Soil organic carbon is not just for soil scientists: measurement recommendations for diverse practitioners.

Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. We advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.

Varicella-zoster DNA in saliva of patients with meningoencephalitis: a preliminary study.

OBJECTIVES: Since the routine use of polymerase chain reaction testing (PCR) in diagnosing herpes infections, varicella-zoster virus is increasingly recognized as a cause of varicella-zoster meningoencephalitis (VZV ME) among immunocompetent patients. We were interested to determine whether patients with VZV ME had VZV DNA in their saliva during the acute phase of the illness. MATERIALS AND METHODS: Forty-five consecutive patients who underwent a lumbar puncture for diagnostic purposes were included in the study. The cerebrospinal fluid was examined for the presence of VZV DNA by PCR, and patients with positive findings were treated with acyclovir. The saliva was later analyzed in a blinded fashion for the presence of VZV DNA. RESULTS: VZV DNA was found in saliva in four of five (80%) patients with PCR confirmed VZV ME (sensitivity 0.8, specificity 0.84, and likelihood ratio 5). This was significantly more than in patients with non-zoster viral ME (0%, P = 0.009), parainfectious headache (12%, P = 0.03) and controls (9.5%, P = 0.007). In immunocompromised patients with systemic lymphoma and AIDS, VZV DNA was present at a similar rate (67%, P = 0.6). CONCLUSIONS: We have found VZV DNA in saliva of patients with PCR confirmed VZV ME at a higher proportion than in controls and patients with non-VZV viral ME. This finding might be of clinical importance, especially in immunocompetent individuals with suspected VZV ME where the results of genetic and immunological testing are not conclusive.

Multiple latent viruses reactivate in astronauts during Space Shuttle missions.

Latent virus reactivation and diurnal salivary cortisol and dehydroepiandrosterone were measured prospectively in 17 astronauts (16 male and 1 female) before, during, and after short-duration (12-16 days) Space Shuttle missions. Blood, urine, and saliva samples were collected during each of these phases. Antiviral antibodies and viral load (DNA) were measured for Epstein-Barr virus (EBV), varicella-zoster virus (VZV), and cytomegalovirus (CMV). Three astronauts did not shed any virus in any of their samples collected before, during, or after flight. EBV was shed in the saliva in all of the remaining 14 astronauts during all 3 phases of flight. Seven of the 14 EBV-shedding subjects also shed VZV during and after the flight in their saliva samples, and 8 of 14 EBV-shedders also shed CMV in their urine samples before, during, and after flight. In 6 of 14 crewmembers, all 3 target viruses were shed during one or more flight phases. Both EBV and VZV DNA copies were elevated during the flight phase relative to preflight or post-flight levels. EBV DNA in peripheral blood was increased preflight relative to post-flight. Eighteen healthy controls were also included in the study. Approximately 2-5% of controls shed EBV while none shed VZV or CMV. Salivary cortisol measured preflight and during flight were elevated relative to post-flight. In contrast DHEA decreased during the flight phase relative to both preflight and post-flight. As a consequence, the molar ratio of the area under the diurnal curve of cortisol to DHEA with respect to ground (AUCg) increased significantly during flight. This ratio was unrelated to viral shedding. In summary, three herpes viruses can reactivate individually or in combination during spaceflight.

Reactivation of latent viruses is associated with increased plasma cytokines in astronauts.

