Effects of stand age, tree species, and climate on water table fluctuations and estimated evapotranspiration in managed peatland forests.

Lowland conifer forests dominated by black spruce (Picea mariana) and tamarack (Larix laricina) typically occur in peatlands in the boreal North American forest with near-surface water tables throughout the year. These forests are ecologically and economically important resources that may be impacted by climate change. However, information characterizing effects of forest disturbance, such as even-aged harvest on water table dynamics is needed to evaluate which forest tree species cover types are most hydrologically susceptible to even-aged harvest and changes in precipitation. We used a chronosequence approach to evaluate water table fluctuations and evapotranspiration across four stand age classes (<10, 15-30, 40-80, and >100-years old) and three distinct forest cover types (productive black spruce, stagnant black spruce, and tamarack) for a period of three years in Minnesota, USA. In general, there is limited evidence for elevated water tables in the younger age classes; the <10-year age class had no significant difference in mean weekly water table depth compared to the older age classes across all cover types. Estimated actual daily evapotranspiration (ET) generally agreed with the water table observations, with the exception of the tamarack cover type where ET was significantly lower in the <10-year age class. Productive black spruce sites that are 40-80-years old had higher evapotranspiration, and lower water table, possibly reflecting increased transpiration associated with the stem exclusion stage of stand development. Tamarack in the 40-80-year age class had higher water tables but no difference in ET compared to all other age classes, indicating that other external factors are driving higher water tables in that age class. To evaluate susceptibility to changing climate, we also assessed the sensitivity and response of water table dynamics to pronounced differences in growing season precipitation that occurred across study years. In general, tamarack forests are more sensitive to changes in precipitation compared to the two black spruce forest cover types. These findings can inform expected responses of site hydrology for a range of precipitation scenarios that may occur under future climate and be used by forest managers to evaluate hydrologic impacts of forest management activities across lowland conifer forest cover types.

Surveillance of multi-drug resistance phenotypes in Staphylococcus aureus in Japan and correlation with whole-genome sequence findings.

BACKGROUND: Antimicrobial resistance in Staphylococcus aureus imposes a high disease burden. Both phenotypic and genotypic monitoring are key to understanding and containing emerging resistant strains. AIM: Phenotypic monitoring of emerging resistance in S. aureus and correlation of priority strain phenotypes with whole-genome sequencing (WGS) findings. METHODS: Antimicrobial susceptibility test results of >40,000 isolates from 213 participating hospitals from 2011 to 2019 were exported from the national Japan Nosocomial Infections Surveillance (JANIS) database. Longitudinal and geographic distribution and prevalence of distinct multi-drug resistance phenotypes ('resistance profiles') of S. aureus were examined among hospitals and prefectures. We further conducted a genome sequence analysis of strains with specific resistance profiles of concern. FINDINGS: The overall prevalence of meticillin-resistant S. aureus (MRSA) decreased from 40.3% to 35.1% from 2011 to 2019. However, among dozens of S. aureus resistance profiles, only one profile of a type of MRSA, exhibited a statistically significant increase in inpatient frequency, exceeding 10% during the nine years. This MRSA profile showed resistance to oxacillin, erythromycin and levofloxacin. Analysis of WGS results of S. aureus isolates with this phenotype revealed that most belonged to clonal complex 8, and all carried SCCmec IV, typical of community-acquired MRSA. CONCLUSION: Tracking distinct resistance profiles deepened our understanding of the overall decrease in MRSA and led to recognition of the emergence of a new resistance phenotype. This study provides a model for future epidemiological research on antimicrobial resistance correlating multi-drug resistance phenotypes with selective genome sequencing, which can be applied to other bacterial species.

Automated detection of outbreaks of antimicrobial-resistant bacteria in Japan.

BACKGROUND: Hospital outbreaks of antimicrobial-resistant (AMR) bacteria should be detected and controlled as early as possible. AIM: To develop a framework for automatic detection of AMR outbreaks in hospitals. METHODS: Japan Nosocomial Infections Surveillance (JANIS) is one of the largest national AMR surveillance systems in the world. For this study, all bacterial data in the JANIS database were extracted between 2011 and 2016. WHONET, a free software for the management of microbiology data, and SaTScan, a free cluster detection tool embedded in WHONET, were used to analyse 2015-2016 data of eligible hospitals. Manual evaluation and validation of 10 representative hospitals around Japan were then performed using 2011-2016 data. FINDINGS: Data from 1031 hospitals were studied; mid-sized (200-499 beds) hospitals accounted for 60%, followed by large hospitals (≥500 beds; 24%) and small hospitals (<200 beds; 16%). More clusters were detected in large hospitals. Most of the clusters included five or fewer patients. From the in-depth analysis of 10 hospitals, ∼80% of the detected clusters were unrecognized by infection control staff because the bacterial species involved were not included in the priority pathogen list for routine surveillance. In two hospitals, clusters of more susceptible isolates were detected before outbreaks of more resistant pathogens. CONCLUSION: WHONET-SaTScan can automatically detect clusters of epidemiologically related patients based on isolate resistance profiles beyond lists of high-priority AMR pathogens. If clusters of more susceptible isolates can be detected, it may allow early intervention in infection control practices before outbreaks of more resistant pathogens occur.

Review of patient decision-making factors and attitudes regarding preimplantation genetic diagnosis.

