Refining similarity scoring to enable decoy‐free validation in spectral library searching

Spectral library searching is a maturing approach for peptide identification from MS/MS, offering an alternative to traditional sequence database searching. Spectral library searching relies on direct spectrum‐to‐spectrum matching between the query data and the spectral library, which affords better discrimination of true and false matches, leading to improved sensitivity. However, due to the inherent diversity of the peak location and intensity profiles of real spectra, the resulting similarity score distributions often take on unpredictable shapes. This makes it difficult to model the scores of the false matches accurately, necessitating the use of decoy searching to sample the score distribution of the false matches. Here, we refined the similarity scoring in spectral library searching to enable the validation of spectral search results without the use of decoys. We rank‐transformed the peak intensities to standardize all spectra, making it possible to fit a parametric distribution to the scores of the nontop‐scoring spectral matches. The statistical significance of the top‐scoring match can then be estimated in a rigorous manner according to Extreme Value Theory. The overall result is a more robust and interpretable measure of the quality of the spectral match, which can be obtained without decoys. We tested this refined similarity scoring function on real datasets and demonstrated its effectiveness. This approach reduces search time, increases sensitivity, and extends spectral library searching to situations where decoy spectra cannot be readily generated, such as in searching unidentified and nonpeptide spectral libraries.     

Genetic risk assessment of the joint effect of several genes: Critical appraisal

When assessing the combined action of genes on the quantitative or qualitative phenotype we encounter a phenomenon that could be named the “paradox of the risk score summation.” It arises when the search of risk allele and assessment of their combined action are performed with the same single dataset. Too often such methodological error occurs when calculating the so called genetic risk score (GRS), which refers to the total number of alleles associated with the disease. Examples from numerous published genetic association studies are considered in which the claimed statistically significant effects can be attributed to the “risk score summation paradox.” In the second section of the review we discuss the current modifications of multiple regression analysis addressed to the so called “n ? p problem” (the number of points is much smaller than the number of possible predictors). Various algorithms for the model selection (searching the significant predictor combinations) are considered, beginning from the common marginal screening of the “top” predictors to LASSO and other modern algorithms of compressed sensing.     

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A strategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.     

Accuracy of prediction scores and novel biomarkers for predicting nonalcoholic fatty liver disease in obese children

Background:

Accurate prediction scores for liver steatosis are demanded to enable clinicians to noninvasively screen for nonalcoholic fatty liver disease (NAFLD). Several prediction scores have been developed, however external validation is lacking.

Objective:

The aim was to determine the diagnostic accuracy of four existing prediction scores in severely obese children, to develop a new prediction score using novel biomarkers and to compare these results to the performance of ultrasonography.

Design and Results:

Liver steatosis was measured using proton magnetic resonance spectroscopy in 119 severely obese children (mean age 14.3 ± 2.1 years, BMI z‐score 3.35 ± 0.35). Prevalence of steatosis was 47%. The four existing predictions scores (“NAFLD liver fat score,” “fatty liver index,” “hepatic steatosis index,” and the pediatric prediction score) had only moderate diagnostic accuracy in this cohort (positive predictive value (PPV): 70, 61, 61, 69% and negative predictive value (NPV) 77, 69, 68, 75%, respectively). A new prediction score was built using anthropometry, routine biochemistry and novel biomarkers (leptin, adiponectin, TNF‐alpha, IL‐6, CK‐18, FGF‐21, and adiponutrin polymorphisms). The final model included ALT, HOMA, sex, and leptin. This equation (PPV 79% and NPV 80%) did not perform substantially better than the four other equations and did not outperform ultrasonography for excluding NAFLD (NPV 82%).

Conclusion:

The conclusion is in severely obese children and adolescents existing prediction scores and the tested novel biomarkers have insufficient diagnostic accuracy for diagnosing or excluding NAFLD.     

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. In spectral library searching, a spectral library is first meticulously compiled from a large collection of previously observed peptide MS/MS spectra that are conclusively assigned to their corresponding amino acid sequence. An unknown spectrum is then identified by comparing it to all the candidates in the spectral library for the most similar match. This review discusses the basic principles of spectral library building and searching, describes its advantages and limitations, and provides a primer for researchers interested in adopting this new approach in their data analysis. It will also discuss the future outlook on the evolution and utility of spectral libraries in the field of proteomics.     

