Assembly and analysis of the genome of Notholithocarpus densiflorus.

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to 'sudden oak death' (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread mortality of tanoaks. Here, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using co-barcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore (ONT) long reads to 30X coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using co-barcoded data we were able to generate complete haplotype coverage of all 11 genomes.

Development of a semi-automated MHC-associated peptide proteomics (MAPPs) method using streptavidin bead-based immunoaffinity capture and nano LC-MS/MS to support immunogenicity risk assessment in drug development.

Major histocompatibility complex (MHC)-Associated Peptide Proteomics (MAPPs) is an ex vivo method used to assess the immunogenicity risk of biotherapeutics. MAPPs can identify potential T-cell epitopes within the biotherapeutic molecule. Using adalimumab treated human monocyte derived dendritic cells (DCs) and a pan anti-HLA-DR antibody (Ab), we systematically automated and optimized biotin/streptavidin (SA)-capture antibody coupling, lysate incubation with capture antibody, as well as the washing and elution steps of a MAPPs method using functionalized magnetic beads and a KingFisher Magnetic Particle processor. Automation of these steps, combined with capturing using biotinylated-Ab/SA magnetic beads rather than covalently bound antibody, improved reproducibility as measured by minimal inter-and intra-day variability, as well as minimal analyst-to-analyst variability. The semi-automated MAPPs workflow improved sensitivity, allowing for a lower number of cells per analysis. The method was assessed using five different biotherapeutics with varying immunogenicity rates ranging from 0.1 to 48% ADA incidence in the clinic. Biotherapeutics with ≥10%immunogenicity incidence consistently presented more peptides (1.8-28 fold) and clusters (10-21 fold) compared to those with <10% immunogenicity incidence. Our semi-automated MAPPs method provided two main advantages over a manual workflow- the robustness and reproducibility affords confidence in the epitopes identified from as few as 5 to 10 donors and the method workflow can be readily adapted to incorporate different capture Abs in addition to anti-HLA-DR. The incorporation of semi-automated MAPPs with biotinylated-Ab/SA bead-based capture in immunogenicity screening strategies allows the generation of more consistent and reliable data, helping to improve immunogenicity prediction capabilities in drug development. MHC associated peptide proteomics (MAPPs), Immunogenicity risk assessment, in vitro/ex vivo, biotherapeutics, Major Histocompatibility Complex Class II (MHC II), LC-MS, Immunoaffinity Capture, streptavidin magnetic beads.

Racial-ethnic socialization, racial discrimination, and internalization of the model minority myth in East Asian families.

Guided by the integrative model, this study investigated the moderating effect of East Asian American youth-reported (N = 143) racial-ethnic socialization (RES) in the relationship between the youth's experiences of discrimination and internalization of the model minority myth. The results suggest that there was a significant interaction between youth's racial discrimination and youth-reported awareness of discrimination on youth's internalization of the model minority myth (b = 3.52, p < .05). No significant interaction effect emerged between racial discrimination and maintenance of heritage culture on internalization of model minority myth. The findings offer several contributions to inform research, family, and communities in understanding the ways caregivers respond to youth's racialized settings, which also contribute to youth's positive outcomes.

Prevalence and Correlates of Prescription Stimulant Misuse Among US College Students: Results From a National Survey.

