bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon Accumulation and Partitioning Above and Belowground under Coppiced and Replanted Eucalypt Plantations
Authors: Pegoraro Rodinei F , Silva Ivo R , Souza Ivan F , Novais Roberto F , Barros Nairam F , Fonseca Sebastião 
Published: December 2021

Abstract
The extent to which the C sink strength of eucalypt plantations can be affected by coppicing or replanting remains unclear. To address this issue, we evaluated variations in C stocks under coppiced or replanted eucalypt stands formed by clones or seedlings. For each field assessment (0 [T0], 2.5, 3.5, 4.5, 5.5 and 7.0 years [at harvest]), tree biomass, litterfall, and soil C stocks (0–120 cm depth) were determined. At harvest, debarked stemwood productivity was similar under coppice or replanting, about 50.0 Mg C ha–1. Generally, coppiced stands favored subsoil C storage (40–100 cm), whereas replanted stands favored soil C accrual in topsoil (0–20 cm), depending on the genetic material. Relative to T0, soil C increased about 2.14, 1.91, and 1.84 Mg C ha–1 yr–1 under coppice, replanting with seedlings and clones, respectively. Coarse root biomass under these stands were about 17.3, 13.4, and 9.5 Mg C ha–1, respectively, equivalent to 50% of total harvest residues. Hence, inputs from coarse roots could represent a large contribution to soil C over multiple rotations under coppiced or replanted stands. Otherwise, short-term C losses can be high where stumps and coarse roots are harvested, especially following successive coppice cycles.
Study Implications: Our findings have important implications for forest managers growing eucalypt plantations aiming to maximize C accumulation. Both coppiced and replanted stands can fix up to 50 Mg C ha−1 only in debarked stemwood over 7 years, with a comparatively higher C storage in coarse roots under coppice. Despite the increasing demand for forest residues in bioenergy production, harvesting stumps and coarse roots should be avoided, especially upon replanting eucalypt stands after successive coppice cycles.
Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature
Authors: Lange Matthias , Alako Blaise T F , Cochrane Guy , Ghaffar Mehmood , Mascher Martin , Habekost Pia-Katharina , Hillebrand Upneet , Scholz Uwe , Schorch Florian , Freitag Jens , Scholz Amber Hartman 
Published: December 2021

Abstract

Background
Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.

Findings
We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.

Conclusions
The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.
Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season
Authors: Harris Zachary N , Awale Mani , Bhakta Niyati , Chitwood Daniel H , Fennell Anne , Frawley Emma , Klein Laura L , Kovacs Laszlo G , Kwasniewski Misha , Londo Jason P , Ma Qin , Migicovsky Zoë , Swift Joel F , Miller Allison J 
Published: December 2021

Abstract

Background
Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown.

Results
Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season.

Conclusions
These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.
Modeling Culinary Value
Authors: Engisch Patrik 
Published: December 2021

AbstractCulinary products have culinary value. That is, they have value qua culinary products. However, what is the nature of culinary value and what elements determine it? In the light of the central and universal role that culinary products play in our lives, offering a philosophical analysis of culinary value is a matter of interest. This article attempts to do just this. It develops three different possible models of culinary value, two rather restricted ones and a third more encompassing one, rejects the first two, and defends the third one.
Effects of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in gilts
Authors: Knox Robert V , Arend Lidia S , Buerkley Ashley L , Patterson Jennifer L , Foxcroft George R 
Published: December 2021

AbstractThe present study was part of a larger experiment that evaluated litter of origin effects on gilt production. The objectives of this study were to determine the effect of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in a commercial farm environment. The experiment was performed in three replicates. Prepubertal gilts were assigned by pen (13/pen) to receive 15 min of daily Fenceline (FBE, n = 153) or Physical (PBE, n = 154) Boar Exposure (BE) for 3 weeks starting at 184 d of age in a purpose-designed Boar Exposure Area (BEAR). At the start of week 3, prepubertal gilts were randomly assigned to receive PG600 or none (Control). From weeks 4 to 6, estrus was checked using only FBE. During weeks 1 to 3, measures of reproductive status were obtained weekly or until expression of estrus. Upon detection of first estrus, gilts were relocated into stalls and inseminated at second estrus. PBE reduced age (P = 0.001) and days to puberty (P = 0.002), increased the proportion of gilts in estrus (P = 0.04) in week 1 (38.3 vs. 27.5%), and tended (P = 0.08) to improve estrus in week 2 (37.6 vs. 26.1%) compared to FBE, respectively. In week 3, more prepubertal gilts receiving PBE-PG600 exhibited estrus (P = 0.04; 81.8%) compared to PBE-Control (40.3%), FBE-PG600 (56.4%), and FBE-Control (47.8%). Overall, expression of estrus through week 6 tended (P = 0.08) to be greater for PBE than FBE (91.5 vs. 85.0%). PBE increased (P ≤ 0.05) or tended to increase (P &gt; 0.05 and ≤0.10) service and farrowing rates in parities 1 through 4, but within parity, there were no effects (P &gt; 0.10) on pig production or wean to service interval. Analyses also indicated that weeks from start of boar exposure to puberty, litter of origin traits, and follicle measures at puberty were related to the subsequent fertility. The results of this study confirm the advantages of using increased intensity of boar exposure, combined with PG600 treatment, for effective induction of pubertal estrus in a commercial setting.
Effect of bupivacaine liposome suspension administered as a local anesthetic block on indicators of pain and distress during and after surgical castration in dairy calves
Authors: Martin Miriam S , Kleinhenz Michael D , Viscardi Abbie V , Curtis Andrew K , Johnson Blaine T , Montgomery Shawnee R , Lou Maria E , Coetzee Johann F 
Published: December 2021