Success of long duration space missions will depend upon robust immunity. Decreased immunity has been observed in astronauts during short duration missions, as evident by the reactivation of latent herpes viruses. Seventeen astronauts were studied for reactivation and shedding of latent herpes viruses before, during, and after 9-14 days of 8 spaceflights. Blood, urine, and saliva samples were collected 10 days before the flight (L-10), during the flight (saliva only), 2-3h after landing (R+0), 3 days after landing (R+3), and 120 days after landing (R+120). Values at R+120 were used as baseline levels. No shedding of viruses occurred before flight, but 9 of the 17 (designated "virus shedders") shed at least one or more viruses during and after flight. The remaining 8 astronauts did not shed any of the 3 target viruses (non-virus shedders). Virus-shedders showed elevations in 10 plasma cytokines (IL-1α, IL-6, IL-8, IFNγ, IL-4, IL-10, IL-12, IL-13, eotaxin, and IP-10) at R+0 over baseline values. Only IL-4 and IP-10 were elevated in plasma of non-virus shedders. In virus shedders, plasma IL-4 (a Th2 cytokine) was elevated 21-fold at R+0, whereas IFNγ (a Th1 cytokine) was elevated only 2-fold indicating a Th2 shift. The inflammatory cytokine IL-6 was elevated 33-fold at R+0. In non-shedding astronauts at R+0, only IL-4 and IP-10 levels were elevated over baseline values. Elevated cytokines began returning to normal by R+3, and by R+120 all except IL-4 had returned to baseline values. These data show an association between elevated plasma cytokines and increased viral reactivation in astronauts.

Three-dimensional growth of extravillous cytotrophoblasts promotes differentiation and invasion.

Human trophoblast research relies on a combination of in vitro models, including isolated primary cultures, explant cultures, and trophoblast cell lines. In the present study, we have utilized the rotating wall vessel (RWV) bioreactor to generate a three-dimensional (3-D) model of human placentation for the study of cytotrophoblast (CTB) invasion. The RWV supported the growth of the human CTB cell line SGHPL-4 and allowed for the formation of complex, multilayered 3-D aggregates that were morphologically, phenotypically, and functionally distinct from SGHPL-4 monolayers. The cells cultured three-dimensionally differentiated into an aggressively invasive cell population characterized by the upregulation of matrix metalloproteinase-2 (MMP-2), MMP-3, MMP-9 and urokinase-type plasminogen activator (uPA) secretion and activation. Microarray analysis of the 3-D and 2-D cultured cells revealed increased expression in the 3-D cells of various genes that are known mediators of invasion, including MT1-MMP, PECAM-1 and L-selectin, as well as genes not previously associated with CTB differentiation such as MMP-13 and MT5-MMP. These results were verified by quantitative real-time PCR. These findings suggest that when cultured in 3-D, SGHPL-4 cells closely mimic differentiating in utero CTBs, providing a novel approach for the in vitro study of the molecular mechanisms that regulate CTB differentiation and invasion.

Leukocyte subsets and neutrophil function after short-term spaceflight.

Changes in leukocyte subpopulations and function after spaceflight have been observed but the mechanisms underlying these changes are not well defined. This study investigated the effects of short-term spaceflight (8-15 days) on circulating leukocyte subsets, stress hormones, immunoglobulin levels, and neutrophil function. At landing, a 1.5-fold increase in neutrophils was observed compared with preflight values; lymphocytes were slightly decreased, whereas the results were variable for monocytes. No significant changes were observed in plasma levels of immunoglobulins, cortisol, or adrenocorticotropic hormone. In contrast, urinary epinephrine, norepinephrine, and cortisol were significantly elevated at landing. Band neutrophils were observed in 9 of 16 astronauts. Neutrophil chemotactic assays showed a 10-fold decrease in the optimal dose response after landing. Neutrophil adhesion to endothelial cells was increased both before and after spaceflight. At landing, the expression of MAC-1 was significantly decreased while L-selectin was significantly increased. These functional alterations may be of clinical significance on long-duration space missions.

Subcutaneous and mediastinal emphysema. Pathophysiology, diagnosis, and management.

Subcutaneous emphysema and pneumomediastinum occur frequently in critically ill patients in association with blunt or penetrating trauma, soft-tissue infections, or any condition that creates a gradient between intra-alveolar and perivascular interstitial pressures. A continuum of fascial planes connects cervical soft tissues with the medlastinum and retroperitoneum, permitting aberrant air arising in any one of these areas to spread elsewhere. Diagnosis is made in the appropriate clinical setting by careful physical examination and inspection of the chest roentgenogram. While the presence of air in subcutaneous or mediastinal tissue is not dangerous in itself, prompt recognition of the underlying cause is essential. Certain trauma-related causes may require surgical intervention, but the routine use of chest tubes tracheostomy, or mediastinal drains is not recommended.

Multiple plasmacytomas with thoracic and biliary involvement.

