Selecting the right tool for the job.
Ontology highlight
ABSTRACT:
SUBMITTER: Caplan AL
PROVIDER: S-EPMC5572069 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Normal DNA replication is blocked by DNA damage in the template strand. Translesion synthesis is a major pathway for overcoming these replication blocks. In this process, multiple non-classical DNA polymerases are thought to form a complex at the stalled replication fork that we refer to as the mutasome. This hypothetical multi-protein complex is structurally organized by the replication accessory factor PCNA and the non-classical polymerase Rev1. One of the non-classical polymerases within this complex then catalyzes replication through the damage. Each non-classical polymerase has one or more cognate lesions, which the enzyme bypasses with high accuracy and efficiency. Thus, the accuracy and efficiency of translesion synthesis depends on which non-classical polymerase is chosen to bypass the damage. In this review article, we discuss how the most appropriate polymerase is chosen. In so doing, we examine the structural motifs that mediate the protein interactions in the mutasome; the multiple architectures that the mutasome can adopt, such as PCNA tool belts and Rev1 bridges; the intrinsically disordered regions that tether the polymerases to PCNA and to one another; and the kinetic selection model in which the most appropriate polymerase is chosen via a competition among the multiple polymerases within the mutasome.
| S-EPMC6340752 | biostudies-literature
Project description:Eggs are the rarest cell in the human body, yet their study is essential for the fields of fertility, reproduction, and fetal health. Guo et al. (Proteomics 2015, 15, 4080-4095) use a "surrogate" animal to discover the phosphoproteomic pathways involved in egg activation. With datasets of several thousand phosphosites on 2500 different proteins, these investigators have defined new pathways, connections to pathways, and priorities in searches for how eggs are activated at fertilization. These results in a sea urchin are now transposable to mammals for testing on a per candidate strategy.
| S-EPMC5093332 | biostudies-literature
Project description:Estimating the causal effect of an exposure (vs. some control) on an outcome using observational data often requires addressing the fact that exposed and control groups differ on pre-exposure characteristics that may be related to the outcome (confounders). Propensity score methods have long been used as a tool for adjusting for observed confounders in order to produce more valid causal effect estimates under the strong ignorability assumption. In this article, we compare two promising propensity score estimation methods (for time-invariant binary exposures) when assessing the average treatment effect on the treated: the generalized boosted models and covariate-balancing propensity scores, with the main objective to provide analysts with some rules-of-thumb when choosing between these two methods. We compare the methods across different dimensions including the presence of extraneous variables, the complexity of the relationship between exposure or outcome and covariates, and the residual variance in outcome and exposure. We found that when noncomplex relationships exist between outcome or exposure and covariates, the covariate-balancing method outperformed the boosted method, but under complex relationships, the boosted method performed better. We lay out criteria for when one method should be expected to outperform the other with no blanket statement on whether one method is always better than the other.
| S-EPMC5617809 | biostudies-literature
Project description:BackgroundDue to the recent increased use of the McMaster (MM) fecal egg counting method for assessing benzimidazole drug efficacy for treating soil-transmitted helminth (STH) infections, the aim of the current study was to determine the operational value of including the MM method alongside the Kato-Katz (KK) fecal thick smear to increase the diagnostic sensitivity when STHs are co-endemic with trematode helminths (e.g., Schistosoma mansoni).MethodsA cross-sectional study was conducted in school-aged children aged 4-18 years in the northeastern region of the State of Minas Gerais (Brazil), where Necator americanus, Ascaris lumbricoides, Trichuris trichiura, and S. mansoni are co-endemic. One fecal sample from each participant was collected and transported to the field laboratory for analysis. Coprological diagnosis was performed on each fecal sample by three different methods: Formalin-Ether Sedimentation (FES), KK and the MM technique. The diagnostic sensitivity and negative predictive value (NPV) of each technique was calculated using the combination of all three techniques as the composite standard. In order to determine the agreement between the three techniques Fleiss´ kappa was used. Both the Cure Rate (CR) and the Fecal Egg Count Reduction (FECR) were calculated using the two quantification techniques (i.e., the MM and KK).ResultsFecal samples from 1260 children were analyzed. The KK had higher diagnostic sensitivity than the MM for the detection of both A. lumbricoides (KK 97.3%, MM 69.5%) and hookworm (KK 95.1%, MM 80.8%). The CR of a single dose of mebendazole varied significantly between the KK and MM for both A. lumbricoides (p = 0.016) and hookworm (p = 0.000), with lower rates obtained with the KK. On the other hand, the FECR was very similar between both techniques for both A. lumbricoides and hookworm.ConclusionThe MM did not add any diagnostic value over the KK in areas where both STHs and trematodes were co-endemic. The lower sensitivity of the MM would have an important impact on the administration of selective school-based treatment in this area since if only the MM were used, 36 (13.9%) children diagnosed with A. lumbricoides would have gone untreated.
