Implantable sensor technology: measuring bone and joint biomechanics of daily life in vivo

Stresses and strains are major factors influencing growth, remodeling and repair of musculoskeletal tissues. Therefore, knowledge of forces and deformation within bones and joints is critical to gain insight into the complex behavior of these tissues during development, aging, and response to injury and disease. Sensors have been used in vivo to measure strains in bone, intraarticular cartilage contact pressures, and forces in the spine, shoulder, hip, and knee. Implantable sensors have a high impact on several clinical applications, including fracture fixation, spine fixation, and joint arthroplasty. This review summarizes the developments in strain-measurement-based implantable sensor technology for musculoskeletal research.     

The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics

Training and testing of conventional machine learning models on binary classification problems depend on the proportions of the two outcomes in the relevant data sets. This may be especially important in practical terms when real-world applications of the classifier are either highly imbalanced or occur in unknown proportions. Intuitively, it may seem sensible to train machine learning models on data similar to the target data in terms of proportions of the two binary outcomes. However, we show that this is not the case using the example of prediction of deleterious and neutral phenotypes of human missense mutations in human genome data, for which the proportion of the binary outcome is unknown. Our results indicate that using balanced training data (50% neutral and 50% deleterious) results in the highest balanced accuracy (the average of True Positive Rate and True Negative Rate), Matthews correlation coefficient, and area under ROC curves, no matter what the proportions of the two phenotypes are in the testing data. Besides balancing the data by undersampling the majority class, other techniques in machine learning include oversampling the minority class, interpolating minority-class data points and various penalties for misclassifying the minority class. However, these techniques are not commonly used in either the missense phenotype prediction problem or in the prediction of disordered residues in proteins, where the imbalance problem is substantial. The appropriate approach depends on the amount of available data and the specific problem at hand.     

Escherichia coli cells with increased levels of DnaA and deficient in recombinational repair have decreased viability

The dnaA operon of Escherichia coli contains the genes dnaA, dnaN, and recF encoding DnaA, beta clamp of DNA polymerase III holoenzyme, and RecF. When the DnaA concentration is raised, an increase in the number of DNA replication initiation events but a reduction in replication fork velocity occurs. Because DnaA is autoregulated, these results might be due to the inhibition of dnaN and recF expression. To test this, we examined the effects of increasing the intracellular concentrations of DnaA, beta clamp, and RecF, together and separately, on initiation, the rate of fork movement, and cell viability. The increased expression of one or more of the dnaA operon proteins had detrimental effects on the cell, except in the case of RecF expression. A shorter C period was not observed with increased expression of the beta clamp; in fact, many chromosomes did not complete replication in runout experiments. Increased expression of DnaA alone resulted in stalled replication forks, filamentation, and a decrease in viability. When the three proteins of the dnaA operon were simultaneously overexpressed, highly filamentous cells were observed (>50 micro m) with extremely low viability and, in runout experiments, most chromosomes had not completed replication. The possibility that recombinational repair was responsible for the survival of cells overexpressing DnaA was tested by using mutants in different recombinational repair pathways. The absence of RecA, RecB, RecC, or the proteins in the RuvABC complex caused an additional approximately 100-fold drop in viability in cells with increased levels of DnaA, indicating a requirement for recombinational repair in these cells.     

A chemical,genetic, and structural analysis of the nuclear bile acid receptor FXR

The farnesoid X receptor (FXR) functions as a bile acid (BA) sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. However, BAs are poor reagents for characterizing FXR functions due to multiple receptor independent properties. Accordingly, using combinatorial chemistry we evolved a small molecule agonist termed fexaramine with 100-fold increased affinity relative to natural compounds. Gene-profiling experiments conducted in hepatocytes with FXR-specific fexaramine versus the primary BA chenodeoxycholic acid (CDCA) produced remarkably distinct genomic targets. Highly diffracting cocrystals (1.78 A) of fexaramine bound to the ligand binding domain of FXR revealed the agonist sequestered in a 726 A(3) hydrophobic cavity and suggest a mechanistic basis for the initial step in the BA signaling pathway. The discovery of fexaramine will allow us to unravel the FXR genetic network from the BA network and selectively manipulate components of the cholesterol pathway that may be useful in treating cholesterol-related human diseases.     

The Assemblage of Birds Foraging in Native West Indian Pine (Pinus occidentalis) Forests of the Dominican Republic during the Nonbreeding Season1

We studied avian resource use in a native West Indian pine (Pinus occidentalis) forest in the Cordillera Central of the Dominican Republic during the nonbreeding season. The forest is characterized by a fairly open pine canopy and a dense mixed-broadleaf and pine understory. We used a principal components analysis of 23 foraging characters for 23 bird species, including foraging height, the proportional use of 5 different foraging methods, 3 horizontal positions and foliage densities, and 11 foraging substrates. Five principal components accounted for 74 percent of the total variance of the assemblage variables and resulted in the delineation of at least 5 foraging guilds. 78 percent of bird species had mean foraging heights of 5.0–10.0 m, corresponding to the region of overlap of pine and broadleaf vegetation. As a result, the diversity of foraging substrates and maneuvers used by birds, rather than foraging height, appears to be the primary means by which birds that exploit this habitat separate ecologically. Migrant wood warblers (Parulinae) are probably able to integrate into the community because of little diet overlap between residents and migrants, and the fairly specialized nature of their largely insectivorous foraging habits. Avian foraging in this habitat may reflect the effects of frequent disturbance such as hurricanes.     