Objective: There is a high prevalence of prescription stimulant misuse (PSM) among college students in the United States (US). Preventing and identifying PSM requires an understanding of risk factors and correlates, but large-scale surveys regarding this issue have been lacking. We present the largest multi-institution study to date on the correlates of PSM among US college students.Methods: We performed a secondary analysis of the 2017 American College Health Association-National College Health Assessment (ACHA-NCHA), an annual national survey on the demographics, health, and academic experiences of US college students. Logistic regression models examined associations between past-year PSM in 40,645 undergraduate college students and hypothesized risk factors.Results: PSM was reported in 8% of college students. PSM was associated with past-year diagnosis or treatment of depression (adjusted odds ratio [AOR] = 1.16; 99% CI, 1.01-1.33), anorexia (AOR = 1.44; 99% CI, 1.02-2.03), attention-deficit/hyperactivity disorder (AOR = 1.66; 99% CI, 1.41-1.95), and substance use disorder/other addiction (AOR = 1.79; 99% CI, 1.30-2.46). The odds of PSM were 5.5 times higher for students who endorsed past-month use of "Legal drugs" and 8 times higher for students who endorsed past-month use of "Illegal drugs" than for those who did not. Other factors associated with PSM included academic difficulty, daytime sleepiness, fraternity or sorority involvement, White race, and cis-male gender.Conclusions: This study identifies many potential risk factors for PSM among US undergraduate college students. Targeted outreach, prevention, and clinical management are discussed. As the COVID-19 pandemic has exacerbated psychiatric distress, sleep difficulties, substance use, and attentional challenges among college students, this study may serve as a baseline for future studies examining the impact of COVID-19 on PSM among college students.

Transitioning to Digital Systems: The Role of World Health Organization's Digital Adaptation Kits in Operationalizing Recommendations and Interoperability Standards.

INTRODUCTION: The transition from paper to digital systems requires quality assurance of the underlying content and application of data standards for interoperability. The World Health Organization (WHO) developed digital adaptation kits (DAKs) as an operational and software-neutral mechanism to translate WHO guidelines into a standardized format that can be more easily incorporated into digital systems. METHODS: WHO convened health program area and digital leads, reviewed existing approaches for requirements gathering, mapped to established standards, and incorporated research findings to define DAK components. RESULTS: For each health domain area, the DAKs distill WHO guidelines to specify the health interventions, personas, user scenarios, business process workflows, core data elements mapped to terminology codes, decision-support logic, program indicators, and functional and nonfunctional requirements. DISCUSSION: DAKs aim to catalyze quality of care and facilitate data use and interoperability as part of WHO's vision of SMART (Standards-based, Machine-readable, Adaptive, Requirements-based, and Testable) guidelines. Efforts will be needed to strengthen a collaborative approach for the uptake of DAKs within the local digital ecosystem and national health policies.

Characterization of Tissue Distribution, Catabolism, and Elimination of an Anti-Staphylococcus aureus THIOMAB Antibody-Antibiotic Conjugate in Rats.

Invasive Staphylococcus aureus infection is a leading cause of infectious disease-related deaths because S. aureus survives within host phagocytic cells, from which the bacteria are not adequately eliminated using current antibiotic treatments. Anti-S. aureus THIOMAB antibody-antibiotic conjugate (TAC), an anti-S. aureus antibody conjugated with antibiotic payload dmDNA31, was designed to deliver antibiotics into phagocytes, thereby killing intracellular S. aureus Herein, we present the distribution, metabolism/catabolism, and elimination properties for this modality. The tissue distribution of TAC and the release and elimination of its payload dmDNA31 were characterized in rats using multiple approaches. Intravenous injection of unconjugated [14C]dmDNA31 to rats resulted in a rapid clearance in both systemic circulation and tissues, with biliary secretion as the major route of elimination. Six major metabolites were identified. When [14C]dmDNA31 was conjugated to an antibody as TAC and administered to rat intravenously, a sustained exposure was observed in both systemic circulation and tissues. The dmDNA31 in blood and tissues mainly remained in conjugated form after administering TAC, although minimal deconjugation of dmDNA31 from TAC was also observed. Several TAC catabolites were identified, which were mainly eliminated through the biliary-fecal route, with dmDNA31 and deacetylated dmDNA31 as the most abundant catabolites. In summary, these studies provide a comprehensive characterization of the distribution, metabolism/catabolism, and elimination properties of TAC. These data fully support further clinical development of TAC for the invasive and difficult-to-treat S. aureus infection. SIGNIFICANCE STATEMENT: The present studies provide a comprehensive investigation of the absorption, distribution, metabolism/catabolism, and elimination of the first antibody-antibiotic conjugate developed for the treatment of an infectious disease. Although many antibody-drug conjugates are in development for various disease indications, only a limited amount of absorption, distribution, metabolism/catabolism, and elimination information is available in the literature. This study demonstrates the use of radiolabeling technology to delineate the absorption, distribution, metabolism/catabolism, and elimination properties of a complex modality and help address the key questions related to clinical pharmacological studies.

