Negative binomial mixture model for identification of noise in antibody-antigen specificity predictions from single-cell data.

Motivation: LIBRA-seq (linking B cell receptor to antigen specificity by sequencing) provides a powerful tool for interrogating the antigen-specific B cell compartment and identifying antibodies against antigen targets of interest. Identification of noise in single-cell B cell receptor sequencing data, such as LIBRA-seq, is critical for improving antigen binding predictions for downstream applications including antibody discovery and machine learning technologies.

Results: In this study, we present a method for denoising LIBRA-seq data by clustering antigen counts into signal and noise components with a negative binomial mixture model.

A potently neutralizing and protective human antibody targeting antigenic site V on RSV and hMPV fusion glycoprotein.

Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are frequent drivers of morbidity and mortality in susceptible populations, most often infantile, older adults, and immunocompromised. The primary target of neutralizing antibodies is the fusion (F) glycoprotein on the surface of the RSV and hMPV virion. As a result of the structural conservation between RSV and hMPV F, three antigenic regions are known to induce cross-neutralizing responses: sites III, IV, and V.

Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families.

Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage members, antibodies 2526 and 546, were confirmed to bind to a large panel of diverse antigens, including several strains of HIV-1 Env, influenza HA, coronavirus (CoV) spike, hepatitis C virus (HCV) E protein, Nipah virus (NiV) F protein, and Langya virus (LayV) F protein.

Antibody sequence determinants of viral antigen specificity.

Throughout life, humans experience repeated exposure to viral antigens through infection and vaccination, resulting in the generation of diverse, antigen-specific antibody repertoires. A paramount feature of antibodies that enables their critical contributions in counteracting recurrent and novel pathogens, and consequently fostering their utility as valuable targets for therapeutic and vaccine development, is the exquisite specificity displayed against their target antigens. Yet, there is still limited understanding of the determinants of antibody-antigen specificity, particularly as a function of antibody sequence.

Development of LIBRA-seq for the guinea pig model system as a tool for the evaluation of antibody responses to multivalent HIV-1 vaccines.

Consistent elicitation of serum antibody responses that neutralize diverse clades of HIV-1 remains a primary goal of HIV-1 vaccine research. Prior work has defined key features of soluble HIV-1 Envelope (Env) immunogen cocktails that influence the neutralization breadth and potency of multivalent vaccine-elicited antibody responses including the number of Env strains in the regimen. We designed immunization groups that consisted of different numbers of SOSIP Env strains to be used in a cocktail immunization strategy: the smallest cocktail (group 2) consisted of a set of two Env strains, which were a subset of the three Env strains that made up group 3, which, in turn, were a subset of the six Env strains that made up group 4.

Negative Binomial Mixture Model for Identification of Noise in Antigen-Specificity Predictions by LIBRA-seq.

Motivation: LIBRA-seq (linking B cell receptor to antigen specificity by sequencing) provides a powerful tool for interrogating the antigen-specific B cell compartment and identifying antibodies against antigen targets of interest. Identification of noise in LIBRA-seq antigen count data is critical for improving antigen binding predictions for downstream applications including antibody discovery and machine learning technologies.

Results: In this study, we present a method for denoising LIBRA-seq data by clustering antigen counts into signal and noise components with a negative binomial mixture model.

Pre-sleep feeding, sleep quality, and markers of recovery in division I NCAA female soccer players.

Pre-sleep nutrition habits in elite female athletes have yet to be evaluated. A retrospective analysis was performed with 14 NCAA Division I female soccer players who wore a WHOOP, Inc. band - a wearable device that quantifies recovery by measuring sleep, activity, and heart rate metrics through actigraphy and photoplethysmography, respectively - 24 h a day for an entire competitive season to measure sleep and recovery.

Comparison of VOpeak from the Progressive Aerobic Cardiovascular Endurance Run (PACER) and treadmill in children.

Background/objectives: The purpose of this study was to investigate the difference in peak oxygen consumption (VOpeak) during a graded treadmill test and the Progressive Aerobic Cardiovascular Endurance Run (PACER) in a sample of 7-14 year old children.

