Number Of Positive Interactions Research Articles

UnbiasedDTI: Mitigating Real-World Bias of Drug-Target Interaction Prediction by Using Deep Ensemble-Balanced Learning

Drug-target interaction (DTI) prediction through in vitro methods is expensive and time-consuming. On the other hand, computational methods can save time and money while enhancing drug discovery efficiency. Most of the computational methods frame DTI prediction as a binary classification task. One important challenge is that the number of negative interactions in all DTI-related datasets is far greater than the number of positive interactions, leading to the class imbalance problem. As a result, a classifier is trained biased towards the majority class (negative class), whereas the minority class (interacting pairs) is of interest. This class imbalance problem is not widely taken into account in DTI prediction studies, and the few previous studies considering balancing in DTI do not focus on the imbalance issue itself. Additionally, they do not benefit from deep learning models and experimental validation. In this study, we propose a computational framework along with experimental validations to predict drug-target interaction using an ensemble of deep learning models to address the class imbalance problem in the DTI domain. The objective of this paper is to mitigate the bias in the prediction of DTI by focusing on the impact of balancing and maintaining other involved parameters at a constant value. Our analysis shows that the proposed model outperforms unbalanced models with the same architecture trained on the BindingDB both computationally and experimentally. These findings demonstrate the significance of balancing, which reduces the bias towards the negative class and leads to better performance. It is important to note that leaning on computational results without experimentally validating them and by relying solely on AUROC and AUPRC metrics is not credible, particularly when the testing set remains unbalanced.

Human-Animal Interactions in Dairy Buffalo Farms.

Simple SummaryThe quality of the human-animal relationship plays a central role in determining animal welfare. In this study, we assessed the relationship between stockperson behavior and buffalo behavior. In particular, during milking, we recorded the behavior of stockpeople in terms of quality and quantity of interactions, and we recorded the behavior of animals in terms of restlessness, whereas at the feeding place, we measured the avoidance distance. Avoidance distance of an animal can be defined as the distance to which the animal will allow an unknown person to approach before moving to the side or away. We found that a high percentage of negative stockperson interactions (shouting, talking impatiently, slapping, and handling forcefully) were associated with a high avoidance distance at the feeding place and restlessness during milking. Therefore, appropriate stockpeople training should be conducted to improve the human-animal relationship with positive effects on animal welfare, productivity, and stockpeople safety.This study aimed to assess the relationship between stockperson behavior and buffalo behavior. The research was carried out in 27 buffalo farms. The behavior of stockpeople and animals during milking and the avoidance distance at the feeding place were recorded. Recordings were repeated within one month to assess test-retest reliability. A high degree of test-retest reliability was observed for all the variables with Spearman rank correlation coefficients (rs) ranging from 0.578 (p = 0.002, df = 25) for the number of kicks performed during milking to 0.937 (p < 0.001, df = 25) for the percentage of animals moving when approached by ≤ 0.5 m. The number of negative stockperson interactions correlated positively with the number of kicks during milking (rs = 0.421, p < 0.028, df = 25) and the percentage of animals injected with oxytocin (rs = 0.424, p < 0.027), whereas the percentage of negative stockperson interactions correlated positively with the percentage of buffaloes moving when approached at a distance >1 m (rs = 0.415, p < 0.031, df = 25). In a subsample of 14 farms, milk yield was correlated positively with the number of positive interactions (rs = 0.588, p < 0.027, df = 12) and correlated negatively with the number of steps performed by the animals during milking (rs = −0.820, p < 0.001, df = 12). This study showed that the quality of stockpeople interactions may affect buffalo behavior and production.

Yeast Two-Hybrid System for Studying Protein-Protein Interactions--Stage 4: Isolation of Library Plasmid Insert and Second Confirmation of Positive Interactions

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the "yeast two-hybrid system," uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term "two-hybrid" derives from the two classes of chimeric, or "hybrid," proteins used in each screen. The first, commonly referred to as the "bait," is a fusion of a protein of interest "x" with a DNA-binding domain (DBD-x). The second, sometimes called the "prey," is a fusion of a cDNA library "y" to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. Stage 4, described here, outlines a series of first-order and subsequent control experiments designed to establish whether an interacting protein is likely to be biologically significant. The number of positive interactions obtained will vary drastically from bait to bait. Subsequent processing methods will depend on the number initially obtained and on the preference of the individual investigator.

Reliability and validity of a cost-efficient sociometric measure

Sociometric measures have been used frequently to measure social status; however, reliable sociograms for young children usually involve time-consuming administrations. A group-administered, peer-rating sociogram, the Sociometric Peer-Rating Scale (SPRS), was devised and given to 217 first and second graders. Concomitantly, teacher nominations of children most liked, aggressive, or withdrawn and behavioral observations of the high- and low-SPRS children were obtained. After 7 months, the SPRS was readministered. On a separate population of eight kindergarten children, this sociogram and a similar, individually administered sociogram were given. Normative data, test-retest reliability, and split-half reliability were reported. The test-retest reliability was comparable to the reported reliability of other peer-rating sociograms, and the SPRS correlated significantly with teacher ratings of aggressiveness and likability and with the individually administered sociogram. The number of positive interactions was significantly different for high-versus low-SPRS children. The usefulness of the SPRS as a measure of social competence was discussed.

The effect of phorbols on metabolic cooperation between human fibroblasts

Autoradiography has been used to study the effect of 12-O-tetradecanoylphorbol-13-acetate (TPA), 4-O-methyl TPA, and phorbol on metabolic cooperation between human diploid fibroblasts. When the donors, hypoxanthine-guanine phosphoribosyl transferase+ (HGPRT+) cells, and recipients, HGPRT- cells, were plated together in the presence of [3H]hypoxanthine and either 4-O-methyl TPA or phorbol, nearly all interactions that developed in 4 h were positive for metabolic cooperation whereas when high concentrations of TPA were used, the number of positive interactions was significantly less than the control. If the phorbol analogs were added after the donors and recipients had made contact, the number of positive interactions was the same as the control in all cases. However, although primary recipients in the cultures that had been treated with phorbol had the same number of grains as those in the control, primary recipients in cultures that had been treated with TPA or high concentrations of 4-O-methyl TPA had significantly fewer grains than those in the control. TPA treatment for 4 h had no effect on total [3H]hypoxanthine incorporation or incorporation into acid-soluble and acid-insoluble fractions. Thus, the effect of TPA on metabolic cooperation is interpreted as a reduction in the transfer of [3H]nucleotides and is an indication of an interference with intercellular communication.