Maternal feeding strategies, child eating behaviors, and child BMI in low-income African-American preschoolers

Objective: To test the hypothesis that low‐income African‐American preschool children would have a higher BMI if their mothers reported greater “restriction” and “control” in feeding and if mothers reported that children showed greater “food responsiveness” and “desire to drink.” In addition, to test whether higher maternal “pressure to eat” would be associated with lower child BMI. Research Methods and Procedures: A questionnaire was completed by 296 low‐income African‐American mothers of preschool children. It assessed three constructs on maternal feeding strategies (“restriction,” “pressure to eat,” and “control”) and two on child eating behaviors (“food responsiveness” and “desire to drink”). Children's BMI was measured, and mothers’ BMI was self‐reported. Results: The mean (standard deviation) BMI z‐score of the children was 0.34 (1.5), and 44% of the mothers were obese (BMI ≥30 kg/m²). Only maternal “pressure to eat” had a significant overall association with child BMI z‐score (r = ?0.16, p < 0.01). Both maternal “restriction” and “control” were positively associated with children's BMI z‐score in the case of obese mothers (r = 0.20, p = 0.03 and r = 0.24, p = 0.007, respectively), but this was not so in the case of non‐obese mothers (r = ?0.16, p = 0.05 and r = ?0.07, p = 0.39, respectively). Discussion: Among low‐income African Americans, the positive association between maternal restriction and control in feeding and their preschoolers’ BMI was limited to obese mothers. Relations between parent feeding strategies and child weight status in this population may differ on the basis of maternal weight status.     

Does Dieting Lead to Weight Gain? A Four‐Year Longitudinal Study of Middle School Girls

Objective: A majority of the published longitudinal research on children has reported that dieting is related to weight gain at a later point in time. The purpose of this study was to look at weight control behaviors and patterns of weight gain and loss, specifically whether dieting is related to weight gain. Research Methods and Procedures: Baseline data were collected from 1358 female students in grades 6 to 9 from schools in Hayward, CA, and Tucson, AZ. Data were obtained annually over a 4‐year period. Paper‐and‐pencil questionnaires and height and weight were obtained during the students’ regular classroom periods. Dieting was measured both with the single item, “In the past year, how often have you been on a diet to lose weight?” scored from “never” to “always,” and with a Dieting Behavior Scale including five items on weight control behaviors. Changes in BMI z‐scores were analyzed. Results: On average, girls who reported “never” dieting were most likely to have an increased BMI z‐score at the next measurement, and those who reported “always” dieting were most likely to have a decreased BMI z‐score. The same pattern was true for the Dieting Behavior Scale. Discussion: Our finding that dieting and weight gain were not related, independently of initial BMI, does not mean that dieting to lose weight is appropriate, especially among young girls. Additional research is needed both to examine this relationship and to determine exactly what behaviors children are engaging in when they report that they are dieting.     

AN ACTIGRAPHIC STUDY COMPARING COMMUNITY DWELLING POOR SLEEPERS WITH NON-DEMENTED CARE HOME RESIDENTS

Sleep disturbances are a common problem among institutionalized older people. Studies have shown that this population experiences prolonged sleep latency, increased fragmentation and wake after sleep onset, more disturbed circadian rhythms, and night-day reversal. However, studies have not examined the extent to which this is because of individual factors known to influence sleep (such as age) or because of the institutional environment. This article compares actigraphic data collected for 14 days from 122 non-demented institutional care residents (across ten care facilities) with 52 community dwelling poor sleepers >65 yrs of age. Four dependent variables were analyzed: (i) “interdaily stability” (IS); (ii) “intradaily variability” (IV); (iii) relative amplitude (RA) of the activity rhythm; and (iv) mean 24?h activity level. Data were analyzed using a fixed-effect, single-level model (using MLwiN). This model enables comparisons between community and institutional care groups to be made while conditioning out possible “individual” effects of “age,” “sex,” “level of dependency,” “level of incontinence care,” and “number of regular daily/prescribed medications.” After controlling for the effects of a range of individual level factors, and after controlling for unequal variance across groups (heteroscedascity), there was little difference between community dwelling older adults and institutional care residents in IS score, suggesting that the stability of day-to-day patterns (such as bed get-up, lunch times, etc.) is similar within these two resident groups. However, institutional care residents experienced more fragmented rest/wake patterns (having significantly higher IV scores and significantly lower mean activity values). Our findings strongly suggest that the institutional care environment itself has a negative association with older people's rest/wake patterns; although, longitudinal studies are required to fully understand any causal relationships. (Author correspondence: r.meadows@surrey.ac.uk)     

A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries

Spectral library searching is a promising alternative to sequence database searching in peptide identification from MS/MS spectra. The key advantage of spectral library searching is the utilization of more spectral features to improve score discrimination between good and bad matches, and hence sensitivity. However, the coverage of reference spectral library is limited by current experimental and computational methods. We developed a computational approach to expand the coverage of spectral libraries with semi-empirical spectra predicted from perturbing known spectra of similar sequences, such as those with single amino acid substitutions. We hypothesized that the peptide of similar sequences should produce similar fragmentation patterns, at least in most cases. Our results confirm our hypothesis and specify when this approach can be applied. In actual spectral searching of real data sets, the sensitivity advantage of spectral library searching over sequence database searching can be mostly retained even when all real spectra are replaced by semi-empirical ones. We demonstrated the applicability of this approach by detecting several known non-synonymous single-nucleotide polymorphisms in three large human data sets by spectral searching.     

