lab: an R package for generating analysis-ready data from laboratory records.

Background: Electronic health records (EHRs) play a crucial role in healthcare decision-making by giving physicians insights into disease progression and suitable treatment options. Within EHRs, laboratory test results are frequently utilized for predicting disease progression. However, processing laboratory test results often poses challenges due to variations in units and formats. In addition, leveraging the temporal information in EHRs can improve outcomes, prognoses, and diagnosis predication. Nevertheless, the irregular frequency of the data in these records necessitates data preprocessing, which can add complexity to time-series analyses. Methods: To address these challenges, we developed an open-source R package that facilitates the extraction of temporal information from laboratory records. The proposed lab package generates analysis-ready time series data by segmenting the data into time-series windows and imputing missing values. Moreover, users can map local laboratory codes to the Logical Observation Identifier Names and Codes (LOINC), an international standard. This mapping allows users to incorporate additional information, such as reference ranges and related diseases. Moreover, the reference ranges provided by LOINC enable us to categorize results into normal or abnormal. Finally, the analysis-ready time series data can be further summarized using descriptive statistics and utilized to develop models using machine learning technologies. Results: Using the lab package, we analyzed data from MIMIC-III, focusing on newborns with patent ductus arteriosus (PDA). We extracted time-series laboratory records and compared the differences in test results between patients with and without 30-day in-hospital mortality. We then identified significant variations in several laboratory test results 7 days after PDA diagnosis. Leveraging the time series-analysis-ready data, we trained a prediction model with the long short-term memory algorithm, achieving an area under the receiver operating characteristic curve of 0.83 for predicting 30-day in-hospital mortality in model training. These findings demonstrate the lab package's effectiveness in analyzing disease progression. Conclusions: The proposed lab package simplifies and expedites the workflow involved in laboratory records extraction. This tool is particularly valuable in assisting clinical data analysts in overcoming the obstacles associated with heterogeneous and sparse laboratory records.

Virtual 3D tooth creation for personized haptic simulation training in access cavity preparation.

Personalized medicine is a new medical concept to achieve patient-centered care. In dentistry, it is recognized for the customization of operative strategies and managements for oral diseases. Access cavity preparation in endodontic treatment is an irreversible procedure. Endodontic training will be more realistic by the implementation of clinical relevant 3D virtual reality technology. In this article, the authors first presented a personized case from a real patient to provide assess cavity preparation in haptic virtual reality dental simulator Simodont® (Nissin Dental Products Inc., Nieuw-Vennep, Netherlands). The practical framework to generate STL from cone beam computed tomography was demonstrated. A case of virtual tooth #26 access cavity preparation in Simodont® was established for trainee unlimited practices before performing the clinical procedure on a real patient. Taken together, access cavity preparation in a virtual environment using a 3D personized tooth may minimize procedural errors and facilitate clinical treatment outcome.

Safety assessment of Mpp75Aa1.1, a new ETX_MTX2 protein from Brevibacillus laterosporus that controls western corn rootworm.

The recently discovered insecticidal protein Mpp75Aa1.1 from Brevibacillus laterosporus is a member of the ETX_MTX family of beta-pore forming proteins (ß-PFPs) expressed in genetically modified (GM) maize to control western corn rootworm (WCR; Diabrotica virgifera virgifera LeConte). In this manuscript, bioinformatic analysis establishes that although Mpp75Aa1.1 shares varying degrees of similarity to members of the ETX_MTX2 protein family, it is unlikely to have any allergenic, toxic, or otherwise adverse biological effects. The safety of Mpp75Aa1.1 is further supported by a weight of evidence approach including evaluation of the history of safe use (HOSU) of ETX_MTX2 proteins and Breviballus laterosporus. Comparisons between purified Mpp75Aa1.1 protein and a poly-histidine-tagged (His-tagged) variant of the Mpp75Aa1.1 protein demonstrate that both forms of the protein are heat labile at temperatures at or above 55°C, degraded by gastrointestinal proteases within 0.5 min, and have no adverse effects in acute mouse oral toxicity studies at a dose level of 1920 or 2120 mg/kg body weight. These results support the use of His-tagged proteins as suitable surrogates for assessing the safety of their non-tagged parent proteins. Taken together, we report that Mpp75Aa1.1 is the first ETX-MTX2 insecticidal protein from B. laterosporus and displays a similar safety profile as typical Cry proteins from Bacillus thuringiensis.

