Spectral characteristics of urine from patients with end-stage kidney disease analyzed using Raman Chemometric Urinalysis (Rametrix).

Raman Chemometric Urinalysis (RametrixTM) was used to discern differences in Raman spectra from (i) 362 urine specimens from patients receiving peritoneal dialysis (PD) therapy for end-stage kidney disease (ESKD), (ii) 395 spent dialysate specimens from those PD therapies, and (iii) 235 urine specimens from healthy human volunteers. RametrixTM analysis includes spectral processing (e.g., truncation, baselining, and vector normalization); principal component analysis (PCA); statistical analyses (ANOVA and pairwise comparisons); discriminant analysis of principal components (DAPC); and testing DAPC models using a leave-one-out build/test validation procedure. Results showed distinct and statistically significant differences between the three types of specimens mentioned above. Further, when introducing "unknown" specimens, RametrixTM was able to identify the type of specimen (as PD patient urine or spent dialysate) with better than 98% accuracy, sensitivity, and specificity. RametrixTM was able to identify "unknown" urine specimens as from PD patients or healthy human volunteers with better than 96% accuracy (with better than 97% sensitivity and 94% specificity). This demonstrates that an entire Raman spectrum of a urine or spent dialysate specimen can be used to determine its identity or the presence of ESKD by the donor.

Spectral characteristics of urine specimens from healthy human volunteers analyzed using Raman chemometric urinalysis (Rametrix).

Raman chemometric urinalysis (Rametrix™) was used to analyze 235 urine specimens from healthy individuals. The purpose of this study was to establish the "range of normal" for Raman spectra of urine specimens from healthy individuals. Ultimately, spectra falling outside of this range will be correlated with kidney and urinary tract disease. Rametrix™ analysis includes direct comparisons of Raman spectra but also principal component analysis (PCA), discriminant analysis of principal components (DAPC) models, multivariate statistics, and it is available through GitHub as the Rametrix™ LITE Toolbox for MATLAB®. Results showed consistently overlapping Raman spectra of urine specimens with significantly larger variances in Raman shifts, found by PCA, corresponding to urea, creatinine, and glucose concentrations. A 2-way ANOVA test found that age of the urine specimen donor was statistically significant (p < 0.001) and donor sex (female or male identification) was less so (p = 0.0526). With DAPC models and blind leave-one-out build/test routines using the Rametrix™ PRO Toolbox (also available through GitHub), an accuracy of 71% (sensitivity = 72%; specificity = 70%) was obtained when predicting whether a urine specimen from a healthy unknown individual was from a female or male donor. Finally, from female and male donors (n = 4) who contributed first morning void urine specimens each day for 30 days, the co-occurrence of menstruation was found statistically insignificant to Rametrix™ results (p = 0.695). In addition, Rametrix™ PRO was able to link urine specimens with the individual donor with an average of 78% accuracy. Taken together, this study established the range of Raman spectra that could be expected when obtaining urine specimens from healthy individuals and analyzed by Rametrix™ and provides the methodology for linking results with donor characteristics.

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding.

RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal information about the sequenced RNA. Here we report TimeLapse-seq, which uses oxidative-nucleophilic-aromatic substitution to convert 4-thiouridine into cytidine analogs, yielding apparent U-to-C mutations that mark new transcripts upon sequencing. TimeLapse-seq is a single-molecule approach that is adaptable to many applications and reveals RNA dynamics and induced differential expression concealed in traditional RNA-seq.

Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa.

Polyphosphate (polyP) granule biogenesis is an ancient and ubiquitous starvation response in bacteria. Although the ability to make polyP is important for survival during quiescence and resistance to diverse environmental stresses, granule genesis is poorly understood. Using quantitative microscopy at high spatial and temporal resolution, we show that granule genesis in Pseudomonas aeruginosa is tightly organized under nitrogen starvation. Following nucleation as many microgranules throughout the nucleoid, polyP granules consolidate and become transiently spatially organized during cell cycle exit. Between 1 and 3 h after nitrogen starvation, a minority of cells have divided, yet the total granule number per cell decreases, total granule volume per cell dramatically increases, and individual granules grow to occupy diameters as large as ∼200 nm. At their peak, mature granules constitute ∼2% of the total cell volume and are evenly spaced along the long cell axis. Following cell cycle exit, granules initially retain a tight spatial organization, yet their size distribution and spacing relax deeper into starvation. Mutant cells lacking polyP elongate during starvation and contain more than one origin. PolyP promotes cell cycle exit by functioning at a step after DNA replication initiation. Together with the universal starvation alarmone (p)ppGpp, polyP has an additive effect on nucleoid dynamics and organization during starvation. Notably, cell cycle exit is temporally coupled to a net increase in polyP granule biomass, suggesting that net synthesis, rather than consumption of the polymer, is important for the mechanism by which polyP promotes completion of cell cycle exit during starvation.

Azacitidine: a novel agent for myelodysplastic syndromes.