An alphabetic code based atomic level molecular similarity search in databases

Atomic level molecular similarity and diversity studies have gained considerable importance through their wide application in Bioinformatics and Chemo-informatics for drug design. The availability of large volumes of data on chemical compounds requires new methodologies for efficient and effective searching of its archives in less time with optimal computational power. We describe an alphabetic algorithm for similarity searching based on atom-atom bonding preference for ligands. We represented 170 cyclindependent kinase 2 inhibitors using strings of pre-defined alphabets for searching using known protein sequence alignment tools. Thus, a common pattern was extracted using this set of compounds for database searching to retrieve similar active compounds. Area under the receiver operating characteristic (ROC) curve was used for the discrimination of similar and dissimilar compounds in the databases. An average retrieval rate of about 60% is obtained in cross-validation using the home-grown dataset and the directory of useful decoys (DUD, formally known as the ZINC database) data. This will help in the effective retrieval of similar compounds using database search.     

PROP taster status interacts with the built environment to influence children's food acceptance and body weight status

Objectives:

Eating behaviors and obesity are complex phenotypes influenced by genes and the environment, but few studies have investigated the interaction of these two variables. The purpose of this study was to use a gene‐environment interaction model to test for differences in children's food acceptance and body weights.

Design and Methods:

Inherited ability to taste 6‐n‐propylthiouracil (PROP) was assessed as a marker of oral taste responsiveness. Food environment was classified as “healthy” or “unhealthy” based on proximity to outlets that sell fruits/vegetables and fast foods using Geographic Information Systems (GIS). The cohort consisted of 120 children, ages 4‐6 years, recruited from New York City over 2005‐2010. Home address and other demographic variables were reported by parents and PROP status, food acceptance, and anthropometrics were assessed in the laboratory. Based on a screening test, children were classified as PROP tasters or non‐tasters. Hierarchical linear models analysis of variance was performed to examine differences in food acceptance and body mass index (BMI) z‐scores as a function of PROP status, the food environment (“healthy” vs. “unhealthy”), and their interaction.

Results and Conclusion:

Results showed an interaction between taster status and the food environment on BMI z‐score and food acceptance. Non‐taster children living in healthy food environments had greater acceptance of vegetables than taster children living in healthy food environments (P ≤ 0.005). Moreover, non‐tasters from unhealthy food environments had higher BMI z‐scores than all other groups (P ≤ 0.005). Incorporating genetic markers of taste into studies that assess the built environment may improve the ability of these measures to predict risk for obesity and eating behaviors. Obesity (2012)     

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.     

BIOGEOGRAPHIC ANALYSIS OF THE GLOBALLY DISTRIBUTED HARMFUL ALGAL BLOOM SPECIES ALEXANDRIUM MINUTUM (DINOPHYCEAE) BASED ON rRNA GENE SEQUENCES AND MICROSATELLITE MARKERS1

The toxic dinoflagellate Alexandrium minutum Halim is one of three species that comprise the “minutum” species complex. This complex is notable due to its role in the etiology of paralytic shellfish poisoning (PSP). Recent increases in PSP incidence and the geographic expansion of toxin‐producing Alexandrium dinoflagellates have prompted the intensive examination of genetic relationships among globally distributed strains to address questions regarding their present distribution and reasons for their apparent increase. The biogeography of A. minutum was studied using large subunit ribosomal DNA gene (LSU rRNA) and internal transcribed spacer (ITS) sequences and genotypic data from 12 microsatellite loci. rRNA gene and ITS sequencing data distinguished between two clades, herein termed the “Global” and the “Pacific”; however, little to no resolution was seen within each clade. Genotypic data from 12 microsatellite loci provided additional information regarding genetic relationships within the Global clade, but it was not possible to amplify DNA from the Pacific clade using these markers. With the exception of isolates from Italy and Spain, strains generally clustered according to origin, revealing geographic structuring within the Global clade. Additionally, no evidence supported the separation of A. lusitanicum and A. minutum as different species. With the use of microsatellites, it is now possible to initiate studies on the origin, history, and genetic heterogeneity of A. minutum that were not previously possible using only rRNA gene sequence data. This study demonstrates the power of combining a marker with intermediate resolution (rRNA sequences) with finer‐scale markers (microsatellites) to examine intraspecies variability among globally distributed isolates and represents the first effort to employ this technique in A. minutum.     

