BioTIME: A database of biodiversity time series for the Anthropocene

MOTIVATION

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

MAIN TYPES OF VARIABLES INCLUDED

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

SPATIAL LOCATION AND GRAIN

BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

TIME PERIOD AND GRAIN

BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

MAJOR TAXA AND LEVEL OF MEASUREMENT

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

SOFTWARE FORMAT

.csv and .SQL.

Induction of micronuclei in human fibroblasts across the Bragg curve of energetic heavy ions

The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LEpsilonTau gamma or X rays, the presence of shielding does not always reduce the radiation risks for energetic charged-particle exposure. The dose delivered by the charged particle increases sharply as the particle approaches the end of its range, a position known as the Bragg peak. However, the Bragg curve does not necessarily represent the biological damage along the particle path since biological effects are influenced by the track structures of both primary and secondary particles. Therefore, the "biological Bragg curve" is dependent on the energy and the type of the primary particle and may vary for different biological end points. Here we report measurements of the biological response across the Bragg curve in human fibroblasts exposed to energetic silicon and iron ions in vitro at two different energies, 300 MeV/nucleon and 1 GeV/nucleon. A quantitative biological response curve generated for micronuclei per binucleated cell across the Bragg curve did not reveal an increased yield of micronuclei at the location of the Bragg peak. However, the ratio of mono- to binucleated cells, which indicates inhibition of cell progression, increased at the Bragg peak location. These results confirm the hypothesis that severely damaged cells at the Bragg peak are more likely to go through reproductive death and not be evaluated for micronuclei.

Experience with over 3,000 open and laparoscopic bariatric procedures: multivariate analysis of factors related to leak and resultant mortality

BACKGROUND

Intestinal leak is a potentially lethal complication of Roux en-Y gastric bypass (GBP). Identification of patients at high risk for leak may reduce complication rates of surgeons early in the procedure learning curve.

METHODS

A total of 3073 patients who underwent GBP were analyzed using univariate and multivariate logistic regression analyses of the following preoperative factors: hypertension (HTN), diabetes mellitus (DM), sleep apnea (SA), age, gender, weight, body mass index (BMI), and surgery type. Multivariate logistic regression analysis was performed for each procedure type.

RESULTS

There were 48 (1.5%) deaths. Independent risk factors for death included leak, weight, procedure type, and HTN. A total of 102 (3.2%) leaks were found. Independent factors for leak included age, male gender, SA, and procedure type.

CONCLUSION

The data suggests that older, heavier male patients with multiple comorbid conditions are at increased risk for leak and mortality. Surgeons early in their learning curve should avoid these high-risk patients to reduce complications.

Hand-assisted laparoscopic gastric bypass does not improve outcome and increases costs when compared to open gastric bypass for the surgical treatment of obesity

BACKGROUND

Hand-assisted laparoscopic Roux-en-Y gastric bypass (Hand-Lap GB) has been adopted by some surgeons to treat morbid obesity because it is easier to perform than the total laparoscopic procedure, but to date no study has compared the outcomes of patients undergoing the Hand-Lap GB to those obtained with the open procedure (Open GB). We hypothesized that patients undergoing Hand-Lap GB would lose a similar amount of weight when compared to Open GB patients, while experiencing no increase in complications, a shorter hospital stay, and lower overall costs of care, in part as a result of fewer incisional hernias requiring subsequent surgery.

METHODS

Nonrandomized, prospective data were collected on all patients undergoing proximal GB via Hand-Lap or open approaches between May 1998 and July 1999. Our first 25 Hand-Lap GB procedures, performed in selected patients (with no extensive previous abdominal surgery) referred to two of us (E.J.D, M.A.S), were compared to all other (n = 62) concurrent open proximal GB performed by the group during this period of time in patients with body mass index (BMI) <50 kg/m2.

RESULTS

Preoperatively, Hand-Lap GB patients did not differ from Open GB patients in age (40 +/- 11 vs 43 +/- 11 years), gender (92% female vs 81% female), incidence or type of preoperative comorbid conditions, preoperative weight (282 +/- 33 vs 280 +/- 37 lb), or BMI (45.5 +/- 5.4 vs 44.1 +/- 3.3 kg/m2). (Data given as mean +/- standard deviation). Although length of hospital stay did not differ between groups (3.6 +/- 1.3 vs 4.2 +/- 4.6 days), total hospital costs were significantly higher for Hand-Lap GB ($14,725 +/- 3089 vs. $10,281 +/- 3687, p <0.01 ANOVA). One patient in the Open GB group developed an anastomotic leak from the gastrojejunostomy. Follow-up revealed that Hand-Lap GB patients had a similar risk of postoperative complications as the Open GB group, including marginal ulcer (16% vs 14.5%), stomal stenosis (24% vs 23%), and, most notably, incisional hernia (20% vs 27%). There were no major wound infections or deaths in either group. One patient in each group developed a postoperative small bowel obstruction. Loss of excess weight in Hand-Lap GB patients at 12 months postoperatively was 66 +/- 14% vs 77 +/- 14% in the Open GB group.