Abstract
Castration is a routine procedure performed on beef and dairy operations in the United States. All methods of castration cause behavioral, physiologic, and neuroendocrine changes associated with pain. The American Veterinary Medical Association and the American Association of Bovine Practitioners recommend that anesthesia and analgesia be administered during castration. The objective of this study was to evaluate the effectiveness of bupivacaine liposome suspension, a novel, long-acting, local anesthetic formulation administered as a nerve block at castration. The authors chose to investigate this novel formulation as an alternative to the current industry standards using lidocaine nerve blocks alone or in combination with meloxicam. Thirty male Holstein calves, 16 to 20 wk of age, were enrolled and randomly assigned to one of the four treatment groups prior to surgical castration: 1) bupivacaine liposome suspension block + oral placebo (BUP), 2) lidocaine block + oral placebo (LID), 3) lidocaine block + oral meloxicam (1 mg/kg) (LID + MEL), and 4) saline block + oral placebo (CON). Biomarkers were collected at −24 h and from 0 to 120 h post-castration and included infrared thermography, pressure mat gait analysis, chute defense and behavior scoring (pain and activity), and blood sampling for serum cortisol and prostaglandin E2 metabolites (PGEMs). Responses were analyzed using repeated measures, with calf nested in treatment as a random effect, and treatment, time, and their interaction designated as fixed effects. The results from pressure mat gait analysis show that the CON had a shorter front limb stance time from baseline (−8.73%; 95% confidence interval [CI]: −24.84% to 7.37%) compared with BUP and LID + MEL (&gt;5.70%; 95% CI: −22.91% to 23.79%) (P &lt; 0.03). The CON tended to have an increase in front limb force from baseline (6.31%; 95% CI: −1.79% to 14.41%) compared with BUP, LID, and LID + MEL (&lt;−5.06%; 95% CI: −14.22% to 0.95%) (P &lt; 0.04). The CON displayed higher counts of hunched standing (2.00; 95% CI: 1.68 to 2.32) compared with LID + MEL (1.43; 95% CI: 1.13 to 1.72) (P = 0.05). The CON had higher cortisol concentrations at 24 h (7.70 ng/mL; 95% CI: 1.52 to 13.87 ng/mL) relative to BUP (3.11 ng/mL; 95% CI: −2.56 to 8.79 ng/mL) (P = 0.002). At 4 and 24 h, LID + MEL had lower PGEM concentrations from baseline (−32.42% and −47.84%; 95% CI: −78.45% to −1.80%) compared with CON (27.86% and 47.63%; 95% CI: 7.49% to 82.98%) (P &lt; 0.02). The administration of bupivacaine liposome suspension as a local anesthetic block at the time of castration was as effective at controlling pain as a multimodal approach of lidocaine and meloxicam.
Ever-expanding NGLY1 biology
Authors: Suzuki Tadashi , Yoshida Yukiko 
Published: December 2021