The course of a patient who had nonsecretory multiple myeloma was characterized by extraosseous plasmacytomas that were initially limited to pleural lesions with effusion and subcutaneous masses. Subsequently, we noted the development of obstructive jaundice caused by a mass at the head of the pancreas, which was diagnosed by abdominal ultrasound and responded to radiation therapy, and bilateral pulmonary nodules, which were visualized by fiberoptic bronchoscopy. Forceps biopsy of an endobronchial lesion showed plasmacytoma similar in histologic features to her original osseous lesions. The pulmonary nodules responded to cyclophosphamide and prednisone. During her course, she had three forms of intrathoracic myeloma: rib lesions extending into pulmonary tissue, pleural disease, and multiple endobronchial masses. The biliary and pulmonary manifestations of plasmacytomas are rarely seen. Diagnosis by noninvasive procedures and rapid response to conservative therapy were important in this patient's care.

Prolactin response to electroconvulsive therapy: effects of electrode placement and stimulus dosage.

BACKGROUND: It is unclear whether the serum prolactin (PRL) surge following electroconvulsive therapy (ECT) is a marker of optimal ECT administration. We investigated the relations among PRL surge, stimulus parameters, and outcome in major depressive disorder (MDD). METHODS: Seventy-nine patients with MDD were randomized in a double-blind trial to right unilateral (RUL) or bilateral (BL), and to low-dose (just above seizure threshold) or high-dose (2.5 x threshold) ECT. RESULTS: Change in PRL (delta PRL) varied among treatment groups, with significant effects of electrode placement (BL > RUL, p < .006), electrical dosage (high > low, p < .04), and gender (female > male, p < .005). There was no evidence that clinical improvement was associated with greater PRL surge. CONCLUSIONS: Although delta PRL varied with parameters impacting on response rates, these data indicate the PRL surge cannot serve as a useful index of clinically effective treatment. This finding does not support the view that diencephalic seizure propagation is necessary for ECT to exert therapeutic effects.

Routine detection of Epstein-Barr virus specific T-cells in the peripheral blood by flow cytometry.

The ability to detect cytomegalovirus-specific T-cells (CD4(+)) in the peripheral blood by flow cytometry has been recently described by Picker et al. In this method, cells are incubated with viral antigen and responding (cytokine producing) T-cells are then identified by flow cytometry. To date, this technique has not been reliably used to detect Epstein-Barr virus (EBV)-specific T-cells primarily due to the superantigen/mitogenic properties of the virus which non-specifically activate T-cells. By modifying culture conditions under which the antigens are presented, we have overcome this limitation and developed an assay to detect and quantitate EBV-specific T-cells. The detection of cytokine producing T-cells by flow cytometry requires an extremely strong signal (such as culture in the presence of PMA and ionomycin). Our data indicate that in modified culture conditions (early removal of viral antigen) the non-specific activation of T-cells by EBV is reduced, but antigen presentation will continue uninhibited. Using this method, EBV-specific T-cells may be legitimately detected using flow cytometry. No reduction in the numbers of antigen-specific T-cells was observed by the early removal of target antigen when verified using cytomegalovirus antigen (a virus with no non-specific T-cell activation properties). In EBV-seropositive individuals, the phenotype of the EBV-specific cytokine producing T-cells was evaluated using four-color flow cytometry and found to be CD45(+), CD3(+), CD4(+), CD45RA(-), CD69(+), CD25(-). This phenotype indicates the stimulation of circulating previously unactivated memory T-cells. No cytokine production was observed in CD4(+) T-cells from EBV-seronegative individuals, confirming the specificity of this assay. In addition, the use of four color cytometry (CD45, CD3, CD69, IFNgamma/IL-2) allows the total quantitative assessment of EBV-specific T-cells while monitoring the interference of EBV non-specific mitogenic activity. This method may have significant utility for the monitoring of the immune response to latent virus infection/reactivation.

Decreased hypoxic ventilatory drive in the obesity-hypoventilation syndrome.

