SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing.

BACKGROUND: Single-cell RNA-sequencing is revolutionising the study of cellular and tissue-wide heterogeneity in a large number of biological scenarios, from highly tissue-specific studies of disease to human-wide cell atlases. A central task in single-cell RNA-sequencing analysis design is the calculation of cell type-specific genes in order to study the differential impact of different replicates (e.g. tumour vs. non-tumour environment) on the regulation of those genes and their associated networks. The crucial task is the efficient and reliable calculation of such cell type-specific 'marker' genes. These optimise the ability of the experiment to isolate highly-specific cell phenotypes of interest to the analyser. However, while methods exist that can calculate marker genes from single-cell RNA-sequencing, no such method places emphasise on specific cell phenotypes for downstream study in e.g. differential gene expression or other experimental protocols (spatial transcriptomics protocols for example). Here we present SMaSH, a general computational framework for extracting key marker genes from single-cell RNA-sequencing data which reliably characterise highly-specific and niche populations of cells in numerous different biological data-sets. RESULTS: SMaSH extracts robust and biologically well-motivated marker genes, which characterise a given single-cell RNA-sequencing data-set better than existing computational approaches for general marker gene calculation. We demonstrate the utility of SMaSH through its substantial performance improvement over several existing methods in the field. Furthermore, we evaluate the SMaSH markers on spatial transcriptomics data, demonstrating they identify highly localised compartments of the mouse cortex. CONCLUSION: SMaSH is a new methodology for calculating robust markers genes from large single-cell RNA-sequencing data-sets, and has implications for e.g. effective gene identification for probe design in downstream analyses spatial transcriptomics experiments. SMaSH has been fully-integrated with the ScanPy framework and provides a valuable bioinformatics tool for cell type characterisation and validation in every-growing data-sets spanning over 50 different cell types across hundreds of thousands of cells.

Powdery Mildew Outbreaks caused by Podosphaera macularis on Hop Cultivars Possessing the Resistance Gene R6 in the Pacific Northwestern United States.

Resistant cultivars of hop (Humulus lupulus) have been grown, with the aim of helping to manage powdery mildew in the Pacific Northwest since the first report of the disease in the field in 1997 (4). A major objective of many breeding programs is development of resistance to powdery mildew, and this has generally been achieved by single resistance genes (qualitative resistance). One such gene, R6 (3), has been utilized extensively in new cultivars and has prevented epidemics of the disease in those cultivars across the Pacific Northwestern United States for approximately 15 years. In 2011, a grower in Washington State reported outbreaks of powdery mildew on cv. Apollo, which is thought to possess powdery mildew resistance derived from R6. Fungicides and cultural control measures were applied, and the grower reported no substantial crop damage from the disease. During the winter of 2012, the same grower planted rhizomes of cv. Apollo in a greenhouse in the Yakima Valley of Washington State and later found the plants to be affected by powdery mildew. Affected leaves from plants of cvs. Apollo, Newport, and Nugget (all reported [3] or assumed to possess R6 based on pedigree) grown in the same greenhouse were later provided to the authors. Conidia obtained from each affected plants were transferred to plants of the highly susceptible cv. Symphony, which is not known to contain any resistance genes. After 10 to 14 days of incubation, resultant conidia from each cultivar above (total of three isolates) were transferred to greenhouse grown plants of cvs. Nugget and Symphony and incubated at 18°C. Within 7 days, all three isolates produced powdery mildew colonies characteristic of P. macularis (2) on both cultivars. Cleistothecia did not develop in any colonies. In addition, Nugget and Symphony plants were inoculated with a field population of P. macularis originating from cultivars lacking R6 in Oregon. These inoculations on Nugget did not develop powdery mildew whereas Symphony plants did. Non-inoculated controls remained free of powdery mildew. Results were identical in two additional experiments. The sequence of the mating type idiomorph, MAT1-1, was obtained to confirm identity of the pathogen as P. macularis as described previously (1). The sequences were identical among the three isolates obtained from the greenhouse in Washington and isolates of P. macularis obtained previously from Oregon and Washington. MAT1-2 idiomorph was not detected in the isolates collected. While R6-virulent strains have been detected previously in race characterization experiments, these strains have not caused widespread epidemics of powdery mildew. The increasing prevalence of virulent strains of P. macularis and outbreaks of powdery mildew on formerly resistant cultivars necessitates changes in breeding strategies and disease management efforts to minimize damage resulting from the disease. The distribution of virulent strains of the pathogen and susceptibility of formerly resistance cultivars to powdery mildew are currently under investigation. References: (1) B. Asalfet et al. Phytopathology 103:717, 2013. (2) R. Bélanger et al. The Powdery Mildews: a Comprehensive Treatise. APS Press, St. Paul, MN, 2002. (3) P. Darby. Brew Hist. 121:94, 2005. (4) C. Ocamb et al. Plant Dis. 83:1072, 1999.