| S-EPMC4524677 | biostudies-literature
Project description:INTRODUCTION:Metformin is the recommended initial treatment in type 2 diabetes mellitus (T2DM), but when this does not give adequate glucose control the choice of which second-line drug to use is uncertain as none have been found to have a better overall glycaemic response. In this real-world study dipeptidyl peptidase 4 inhibitors (DPP4i), sulphonylureas (SU), thiazolidinediones (TZD) and sodium glucose co-transporter 2 inhibitors (SGLT2i) were compared for their effectiveness in lowering glycated haemoglobin (HbA1c) levels for a particular individual based on their clinical characteristics. METHODS:A retrospective analysis was undertaken of electronic health records of people with T2DM prescribed metformin alongside a DPP4i, SU, TZD or SGLT2i at second-line. Regression modelling was used to model the changes in HbA1c from baseline at month 6 and month 12 for the individual therapies, adjusting for demographic and clinical characteristics. RESULTS:There were 7170 people included in the study. Treatment at second-line with SUs, DPP4i, TZDs and SGLT2i resulted in similar percentages of people achieving the recommended HbA1c target of?<?7.5% (58 mmol/mol) at both 6 and 12 months. For those receiving SGLT2i and SUs, the greatest improvement in HbA1c was observed in relatively younger and older people, respectively. Trends were detected between other baseline characteristics and HbA1c improvement by drug class, but they were not statistically significant. Non-adherence rates were low for all drug classes. People with a higher medication possession ratio (??80%) also had greater improvements in HbA1c at 12 months. CONCLUSION:This study identified patients' phenotypic characteristics that may have the potential to influence individual treatment response. Accounting for these characteristics in clinical treatment decisions may facilitate individualised prescribing by being able to select the right drug for the right patient.
| S-EPMC7261289 | biostudies-literature
Project description:Tools pose a challenge to the need to select actions appropriate for task goals and environmental constraints. For many tools (e.g., calculator), actions for "using" and "grasping-to-move" conflict with each other and may compete during selection. To date, little is known about the mechanisms that enable selection between possible tool actions or their neural substrates. The study of patients with chronic left hemisphere stroke, many of whom are deficient in tool-use action (apraxic), provides an opportunity to elucidate these issues. Here, 31 such patients pantomimed or recognized tool use actions for "conflict" and "non-conflict" tools. Voxel-based lesion-symptom mapping (VLSM), lesion subtraction, and tractographic overlap analyses were used to determine brain regions necessary for selecting among tool-directed actions. Lesions to posterior middle temporal gyrus (pMTG) and anterior intraparietal sulcus (aIPS) tended to impair production of use actions similarly for both conflict and non-conflict tools. By contrast, lesions to the supramarginal gyrus (SMG), inferior frontal gyrus (IFG)/anterior insula, and superior longitudinal fasciculus (SLF) specifically impaired production of use actions for conflict tools. Patients' errors on conflict tools suggested inappropriate selection of grasping actions and difficulty selecting single actions. Use/grasp conflict had no effect on action recognition. We suggest that the SMG/SLF/IFG pathway implements biased competition between possible tool actions, while aIPS and pMTG compute the structure-based and skilled use actions, respectively, that constitute input to this competitive process. This is the first study to demonstrate a reliable link between a characteristic of single tools (i.e., their association with different use and grasp actions) and action selection difficulties. Additionally, the data allow us to posit an SMG-involved subtype of apraxia characterized by an inability to resolve action competition.
| S-EPMC4385438 | biostudies-literature
Project description:Variations in candidate and donor acceptance criteria may influence access and mortality for liver transplantation. We sought to understand how recipient and donor characteristics vary across centers and how patients interpret this information, and we used these data to develop a tool to provide tailored information to candidates seeking a center (www.transplantcentersearch.org). We analyzed liver recipient data from the Scientific Registry of Transplant Recipients to determine how recipient and donor characteristics (eg, age, Medicaid use, and human immunodeficiency virus status) varied across programs. Data included recipients and donors at each US program between January 1, 2015, and December 31, 2017. The variation in characteristics was plotted with centers stratified by total transplant volume and by volume of each characteristic. A subset of characteristics was plotted to show variation over 3 years. We created mockups of potential reports displaying recipient characteristics alongside pretransplant and posttransplant outcomes and solicited feedback at patient and family interviews and focus groups, which included 39 individuals: 10 pilot interviews with candidates seeking liver transplant at the University of Minnesota-Fairview (UMNF) and 5 focus groups with 13 UMNF candidates, 6 UMNF family members, and 10 national recipients. Transcripts were analyzed using a thematic analysis. Several themes emerged: (1) Candidates experience gaps in existing education about center options; (2) patients requested information about how selection criteria might impact access to transplant; and (3) information tailored to a candidate's medical characteristics can inform decisions. Characteristics shown on mockups varied across centers (P < 0.01). Variation was widespread for small and large centers. In conclusion, variation exists in recipient and donor characteristics across centers. Liver transplant patients provide positive feedback upon viewing patient-specific search tools.