Abstract
The cytosolic peptide:N-glycanase (PNGase; NGLY1 in humans) is a deglycosylating enzyme that is widely conserved in eukaryotes. This enzyme is involved in the degradation of misfolded N-glycoproteins that are destined for proteasomal degradation in the cytosol, a process that is called endoplasmic reticulum-associated degradation. Although the physiological significance of NGLY1 remained unknown until recently, the discovery of NGLY1 deficiency, a human genetic disorder bearing mutations in the NGLY1 gene, has led to explosive research progress regarding the functional characterization of this enzyme. For example, it is now known that NGLY1 can also act as an ‘editing enzyme’ to convert N-glycosylated asparagine residues to aspartate residues, thus introducing negative charges into a core peptide and modulating the function of the target molecule. Diverse biological processes have also been found to be affected by compromised NGLY1 activity. In this special issue, recent research progress on the functional characterization of NGLY1 and its orthologues in worm/fly/rodents, assay methods/biomarkers useful for the development of therapeutics and the comprehensive transcriptome/proteome of NGLY1-KO cells as well as patient-derived cells are discussed.
Factors Influencing the Efficacy of Novel Attract-and-Kill (ACTTRA SWD) Formulations Against Drosophila suzukii
Authors: Babu Arun , Rodriguez-Saona Cesar , Sial Ashfaq A 
Published: December 2021

Abstract
In the continental United States, the invasive spotted-wing drosophila (SWD), Drosophila suzukii Matsumura, has become a primary pest of multiple stone and soft-skinned fruits. A new innovative adjuvant formulation, ACTTRA SWD, mixed with a suitable insecticide, constitutes a novel attract-and-kill tactic to manage D. suzukii in fruit crops. We hypothesized that background odors present in crop fields, particularly odors from host fruits, negatively affect the effectiveness of this attract-and-kill formulation, as odors from these sources can compete for insect attraction. Additionally, we evaluated the influence of adult D. suzukii sex and physiological status (age and mating status), and fruit ripeness on its response to the ACTTRA SWD formulation. For this, we used two-choice bioassays to test the response of adult D. suzukii to three ACTTRA SWD formulations (named OR1, TD, and HOOK SWD) in the presence and absence of host fruits (blueberries, raspberries, blackberries, and strawberries). Odors from raspberries were significantly more attractive than those from the TD formulation mixed with spinosad (Entrust). For the HOOK SWD formulation and OR1+Entrust formulation, odors from all the fruit types tested were significantly more attractive than the adjuvants. Compared with females, male D. suzukii were more attracted to the TD formulation over the blueberry fruits. Additionally, age and female mating status but not fruit ripeness influenced D. suzukii attraction to both OR1 and TD formulations. The results from this study indicate that D. suzukii physiological status and host fruit availability impact the efficacy of new attract-and-kill adjuvants such as ACTTRA SWD.
Evaluation of Pharmacogenomics Testing of Cytochrome P450 Enzymes in the Military Health System From 2015 to 2020
Authors: Por Elaine D , Selig Daniel J , Chin Geoffrey C , DeLuca Jesse P , Oliver Thomas G , Livezey Jeffrey R 
Published: December 2021

ABSTRACT
Pharmacogenomics (PGx) plays a fundamental role in personalized medicine, providing an evidence-based treatment approach centered on the relationship between genomic variations and their effect on drug metabolism. Cytochrome P450 (CYP450) enzymes are responsible for the metabolism of most clinically prescribed drugs and a major source of variability in drug pharmacokinetics and pharmacodynamics. To assess the prevalence of PGx testing within the Military Health System (MHS), testing of specific CYP450 enzymes was evaluated. Data were retrospectively obtained from the Military Health System Management Analysis and Reporting Tool (M2) database. Patient demographics were identified for each test, along with TRICARE status, military treatment facility, clinic, and National Provider Identifier. A total of 929 patients received 1,833 PGx tests, predominantly composed of active duty/guard service members (N = 460; 49.5%), with highest testing rates in the army (51.5%). An even distribution in testing was observed among gender, with the highest rates in Caucasians (41.7%). Of the CYP enzymes assessed, CYP2C19 and CYP2D6 accounted for 87.8% of all PGx CYP testing. The majority of patients were tested in psychiatry clinics (N = 496; 53.4%) and primary care clinics (N = 233; 25.1%), accounting for 56.4% and 24.8% of all tests, respectively. Testing was found to be provider driven, suggesting a lack of a standardized approach to PGx and its application in patient care within the MHS. We initially recommend targeted education and revising testing labels to be more uniform and informative. Long-term recommendations include establishing pharmacy-driven protocols and point-of-care PGx testing to optimize patient outcomes.
Applying Pharmacogenomic Guidelines to Combat Medical Care
Authors: DeLuca Jesse , Oliver Thomas , Hulsopple Chad , Selig Daniel , Por Elaine , Turner Clesson , Hellwig Lydia , Livezey Jeffrey 
Published: December 2021