A fossil grass (gramineae: chloridoideae) from the miocene with kranz anatomy.

A fossil leaf fragment collected from the Ogallala Formation of northwestern Kansas exhibits features found in taxa of the modern grass subfamily Chloridoideae. These include bullet-shaped, bicellular microhairs, dumbbell-shaped silica bodies, cross-shaped suberin cells, papillae, stomata with low dome- to triangular-shaped subsidiary cells, and Kranz leaf anatomy. The leaf fragment extends the fossil record of plants that show both anatomical and external micromorphological features indicating C(4) photo-synthesis back to the Miocene. On the basis of associated mammals, the leaf fragment is assigned a Hemphillian age (7 to 5 million years ago).

Deployment and early experience with remote-presence patient care in a community hospital.

BACKGROUND: The introduction of the RP6 (InTouch Health, Santa Barbara, CA, USA) remote-presence "robot" appears to offer a useful telemedicine device. The authors describe the deployment and early experience with the RP6 in a community hospital and provided a live demonstration of the system on April 16, 2005 during the Emerging Technologies Session of the 2005 SAGES Meeting in Fort Lauderdale, Florida. METHODS: The RP6 is a 5-ft 4-in. tall, 215-pound robot that can be remotely controlled from an appropriately configured computer located anywhere on the Internet (i.e., on this planet). The system is composed of a control station (a computer at the central station), a mechanical robot, a wireless network (at the remote facility: the hospital), and a high-speed Internet connection at both the remote (hospital) and central locations. The robot itself houses a rechargeable power supply. Its hardware and software allows communication over the Internet with the central station, interpretation of commands from the central station, and conversion of the commands into mechanical and nonmechanical actions at the remote location, which are communicated back to the central station over the Internet. The RP6 system allows the central party (e.g., physician) to control the movements of the robot itself, see and hear at the remote location (hospital), and be seen and heard at the remote location (hospital) while not physically there. RESULTS: Deployment of the RP6 system at the hospital was accomplished in less than a day. The wireless network at the institution was already in place. The control station setup time ranged from 1 to 4 h and was dependent primarily on the quality of the Internet connection (bandwidth) at the remote locations. Patients who visited with the RP6 on their discharge day could be discharged more than 4 h earlier than with conventional visits, thereby freeing up hospital beds on a busy med-surg floor. Patient visits during "off hours" (nights and weekends) were three times more efficient than conventional visits during these times (20 min per visit vs 40-min round trip travel + 20-min visit). Patients and nursing personnel both expressed tremendous satisfaction with the remote-presence interaction. CONCLUSIONS: The authors' early experience suggests a significant benefit to patients, hospitals, and physicians with the use of RP6. The implications for future development are enormous.

Effect of Structured Physical Activity and Nutritional Supplementation on Physical Function in Mobility-Limited Older Adults: Results from the VIVE2 Randomized Trial.

