and stand measurements ; latewood ; earlywood
Language	English
Size	p. 19-60.
Document type	Article
ZDB-ID	1160736-1
ISSN	1054-9811
ISSN	1054-9811
Database	NAL-Catalogue (AGRICOLA)

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Article: Influences of Mechanized Thinning and Prescribed Fire on Natural Regeneration in an Uneven-Aged Jeffrey Pine Stand

Salverson, Wade G / Walker, Roger F / Fecko, Robert M / Frederick, Wesley B / Miller, Watkins W / Johnson, Dale W

Journal of sustainable forestry. 2011 Nov. 1, v. 30, no. 7

2011

Abstract: ... evaluated for their effects on seedling and sapling demography in a pure, uneven-aged Jeffrey pine ... with thinning was followed by a recovery largely confined to Jeffrey pine in the whole-tree treatment ... for establishment of Jeffrey pine than white fir seedlings, and the largest increase in seedling counts between ...

Abstract	Thinnings using cut-to-length or whole-tree harvesting systems followed by underburning were evaluated for their effects on seedling and sapling demography in a pure, uneven-aged Jeffrey pine (Pinus jeffreyi Grev. & Balf.) stand containing a minor component of California white fir (Abies concolor var. lowiana [Gord.] Lemm.). Depression of seedling counts due to forest floor disturbance associated with thinning was followed by a recovery largely confined to Jeffrey pine in the whole-tree treatment where final seedling counts exceeded those found initially. The postburn substrate was more favorable for establishment of Jeffrey pine than white fir seedlings, and the largest increase in seedling counts between the initial and final inventories occurred in the burned portion of the whole-tree treatment. Live sapling losses from thinning were greatest in the cut-to-length treatment, while underburning induced complete sapling mortality. Absent treatment, several stand and site variables influenced seedling and sapling abundance, prominent among them a propensity for mahala mat (Ceanothus prostratus Benth.) to elevate counts of white fir within both size classes. These results provide land managers insight into the impacts of six combinations of thinning and burning treatment on natural regeneration in eastern Sierra Nevada Jeffrey pine and similar dry site forest types.
Keywords	Abies concolor ; Ceanothus ; Pinus jeffreyi ; demography ; forest litter ; forest types ; harvesting ; managers ; mechanization ; mortality ; natural regeneration ; prescribed burning ; seedlings ; California ; Sierra Nevada (California)
Language	English
Dates of publication	2011-1101
Size	p. 654-676.
Publishing place	Taylor & Francis Group
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2011.567937
Database	NAL-Catalogue (AGRICOLA)

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Article: Influences of Mechanized Thinning and Prescribed Fire on Understory Vegetation in an Uneven-Aged Jeffrey Pine Stand

Salverson, Wade G / Walker, Roger F / Fecko, Robert M / Frederick, Wesley B / Johnson, Dale W / Miller, Watkins W

Journal of sustainable forestry. 2011 Dec. 1, v. 30, no. 8

2011

Abstract: ... were assessed for their effects on shrub, forb, and grass understory species in a second-growth Jeffrey ...

Abstract	Thinnings using cut-to-length and whole-tree harvesting systems followed by prescribed underburning were assessed for their effects on shrub, forb, and grass understory species in a second-growth Jeffrey pine (Pinus jeffreyi Grev. & Balf.) stand. Prior to treatment installation, a mixed shrub-dominated understory featuring antelope bitterbrush (Purshia tridentata [Pursh] DC.) with mules ears (Wyethia mollis A. Gray) as the only forb and Sandberg bluegrass (Poa secunda J. Presl) the most prominent among sparse grasses was inventoried such that both percent cover and dry weight by species were revealed. Five growing seasons after thinning and four after underburning, this inventory was repeated. By either abundance measure, bitterbrush was reduced by approximately two-thirds in the cut-to-length treatment and by one-half in the whole-tree treatment in comparison to that in the unthinned control at the final inventory. For the cut-to-length treatment, a similar reduction in mules ears was noted, but that in the whole-tree treatment was somewhat less for this species. Bluegrass was reduced by approximately one-half in the former treatment and by threefourths in the latter. Prescription fire reduced bitterbrush to less than one-tenth and mules ears to approximately one-half of that in the unburned treatment, but bluegrass prevalence was more than 10× greater in the burned than in the unburned treatment. Among an array of regression models used to evaluate selected variables for their predictive capacity regarding understory plants, abundance of each species noted above among others was negatively correlated with overstory density across treatments.
Keywords	Pinus jeffreyi ; Poa secunda ; Purshia tridentata ; Wyethia ; correlation ; forbs ; grasses ; growing season ; harvesting ; mechanization ; overstory ; prescribed burning ; regression analysis ; second growth ; shrubs ; understory ; vegetation
Language	English
Dates of publication	2011-1201
Size	p. 823-849.
Publishing place	Taylor & Francis Group
Document type	Article
ZDB-ID	2094282-5
ISSN	1540-756X ; 1054-9811
ISSN (online)	1540-756X
ISSN	1054-9811
DOI	10.1080/10549811.2011.577401
Database	NAL-Catalogue (AGRICOLA)

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Article: Variation in morphological and biochemical O3 injury attributes of mature Jeffrey pine within canopies and between microsites.

Grulke, N E / Johnson, R / Monschein, S / Nikolova, P / Tausz, M

Tree physiology

2003 Volume 23, Issue 13, Page(s) 923–929

Abstract: ... injury were assessed in the lower, mid- and upper canopy of Jeffrey pine (Pinus jeffreyi Grev. & Balf ... influenced the expression of O3 injury in Jeffrey pine. ...

Abstract	Crown morphology and leaf tissue chemical and biochemical attributes associated with ozone (O3) injury were assessed in the lower, mid- and upper canopy of Jeffrey pine (Pinus jeffreyi Grev. & Balf.) growing in mesic and xeric microsites in Sequoia National Park, California. Microsites were designated mesic or xeric based on topography and bole growth in response to years of above-average precipitation. In mesic microsites, canopy response to O3 was characterized by thinner branches, earlier needle fall, less chlorotic leaf mottling, and lower foliar antioxidant capacity, especially of the aqueous fraction. In xeric microsites, canopy response to O3 was characterized by higher chlorotic leaf mottling, shorter needles, lower needle chlorophyll concentration, and greater foliar antioxidant capacity. Increased leaf chlorotic mottle in xeric microsites was related to drought stress and increased concurrent internal production of highly reactive oxygen species, and not necessarily to stomatal O3 uptake. Within-canopy position also influenced the expression of O3 injury in Jeffrey pine.
MeSH term(s)	Ozone/adverse effects ; Pinus/physiology ; Plant Leaves/anatomy & histology ; Plant Leaves/physiology ; Trees/physiology
Chemical Substances	Ozone (66H7ZZK23N)
Language	English
Publishing date	2003-07-11
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	743341-4
ISSN	1758-4469 ; 0829-318X
ISSN (online)	1758-4469
ISSN	0829-318X
DOI	10.1093/treephys/23.13.923
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