Clinical relevant haptic simulation learning and training in tooth preparation.

Clinical dentistry is a complex activity which the procedure of most dental treatment are almost irreversible changes. Patient safety is a major challenge in clinical dental care. This is the reason why simulation-based learning and training is emphasized in dental education. In this article, the authors presented the clinical relevant haptic simulation learning and training in tooth preparation. The practical framework to set up the simulation environment from real patients in haptic 3D virtual reality dental training simulator Simodont® (Nissin Dental Products Inc., Nieuw-Vennep, Netherlands). Then, the trainee can repeatedly practice in Simodont® before performing the clinical procedure on real patient. Taken together, the implementation of this model in dental education may not only enhance trainees' self-confidence and performance, but also facilitate patient safety during clinical dental care.

Indocyanine Green-Camptothecin Co-Loaded Perfluorocarbon Double-Layer Nanocomposite: A Versatile Nanotheranostics for Photochemotherapy and FDOT Diagnosis of Breast Cancer.

Breast cancer remains the most frequently diagnosed cancer and is the leading cause of neoplastic disease burden for females worldwide, suggesting that effective therapeutic and/or diagnostic strategies are still urgently needed. In this study, a type of indocyanine green (ICG) and camptothecin (CPT) co-loaded perfluorocarbon double-layer nanocomposite named ICPNC was developed for detection and photochemotherapy of breast cancer. The ICPNCs were designed to be surface modifiable for on-demand cell targeting and can serve as contrast agents for fluorescence diffuse optical tomography (FDOT). Upon near infrared (NIR) irradiation, the ICPNCs can generate a significantly increased production of singlet oxygen compared to free ICG, and offer a comparable cytotoxicity with reduced chemo-drug dosage. Based on the results of animal study, we further demonstrated that the ICPNCs ([ICG]/[CPT] = 40-/7.5-µM) in association with 1-min NIR irradiation (808 nm, 6 W/cm2) can provide an exceptional anticancer effect to the MDA-MB-231 tumor-bearing mice whereby the tumor size was significantly reduced by 80% with neither organ damage nor systemic toxicity after a 21-day treatment. Given a number of aforementioned merits, we anticipate that the developed ICPNC is a versatile theranostic nanoagent which is highly promising to be used in the clinic.

Optical profile: A key determinant of antibacterial efficacy of photodynamic therapy in dentistry.

BACKGROUND: Periodontal disease effects 20-50% of the population worldwide, posing a global health challenge. It has been reported to be more prevalent among adults. Actinobacillus actinomycetemcomitans (A. actinomycetemcomitans) is an important organism associated with localized juvenile periodontitis. Photodynamic therapy (PDT) has been widely utilized for the treatment of periodontal disease; however, the effect of laser (light) profile on the antibacterial efficacy of PDT remains to be established. The quantitative measurement of laser profile is required to confirm the in vitro efficacy of PDT. AIM: In the present study, a low cost PDT system comprising of six copper tube waveguides (CTW) was developed to provide more uniform irradiation of the culture plate. METHODS: The antibacterial effect of PDT, in combination with 200 µg/mL methylene blue (MB) as photosensitizer and 60 sec of irradiation, was studied on A. actinomycetemcomitans and Streptococcus mutans (S. mutans). In the present case, 660 nm laser guided with unpolished CTW, polished CTW, and optical fiber waveguide (OFW) provided radiant exposure of 0.86, 1.38, and 1.36 J/cm2, respectively, for a 24-well culture plate. RESULTS: The designed PDT system provided antimicrobial efficacy of 98% and 91% for A. actinomycetemcomitans and S. mutans, respectively, which was significantly higher as compared to OFW guided PDT. CONCLUSION: The results of the study highlighted the importance of laser profile as a key parameter that determines the survival rate of bacteria at the edge of the culture plate. Thus, the dose of PDT at the margin of optical profile is important for antibacterial activity for in vitro evaluation.

dxpr: an R package for generating analysis-ready data from electronic health records-diagnoses and procedures.