OBJECTIVES: The interactions between nutritional supplementation and physical activity on changes in physical function among older adults remain unclear. The primary objective of this study was to examine the impact of nutritional supplementation plus structured physical activity on 400M walk capacity in mobility-limited older adults across two sites (Boston, USA and Stockholm, Sweden). DESIGN: All subjects participated in a physical activity program (3x/week for 24 weeks), involving walking, strength, balance, and flexibility exercises. Subjects were randomized to a daily nutritional supplement (150kcal, 20g whey protein, 800 IU vitamin D) or placebo (30kcal, non-nutritive). SETTING: Participants were recruited from urban communities at 2 field centers in Boston MA USA and Stockholm SWE. PARTICIPANTS: Mobility-limited (Short Physical Performance Battery (SPPB) ≤9) and vitamin D insufficient (serum 25(OH) D 9 - 24 ng/ml) older adults were recruited for this study. MEASUREMENTS: Primary outcome was gait speed assessed by the 400M walk. RESULTS: 149 subjects were randomized into the study (mean age=77.5±5.4; female=46.3%; mean SPPB= 7.9±1.2; mean 25(OH)D=18.7±6.4 ng/ml). Adherence across supplement and placebo groups was similar (86% and 88%, respectively), and was also similar across groups for the physical activity intervention (75% and 72%, respectively). Both groups demonstrated an improvement in gait speed with no significant difference between those who received the nutritional supplement compared to the placebo (0.071 and 0.108 m/s, respectively (p=0.06)). Similar effects in physical function were observed using the SPPB. Serum 25(OH)D increased in supplemented group compared to placebo 7.4 ng/ml versus 1.3 ng/ml respectively. CONCLUSION: Results suggest improved gait speed following physical activity program with no further improvement with added nutritional supplementation.

Brain maps and parallel computers.

It is well known that neural responses in many brain regions are organized in characteristic spatial patterns referred to as brain maps. It is likely that these patterns in some way reflect aspects of the neural computations being performed, but to date there are no general guiding principles for relating the structure of a brain map to the properties of the associated computation. In the field of parallel computing, maps similar to brain maps arise when computations are distributed across the multiple processors of a parallel computer. In this case, the relationship between maps and computations is well understood and general principles for optimally mapping computations onto parallel computers have been developed. In this paper we discuss how these principles may help illuminate the relationship between maps and computations in the nervous system.

MIDN: a spacecraft microdosimeter mission.

MIDN (MIcroDosimetry iNstrument) is a payload on the MidSTAR-I spacecraft (Midshipman Space Technology Applications Research) under development at the United States Naval Academy. MIDN is a solid-state system being designed and constructed to measure microdosimetric spectra to determine radiation quality factors for space environments. Radiation is a critical threat to the health of astronauts and to the success of missions in low-Earth orbit and space exploration. The system will consist of three separate sensors, one external to the spacecraft, one internal and one embedded in polyethylene. Design goals are mass <3 kg and power <2 W. The MidSTAR-I mission in 2006 will provide an opportunity to evaluate a preliminary version of this system. Its low power and mass makes it useful for the International Space Station and manned and unmanned interplanetary missions as a real-time system to assess and alert astronauts to enhanced radiation environments.

Accelerometer Assessment of Physical Activity and Its Association with Physical Function in Older Adults Residing at Assisted Care Facilities.

OBJECTIVES: To describe levels of physical activity among older adults residing at assisted care facilities and their association with physical function. DESIGN: Cross-sectional analysis. SETTING: Assisted care facilities within the greater Boston, MA area. PARTICIPANTS: Older adults aged 65 years and older (N = 65). MEASUREMENTS: Physical Activity Level (PAL) as defined by quartiles from accelerometry (counts and steps), Short Physical Performance Battery (SPPB) Score, gait speed, and handgrip strength. RESULTS: Participants in the most active accelerometry quartile engaged in 25 minutes/week of moderate to vigorous physical activity (MVPA) and walked 2,150 steps/day. These individuals had an SPPB score, 400 meter walk speed, and handgrip strength that was 3.7-3.9 points, 0.3-0.4 meters/second, and 4.5-5.1 kg greater respectively, than individuals in the lowest activity quartile, who engaged in less than 5 min/wk of MVPA or took fewer than 460 steps/day. CONCLUSION: Despite engaging in physical activity levels far below current recommendations (150 min/week of MVPA or > 7000 steps/day), the most active older adults in this study exhibited clinically significant differences in physical function relative to their less active peers. While the direction of causality cannot be determined from this cross-sectional study, these findings suggest a strong association between PAL and physical function among older adults residing in an assisted care facility.