CONCLUSIONS

The Hand-Lap GB yielded good weight reduction in a population of morbidly obese patients, but at a higher cost for hospital care than Open GB. There was no decrease in the incidence of incisional hernias with the Hand-Lap GB procedure. Although Hand-Lap GB appears to be safe and effective, its failure to provide a decrease in hospital stay or risk of incisional hernia requiring subsequent surgical repair is significant. The primary role for the Hand-Lap GB procedure should therefore be to aid surgeons in developing skills to climb the steep learning curve for total laparoscopic gastric bypass, since Hand-Lap GB does not improve patient outcome and increases cost in comparison to the open GB procedure.

Rapid multiserotype detection of human rhinoviruses on optically coated silicon surfaces

BACKGROUND

More than 100 immunologically distinct serotypes of human rhinoviruses (HRV) have been discovered, making detection of surface exposed capsid antigens impractical. However, the non-structural protein 3C protease (3Cpro) is essential for viral replication and is relatively highly conserved among serotypes, making it a potential target for diagnostic testing. The thin film biosensor is an assay platform that can be formatted into a sensitive immunoassay for viral proteins in clinical specimens. The technology utilizes an optically coated silicon surface to convert specific molecular binding events into visual color changes by altering the reflective properties of light through molecular thin films.

OBJECTIVE

To develop a rapid test for detection of HRV by developing broadly serotype reactive antibodies to 3Cpro and utilizing them in the thin film biosensor format.

STUDY DESIGN

Polyclonal antibodies to 3Cpro were purified and incorporated into the thin film assay. The in vitro sensitivity, specificity and multiserotype cross-reactivity of the 3Cpro assay were tested. Nasal washes from naturally infected individuals were also tested to verify that 3Cpro was detectable in clinical specimens.

RESULTS

The 3Cpro assay is a 28-min, non-instrumented room temperature test with a visual limit of detection of 12 pM (picomolar) 3Cpro. In terms of viral titer, as few as 1000 TCID(50) equivalents of HRV2 were detectable. The assay detected 45/52 (87%) of the HRV serotypes tested but showed no cross-reactivity to common respiratory viruses or bacteria. The thin film assay detected 3Cpro in HRV-infected cell culture supernatants coincident with first appearance of cytopathic effect. Data are also presented demonstrating 3Cpro detection from clinical samples collected from HRV-infected individuals. The assay detected 3Cpro in expelled nasal secretions from a symptomatic individual on the first day of illness. In addition, 9/11 (82%) concentrated nasal wash specimens from HRV infected children were positive in the 3Cpro test.

CONCLUSION

We have described a novel, sensitive thin film biosensor for rapid detection of HRV 3Cpro. This test may be suitable for the point of care setting, where rapid HRV diagnostic test results could contribute to clinical decisions regarding appropriate antibiotic or antiviral therapy.

Substituted benzamide inhibitors of human rhinovirus 3C protease: structure-based design, synthesis, and biological evaluation

A series of nonpeptide benzamide-containing inhibitors of human rhinovirus (HRV) 3C protease was identified using structure-based design. The design, synthesis, and biological evaluation of these inhibitors are reported. A Michael acceptor was combined with a benzamide core mimicking the P1 recognition element of the natural 3CP substrate. alpha,beta-Unsaturated cinnamate esters irreversibly inhibited the 3CP and displayed antiviral activity (EC(50) 0.60 microM, HRV-16 infected H1-HeLa cells). On the basis of cocrystal structure information, a library of substituted benzamide derivatives was prepared using parallel synthesis on solid support. A 1.9 A cocrystal structure of a benzamide inhibitor in complex with the 3CP revealed a binding mode similar to that initially modeled wherein covalent attachment of the nucleophilic cysteine residue is observed. Unsaturated ketones displayed potent reversible inhibition but were inactive in the cellular antiviral assay and were found to react with nucleophilic thiols such as DTT.

Outbreak of drug-resistant tuberculosis with second-generation transmission in a high school in California

BACKGROUND

In spring 1993, four students in a high school were diagnosed with tuberculosis resistant to isoniazid, streptomycin, and ethionamide.

