A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

Preconception cystic fibrosis carrier screening: costs and consequences

The objective of the study was to determine net costs of four potential preconception cystic fibrosis (CF) carrier screening strategies, and to identify the most important cost-related parameters. An estimate was made of the costs of screening carried out during general practitioner (GP) consultations, and screening carried out during group educational sessions. Two test strategies were evaluated: single-entry two-step (SETS) and double- entry two-step (DETS). Several sensitivity analyses were performed. Under the baseline assumptions, SETS screening during GP consultations was the least expensive (net costs US dollar 1,111,354 per year). The sensitivity analysis showed that the costs depend greatly on the estimated lifetime costs of care for a CF patient and the strategy used to inform the target population. Adaptations could be made to the screening program, resulting in economic savings while the primary goal of the screening--to enable participants to make an autonomous informed choice--is guaranteed.     

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals

Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P = 4.5×10⁻⁸–1.2×10⁻⁴³). Using a novel method to combine data across ethnicities (N = 4,232 African Americans, N = 1,776 Asians, and N = 29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3×10⁻⁴). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p = 4.3×10⁻³, n = 22,044), increased triglycerides (p = 2.6×10⁻¹⁴, n = 93,440), increased waist-to-hip ratio (p = 1.8×10⁻⁵, n = 77,167), increased glucose two hours post oral glucose tolerance testing (p = 4.4×10⁻³, n = 15,234), increased fasting insulin (p = 0.015, n = 48,238), but with lower in HDL-cholesterol concentrations (p = 4.5×10⁻¹³, n = 96,748) and decreased BMI (p = 1.4×10⁻⁴, n = 121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.     

Role of host fruit color in the behavior of the walnut fly Rhagoletis juglandis

Observations and sticky-trap tests were used to assess the effect of fruit color on the behavior of adult male and female Rhagoletis juglandis Cresson (Diptera: Tephritidae), a tephritid that infests husks of Arizona walnut in southeastern Arizona. In the first experiment, during which flies were observed foraging among walnut models suspended from small walnut trees, models were painted green to appear ripe and uninfested or yellow with brown patches to appear ripe and infested. Flies used for this first experiment were also of two types: prior to observations, one group of flies had access to real walnuts for 1.5 days (prior experience) while the other group of flies was held without real walnut fruits (no prior experience). Regardless of prior experience with real walnut fruits, female flies landed on green models more than yellow/brown models. Experienced males also were more likely to land on green models than on yellow/brown models. More interactions also occurred on green models, because there were more landings.In the field behavioral assay, flies from a natural population given a choice of green, yellow, and yellow/brown models landed most often on green models, and all interactions and oviposition attempts occurred on green models. Flies also distinguished models by color in field sticky trap assays.These results suggest that female response to ripeness cues is innate, while males develop a preference for green based on their encounter rate with females.     

The effect of sheltered load on reproduction in Solanum carolinense, a species with variable self-incompatibility

In previous studies, we have investigated the strength of self-incompatibility (SI) in Solanum carolinense, a highly successful weed with a fully functional SI system that inhabits early successional and other disturbed habitats. We have found that the SI response in S. carolinense is a plastic trait—its strength being affected by the age of the flowers, and the presence of developing fruits and that there are genetic differences among families in their self-fertility. However, in species with a fully functional SI response, selfing would not be that common. As a result, deleterious recessives scattered though the genome of horsenettle are only occasionally exposed to selection. It has been suggested that deleterious recessives accumulate near S-alleles in strong SI species because the S-locus is located in a non-recombining region of the genome and because strong S-alleles are never in the homozygous state, thus sheltering some of the genetic load near the S-locus from selection. We performed a series of laboratory and greenhouse experiments to determine the extent to which sheltered load adds to the overall magnitude of inbreeding depression in horsenettle. Specifically, we amplified and sequenced the S-alleles from 16 genets collected from a large population in Pennsylvania and performed a series of controlled self-pollinations. We then grew the selfed progeny in the greenhouse; recorded various measures of growth and reproductive output; and amplified and sequenced their S-allele(s). We found that the heterozygous progeny of self-pollinations produce more flowers and have a greater ability to set both self and cross seed than S-homozygous progeny. We also found evidence of variation in the magnitude of load among S-alleles. These results suggest that sheltered load might slow the fixation of weak (partially compatible) S-alleles in this population, thus adding to the maintenance of a mixed mating system rather than leading to the fixation of the selfing alleles.     

Public attitudes toward genetic testing: perceived benefits and objections

The aim of this study was to assess public attitudes toward the availability and use of genetic tests to explore support for genomics developments and to help improve public discussion. Questionnaires to assess the assumed advantages and disadvantages of genetic testing were sent to a representative sample of the Dutch population (n = 1,308; age > or =25 years). The response was 63% (817/1,308). Two groups with extreme scores on a four-item scale were distinguished, representing opponents (n = 248) and supporters (n = 264) of the availability and use of genetic tests. Multiple logistic regression analyses showed that those who were familiar with a genetic disease (odds ratio [OR] 0.54; 95% confidence interval [CI] 0.32-0.89; p = 0.015), those who scored higher on a four-item scale on belief in personal benefits of testing (OR 0.29; 95% CI 0.21-0.40; p < 0.0001), and those who believe that knowledge of the genetic background of disease will help people to live more healthy lives (OR 0.48; 95% CI 0.37-0.62; p < 0.0001), were less likely to be opponents. Those who agreed that genetic testing is tampering with nature (OR 1.63; 95% CI 1.32-2.00; p < 0.0001) were more likely to be opponents. Other variables such as belief in genetic determinism, genetic knowledge, level of education, age, and gender were not significantly associated. These results suggest that in addition to moral acceptability, perceived usefulness is a precondition for supporting genetic testing. It is not expected that more information will necessarily result in more positive attitudes.     

Preconception cystic fibrosis carrier couple screening: impact,understanding, and satisfaction

The impact, understanding of test-results, and satisfaction among participating couples in a preconception cystic fibrosis (CF) carrier screening project were assessed 6 months after testing. Questionnaire data were obtained from 17/18 identified carriers, 15 partners of carriers with negative test results, and 794 (73%) other participants. None of the carriers changed their reproductive plans because of their test results. Eight participants were worried about their results, including four carriers. Those who attended a general practitioner (GP) consultation for pretest education were less worried than those who attended an educational session. Seven carriers felt less healthy. Predictors of a correct understanding of test results (correct in 62% of participants) were: positive test results, high level of knowledge of CF, high level of education, attending an educational session, and previously heard of CF. All participants who reported that they were worried, all carriers, and 95% of the other participants said that they would make the same decision to be tested again. Although couples who were educated during a GP consultation were less worried, the results of the study suggest that understanding is more correct in couples attending an educational session. The results further suggest that since satisfaction with the screening was high, worries and feeling less healthy due to the test results are probably not a great burden.