Psychiatric Symptoms and Diagnoses Among U.S. College Students: A Comparison by Race and Ethnicity.

OBJECTIVE: The mental health challenges of college students are a critical public health concern, and they may be exacerbated among racial and ethnic minority groups. Unfortunately, there is a lack of recent large-scale research on this topic. This study provides an update on the mental health experiences of U.S. college students from minority backgrounds. METHODS: This is a retrospective analysis of cross-sectional data from the spring 2015 administration of the American College Health Association-National College Health Assessment (ACHA-NCHA IIB). Survey results from 67,308 undergraduates at 108 colleges were analyzed. RESULTS: Past-year rates of self-reported psychiatric symptoms and diagnoses were high, regardless of race or ethnicity. Students from minority groups generally reported lower rates of both symptoms and diagnoses compared with whites, with notable exceptions. Despite reporting generally lower rates of psychiatric diagnoses compared with whites, students who identified as multiracial (N=7,473) or Asian/Pacific Islander (N=7,166) were more likely to endorse having felt hopeless, so depressed that it was difficult to function, or overwhelmed by anger and were more likely to have considered or attempted suicide. Compared with whites, blacks and Hispanics endorsed lower rates of psychiatric diagnoses but had similar rates of past-year suicide attempts. CONCLUSIONS: Lower rates of formally diagnosed psychiatric illnesses may obscure significant mental health burden among minority students, especially with regard to suicidal thoughts and attempts among Asian/Pacific Islander and multiracial students. Students from racial and ethnic minority backgrounds may have undetected psychiatric problems and, therefore, represent a particularly at-risk group on campus.

The prevalence and predictors of mental health diagnoses and suicide among U.S. college students: Implications for addressing disparities in service use.

BACKGROUND: The college years represent a period of increased vulnerability for a wide range of mental health (MH) challenges. The onset of common psychiatric conditions occurs during this period of development. Increases in depression, anxiety, and suicidality among U.S. college students have been observed. This study identified prevalence and correlates of MH diagnoses and suicidality in a recent sample of U.S. college students. METHODS: The Spring 2015 American College Health Association-National College Health Assessment (ACHA-NCHA) survey assessed MH diagnoses and suicidality from U.S. undergraduate students (n = 67,308) across 108 institutions. RESULTS: Stress was strongly associated with a greater likelihood of suicide attempts and MH diagnoses, even among students reporting 1-2 stressful events (OR [odds ratio] range 1.6-2.6, CI [confidence interval] = 1.2-3.2). Bisexual students were more likely to report MH diagnoses and suicidality, compared to heterosexual and gay/lesbian students (OR range 1.5-3.9, CI = 1.8-4.3), with over half engaging in suicidal ideation and self-harm, and over a quarter reporting suicide attempts. Transgender students reported a higher rate of MH diagnoses and suicidality relative to females (OR range 1.9-2.4, CI = 1.1-3.4). Racial/ethnic minority students were generally less likely to report MH diagnoses relative to Whites, although the likelihood for suicidality was mixed. CONCLUSIONS: The high rate of multiple stress exposures among the U.S. college population and the high impacts of stress on MH and suicidality point to an urgent need for service utilization strategies, especially among racial/ethnic, sexual, or gender minorities. Campuses must consider student experiences to mitigate stress during this developmental period.

A never-before opportunity to strengthen investment and action on adolescent contraception, and what we must do to make full use of it.