METHODS

To investigate potential transmission of drug-resistant tuberculosis, a retrospective cohort study with case investigation and screening by tuberculin skin tests and symptom checks was conducted in a high school of approximately 1400 students. Current and graduated high-school students were included in the investigation. DNA fingerprinting of available isolates was performed.

RESULTS

Eighteen students with active tuberculosis were identified. Through epidemiologic and laboratory investigation, 13 cases were linked; 8 entered 12th grade in fall 1993; 9 of 13 had positive cultures for Mycobacterium tuberculosis with isoniazid, streptomycin, and ethionamide resistance, and all 8 available isolates had identical DNA fingerprints. No staff member had tuberculosis. One student remained infectious for 29 months, from January 1991 to June 1993, and was the source case for the outbreak. Another student was infectious for 5 months before diagnosis in May 1993 and was a treatment failure in February 1994 with development of rifampin and ethambutol resistance in addition to isoniazid, streptomycin, and ethionamide. In the fall 1993 screening, 292 of 1263 (23%) students tested had a positive tuberculin skin test. Risk of infection was highest among 12th graders and classroom contacts of the two students with prolonged infectiousness. An additional 94 of 928 (10%) students tested in spring 1994 had a positive tuberculin skin test; 22 were classroom contacts of the student with treatment failure and 21 of these had documented tuberculin skin test conversions.

CONCLUSION

Extensive transmission of drug-resistant tuberculosis was documented in this high school, along with missed opportunities for prevention and control of this outbreak. Prompt identification of tuberculosis cases and timely interventions should help reduce this public health problem.

Rifampin preventive therapy for tuberculosis infection: experience with 157 adolescents

For persons infected with Mycobacterium tuberculosis resistant to isoniazid (INH), rifampin is recommended for the prevention of active disease. However, the adverse effects and acceptability of this preventive therapy are largely uncharacterized. We prospectively followed 157 high-school students exposed to, and probably infected with, M. tuberculosis strains resistant to INH. All 157 students were prescribed preventive therapy with rifampin (10 mg/kg up to 600 mg daily) for 24 wk. While receiving therapy, 41 (26%) reported one or more adverse effects; of these, 18 had therapy interrupted temporarily, two permanently. Four (2.5%) had alanine aminotransferase elevations greater than two times the upper limit of normal (range, 91 to 161 U/L); of these, one had therapy permanently stopped. Six (3.8%) self-discontinued therapy. No student was found to have active disease during the 2 yr of the study (exact 95% upper confidence limit, 2.2). We assumed that without preventive therapy, seven cases of tuberculosis would have occurred during these 2 yr. Therefore, we estimated that rifampin had a minimum protective effect of 56%. In conclusion, preventive therapy with rifampin was well tolerated and well accepted, and it appears effective in preventing active tuberculosis.

Laparoscopic management of enlarged cystic duct

After laparoscopic exploration of the common bile duct, or when a patient has acute cholecystitis, the cystic duct is sometimes edematous and too large to be ligated safely with an Endoclip. In such cases, ligation of the cystic duct with an Endoloop offers a solution to the problem. The standard technique for application of an Endoloop consists of dividing the cystic duct and then applying the Endoloop. This becomes more difficult if, after the cystic duct is divided, loss of traction on the common bile duct results in retraction of the divided cystic stump outside of the laparoscopic field of view. To avoid this difficulty, the authors apply an Endoloop with the grasping forceps on the cystic duct before the duct is divided so that it cannot retract from operative view and for this task developed an instrument that allows simultaneous introduction of both grasping forceps and the Endoloop through a single port.

Cloning and sequencing the gene encoding Escherichia coli ribonuclease I: exact physical mapping using the genome library

The amino acid (aa) sequence of the N terminus of Escherichia coli RNase I was determined. A mixed oligodeoxynucleotide coding for that sequence was used to probe the 476 lambda clones of Kohara et al. [Cell 50 (1987) 495-508]. DNA from these clones carry almost the entire E. coli chromosome in overlapping segments. Two overlapping clones hybridized to the probe sequence. From one of them DNA containing the rna gene was subcloned and sequenced. The inferred protein contains 245 aa residues and has an Mr of 27,156, which agrees with earlier estimates from sodium dodecyl sulfate-polyacrylamide-gel electrophoresis. RNase I is close to twice the size of pancreatic RNase A, but both enzymes contain eight Cys and four His; those aa are important for structure and function of RNase A. Proximal to the rna gene is a sequence that would code for a 23-aa peptide which conforms to consensus rules for signal peptides, and thus should transport this periplasmic enzyme. Sites for eight restriction enzymes had been mapped on each lambda clone. By relating to the map for that specific region, it was possible to position the rna gene exactly at 659 kb from the thr locus (time zero on a time scale of 100 min). This physical mapping gave a more precise (exact) map position based on distance than was possible using genetic mapping based on a time scale derived from conjugation, and should be applicable for mapping many other E. coli genes.