ABSTRACTPharmacogenomics is a pillar of personalized medicine that has the potential to deliver optimized treatment in many medical settings. Military medicine in the deployed setting is unique and therefore warrants separate assessment pertaining to its potential capabilities and impact. Pharmacogenomics for United States Active Duty Service Members medical care in the deployed setting has not, to our knowledge, been previously reviewed. We present potential applications of pharmacogenomics to forward medical care through two comprehensive references for deployed medical care, the Tactical Combat Casualty Care Guidelines (TCCC) and Emergency War Surgery (EWS) fifth edition. All drugs within the deployment manuals, TCCC guidelines and EWS book, were identified and the list was cross-referenced to the Clinical Pharmacogenetics Implementation Consortium guidelines and genes–drugs interactions list as well as the Food and Drug Administration Table of Pharmacogenomics Biomarkers in Drug Labeling. Ten pharmacologic categories were identified, consisting of 15 drugs, along with the classes, aminogylcosides, beta-blockers, and volatile anesthetics. Drugs and pharmacogenomics liabilities were tabulated. Eight specific drugs or classes are expounded upon given the belief of the authors of their potential for impacting future treatment on the battlefield in the setting of prolonged field care. This review outlines several genes with liabilities in the prolonged field care setting and areas that may produce improved care with further study.
Prescription Patterns and Relationship to Pharmacogenomics Testing in the Military Health System
Authors: Selig Daniel J , Livezey Jeffrey R , Chin Geoffrey C , DeLuca Jesse P , Guillory II Walter O , Kress Adrian T , Oliver Thomas O , Por Elaine D 
Published: December 2021

ABSTRACT

Introduction
Clinical utilization of pharmacogenomics (PGx) testing is highly institutionally dependent, and little information is known about provider practices of PGx testing in the Military Health System (MHS). In this study, we aimed to characterize Clinical Pharmacogenetics Implementation Consortium (CPIC) actionable prescription (Rx) patterns and their temporal relationship with PGx testing in the MHS.

Methods
Using data from the Military Health System Management Analysis and Reporting Tool (M2) database, this retrospective cohort study included all patients receiving at least one PGx test and at least one CPIC actionable Rx from January 2015 to August 2020 (845 patients, 1,471 PGx, 7,725 index CPIC actionable Rxs). Rx patterns and temporal relationships with PGx testing were characterized via descriptive statistics. Binomial regression was used to determine which patient and provider characteristics were associated with a patient receiving a PGx test within 30 days of an index Rx.

Results
Patients had a median of 9 index CPIC actionable Rx’s (range 1–26). Pain medications were most commonly prescribed (N = 794, 94% patients with at least 1 Rx). However, pain medication had the lowest Rx–PGx match rate (40%) compared to an average of 62% Rx–PGx match rate for all CPIC drugs. Antidepressants were also commonly prescribed (N = 668, 79.1% patients with at least 1 Rx), and antidepressants had the highest Rx–PGx match rate of 86.7%. A minority of providers (20%, N = 249) ordered the majority of PGx tests (86.1%, N = 1,266) and only 8.3% of PGx tests (N = 398) matched to a CPIC actionable drug within 30 days of the test (defined by Rxs ordered within 30 days before or after the PGx test). However, approximately 39.8% of patients (N = 317) had at least one drug match to a PGx test within 30 days. The largest predictor of whether a patient received a PGx test within 30 days of any index Rx was whether or not a specific psychiatry provider ordered the PGx test (odds ratio; OR 3.7, 95% CI 2.13–6.54, P &lt; 0.001). Neither the CPIC level of evidence nor FDA PGx actionable or informative labels had a significant effect on PGx test timing.

Conclusions
PGx testing was generally limited to high Rx-drug users and was found to be an under-utilized resource. PGx testing did not typically follow CPIC guidelines. Implementing PGx testing protocols, simplifying PGx test-ordering by incorporating at minimum CYP2D6, CYP2C19, and CYP2C9 into PGx-testing panels, and unifying providers’ PGx knowledgebase in the MHS are feasible and would improve the clinical utilization of PGx tests in the MHS.
Rapid Bedside Ultrasound Evaluation of a Ruptured Abdominal Aortic Aneurysm With a Prior Repair
Authors: Corcillo Juliet , Stierwalt Joshua , Kaelin Andrea , Murray Brian 
Published: December 2021

ABSTRACT
Ruptured aortic aneurysms carry a high risk of morbidity and mortality, particularly if not rapidly identified. We present an 87-year-old male, with a history of hypertension and prior endovascular aortic repair, who presented to the Emergency Department (ED) with several days of epigastric abdominal pain radiating to his back and flanks. The patient acutely deteriorated in the ED, and point-of-care ultrasound rapidly identified active extravasation from an abdominal aortic aneurysm with visualization of prior endograft. Point-of-care ultrasound in this patient expedited the diagnosis, resuscitation, and transfer to the operating room with definitive repair by vascular surgery. The patient recovered and was discharged in stable condition.