Methods: Forty-four participants (25 boys, 19 girls) had VO assessed during a peak treadmill test and the PACER by a portable indirect calorimeter on non-consecutive days. Exercise parameters were compared between exercise tests by paired t-tests.

Development of an Aptamer-Based Electrochemical Microfluidic Device for Viral Vaccine Quantitation.

Global deployment of vaccines poses significant challenges in the distribution and use of the accompanying immunoassays, one of the standard methods for quality control of vaccines, particularly when establishing assays in countries worldwide to support testing/release upon importation. This work describes our effort toward developing an integrated, portable device to carry out affinity assays for viral particles quantification in viral vaccines by incorporating (i) aptamers, (ii) microfluidic devices, and (iii) electrochemical detection. We generated and characterized more than eight aptamers against multiple membrane proteins of cytomegalovirus (CMV), which we used as a model system and designed and fabricated electrochemical microfluidic devices to measure CMV concentrations in a candidate vaccine under development.

Factors associated with nurses emotional distress during the COVID-19 pandemic.

Background: Nurses are among the frontline healthcare workers directly impacted by the burden of the coronavirus disease of 2019 (COVID-19) pandemic. This study aimed to examine the prevalence of emotional distress and the associated factors among nurses practicing in South Dakota during the COVID-19 pandemic.

Methods: An online survey was conducted among practicing, licensed nurses in South Dakota during the pandemic (July 2020 - August 2020).

Combined Sprint Interval, Plyometric, and Strength Training in Adolescent Soccer Players: Effects on Measures of Speed, Strength, Power, Change of Direction, and Anaerobic Capacity.

Ferley, DD, Scholten, S, and Vukovich, MD. Combined sprint interval, plyometric, and strength training in adolescent soccer players: effects on measures of speed, strength, power, change of direction, and anaerobic capacity. J Strength Cond Res 34(4): 957-968, 2020-During winter, many soccer players train indoors to improve the aerobic and anaerobic demands of their sport.

Assessing the Reliability of Using a Horizontal Leg Press Equipped With a Force Plate to Report on Measures of Positive and Negative Neuromuscular Characteristics.

Ferley, DD and Vukovich, MD. Assessing the reliability of using a horizontal leg press equipped with a force plate to report on measures of positive and negative neuromuscular characteristics. J Strength Cond Res 33(2): 360-371, 2019-Individuals participating in sport or returning from a lower-extremity injury routinely perform assessments of lower-body anaerobic capacity and power to gauge fitness or readiness to return to competition.

The Effect of Nitrate Supplementation on Exercise Tolerance and Performance: A Systematic Review and Meta-Analysis.

Van De Walle, GP and Vukovich, MD. The effect of nitrate supplementation on exercise tolerance and performance: a systematic review and meta-analysis. J Strength Cond Res 32(6): 1796-1808, 2018-The purpose of this article was to systematically review the current literature and evaluate the overall efficacy of nitrate supplementation on exercise tolerance and performance by meta-analysis.

Protein Supplementation During a 6-Month Concurrent Training Program: Effect on Body Composition and Muscular Strength in Sedentary Individuals.

We examined the effect of a protein supplement on muscular strength and body composition during 6 months of a 5 days/week concurrent strength and endurance training program. Sedentary males (n = 26) and females (n = 25), 18-25 years, were randomly assigned to receive a protein (PRO, 42 g/serving) or carbohydrate (CON) supplement twice daily. Strength and body composition (dual-energy X-ray absorptiometry) were assessed at baseline, 3 (3M), and 6 (6M) months.

Predicting the Intensity for Performing Supramaximal Incline Treadmill Interval Training in Distance Runners.

Ferley, DD and Vukovich, MD. Predicting the intensity for performing supramaximal incline treadmill interval training in distance runners. J Strength Cond Res 33(5): 1354-1361, 2019-Recent evidence highlights the effectiveness of 30-second bouts paired with level-grade supramaximal interval training (SMIT) and incline treadmill training (INC), respectively, in distance runners.