BACKGROUND: Increasingly, the health and rights of adolescents are being recognized and prioritized on the global agenda. This presents us with a "never-before" opportunity to address adolescent contraception. This is timely, as there are enormous numbers of adolescents who are currently unable to obtain and use contraceptives. From research evidence and programmatic experience, it is clear that we need to do things differently to meet their needs/fulfil their rights. MAIN BODY: In this commentary, we call for action in several key areas to address adolescents' persistent inability to obtain and use contraceptives. We must move away from one-size-fits-all approaches, from a 'condoms-only' mind set, from separate services for adolescents, from ignoring the appeal of pharmacies and shops, and from one-off-training to make health workers adolescent friendly. Our efforts to expand access to quality contraceptive services to adolescents must be combined with efforts to build their desire and ability to use them, and to do so consistently. In order for these changes to be made, action must be taken on several levels. This includes the formulation of sound national policies and strategies, robust programme implementation with monitoring, regular programmatic reviews, and implementation research. Further, high-quality collection, analysis, and dissemination of data must underlie all of our efforts. As we move ahead, we must also recognize and draw lessons from positive examples of large scale and sustained programmes in countries that have led the way in increasing contraceptive use by adolescents. CONCLUSION: This unprecedented moment in history gives us a real opportunity to bring about transformational change, particularly when there is so much at stake.

Secondary ventricular fibrillation or pulseless ventricular tachycardia during cardiac arrest and epinephrine dosing.

BACKGROUND: Development of ventricular fibrillation or pulseless ventricular tachycardia after an initial rhythm of pulseless electrical activity or asystole is associated with significantly increased cardiac arrest mortality. OBJECTIVE: To examine differences in epinephrine administration during cardiac arrest between patients who had a secondary ventricular fibrillation or ventricular tachycardia develop and patients who did not. METHODS: Data were collected for 2 groups of patients with in-hospital cardiac arrest and an initial rhythm of pulseless electrical activity or asystole: those who had a secondary ventricular fibrillation or ventricular tachycardia develop (cases) and those who did not (controls). Dosing of epinephrine during cardiac arrest and other variables were compared between cases and controls. RESULTS: Of the 215 patients identified with an initial rhythm of pulseless electrical activity or asystole, 51 (23.7%) had a secondary ventricular fibrillation or ventricular tachycardia develop. Throughout the total duration of arrest, including periods of return of spontaneous circulation, the dosing interval for epinephrine in patients who had a secondary ventricular fibrillation or ventricular tachycardia develop was 1 mg every 3.4 minutes compared with 1 mg every 5 minutes in controls (P= .001). For the total duration of pulselessness, excluding periods of return of spontaneous circulation during the arrest, the dosing interval for epinephrine in patients who had a secondary ventricular fibrillation or ventricular tachycardia develop was 1 mg every 3.1 minutes versus 1 mg every 4.3 minutes in controls (P= .001). CONCLUSION: More frequent administration of epinephrine during cardiac arrest is associated with development of secondary ventricular fibrillation or ventricular tachycardia.

Oral delivery of double-stranded RNA in larvae of the yellow fever mosquito, Aedes aegypti: implications for pest mosquito control.

RNA interference has already proven itself to be a highly versatile molecular biology tool for understanding gene function in a limited number of insect species, but its widespread use in other species will be dependent on the development of easier methods of double-stranded RNA (dsRNA) delivery. This study demonstrates that RNA interference can be induced in the mosquito Aedes aegypti L. (Diptera: Culicidae) simply by soaking larvae in a solution of dsRNA for two hours. The mRNA transcripts for ß-tubulin, chitin synthase-1 and -2, and heat shock protein 83 were reduced between 30 and 50% three days post-dsRNA treatment. The dsRNA was mixed with a visible dye to identify those individuals that fed on the dsRNA, and based on an absence of RNA interference in those individuals that contained no dye within their guts, the primary route of entry of dsRNA is likely through the gut epithelium. RNA interference was systemic in the insects, inducing measurable knock down of gene expression in tissues beyond the gut. Silencing of the ß-tubulin and chitin synthase-1 genes resulted in reduced growth and/or mortality of the larvae, demonstrating the utility of dsRNA as a potential mosquito larvicide. Silencing of chitin synthase-2 did not induce mortality in the larvae, and silencing of heat shock protein 83 only induced mortality in the insects if they were subsequently subjected to a heat stress. Drosophila melanogaster Meigen (Diptera: Drosophilidae) larvae were also soaked in dsRNA designed to specifically target either their own ß-tubulin gene, or that of A. aegypti, and significant mortality was only seen in larvae treated with dsRNA targeting their own gene, which suggests that dsRNA pesticides could be designed to be species-limited.