BACKGROUND: Enriched electronic health records (EHRs) contain crucial information related to disease progression, and this information can help with decision-making in the health care field. Data analytics in health care is deemed as one of the essential processes that help accelerate the progress of clinical research. However, processing and analyzing EHR data are common bottlenecks in health care data analytics. METHODS: The dxpr R package provides mechanisms for integration, wrangling, and visualization of clinical data, including diagnosis and procedure records. First, the dxpr package helps users transform International Classification of Diseases (ICD) codes to a uniform format. After code format transformation, the dxpr package supports four strategies for grouping clinical diagnostic data. For clinical procedure data, two grouping methods can be chosen. After EHRs are integrated, users can employ a set of flexible built-in querying functions for dividing data into case and control groups by using specified criteria and splitting the data into before and after an event based on the record date. Subsequently, the structure of integrated long data can be converted into wide, analysis-ready data that are suitable for statistical analysis and visualization. RESULTS: We conducted comorbidity data processes based on a cohort of newborns from Medical Information Mart for Intensive Care-III (n = 7,833) by using the dxpr package. We first defined patent ductus arteriosus (PDA) cases as patients who had at least one PDA diagnosis (ICD, Ninth Revision, Clinical Modification [ICD-9-CM] 7470*). Controls were defined as patients who never had PDA diagnosis. In total, 381 and 7,452 patients with and without PDA, respectively, were included in our study population. Then, we grouped the diagnoses into defined comorbidities. Finally, we observed a statistically significant difference in 8 of the 16 comorbidities among patients with and without PDA, including fluid and electrolyte disorders, valvular disease, and others. CONCLUSIONS: This dxpr package helps clinical data analysts address the common bottleneck caused by clinical data characteristics such as heterogeneity and sparseness.

Enhancing osteoblast functions on biofilm-contaminated titanium alloy by concentration-dependent use of methylene blue-mediated antimicrobial photodynamic therapy.

The concentration of methylene blue (MB) photosensitizer could affect the eradication efficacy of antimicrobial photodynamic therapy (aPDT) in the treatment of contaminated implants, which is linked to the osseointegration of the implant. We evaluated osteoblast functions on the contaminated SLA (sandblasting, large-grit and acid-etching) Ti alloy surfaces after the concentration-dependent use of MB-aPDT. Totally 1164 SLA discs were randomly distributed for the analyses of antibacterial efficacy and osteoblast functions. Gram-negative (Aggregatibacter actinomycetemcomitans; A. actinomycetemcomitans) or Gram-positive (Streptococcus mutans; S. mutans) adhered on disc samples was subjected to aPDT with different MB concentrations (200, 250, 300, 350, and 400 µg/mL) using 660 nm diode laser with maximum output 80 mW for 1 min irradiation (4.8 J/cm2). Bactericidal effect was examined by viability, morphology, and lipopolysaccharide (LPS) assays. The disinfected disc surfaces by MB-aPDT to support osteoblast-like MG63 attachment, proliferation, differentiation, and mineralization were assessed for the predetermined culture time intervals. The statistical differences between the means were performed using a one-way analysis of variance (ANOVA) with a post hoc Scheffe test. The results of the morphology observation and bacterial survival examination consistently indicated a remarkably lower quantity of bacterial colonies on biofilm-contaminated surfaces after the aPDT treatment with higher MB concentration. Similarly, the higher MB concentration in aPDT resulted in the lower LPS amounts remaining on the A. actinomycetemcomitans-contaminated surfaces. Intriguingly, the expression of osteoblast cultured on disinfected surfaces using aPDT with higher MB concentration was comparable to the control without contamination. Within the limits of this in vitro model, this formulation of 400 µg/mL MB used in aPDT may be not only the lethal concentration against the 2 bacteria-contaminated implants, but it could also enhance the osteoblast functions on the contaminated implants. Nevertheless, the efficacy in the clinical practice for peri-implantitis therapy remains to be studied.