Multiparameter Particle Display (MPPD): A Quantitative Screening Method for the Discovery of Highly Specific Aptamers.

Aptamers are a promising class of affinity reagents because they are chemically synthesized, thus making them highly reproducible and distributable as sequence information rather than a physical entity. Although many high-quality aptamers have been previously reported, it is difficult to routinely generate aptamers that possess both high affinity and specificity. One of the reasons is that conventional aptamer selection can only be performed either for affinity (positive selection) or for specificity (negative selection), but not both simultaneously.

The effect of six days of dietary nitrate supplementation on performance in trained CrossFit athletes.

Background: While it is well established that dietary nitrate reduces the metabolic cost of exercise, recent evidence suggests this effect is maintained 24 h following the final nitrate dose when plasma nitrite levels have returned to baseline. In addition, acute dietary nitrate was recently reported to enhance peak power production. Our purpose was to examine whether chronic dietary nitrate supplementation enhanced peak power 24 h following the final dose and if this impacted performance in a heavily power-dependent sport.

Time-to-Fatigue During Incline Treadmill Running: Implications for Individualized Training Prescription.

Uphill running has been touted as a key interval training tactic for distance runners despite few scientifically derived recommendations for individualized training prescription. To date, a majority of uphill training research has focused on shorter, faster training bouts; however, longer, slower bouts based on an individual's velocity at maximum oxygen consumption (Vmax) may prove more effective. One potential longer bout length may be associated with the time Vmax can be maintained (Tmax), an approach proven effective in level-grade interval training.

The effects of incline and level-grade high-intensity interval treadmill training on running economy and muscle power in well-trained distance runners.

Despite a paucity of evidence, uphill running has been touted as a sport-specific resistance-to-movement training tactic capable of enhancing metabolic, muscular, and neuromuscular processes in distance runners in ways similar to previously established resistance-to-movement training methods, such as heavy and/or explosive strength training and plyometric training. Therefore, the purpose of this investigation included documenting the effects of incline and level-grade interval treadmill training on indices of running economy (RE) (i.e.

The effects of uphill vs. level-grade high-intensity interval training on VO2max, Vmax, V(LT), and Tmax in well-trained distance runners.

Uphill running represents a frequently used and often prescribed training tactic in the development of competitive distance runners but remains largely uninvestigated and unsubstantiated as a training modality. The purpose of this investigation included documenting the effects of uphill interval training compared with level-grade interval training on maximal oxygen consumption (VO2max), the running speed associated with VO2max (Vmax), the running speed associated with lactate threshold (V(LT)), and the duration for which Vmax can be sustained (Tmax) in well-trained distance runners. Thirty-two well-trained distance runners (age, 27.

Osteogenic index and changes in bone markers during a jump training program: a pilot study.

Purpose: This study was designed as a proof-of-concept study to assess the osteogenic index (OI) and changes in bone markers during an 8-wk jump training program. On the basis of the OI, jumps were completed in one or two daily sessions with total jumps per day being equal.

Methods: Seven males served as controls and participated in their normal strength training program.

Moderate protein intake improves total and regional body composition and insulin sensitivity in overweight adults.

A high protein intake (approximately 40% of energy intake) combined with aerobic and resistance exercise training is more closely associated with improved body composition and cardiovascular risk profile than a traditional protein intake (approximately 15% of intake) combined with moderate-intensity aerobic exercise. However, there is concern that such high-protein diets may adversely affect health. We therefore tested the hypothesis that moderate protein intake (approximately 25% of energy intake) would elicit similar benefits on body composition and metabolic profile as high protein intake.

The impact of varying dietary protein on serum IGF-I, IGFBP-1, and IGFBP-3 during 6 days of physical activity.

This study was designed to investigate the impact of dietary protein intake on serum concentrations of IGF-I and IGFBP-1 and relative amounts of serum IGFBP-3 during 6 d of physical activity. Ten men (23.8 +/- 2.