Most patients with extreme obesity do not exhibit alveolar hypoventilation, but an intriguing minority do. The mechanism(s) of this phenomenon remain unknown. A disorder in ventilatory control has been suggested as a major factor in the pathogenesis of the obesity-hypoventilation syndrome. Accordingly, hypoxic and hypercapnic ventilatory drives were measured in 10 patients with the typical symptoms of the syndrome: obesity, hypersomnolence, hypercapnia, hypoxemia, polycythemia and cor pulmonale. Hypoxic ventilatory drive, measured as the shape parameter A, averaged 21.9 +/- 5.35, approximately one-sixth that in normal controls, A = 126 +/- 8.6 (P less than 0.01). The ventilatory response to hypercapnia also was markedly reduced, the slope of the response averaging 0.51 +/- 0.005, or about one-third the normal value of 1.83 +/- 0.13 (P less than 0.01). This decreased responsiveness in hypoxic and hypercapnic ventilatory drive was consistent throughout the group. The depression in ventilatory drive found in the obesity-hypoventilation syndrome may be causally related to the alveolar hypoventilation manifested by these patients.

Spreadsheet macro for setting up PCR assay tubes.

This article describes a Microsoft Excel macro designed to calculate PCR master mix amounts based on variations in the DNA template amounts added to each tube, the total number of PCR assay tubes being set up or both. This macro uses a dynamic dialog box to quickly calculate and display the new component volumes after changes in one or both of the variables. The PCR assay mix protocol can then be printed in a format suitable for record keeping. This macro was designed for use with the Windows version of Excel but will also run on Macintosh computers.

Effects of ECT on the TRH stimulation test.

The prognostic value of the TRH stimulation test was evaluated in 23 inpatients with major depressive disorder before and after a trial of ECT. In contrast to previous reports, the peak TSH response to TRH was significantly decreased after treatment compared with before treatment. This effect was consistent across individuals and subgroups (responders/nonresponders; unilateral/bilateral ECT). The particular ECT technique used in the study may account for the discrepancies between these findings and those previously reported by other authors.

Legionnaires' disease. Clinical and pulmonary histopathologic features of a sporadic case.

The pulmonary histopathologic features in a sporadic case of Legionnaires' disease are shown. The changes include acute bronchitis with focal ulceration and diffuse acute interstitial pneumonitis. These changes are not those seen with typical bacterial pneumonia but are similar to changes seen when viruses, rickettsiae, chlamydiae, or Mycoplasma pneumoniae organisms are the infecting agents.

Cardiac asystole during an hypoxic drive study in a normal subject.

A healthy 31-year-old man who had previously sojourned to an altitude of 5,000 meters with no detrimental effect developed sudden cardiac asystole during a progressive hypoxic ventilatory response ( HVR ) test. At the moment of asystole, his alveolar PO2 (PAO2) was 41 mm Hg and his arterial oxygen saturation (SaO2) was 81 percent. Cardiopulmonary resuscitation was initiated, and after 20 seconds of asystole and apnea, he recovered normal sinus rhythm and spontaneous respiration. A subsequent ECG and cardiac enzyme levels were normal. During testing, he demonstrated depressed ventilation in response to hypoxia and a slowing of the heart rate. Careful observation of heart rate and breath-by-breath ventilation during HVR tests may predict this potentially fatal complication.

Severe precocious emphysema in intravenous methylphenidate (Ritalin) abusers.

Intravenous (IV) drug abuse is known to cause pulmonary tale granulomatosis. Reports have documented a syndrome of pulmonary vascular sclerosis in long-term IV methylphenidate users. Although this would be expected to produce restrictive lung disease, we hereby report six patients who have severe obstructive lung disease. All had used IV methylphenidate for at least four years. One of these patients died of progressive respiratory insufficiency and the others are clinically disabled. Their symptoms and airflow obstruction are more severe than those of most patients with chronic obstructive pulmonary disease. In these individuals, we cannot say that precocious obstructive lung disease is not due to a combination of smoking and other factors, nor can we be certain that methylphenidate is the offending agent. However, this cluster of cases among methylphenidate abusers suggests that long-term IV exposure to this drug might lead to early severe obstructive lung disease.

A comparison of spirometric values with subjects in standing and sitting positions.