Functional properties of human nicotinic AChRs expressed by IMR-32 neuroblastoma cells resemble those of alpha3beta4 AChRs expressed in permanently transfected HEK cells.

We characterized the functional and molecular properties of nicotinic acetylcholine receptors (AChRs) expressed by IMR-32, a human neuroblastoma cell line, and compared them to human alpha3 AChRs expressed in stably transfected human embryonic kidney (HEK) cells. IMR-32 cells, like neurons of autonomic ganglia, have been shown to express alpha3, alpha5, alpha7, beta2, and beta4 AChR subunits. From these subunits, several types of alpha3 AChRs as well as homomeric alpha7 AChRs could be formed. However, as we show, the properties of functional AChRs in these cells overwhelmingly reflect alpha3beta4 AChRs. alpha7 AChR function was not detected, yet we estimate that there are 70% as many surface alpha7 AChRs in IMR-32 when compared with alpha3 AChRs. Agonist potencies (EC(50) values) followed the rank order of 1,1-dimethyl-4-phenylpiperazinium (DMPP; 16+/-1 microM) > nicotine (Nic; 48 +/- 7 microM) > or = cytisine (Cyt; 57 +/- 3 microM) = acetylcholine (ACh; 59 +/- 6 microM). All agonists exhibited efficacies of at least 80% relative to ACh. The currents showed strong inward rectification and desensitized at a rate of 3 s(-1) (300 microM ACh; -60 mV). Assays that used mAbs confirmed the predominance of alpha3- and beta4-containing AChRs in IMR-32 cells. Although 18% of total alpha3 AChRs contained beta2 subunits, no beta2 subunit was detected on the cell surface. Chronic Nic incubation increased the amount of total, but not surface alpha3beta2 AChRs in IMR-32 cells. Nic incubation and reduced culture temperature increased total and surface AChRs in alpha3beta2 transfected HEK cells. Characterization of various alpha3 AChRs expressed in HEK cell lines revealed that the functional properties of the alpha3beta4 cell line best matched those found for IMR-32 cells. The rank order of agonist potencies (EC(50) values) for this line was DMPP (14 +/- 1 microM) = Cyt (18 +/- 1 microM) > Nic (56 +/- 15 microM > ACh (79 +/- 8 microM). The efficacies of both Cyt and DMPP were approximately 80% when compared with ACh and the desensitization rate was 2 s(-1). These data show that even with the potential to express several human nicotinic AChR subtypes, the functional properties of AChRs expressed by IMR-32 are completely attributable to alpha3beta4 AChRs.

A multicenter comparison of dual-energy X-ray absorptiometers: in vivo and in vitro measurements of bone mineral content and density.

As part of a multicenter research project, we compared dual-energy X-ray absorptiometry (DXA) instruments at three research centers (sites 1, 2 and 3) to determine both intra- and intersite variability of bone mineral content (BMC), bone mineral density (BMD), and bone area (BA). Scans of the total body and lumbar spine were performed in duplicate on five humans (in vivo), and scans of the total body were performed on two whole body phantoms with artificial skeletons and thickness overlays (in vitro) at all sites over 15 days. The average intrasite variability in two consecutive total body BMD measurements, expressed as a percent difference, was significantly higher in vitro, 1.74 +/- 1.97%, than in vivo, 0.71 +/- 0.38% (p < 0.05). Average intrasite variability of the in vivo lumbar spine BMD was 1.08 +/- 1.12%. The intersite coefficients of variation for all BMD, BMC, and BA measurements were < 2.0%. The total body BMD from site 2 was systematically lower than at sites 1 and 3 both in vivo and in vitro (p < 0.05) with no differences in BMC and BA. Although significant, the total body BMD differences between sites were small (< 1.2%) in vivo compared with in vitro (< 2.6%) and are encouraging for the comparison and pooling of human data from multicenter trials, provided that appropriate standardized cross-calibration and analysis procedures are applied.

Hormone and bone mineral status in endurance-trained and sedentary postmenopausal women.