Electrophysiological effects of monophasic and biphasic stimuli in normal and infarcted dogs

Though some biphasic waveforms significantly decrease the energy required for defibrillation, little is known about the effect of biphasic stimulation on the determination of other electrophysiological parameters in normal and infarcted hearts. To evaluate this, nine normal dogs and 12 dogs with myocardial infarction had activation threshold (AT), effective refractory period (ERP), strength-interval curves, and ventricular fibrillation threshold (VFT) determined with constant current stimulation to a pair of right ventricular plunge electrodes, and upper limit of vulnerability (ULV) and defibrillation threshold (DFT) determined with truncated exponential shocks delivered to a pair of wire electrodes coiled to contour the right and left ventricular epicardium. Each electrophysiological parameter was determined with a 5.5 msec monophasic and 5.5-msec biphasic (3.5 msec first phase) waveform. Though AT and VFT were not significantly different for the two waveforms, the ERP was significantly longer, the strength-interval curve shifted rightward, and the threshold for repetitive responses higher for biphasic stimuli. Compared to the monophasic waveform, the ULV and DFT were significantly decreased in a parallel fashion for the biphasic waveform. Neither the presence nor size of myocardial infarction significantly affected any of the measured electrophysiological parameters. In six additional dogs, sigmoid defibrillation probability curves were constructed from biphasic shocks of four energies including that of the DFT and ULV. The ULV energy predicted an effective dose that defibrillated 97% of the time (range 90%-100%). In conclusion, the increased defibrillation efficacy of the biphasic waveform is independent of its ability to activate fully repolarized myocardium and cannot be explained by a greater ability of biphasic waveforms to activate partially depolarized tissue. The parallel decrease in the ULV and DFT for biphasic stimulation and the finding that the ULV energy defibrillates with a high probability of success suggest similar underlying mechanisms for the ULV and defibrillation.

Purification and characterization of Escherichia coli RNase I. Comparisons with RNase M

The endoribonuclease, RNase I, was purified from the periplasm of Escherichia coli. Based on PAGE, it has molecular mass of approximately 27 kDa with a migration rate indistinguishable from that of the recently reported RNase M from E. coli. The amino acid sequence of the two enzymes must be very similar based on two-dimensional mapping of their tryptic peptides and suggests either a post-transcriptional modification to yield different proteins from the same gene or evolution of two genes by gene duplication. However, while RNase I could degrade each of the four ribonucleotide homopolymers, only poly(U) or poly(C) were good substrates for RNase M with possibly some hydrolysis of poly(A). The reaction rate for poly(C) hydrolysis with RNase M was about ten times faster than for poly(U), while for RNase I the rates were about equal. Besides differences in specificity, RNase M was only located in the spheroplasts while RNase I found in the periplasm of growing cells. In terms of function, RNase I is known to cause degradation of rRNA during periods of stress or non-growth, whereas it has been proposed that RNase M is the endonuclease for mRNA degradation in growing cells.

Correction of altered plasma membrane potentials. A possible mechanism of cyclosporin A and verapamil reversal of pleiotropic drug resistance in neoplasia

We have recently shown that cyclosporin A (CsA) reverses pleiotropic drug resistance in human acute lymphatic leukemia in vitro and daunorubicin resistance in Ehrlich ascites tumor in vivo. In the present study we examined the mechanisms by which CsA might reverse pleiotropic drug resistance relative to changes in cellular plasma membrane potentials and intracellular calcium ([Ca2+]i). Membrane potentials were measured with DIOC5 dye flow-cytometrically and [Ca2+]i levels with Quin 2 dye spectrofluorimetrically. All pleiotropic (PDR) drug-resistant tumor sublines had decreased membrane potentials (membrane depolarized) compared with their corresponding drug-sensitive parental tumors. In comparison, the membrane potentials of a control antimetabolite-resistant acute leukemia cell line were unchanged. The basal levels of [Ca2+]i in the PDR sublines were variable compared with those of parental drug-sensitive cell lines. Incubation of all PDR tumor sublines with CsA or verapamil resulted in the restoration of membrane potentials to that characteristic of the corresponding drug-sensitive parental tumor. Cyclosporin A produced variable changes in the levels of [Ca2+]i. These data suggest that alteration of membrane potentials is one of the mechanisms responsible for pleiotropic drug resistance in malignancy and show that this alteration is corrected by CsA and verapamil.