Antimicrobial efficacy of methylene blue-mediated photodynamic therapy on titanium alloy surfaces in vitro.

Bacterial elimination using antimicrobial photodynamic therapy (aPDT) has been considered an alternative therapeutic modality in peri-implantitis treatment. The present in vitro study evaluated the dose-dependent and pH-dependent bactericidal effects of methylene blue (MB)-mediated aPDT at eliminating Gram-negative (P. gingivalis and A. actinomycetemcomitans) and Gram-positive (S. mutans) bacteria on sandblasting, large-grit and acid-etching (SLA)-pretreated titanium alloy. The effects of different MB concentrations (50, 100, and 200 µg/mL), the pH of the MB (4, 7, and 10), and irradiation time (0, 30, and 60 s) on the bacterial viability and residual lipopolysaccharide (LPS) levels were examined. The variations in the pH of the MB solution after aPDT for 60 s on the uncontaminated and contaminated specimens were also detected. The experimental results indicated that MB-mediated PDT could effectively kill the majority of bacteria on the titanium alloy surfaces of biofilm-contaminated implants compared with the MB alone. Of note, aPDT exhibited better antibacterial efficacy with increase in the MB concentration and irradiation time. While treated in an acidic solution on the biofilm-contaminated specimens, aPDT caused the pH to increase. By contrast, the initially high alkaline pH decreased to a value of about pH 8.5 after aPDT. Intriguingly, the neutral pH had minor changes, independent of the MB concentration and bacterial species. As expected, aPDT with higher MB concentration at higher pH environment significantly lowered the LPS concentration of A. actinomycetemcomitans and P. gingivalis. On the basis of the data, the aPDT with 200 µg/mL MB at pH 10 for 60 s of irradiation time might be an effectively treatment to eliminate bacteria and LPS adherent to titanium surface, however, the use of the multispecies biofilm model and the evaluation of in vitro osteogenesis needed to be further evaluated.

Effectiveness of Hypochlorous Acid to Reduce the Biofilms on Titanium Alloy Surfaces in Vitro.

Chemotherapeutic agents have been used as an adjunct to mechanical debridement for peri-implantitis treatment. The present in vitro study evaluated and compared the effectiveness of hypochlorous acid (HOCl), sodium hypochlorite (NaOCl), and chlorhexidine (CHX) at eliminating Gram-negative (E. coli and P. gingivalis) and Gram-positive (E. faecalis and S. sanguinis) bacteria. The effect of irrigating volume and exposure time on the antimicrobial efficacy of HOCl was evaluated, and a durability analysis was completed. Live/dead staining, morphology observation, alamarBlue assay, and lipopolysaccharide (LPS) detection were examined on grit-blasted and biofilm-contaminated titanium alloy discs after treatment with the three chemotherapeutic agents. The results indicated that HOCl exhibited better antibacterial efficacy with increasing irrigating volumes. HOCl achieved greater antibacterial efficacy as treatment time was increased. A decrease in antimicrobial effectiveness was observed when HOCl was unsealed and left in contact with the air. All the irrigants showed antibacterial activity and killed the majority of bacteria on the titanium alloy surfaces of biofilm-contaminated implants. Moreover, HOCl significantly lowered the LPS concentration of P. gingivalis when compared with NaOCl and CHX. Thus, a HOCl antiseptic may be effective for cleaning biofilm-contaminated implant surfaces.