Serum hormone levels and bone mineral status were studied in 18 sedentary and 15 endurance-trained postmenopausal women (mean age, 62 yr). The endurance-trained women had lower body weight, lower body fat, and higher aerobic capacity than the sedentary women (P less than 0.05). There were no differences in current calcium intake between the 2 groups, as assessed by a 7-day food record, but carbohydrate intake (grams per kg BW) was higher in the endurance-trained women (P less than 0.001). Bone mineral density (BMD) of the spine (L1-L3), proximal femur, and radius did not differ between the 2 groups; however, when normalized for body weight, the BMDs of the spine and radius were higher in the endurance-trained than in the sedentary women. Serum estrone and PTH levels were lower, and 1,25-dihydroxyvitamin D and somatomedin-C levels were higher in the endurance-trained than in the sedentary women. Serum GH tended to be higher in the endurance-trained than in the sedentary women (P = 0.08), and there was a postexercise increase in serum GH in the endurance-trained, but not in the sedentary, women (P less than 0.01). The major effect of habitual exercise was on body weight and hormone status. Although leanness and low serum estrone levels are risk factors for osteoporosis, these were not associated with lower BMD in endurance-trained women. Endurance-trained women may have improved calcium absorption as a result of higher carbohydrate intake and higher serum 1,25-dihydroxyvitamin D levels.

Bone mineral content and levels of gonadotropins and estrogens in amenorrheic running women.

Serum gonadotropin and estrogen levels and their relationship to bone mineral content in exercise-related amenorrhea were studied in 11 amenorrheic women and 24 eumenorrheic women, all of whom were runners. Serum estradiol, LH, FSH, estrone, and testosterone were measured in serial blood samples obtained at 15-min intervals for 4 h. The amenorrheic women had lower estradiol, LH, FSH; and estrone levels as well as a higher estrone-estradiol ratio than did the eumenorrheic women. There was no difference in testosterone levels. The amenorrheic women had lower LH pulse amplitudes, whereas no differences were found in FSH pulse amplitudes. LH and FSH pulse frequencies did not differ between the two groups. Bone mineral content of the lumbar spine was lower in amenorrheic women and was positively correlated with estradiol levels in all women. There was no difference in bone mineral content of the radius. These data suggest that, in exercise-related amenorrhea, low serum LH, FSH, and estrogen levels reflect an alteration in the hypothalamic control of gonadotropin release. Reduced circulating estrogen levels in amenorrheic running women may be a cause of low mineral content of the spine.

Effect of exercise and menstrual cycle status on plasma lipids, low density lipoprotein particle size, and apolipoproteins.

Habitual physical exercise has been reported to have beneficial effects on plasma lipoproteins. To examine this question in women, plasma cholesterol, triglyceride, and apolipoprotein (apo) A-I and B levels, and low density lipoprotein (LDL) particle size were determined in 25 women runners (9 of whom had exercise-related secondary amenorrhea) and 36 age-matched nonexercising women (controls). The eumenorrheic runners had significantly lower apo B levels and significantly greater mean apo A-I/apo B ratios and LDL particle sizes than did the control women (P less than 0.05). Lower apo B levels were correlated with decreased body mass index, a known exercise effect (P less than 0.0001). In addition, normally menstruating runners had cholesterol and triglyceride levels that were 7.6% and 25.4% lower, respectively, and apo A-I levels that were 6.4% higher than control women (P = NS). In amenorrheic runners all parameters were similar to values in control women, except that apo B levels were 20% lower (P less than 0.05). Amenorrheic runners had lower plasma apo A-I levels (13%) and significantly lower apo A-I/apo B ratios and estradiol levels than eumenorrheic runners, and serum estradiol values in the runners were correlated with apo A-I levels (P less than 0.01). These data indicate that the beneficial effects of strenuous exercise on plasma apo A-I levels and apo A-I/apo B ratios in women runners can be reversed by exercise-induced amenorrhea and decreased serum estradiol levels, and that women runners have lower apo B levels than nonexercising women, regardless of menstrual status.

Total-body skeletal muscle mass: evaluation of 24-h urinary creatinine excretion by computerized axial tomography.