PURPOSE: The pharmacology, pharmacokinetics, clinical efficacy, dosage and administration, and safety of azacitidine are reviewed. SUMMARY: Azacitidine is the first drug in a new class of compounds, known as DNA hypomethylating agents, to receive FDA-approved labeling for the treatment of myelodysplastic syndromes. It exerts its antineoplastic activity by causing a direct cytotoxic effect on abnormally proliferating hematopoietic cell lines by interfering with nucleic acid metabolism. Azacitidine is rapidly absorbed following subcutaneous injection, with peak plasma concentrations achieved within 30 minutes of administration. Based on promising results in Phase I-II testing, azacitidine entered Phase III testing in all subtypes of myelodysplastic syndromes. Azacitidine was compared with best supportive care, the previous standard therapy for myelodysplastic syndromes, demonstrating improvements in hematologic response, delaying time to progression to acute myelogenous leukemia, and increasing overall survival. Azacitidine is available as sterile lyophilized powder in single-use vials for reconstitution. The recommended dosage of azacitidine for the first treatment cycle is 75 mg/m(2) daily for seven days. The treatment cycle should be repeated every four weeks for a minimum of four cycles. Overall, azacitidine appears to be well tolerated, with the most common adverse effects being myelosuppression, nausea, and vomiting. CONCLUSION: Azacitidine is the first DNA hypomethylating agent approved by FDA for the treatment of myelodysplastic syndromes and has demonstrated superior efficacy and improvements in patients' quality of life and bone marrow function over supportive care.

Physiotherapy, steroid injections, or rest for lateral epicondylosis? What the evidence suggests.

OBJECTIVE: To identify effective lateral epicondylosis interventions and assess the quality of research over time. METHODS: Relevant MEDLINE and EMBASE searches respectively yielded 226 and 187 potential studies. Additional citations were extracted from bibliographies. Thirty controlled trials met inclusion criteria. The Cochrane Collaboration guidelines "quality score" served to rate studies. RESULTS: In the short term (<2 to 3 months) steroid injections and physiotherapy outperformed relative rest. Physiotherapy appears efficacious regardless of time frame. After 3 months, active physiotherapy outperforms injections, but does not appear significantly better than rest. Evidence was neutral or insufficient regarding ultrasound, splinting, or manipulation. Nonsignificant correlations between publication year and study quality score were found. CONCLUSIONS: Overall research quality has not improved with time. Steroid injections appear the most successful short-term intervention for pain relief. Active physiotherapy appears efficacious regardless of time frame.

Effect of a hip flexor-stretching program on gait in the elderly.

OBJECTIVES: To test whether a reduction in peak hip extension during the terminal stance phase of walking in elderly compared with young adult subjects represents a hip flexor contracture impairment rather than some dynamic consequence and to test the hypothesis that stretching the hip flexors improves both static and dynamic peak hip extension, as well as other age-related gait changes about the ankle. DESIGN: A double-blinded, randomized, controlled trial. SETTING: Stretching exercises were performed in the subjects' homes. Pre- and postassessments were performed in a gait laboratory. PARTICIPANTS: Ninety-six healthy elderly individuals in 2 groups: treatment (n=47) and control (n=49). INTERVENTION: The treatment group received a 1-time instruction in hip flexor stretching, whereas the control group received a 1-time instruction in shoulder abductor stretching. Participants in each group were asked to perform stretching exercises on their own twice daily for 10 weeks. MAIN OUTCOME MEASURES: Static and dynamic peak hip extension, peak anterior pelvic tilt, and other peak kinematic and kinetic variables during the gait cycle. RESULTS: There was a modest improvement in static peak hip extension as measured by a goniometer within the treatment group (mean +/- standard deviation, 6.1 degrees +/-2.5 degrees to 7.7 degrees +/-3.6 degrees, P=.032) compared with no change in the control group. At comfortable walking speed, dynamic hip extension tended to increase in the treatment group (5.1 degrees +/-9.7 degrees to 7.1 degrees +/-8.0 degrees, P=.103) compared with no real change in the control group (5.3 degrees +/-8.9 degrees to 5.4 degrees +/-7.5 degrees, P=.928). Similarly, at fast walking speed, dynamic hip extension tended to increase in the treatment group (6.4 degrees +/-9.8 degrees to 8.4 degrees +/-8.0 degrees, P=.093) compared with no change in the control group. Changes in ankle kinematics and kinetics included a significant improvement in peak ankle plantarflexion and a tendency to improved ankle power generation. CONCLUSION: The static and dynamic trends to improvement in peak hip extension were of similar magnitude, suggesting that age-related reduction in peak hip extension during gait is the result of a static hip flexion contracture rather than a dynamic consequence. Additionally, age-related changes in ankle kinematics and kinetics may be secondarily related to hip flexion contracture impairment rather than impairment at the ankle per se. This study was limited by the exercises being unsupervised and relying on 1-time instruction. A more rigorous and supervised hip flexor-stretching exercise program may yield more substantial improvements in gait parameters.