Effects of Surface Conditions of Titanium Dental Implants on Bacterial Adhesion.

OBJECTIVE: The study is to evaluate the effect of surface roughness of titanium implants on bacterial adhesion and then to investigate the efficacy of the three cleaning treatments for bacterial removal in titanium surfaces. BACKGROUND DATA: Although surface debridement is the basic element for treatment of peri-implantitis to reduce bacterial adhesion, adjunctive therapies such as antiseptics and laser debridement have been proposed to improve the nonsurgical treatment options of the peri-implant infection. METHODS: Titanium specimens were divided into five groups: No. 1200 grit sandpaper polishing (Grit), 50 µm (SB50), 100 µm (SB100), and 250 µm Al2O3 sandblasting (SB250), and sandblasting, large-grit, and acid-etching (SLA). Surface roughness (Ra), contact angle, and surface morphology were examined. The subsequent adhesion of Escherichia coli on the different substrates was assayed. After 8 h of bacterial culture, three different cleaning treatments, including plastic curettage, air-powder abrasive system, and Er:YAG laser debridement, were applied on the specimens. RESULTS: The Ra value changed from the lower value of 0.2 µm for the Grit group to the significantly higher value of 2.7 µm for the SB250 group, indicating a significant difference from the SLA group (2.0 µm). The average contact angle of SLA (101°) was significantly higher than the other groups. No significant difference in E. coli bacterial adhesion was found among the all roughened groups, except the SB50 and SB250 groups at 12 h of culture. The use of three cleaning treatments did not induce significant surface alterations. However, the E. coli adhesion was significantly reduced in the air-powder abrasive system and laser debridement in comparison with that treated with the plastic curettage. CONCLUSIONS: Laser debridement could be a useful cleaning method for peri-implantitis therapy.

Common mechanistic themes for the powerstroke of kinesin-14 motors.

Kar3Cik1 is a heterodimeric kinesin-14 from Saccharomyces cerevisiae involved in spindle formation during mitosis and karyogamy in mating cells. Kar3 represents a canonical kinesin motor domain that interacts with microtubules under the control of ATP-hydrolysis. In vivo, the localization and function of Kar3 is differentially regulated by its interacting stoichiometrically with either Cik1 or Vik1, two closely related motor homology domains that lack the nucleotide-binding site. Indeed, Vik1 structurally resembles the core of a kinesin head. Despite being closely related, Kar3Cik1 and Kar3Vik1 are each responsible for a distinct set of functions in vivo and also display different biochemical behavior in vitro. To determine a structural basis for their distinct functional abilities, we used cryo-electron microscopy and helical reconstruction to investigate the 3-D structure of Kar3Cik1 complexed to microtubules in various nucleotide states and compared our 3-D data of Kar3Cik1 with that of Kar3Vik1 and the homodimeric kinesin-14 Ncd from Drosophila melanogaster. Due to the lack of an X-ray crystal structure of the Cik1 motor homology domain, we predicted the structure of this Cik1 domain based on sequence similarity to its relatives Vik1, Kar3 and Ncd. By molecular docking into our 3-D maps, we produced a detailed near-atomic model of Kar3Cik1 complexed to microtubules in two distinct nucleotide states, a nucleotide-free state and an ATP-bound state. Our data show that despite their functional differences, heterodimeric Kar3Cik1 and Kar3Vik1 and homodimeric Ncd, all share striking structural similarities at distinct nucleotide states indicating a common mechanistic theme within the kinesin-14 family.

The ATPase pathway that drives the kinesin-14 Kar3Vik1 powerstroke.