A classic body-composition method is estimation of total-body skeletal muscle mass (SM, in kg) from 24-h urinary creatinine excretion (in g). Two approaches of unknown validity have been used to calculate SM from creatinine: one assumes a constant ratio of SM to creatinine, the so-called creatinine equivalence (k), and that SM = k x creatinine; the other suggests a highly variable ratio of SM to creatinine and is based on regression equations of the form SM = b + a x creatinine. We explored these two extreme possibilities by measuring SM with whole-body computerized axial tomography and collecting urinary creatinine during meat-free dietary conditions in 12 healthy adult men. Prediction equations were developed in the men that fit these two models: SM = 21.8 x creatinine (SD and CV of the ratio of SM to creatinine: 1.3 kg and 6.0%, respectively) and SM = 18.9 x creatinine + 4.1 (r = 0.92, P = 2.55 x 10(-5), SEE = 1.89 kg). The validity of each model is reviewed in the context of theoretical aspects of creatine-creatinine metabolism. This first investigation of the method of measuring urinary creatinine excretion to determine SM by using modern techniques raises important practical and basic questions related to SM prediction.

A 1-y walking program and increased dietary calcium in postmenopausal women: effects on bone.

The effects of a supervised 1-y walking program and increased dietary calcium (milk supplement, 831 mg/d, vs placebo drink, 41 mg/d) on bones were examined in 36 postmenopausal women (60.2 +/- 6.5 y). Trabecular bone-mineral density (BMD) of the lumbar spine (L1-L3), measured by computed tomography, increased by 0.5% in exercising women (n = 18) and decreased by 7.0% in sedentary women (n = 18; P = 0.02). Femoral-neck BMD measured by dual-photon absorptiometry (DPA) increased by 2.0% in women consuming high dietary calcium (n = 18) and decreased by 1.1% in those on moderate calcium intake (n = 18; P = 0.001). Neither exercise nor dietary calcium had an effect on lumbar spine (L2-L4) measured by DPA, distal radius measured by single-photon absorptiometry, or total body calcium measured by in vivo neutron activation. The varying proportions and rates of turnover of trabecular and cortical bone from one site to another suggest that exercise and high dietary calcium may preferentially alter bone density at different skeletal sites.

Analysis of body-composition techniques and models for detecting change in soft tissue with strength training.

The purpose of this study was to compare the ability of various body-composition assessment techniques to detect changes in soft tissue in older, weight-stable women (50-70 y of age) completing a 1-y randomized, controlled trial of progressive resistance training. The intervention group (n = 20) performed high-intensity strength-training 2 d/wk with five different exercises; the control group (n = 19) was untreated. Hydrostatic weighing, 24-h urinary creatinine, computed tomography of thigh sections, total body potassium, and tritium dilution techniques were used to measure increases in total fat-free mass (FFM) and the muscle and water components of FFM. A decrease in fat mass (by hydrostatic weighing) was seen in the strength-trained women compared with the control subjects (P - 0.01-0.0001). Anthropometry, bioelectric impedance, dual-energy X-ray absorptiometry, and total body nitrogen and carbon did not measure any significant change in soft tissue. The choice of a body-composition technique is important when designing a study expected to affect soft tissue, because not all techniques available are precise enough to detect small changes.

Diet and bone status in amenorrheic runners.

Our purpose was to determine the relationship of diet, exercise, and amenorrhea with bone mineral status in trained young women. Bone mineral density of the lumbar spine was significantly lower in amenorrheic compared to normally menstruating runners. Circulating estradiol was also significantly lower. No significant differences between the two groups were found in body composition, maximum aerobic power, or amount of training per week. A 3-day dietary record showed that the amenorrheic women reported a significantly lower daily energy intake, but no difference in the calcium intake. Protein intake was less than the US Recommended Dietary Allowance in 82% of amenorrheic women and 35% of eumenorrheic women. Abnormal eating behaviors may be associated with the development of amenorrhea. Our results show that when weight-bearing exercise and a low energy intake are associated with amenorrhea, the accretion of a large bone mass in young trained women is not favored.

Intrapulmonary cytokine accumulation following BAL and the role of endotoxin contamination.