Spirograms obtained from 235 subjects in standing and sitting positions revealed small differences for the forced vital capacity (FVC) and forced expiratory volume in one second (FEV1). No statistically significant differences were found for the mean forced expiratory flow during the middle half of the FVC (FEF25-75%, or maximal midexpiratory flow) and FEV1/FVC. Sitting values were, on the average, higher for determinations greater than FVC of 2.14 L, FEV1 of 1.68 L, FEF25-75% of 2.16 L/sec, and FEV1/FVC of 75.7 percent. On the average, subjects with less than these values performed slightly better in the standing position.

Carbon dioxide excretion via bronchopleural fistulas in adult respiratory distress syndrome.

Expired gas and gas leaked via thoracostomy tubes was collected in nine patients with the adult respiratory distress syndrome (ARDS) and bronchopleural fistulas. Mean minute ventilation in the group was 23.9 +/- 7.5 L/min with 31 +/- 23 percent of the gas escaping via the leak. Carbon dioxide was present in the leaked gas in every patient, with the fraction of CO2 excreted via the leak highly correlated with the fraction of minute ventilation exiting via the leak (r = 0.86, p less than 0.005). Mean concentration of CO2 in leaked gas was 1.3 +/- 0.5 percent. We conclude that some of the gas leaked via a bronchopleural fistula in such patients participated in gas exchange.

Persistent bronchopleural air leak during mechanical ventilation. A review of 39 cases.

Bronchopleural fistula (BPF), or bronchopleural air leak, is regarded as an ominous complication of ventilator management in acute respiratory failure, but data on its natural course and prognosis are lacking. We reviewed all instances of mechanical ventilation at a major trauma center during a four-year period, and found that 39 of the 1,700 mechanically-ventilated patients developed BPF lasting at least 24 hrs. Overall mortality in these 39 patients was 67 percent, and this was higher when BPF developed late in the illness (16 of 17, or 94 percent, when mean onset was hospital day 13), than when it occurred within 24 hours of admission (ten of 22, or 45 percent, p = 0.002). Survival in patients with chest trauma (12 of 27, 44 percent), most of whom had air leaks on or just after admission, was better than in those with other primary diagnoses (one of 12, 8 percent, p less than 0.005). All eight patients whose maximum air leak exceeded 500 ml per breath died, whereas 13 of 30 with smaller maximum leaks survived (p less than 0.05). Despite leaks as large as 900 ml per breath, however, conventional ventilator adjustments permitted avoidance of severe respiratory acidosis (pH less than 7.30) in all but two patients. We conclude that the occurrence of BPF during mechanical ventilation identifies patients with high mortality, but that unmanageable respiratory acidosis from this complication is rare.

Prediction of successful ventilator weaning using airway occlusion pressure and hypercapnic challenge.

We studied eleven patients during 14 attempts at weaning from mechanical ventilation to determine whether central ventilatory drive, measured as airway occlusion pressure 0.1 s after onset of inspiration (P 0.1), during spontaneous breathing before and during a brief hypercapnic challenge, could accurately predict the success or failure of the attempt. All patients were recovering from acute respiratory failure and could breathe spontaneously for 20 minutes on a T-piece but were judged clinically to be marginal weaning candidates. Minute ventilation (VI) and P 0.1 were measured while breathing spontaneously and were repeated during a hypercapnic challenge that raised end-tidal PCO2 approximately 10 mm Hg. Seven of the 14 weaning attempts were unsuccessful, requiring reinstitution of mechanical ventilation. Although the failure group had lower mean maximum inspiratory force and higher spontaneous respiratory rate, no threshold value separated the failure from the success group. Ventilation increased more during hypercapnic challenge in those patients whose weaning attempt was successful, but overlap of results between the two groups rendered this test inaccurate for predicting weaning success. In contrast, successfully weaned patients had greater augmentation of P 0.1 during hypercapnia, expressed as the ratio of P 0.1 during CO2-stimulated to P 0.1 during baseline values, than did those who failed weaning (p less than 0.005). This ratio succeeded, and was thus both specific and sensitive as a predictor of successful weaning from mechanical ventilation in these patients.