Discovery and characterization of a potent and selective antagonist of melanin-concentrating hormone receptor 2.

A series of spiropiperidine carbazoles were synthesized and evaluated as MCHR2 antagonists using a FLIPR assay. The pharmacokinetic properties of selected compounds have also been studied. This effort led to the discovery of potent and specific MCHR2 antagonists. Compound 38 demonstrated good pharmacokinetic properties across rat, beagle dog and rhesus monkey and had a favorable selectivity profile against a number of other receptors. These MCHR2 antagonists are considered appropriate tool compounds for study of the function of MCHR2 in vivo.

Addressing diversity in adolescent sexual and reproductive health services.

The social, economic, and biological events that mark adolescence profoundly influence and shape future adult lives. Sexual and reproductive health (SRH) services, education, and other social programs are needed to support young people for a healthy start. As adolescents transition into adulthood, SRH programs and services that have skilled health providers, in combination with other social services including comprehensive sexuality education, can help prevent unwanted pregnancies, maternal mortality and morbidity, as well as sexually transmitted infections including HIV/AIDS. Programs and services can also provide counseling to prevent sexual violence and abuse and deal with its consequences. Adolescent SRH programs can be more effective if the demographic diversity of this age group is studied. Vulnerable adolescents should be targeted as priority recipients of youth-friendly SRH and other social support services. Data demonstrate that adolescent girls living in rural areas who are not in school and who are often married as children are vulnerable to maternal mortality and morbidity, unwanted pregnancies, unsafe abortion, HIV infection, and sexual violence and abuse. Building adolescent capacities and opportunities requires programs that support adolescent social, economic, and health assets so that they can contribute socially and economically to their societies. A healthy adolescent population is critical for low-resource countries, where a rising proportion of the population is under 24 years of age. Recommendations for strengthening the effectiveness of SRH programs detailed at the FIGO World Congress in 2009 are discussed.

Ingested double-stranded RNAs can act as species-specific insecticides.

A serious shortcoming of many insecticides is that they can kill non-target species. To address this issue, we harnessed the sequence specificity of RNA interference (RNAi) to design orally-delivered double-stranded (ds) RNAs that selectively killed target species. Fruit flies (Drosophila melanogaster), flour beetles (Tribolium castaneum), pea aphids (Acyrthosiphon pisum), and tobacco hornworms (Manduca sexta) were selectively killed when fed species-specific dsRNA targeting vATPase transcripts. We also demonstrate that even closely related species can be selectively killed by feeding on dsRNAs that target the more variable regions of genes, such as the 3' untranslated regions (UTRs): four species of the genus Drosophila were selectively killed by feeding on short (<40 nt) dsRNAs that targeted the 3' UTR of the gamma-tubulin gene. For the aphid nymphs and beetle and moth larvae, dsRNA could simply be dissolved into their diets, but to induce RNAi in the drosophilid species, the dsRNAs needed to be encapsulated in liposomes to help facilitate uptake of the dsRNA. This is the first demonstration of RNAi following ingestion of dsRNA in all of the species tested, and the method offers promise of both higher throughput RNAi screens and the development of a new generation of species-specific insecticides.

An inhibitory metabolite leads to dose- and time-dependent pharmacokinetics of (R)-N-{1-[3-(4-ethoxy-phenyl)-4-oxo-3,4-dihydro-pyrido[2,3-d]pyrimidin-2-yl]-ethyl}-N-pyridin-3-yl-methyl-2-(4-trifluoromethoxy-phenyl)-acetamide (AMG 487) in human subjects after multiple dosing.