STUDY OBJECTIVES: BAL induces alveolar inflammation, but its effects on intrapulmonary cytokines and the mechanisms causing inflammation are uncertain. The objectives of this study were: (1) to characterize cytokine response in the lungs to BAL, and (2) to determine whether endotoxin is introduced into the lungs during BAL, which could promote BAL-induced inflammation. DESIGN AND METHODS: We performed two BAL procedures in healthy volunteers separated by 4 (n=6), 24 (n=5), or 72 h (n=3). The initial BAL was performed in the right middle lobe (RML) and the second BAL was performed in the same location and the lingula. Concentrations of interleukin-8 (IL-8), interleukin-1 (IL-1beta), and transforming growth factor-beta were measured by enzyme-linked immunosorbent assay and tumor necrosis factor-alpha (TNF-alpha) bioactivity was determined. Endotoxin contents of saline (10 and 20 mL) infused through bronchoscopes as well as BAL fluids recovered from six subjects were assessed by limulus amebocyte assay. RESULTS: At 4 h after the initial lavage, but not at later times, BAL fluid recovered from the RML contained increased concentrations of IL-8 and IL-1beta, and increased TNF-alpha bioactivity. BAL fluid recovered from the lingula contained increased concentrations of TNF-alpha only at 4 h. All BAL samples tested contained detectable endotoxin as did all saline aliquots instilled through bronchoscopes. CONCLUSIONS: There is intrapulmonary accumulation of the cytokines TNF-alpha, IL-8, and IL-1beta in the lavaged lung within 4 h after BAL; this accumulation resolves by 24 h. Endotoxin contamination of the lungs during bronchoscopy may contribute to BAL-induced lung inflammation.

Transferrin concentrations in serum and lower respiratory tract fluid of mechanically ventilated patients with COPD or ARDS.

Transferrin serves as the primary iron transport protein in serum, but it also is present in the lower respiratory tract where it has antioxidant and antibacterial properties. Prior studies indicate that patients with respiratory failure (RF) due to ARDS have increased concentrations of transferrin in the lower respiratory tract, which is attributed to increased lung vascular permeability. It is unclear whether mechanical ventilation contributes to increased lung transferrin content in patients with ARDS, although mechanical ventilation may increase lung microvascular permeability. To assess whether mechanical ventilation in patients with RF due to causes other than ARDS is also associated with increased respiratory tract concentrations of transferrin, we compared transferrin concentrations in serum and lung lavage fluid obtained from 12 mechanically ventilated patients with RF attributable to COPD, 6 patients with ARDS, and 15 healthy volunteers. Serum transferrin concentrations in patients with RF due to COPD were variable, but mean concentrations were similar to those in control subjects (336 +/- 58 vs 307 +/- 9 [SE] mg/dL), whereas serum transferrin concentrations were decreased in patients with ARDS (182 +/- 68 mg/dL; p < 0.05). Compared with control subjects, lavage fluid recovered from patients with RF due to COPD contained significantly decreased concentrations of transferrin (1.56 +/- 0.24 vs 4.27 +/- 0.44 micrograms/mL; p < 0.001), whereas transferrin concentrations in lavage fluid recovered from patients with ARDS were increased (15.72 +/- 2.01 micrograms/mL; p < 0.001). Transferrin concentrations of lavage fluid also were decreased in COPD patients when normalized for lavage fluid protein content (4.35 +/- 0.72 vs 19.96 +/- 3.13 micrograms/mg in control subjects, p < 0.001). These data indicate that mechanical ventilation of patients with COPD is associated with decreased lung transferrin concentrations, in contrast to an increased transferrin concentration found in patients with ARDS. Decreased transferrin concentrations in the lower respiratory tract may decrease defenses against oxidant injury and bacterial infection in patients with RF due to COPD.

Counteracting the effects of mydriatics. Does it benefit the patient?

The effect of 2% pilocarpine nitrate in countering mydriasis, cycloplegia, and change in visual acuity due to 0.5% tropicamide was studied in 23 healthy volunteers. There was no significant difference in the decrease in pupil size or the rate of return of accommodation between the eye that received pilocarpine and the control eye. The effect of tropicamide on visual acuity was slight. In four (17%) of 23 eyes that received pilocarpine, visual acuity was reduced to 6/36 or worse. It is suggested that the use of 2% pilocarpine in the attempted reversal of 0.5% tropicamide to improve a patient's vision is not helpful and may possibly be harmful.