Purification and characterization of toxin B from Clostridium difficile

Toxin B from Clostridium difficile was purified to homogeneity and characterized. Purification of toxin B was achieved by gel filtration, chromatography on two consecutive anion-exchange columns, and chromatography on a high-resolution anion-exchange column in the presence of 50 mM CaCl2. The molecular weight of toxin B was estimated to be 250,000 by denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and 500,000 by gel filtration. No subunits were apparent when the toxin was reduced and analyzed by SDS-PAGE. The estimated molecular weight of native toxin B indicated that dimers may form in solution. Toxin B was homogeneous by SDS-PAGE, native PAGE, and high-resolution anion-exchange chromatography. No secondary sequences were detected when the amino terminus of the toxin was sequenced, which also indicated that contaminating peptides were absent from the preparation. The amino terminus of toxin B was determined to be NH3-Trp-Leu-Val-Asn-Arg-Lys-Gln-Leu-Glu-Lys-Met-Ala-Asn-Val-ARg-Phe-Arg. One cytotoxic unit of toxin B was estimated to be 0.2 to 0.8 pg.

Molybdate stabilized rat uterine progesterone receptors: evidence for two mechanisms

Molybdate (Mo), EGTA, or protease inhibitors substantially increase detectable rat uterine progesterone (Pg) receptors. Rehomogenization experiments demonstrated that receptor levels decreased in the absence of Mo or protease inhibitors and were not regenerated. Thus Mo prevents an EGTA and protease-inhibitor-sensitive loss of uterine Pg receptors during homogenization. This effect was compared with receptor stabilization at elevated temperature. In contrast to the stability of receptors in the presence of Mo, receptors decreased rapidly to minimal levels by 30 min at 30 degrees C in TESHG (10 mM Tris, 1.5 mM EGTA, 12 mM thioglycerol, 10% glycerol) or TG buffers. The ability of EGTA to mimic receptor stabilization by Mo during homogenization, compared with its ineffectiveness at 30 degrees C, suggested fundamentally different mechanisms for these two phenomena. Similarly, 0.3 M KCl prevented Mo stabilization of the receptors at 30 degrees C, but did not change their recovery after homogenization. Results with protease inhibitors were also consistent: addition of 2-5 mM leupeptin and 500 microM PMSF to TG during homogenization resulted in substantially increased (P less than 0.01) receptor recovery, but leupeptin (+/- the temperature-labile PMSF) did not prevent the Pg receptor losses at 30 degrees C. The transformation state of the receptors may be important, since receptors were untransformed in the presence of either EGTA or Mo. Moreover, KCl transformed the receptors in parallel to their instability at 30 degrees C. In conclusion, Mo stabilizes Pg receptors during temperature elevation by a different mechanism from that involved during homogenization. Although the parallel effects by EGTA, molybdate, and the protease-inhibitors during homogenization is consistent with inhibition of Ca2+-dependent proteolysis, other possible mechanisms must be considered in future studies.

Enhancement by cyclosporin A of daunorubicin efficacy in Ehrlich ascites carcinoma and murine hepatoma 129

Cyclosporin A abrogates pleiotropic drug resistance in certain experimental tumors. Its impact on drug-sensitive tumors has not been investigated. Our studies show that in drug-sensitive Ehrlich ascites carcinoma and hepatoma 129 cyclosporin A enhances daunorubicin inhibition of DNA synthesis in vitro and prolongs survival of host mice in vivo. Of particular interest is that cyclosporin A converts ineffective daunorubicin regimens into those which result in prolongation of host mice survival. Other agents known to reverse pleiotropic drug resistance are reported to exert their effects by increasing intracellular drug accumulation. In contrast, our studies of drug transport in drug-sensitive Ehrlich ascites carcinoma and hepatoma 129 show that cyclosporin A causes minimal enhancement of [3H]daunorubicin uptake without inhibition of [3H]daunorubicin efflux in both the presence and absence of interrupted active daunorubicin efflux. This suggests that the mechanism of action of daunorubicin enhancement by cyclosporin A in drug-sensitive tumors is not simply the result of increased intracellular daunorubicin accumulation. In vivo dosages of cyclosporin A in the current study are comparable to those which can be used with reasonable safety in humans. We conclude that cyclosporin A may be useful in the potentiation of anthracycline antibiotic therapy directed against drug-sensitive as well as drug-resistant tumors.

Kaposi's sarcoma presenting as homogeneous pulmonary infiltrates in a patient with acquired immunodeficiency syndrome

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