Short-range Navigation of the Weakly Electric Fish,Gnathonemus petersii L. (Mormyridae,Teleostei), in Novel and Familiar Environments

We investigated the electrolocation performance of the weakly electric fish, Gnathonemus petersii, in novel and familiar environments. By selectively interfering with the fish's sensory input, we determined the sensory channels necessary for navigation and orientation. The fish's task was to locate a circular aperture (diameter: 64 mm) in a wall dividing a 200–1 aquarium into two equal compartments. To assess the fish's performance, we measured (1) the time it took the fish to locate the aperture, (2) the height at which it contacted the divider, (3) its electric organ discharge rate, and (4) the frequency of divider crossings. In the first experiment (novel environment), 50 naive G. petersii assigned to five groups of 10 fish each (intact, blind, electrically “silent,” blind and “silent,” and shamoperated animals) were tested with the aperture presented randomly in one of three positions (aperture center: 7.6, 17.7, 27.8 cm from the bottom). In a novel environment, G. petersii depend on active electrolocation. Despite the changing aperture position, over the 15 trials, fish with a functioning electric organ found the aperture, whereas those without one did not. The electric organ discharge rate was inversely correlated with the amount of time spent searching for the aperture. In a second experiment (familiar environment) 20 intact fish learned the position of a fixed aperture. When we subsequently denervated the electric organ in 10 of these animals, their performance did not differ significantly from that of their conspecifics. Thus, once the fish were familiar with the aperture's position, they no longer depended on active electrolocation. We interpret and discuss this behavior as evidence for a “central expectation” and discuss its possible role in electronavigation.     

A dysmorphology score system for assessing embryo abnormalities in rat whole embryo culture

BACKGROUND: The rodent whole embryo culture (WEC) system is a well‐established model for characterizing developmental toxicity of test compounds and conducting mechanistic studies. Laboratories have taken various approaches in describing type and severity of developmental findings of organogenesis‐stage rodent embryos, but the Brown and Fabro morphological score system is commonly used as a quantitative approach. The associated score criteria is based upon developmental stage and growth parameters, where a series of embryonic structures are assessed and assigned respective scores relative to their gestational stage, with a Total Morphological Score (TMS) assigned to the embryo. This score system is beneficial because it assesses a series of stage‐specific anatomical landmarks, facilitating harmonized evaluation across laboratories. Although the TMS provides a quantitative approach to assess growth and determine developmental delay, it is limited to its ability to identify and/or delineate subtle or structure‐specific abnormalities. Because of this, the TMS may not be sufficiently sensitive for identifying compounds that induce structure or organ‐selective effects. METHOD: This study describes a distinct morphological score system called the “Dysmorphology Score System (DMS system)” that has been developed for assessing gestation day 11 (approximately 20–26 somite stage) rat embryos using numerical scores to differentiate normal from abnormal morphology and define the respective severity of dysmorphology of specific embryonic structures and organ systems. This method can also be used in scoring mouse embryos of the equivalent developmental stage. RESULT AND CONCLUSION: The DMS system enhances capabilities to rank‐order compounds based upon teratogenic potency, conduct structure‐ relationships of chemicals, and develop statistical prediction models to support abbreviated developmental toxicity screens. Birth Defects Res (Part B) 89:485–492, 2010. © 2010 Wiley‐Liss, Inc.     

A Reliability and Validity Study of the Bergen Shift Work Sleep Questionnaire in Nurses Working Three-Shift Rotations