Inactivation of Feline Calicivirus and Adenovirus Type 40 by UV Radiation

Little information regarding the effectiveness of UV radiation on the inactivation of caliciviruses and enteric adenoviruses is available. Analysis of human calicivirus resistance to disinfectants is hampered by the lack of animal or cell culture methods that can determine the viruses' infectivity. The inactivation kinetics of enteric adenovirus type 40 (AD40), coliphage MS-2, and feline calicivirus (FCV), closely related to the human caliciviruses based on nucleic acid organization and capsid architecture, were determined after exposure to low-pressure UV radiation in buffered demand-free (BDF) water at room temperature. In addition, UV disinfection experiments were also carried out in treated groundwater with FCV and AD40. AD40 was more resistant than either FCV or coliphage MS-2 in both BDF water and groundwater. The doses of UV required to achieve 99% inactivation of AD40, coliphage MS-2, and FCV in BDF water were 109, 55, and 16 mJ/cm², respectively. The doses of UV required to achieve 99% inactivation of AD40, coliphage MS-2, and FCV in groundwater were slightly lower than those in BDF water. FCV was inactivated by 99% by 13 mJ/cm² in treated groundwater. A dose of 103 mJ/cm² was required for 99% inactivation of AD40 in treated groundwater. The results of this study indicate that if FCV is an adequate surrogate for human caliciviruses, then their inactivation by UV radiation is similar to those of other single-stranded RNA enteric viruses, such as poliovirus. In addition, AD40 appears to be more resistant to UV disinfection than previously reported.     

Mycotoxin fumonisin B1 increases intestinal colonization by pathogenic Escherichia coli in pigs

Fumonisin B(1) (FB(1)) is a mycotoxin that commonly occurs in maize. FB(1) causes a variety of toxic effects in different animal species and has been implicated as a contributing factor of esophageal cancers in humans. In the present study, we examined the effect of dietary exposure to FB(1) on intestinal colonization by pathogenic Escherichia coli associated with extraintestinal infection. Three-week-old weaned pigs were given FB(1) by gavage as a crude extract or as a purified toxin at a dose of 0.5 mg/kg of body weight daily for 6 days. On the last day of the toxin treatment, the pigs were orally inoculated with an extraintestinal pathogenic E. coli strain. All animals were euthanized 24 h later, necropsies were performed, and tissues were taken for bacterial counts and light microscopic examination. Ingestion of FB(1) had only a minimal effect on animal weight gain, did not cause any macroscopic or microscopic lesions, and did not change the plasma biochemical profile. However, colonization of the small and large intestines by an extraintestinal pathogenic E. coli strain was significantly increased. Our results show that FB(1) is a predisposing factor to infectious disease and that the pig can be used as a model for the study of the consequences of ingesting mycotoxin-contaminated food.     

Noninfectious human immunodeficiency virus type 1 mutants deficient in genomic RNA.

All retroviruses contain, in the nucleocapsid domain of the Gag protein, one or two copies of the sequence Cys-X2-Cys-X4-His-X4-Cys. We have generated a series of mutants in the two copies of this motif present in human immunodeficiency virus type 1. These mutants encoded virus particles that were apparently composed of the normal complement of viral proteins but contained only 2 to 20% of the normal level of genomic RNA. No infectivity could be detected in the mutant particles, while 10(5) infectious U were present in an equivalent amount of wild-type particles. Thus, the mutants have another defect in addition to the inefficiency with which they encapsidate genomic RNA. Our results show that both copies of the motif are required for normal RNA packaging and for infectivity. Mutants of this type may have important applications, including nonhazardous materials for research, immunogens in vaccine and immunotherapy studies, and diagnostic reagents.     

What is Communicated in the Antipredator Calls of Lemurs: Evidence from Playback Experiments with Ringtailed and Ruffed Lemurs

Two hypotheses of signal specificity in antipredator calls (“referential signalling” and “response urgency”) are discussed in light of prior research on ground squirrels and vervet monkeys. These hypotheses then are examined with data on responses of semi-captive ringtailed and ruffed lemurs to antipredator call playbacks. Although the responses of ringtailed lemurs support a referential-signalling interpretation of their antipredator calls, those of ruffed lemurs do not conform well to either hypothesis. Rather, ruffed lemur antipredator calls seem best viewed as “affective” signals that may only reflect underlying emotional/motivational states.