(R)-N-{1-[3-(4-Ethoxy-phenyl)-4-oxo-3,4-dihydro-pyrido[2,3-d]-pyrimidin-2-yl]-ethyl}-N-pyridin-3-yl-methyl-2-(4-trifluoromethoxyphenyl)-acetamide (AMG 487) is a potent and selective orally bioavailable chemokine (C-X-C motif) receptor 3 (CXCR3) antagonist that displays dose- and time-dependent pharmacokinetics in human subjects after multiple oral dosing. Although AMG 487 exhibited linear pharmacokinetics on both days 1 and 7 at the 25-mg dose, dose- and time-dependent kinetics were evident at the two higher doses. Nonlinear kinetics were more pronounced after multiple dosing. Area under the plasma concentration-time curve from 0 to 24 h [AUC((0-24 h))] increased 96-fold with a 10-fold increase in dose on day 7 compared with a 28-fold increase in AUC((0-24 h)) on day 1. These changes were correlated with time- and dose-dependent decreases in the metabolite to parent plasma concentrations, suggesting that these changes result from a decrease in the oral clearance (CL) of AMG 487 (e.g., intestinal/hepatic first-pass metabolism and systemic CL). The biotransformation of AMG 487 is dependent on CYP3A and results in the formation of two primary metabolites, a pyridyl N-oxide AMG 487 (M1) and an O-deethylated AMG 487 (M2). One of these metabolites, M2, undergoes further metabolism by CYP3A. M2 has also been demonstrated to inhibit CYP3A in a competitive (K(i)=0.75 microM) manner as well as via mechanism-based inhibition (unbound K(I)=1.4 microM, k(inact)=0.041 min(-1)). Data from this study implicate M2-mediated CYP3A mechanism-based inhibition as the proximal cause for the time-dependent pharmacokinetics of AMG 487. However, the sequential metabolism of M2, nonlinear AMG 487 pharmacokinetics, and the inability to accurately determine the role of intestinal AMG 487 metabolism complicates the correlation between M2 plasma concentrations and the time-dependent AMG 487 pharmacokinetic changes.

A double-blind, randomized controlled trial on the use of a 50:50 mixture of nitrous oxide/oxygen in pain relief during suction evacuation for the first trimester pregnancy termination.

BACKGROUND: This prospective study assessed the role of a 50:50 mixture of nitrous oxide (N2O) and oxygen for pain relief during the termination of first trimester pregnancies by suction evacuation under conscious sedation. METHODS: Ninety women undergoing suction evacuation up to 12 weeks of gestation were randomized by a computer-generated randomization list and allocated using sealed envelopes to receive the N2O/O2 mixture or air during the operation. Pain scores during and after suction evacuation, post-operative side effects and satisfaction level were compared. RESULTS: No statistically significant differences in pain scores, post-operative side effects and satisfaction levels were found between the two groups. CONCLUSION: N2O/O2 did not reduce the pain level during suction evacuation for the first trimester pregnancy termination under conscious sedation.

Identification of Src transformation fingerprint in human colon cancer.

We used a classical rodent model of transformation to understand the transcriptional processes, and hence the molecular and cellular events a given cell undergoes when progressing from a normal to a transformed phenotype. Src activation is evident in 80% of human colon cancer, yet the myriad of cellular processes effected at the level of gene expression has yet to be fully documented. We identified a Src 'transformation fingerprint' within the gene expression profiles of Src-transformed rat 3Y1 fibroblasts demonstrating a progression in transformation characteristics. To evaluate the role of this gene set in human cancer development and progression, we extracted the orthologous genes present on the Affymetrix Hu95A GeneChip (12k named genes) and compared expression profiles between the Src-induced rodent cell line model of transformation and staged colon tumors where Src is known to be activated. A similar gene expression pattern between the cell line model and staged colon tumors for components of the cell cycle, cytoskeletal associated proteins, transcription factors and lysosomal proteins suggests the need for co-regulation of several cellular processes in the progression of cancer. Genes not previously implicated in tumorigenesis were detected, as well as a set of 14 novel, highly conserved genes with here-to-fore unknown function. These studies define a set of transformation associated genes whose up-regulation has implications for understanding Src mediated transformation and strengthens the role of Src in the development and progression of human colon cancer. Supportive Supplemental Data can be viewed at http://pga.tigr.org/PGApubs.shtml.