The “Bergen Shift Work Sleep Questionnaire” (BSWSQ) was developed to systematically assess discrete sleep problems related to different work shifts (day, evening, night shifts) and rest days. In this study, we assessed the psychometric properties of the BSWSQ using a sample of 760 nurses, all working in a three-shift rotation schedule: day, evening, and night shifts. BSWSQ measures insomnia symptoms using seven questions: >30-min sleep onset latency, >30-min wake after sleep onset, >30-min premature awakenings, nonrestorative sleep, being tired/sleepy at work, during free time on work days, and when not working/on vacation. Symptoms are assessed separately for each work shift and rest days, as “never,” “rarely,” “sometimes,” “often,” “always,” or “not applicable.” We investigated the BSWSQ model fit, reliability (test-retest of a subsample, n?=?234), and convergent and discriminant validity between the BSWSQ and Epworth Sleepiness Scale, Fatigue Questionnaire, and Hospital Anxiety Depression Scale. We also investigated differences in mean scores between the different insomnia symptoms with respect to different work shifts and rest days. BSWSQ demonstrated an adequate model fit using structural equation modeling: root mean square error of approximation?=?.071 (90% confidence interval [CI]?=?.066–.076), comparative fit index?=?.91, and chi-square/degrees of freedom?=?4.41. The BSWSQ demonstrated good reliability (test-retest coefficients p?<?.001). We found good convergent and discriminant validity between BSWSQ and the other scales (all coefficients p?<?.001). There were significant differences between the overall/composite scores of the various work shifts. Night shift showed the highest score compared to day and evening shifts as well as to rest days (all post hoc comparisons p?<?.001). Mean scores of different symptoms also varied significantly within the individual work shifts. We conclude that the BSWSQ meets the necessary psychometric standards, enabling systematic study of discrete insomnia symptoms in different work shifts. (Author correspondence: elisabeth.flo@psykp.uib.no)     

Sleepiness during shift work in Japanese nurses: A comparison study using JESS,SSS, and actigraphy

The present cross-sectional survey of shift-working nurses investigated the characteristics of the Japanese version of the Epworth Sleepiness Scale (JESS), the Stanford Sleepiness Scale (SSS) and actigraphy. Subjects comprised 51 nurses recruited from among participants of the Gunma Nurses’ Health Study. The self-check lists used were the JESS for “recent sleepiness” and the SSS for “current sleepiness.” Actigraphy was performed using an Actiwatch worn for 7–9 days. Subjects also kept a sleep diary. Prevalence of excessive daytime sleepiness was determined using a cut-off value of 11 for total JESS score. SSS was administered at 2-h intervals from the time of starting work until shift completion. Mean (±standard deviation) JESS score was 10.4 ± 3.6; scores were significantly higher for shift workers than for non-shift workers (P > 0.05). Agreement and sensitivity/specificity of JESS score based on maximum SSS score were investigated by varying thresholds for each. JESS score (0–10/11–24) and maximum SSS score (1–3/4–7) showed intermediate agreement (k= 0.416). When the JESS score threshold was 0–10/11–24 and the maximum SSS score threshold was 1–3/4–7, the Youden index (calculated from sensitivity and specificity) was 0.51, indicating those thresholds as cut-off points facilitating detection of sleepiness. Actiwatch-determined sleep variables were uncorrelated to JESS scores, but sleepiness as determined by JESS and actigraphy exhibited a weak correlation. Our findings suggest that the JESS is a scale that reflects SSS, representing current sleepiness, and is an easy-to-use and effective tool for detecting sleepiness. The JESS is useful for self-monitoring, and SSS and Actiwatch can be applied when JESS score is high.

     

CELL SIZE DIFFERENTIATION IN THE BLOOM-FORMING DINOFLAGELLATE GYMNODINIUM CF. NAGASAKIENSE1

Two subpopulations differing essentially by their mean cell size were observed regularly in cultures and natural samples of the naked dinoflagellate Gymnodinium cf. nagasakiense Takayama et Adachi (currently known as Gyrodinium aureolum Hulburt), a species which frequently forms red tides in North European seas. “Large” cells represented the typical forms; they were morphologically similar to cells of the closely related Japanese species G. nagasakiense, which did not form any subpopulation of reduced size. “Small” and “large” cells of G. cf. nagasakiense had the same DNA content, but the nucleus of the former appeared to be much more condensed during interphase. Each cell type was able to divide and had its own growth dynamics; therefore, any intermediary between pure populations of “small” and of “large” cells were observed in culture. The “large” form generated a “small” cell by an atypical budding-like division, whereas the “small” form gave back a “large” form, once it ceased to divide, by simple enlargement of its cell body. Factory inducing cell size differentiation are yet unclear. Neither nitrogen nor phosphorus starvation induced a significant increase in the relative proportion of “small” and budding cells. Although cell size differentiation is associated with the formation of gametes in a variety of dinoflagellates, we demonstrated that “small” cells of G. cf. nagasakiense are able to divide asexually, in contrast to gametes of most other species. The high proliferative power of “small” cells as compared with normal cells suggests that they could play a significant role during red tides of G. cf. nagasakiense; in contrast, cells of the Japanese species G. Nagasakiense could sustain high growth rates with larger cell size because this species generally blooms in waters much warmer than those found in northern Europe.