| S-EPMC8193801 | biostudies-literature
Project description:Literature has demonstrated the successful application of various prompts and prompt-fading procedures for teaching clients with intellectual and developmental disabilities. However, few practical resources exist to guide behavior analysts in the evaluation and selection of a prompting strategy for a given client and a targeted skill. In this article, we describe the development of a decision-making tool for selecting and evaluating prompting strategies, highlighting steps needed prior to evaluating clinical outcomes associated with the use of the tool. We used a multiple baseline across participants design to assess the ease with which graduate students could apply the decision-making tool with clients across a variety of skills. Results indicated that the participants learned to apply the decision-making tool with relatively limited involvement from a trainer. Social validity data collected from participants suggested that they found the tool helpful. Results contribute to the literature on the development of decision-making tools to guide behavior analysts in the selection of interventions to use with clients.Supplementary informationThe online version contains supplementary material available at 10.1007/s40617-022-00722-8.
| S-EPMC9177132 | biostudies-literature
Project description:Deubiquitinases (DUBs) have been the subject of intense scrutiny in recent years. Many of their diverse enzymatic mechanisms are well characterized in vitro; however, our understanding of these enzymes at the cellular level lags due to the lack of quality tool reagents. DUBs play a role in seemingly every biological process and are central to many human pathologies, thus rendering them very desirable and challenging therapeutic targets. This review aims to provide researchers entering the field of ubiquitination with knowledge of the pharmacological modulators and tool molecules available to study DUBs. A focus is placed on small molecule inhibitors, ubiquitin variants (UbVs), and activity-based probes (ABPs). Leveraging these tools to uncover DUB biology at the cellular level is of particular importance and may lead to significant breakthroughs. Despite significant drug discovery efforts, only approximately 15 chemical probe-quality small molecule inhibitors have been reported, hitting just 6 of about 100 DUB targets. UbV technology is a promising approach to rapidly expand the library of known DUB inhibitors and may be used as a combinatorial platform for structure-guided drug design.
| S-EPMC9139131 | biostudies-literature
Project description:Cover crop mixtures have the potential to provide more ecosystem services than cover crop monocultures. However, seeding rates that are typically recommended (i.e. seeding rate of monoculture divided by the number of species in the mixture) are non-optimized and often result in the competitive species dominating the mixture, and therefore limiting the amount of ecosystem services that are provided. We created an analytical framework for selecting seeding rates for cover crop mixtures that maximize multifunctionality while minimizing seed costs. The framework was developed using data from a field experiment, which included six response surface designs of two-species mixtures, as well as a factorial replacement design of three-species and four-species mixtures. We quantified intraspecific and interspecific competition among two grasses and two legume cover crop species with grass and legume representing two functional groups: pearl millet [Pennisetum glaucum (L.) R.Br.], sorghum sudangrass [Sorghum bicolor (L.) Moench × Sorghum sudanense (Piper) Stapf], sunn hemp (Crotalaria juncea L.), and cowpea [Vigna unguiculata (L.) Walp]. Yield-density models were fit to estimate intraspecific and interspecific competition coefficients for each species in biculture. The hierarchy from most to least competitive was sorghum sudangrass > sunn hemp > pearl millet > cowpea. Intraspecific competition of a less competitive species was the greatest when the biculture was composed of two species in the same functional group. Competition coefficients were used to build models that estimated the biomass of each cover crop species in three-species and four-species mixtures. The competition coefficients and models were validated with an additional nine site-years testing the same cover crop mixtures. The biomass of a species in a site-year was accurately predicted 69% of the time (low root mean square error, correlation > 0.5, not biased, r2 > 0.5). Applying the framework, we designed three-species and four-species mixtures by identifying relative seeding rates that produced high biomass with high species evenness (i.e. high multifunctionality) at low seed costs based on a Pareto front analysis of 10,418 mixtures. Accounting for competition when constructing cover crop mixtures can improve the ecosystem services provided, and such an advancement is likely to lead to greater farmer adoption.
| S-EPMC9285019 | biostudies-literature