Kar3, a Saccharomyces cerevisiae microtubule minus-end-directed kinesin-14, dimerizes with either Vik1 or Cik1. The C-terminal globular domain of Vik1 exhibits the structure of a kinesin motor domain and binds microtubules independently of Kar3 but lacks a nucleotide binding site. The only known function of Kar3Vik1 is to cross-link parallel microtubules at the spindle poles during mitosis. In contrast, Kar3Cik1 depolymerizes microtubules during mating but cross-links antiparallel microtubules in the spindle overlap zone during mitosis. A recent study showed that Kar3Vik1 binds across adjacent microtubule protofilaments and uses a minus-end-directed powerstroke to drive ATP-dependent motility. The presteady-state experiments presented here extend this study and establish an ATPase model for the powerstroke mechanism. The results incorporated into the model indicate that Kar3Vik1 collides with the microtubule at 2.4 µm(-1) s(-1) through Vik1, promoting microtubule binding by Kar3 followed by ADP release at 14 s(-1). The tight binding of Kar3 to the microtubule destabilizes the Vik1 interaction with the microtubule, positioning Kar3Vik1 for the start of the powerstroke. Rapid ATP binding to Kar3 is associated with rotation of the coiled-coil stalk, and the postpowerstroke ATP hydrolysis at 26 s(-1) is independent of Vik1, providing further evidence that Vik1 rotates with the coiled coil during the powerstroke. Detachment of Kar3Vik1 from the microtubule at 6 s(-1) completes the cycle and allows the motor to return to its initial conformation. The results also reveal key differences in the ATPase cycles of Kar3Vik1 and Kar3Cik1, supporting the fact that these two motors have distinctive biological functions.

Kar3Vik1, a member of the kinesin-14 superfamily, shows a novel kinesin microtubule binding pattern.

Kinesin-14 motors generate microtubule minus-end-directed force used in mitosis and meiosis. These motors are dimeric and operate with a nonprocessive powerstroke mechanism, but the role of the second head in motility has been unclear. In Saccharomyces cerevisiae, the Kinesin-14 Kar3 forms a heterodimer with either Vik1 or Cik1. Vik1 contains a motor homology domain that retains microtubule binding properties but lacks a nucleotide binding site. In this case, both heads are implicated in motility. Here, we show through structural determination of a C-terminal heterodimeric Kar3Vik1, electron microscopy, equilibrium binding, and motility that at the start of the cycle, Kar3Vik1 binds to or occludes two αß-tubulin subunits on adjacent protofilaments. The cycle begins as Vik1 collides with the microtubule followed by Kar3 microtubule association and ADP release, thereby destabilizing the Vik1-microtubule interaction and positioning the motor for the start of the powerstroke. The results indicate that head-head communication is mediated through the adjoining coiled coil.

Kinesin Kar3Cik1 ATPase pathway for microtubule cross-linking.

Kar3Cik1 is a Saccharomyces cerevisiae kinesin-14 that functions to shorten cytoplasmic microtubules (MTs) during yeast mating yet maintains mitotic spindle stability by cross-linking anti-parallel interpolar MTs. Kar3 contains both an ATP- and a MT-binding site, yet there is no evidence of a nucleotide-binding site in Cik1. Presteady-state and steady-state kinetic experiments were pursued to define the regulation of Kar3Cik1 interactions with the MT lattice expected during interpolar MT cross-linking. The results reveal that association of Kar3Cik1 with the MT occurs at 4.9 µM(-1) s(-1), followed by a 5-s(-1) structural transition that limits ADP release from the Kar3 head. Mant-ATP binding occurred at 2.1 µM(-1) s(-1), and the pulse-chase experiments revealed an ATP-promoted isomerization at 69 s(-1). ATP hydrolysis was observed as a rapid step at 26 s(-1) and was required for the Kar3Cik1 motor to detach from MT. The conformational change at 5 s(-1) that occurred after Kar3Cik1 MT association and prior to ADP release was hypothesized to be the rate-limiting step for steady-state ATP turnover. We propose a model in which Kar3Cik1 interacts with the MT lattice through an alternating cycle of Cik1 MT collision followed by Kar3 MT binding with head-head communication between Kar3 and Cik1 modulated by the Kar3 nucleotide state and intramolecular strain.