The increasing technical complexity and evolving options for repro-genetic testing have direct implications for information processing and decision making, yet the research among patients considering preimplantation genetic diagnosis (PGD) is narrowly focused. This review synthesizes the literature regarding patient PGD decision-making factors, and illuminates gaps for future research and clinical translation. Twenty-five articles met the inclusion criteria for evaluating experiences and attitudes of patients directly involved in PGD as an intervention or considering using PGD. Thirteen reports were focused exclusively on a specific disease or condition. Five themes emerged: (1) patients motivated by prospects of a healthy, genetic-variant-free child, (2) PGD requires a commitment of time, money, energy and emotions, (3) patients concerned about logistics and ethics of discarding embryos, (4) some patients feel sense of responsibility to use available technologies, and (5) PGD decisions are complex for individuals and couples. Patient research on PGD decision-making processes has very infrequently used validated instruments, and the data collected through both quantitative and qualitative designs have been inconsistent. Future research for improving clinical counseling is needed to fill many gaps remaining in the literature regarding this decision-making process, and suggestions are offered.

Note: Parameter-independent bounding of the stochastic Michaelis-Menten steady-state intrinsic noise variance.

Using the (slow-scale) linear noise approximation, we give parameter-independent bounds to the substrate and product intrinsic noise variance for the stochastic Michaelis-Menten approximation at steady state.

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.

Many different definitions for multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) bacteria are being used in the medical literature to characterize the different patterns of resistance found in healthcare-associated, antimicrobial-resistant bacteria. A group of international experts came together through a joint initiative by the European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC), to create a standardized international terminology with which to describe acquired resistance profiles in Staphylococcus aureus, Enterococcus spp., Enterobacteriaceae (other than Salmonella and Shigella), Pseudomonas aeruginosa and Acinetobacter spp., all bacteria often responsible for healthcare-associated infections and prone to multidrug resistance. Epidemiologically significant antimicrobial categories were constructed for each bacterium. Lists of antimicrobial categories proposed for antimicrobial susceptibility testing were created using documents and breakpoints from the Clinical Laboratory Standards Institute (CLSI), the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the United States Food and Drug Administration (FDA). MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories, XDR was defined as non-susceptibility to at least one agent in all but two or fewer antimicrobial categories (i.e. bacterial isolates remain susceptible to only one or two categories) and PDR was defined as non-susceptibility to all agents in all antimicrobial categories. To ensure correct application of these definitions, bacterial isolates should be tested against all or nearly all of the antimicrobial agents within the antimicrobial categories and selective reporting and suppression of results should be avoided.

Distribution-based sensitivity metric for highly variable biochemical systems.

Classical sensitivity analysis is routinely used to identify points of fragility or robustness in biochemical networks. However, intracellular systems often contain components that number in the thousands to tens or less and consequently motivate a stochastic treatment. Although methodologies exist to quantify sensitivities in stochastic models, they differ substantially from those used in deterministic regimes. Therefore it is not possible to tell whether observed differences in sensitivity measured in deterministic and stochastic elaborations of the same network are the result of methodology or model form. The authors introduce here a distribution-based methodology to measure sensitivity that is equally applicable in both regimes, and demonstrate its use and applicability on a sophisticated mathematical model of the mouse circadian clock that is available in both deterministic and stochastic variants. The authors use the method to produce sensitivity measurements on both variants. They note that the rank-order sensitivity of the clock to parametric perturbations is extremely well conserved across several orders of magnitude. The data show that the clock is fragile to perturbations in parameters common to the cellular machinery ('global' parameters) and robust to perturbations in parameters that are clock-specific ('local' parameters). The sensitivity measure can be used to reduce the model from its original 73 ordinary differential equations (ODEs) to 18 ODEs and to predict the degree to which parametric perturbation can distort the phase response curve of the clock. Finally, the method is employed to evaluate the effect of transcriptional and translational noise on clock function. [Includes supplementary material].

Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes.

Antimicrobial resistance is a priority emerging public health threat, and the ability to detect promptly outbreaks caused by resistant pathogens is critical for resistance containment and disease control efforts. We describe and evaluate the use of an electronic laboratory data system (WHONET) and a space-time permutation scan statistic for semi-automated disease outbreak detection. In collaboration with WHONET-Argentina, the national network for surveillance of antimicrobial resistance, we applied the system to the detection of local and regional outbreaks of Shigella spp. We searched for clusters on the basis of genus, species, and resistance phenotype and identified 19 statistical 'events' in a 12-month period. Of the six known outbreaks reported to the Ministry of Health, four had good or suggestive agreement with SaTScan-detected events. The most discriminating analyses were those involving resistance phenotypes. Electronic laboratory-based disease surveillance incorporating statistical cluster detection methods can enhance infectious disease outbreak detection and response.

Computational design of synthetic gene circuits with composable parts.

MOTIVATION: In principle, novel genetic circuits can be engineered using standard parts with well-understood functionalities. However, no model based on the simple composition of these parts has become a standard, mainly because it is difficult to define signal exchanges between biological units as unambiguously as in electrical engineering. Corresponding concepts and computational tools for easy circuit design in biology are missing. RESULTS: Taking inspiration from (and slightly modifying) ideas in the 'MIT Registry of Standard Biological Parts', we developed a method for the design of genetic circuits with composable parts. Gene expression requires four kinds of signal carriers: RNA polymerases, ribosomes, transcription factors and environmental 'messages' (inducers or corepressors). The flux of each of these types of molecules is a quantifiable biological signal exchanged between parts. Here, each part is modeled independently by the ordinary differential equations (ODE) formalism and integrated into the software ProMoT (Process Modeling Tool). In this way, we realized a 'drag and drop' tool, where genetic circuits are built just by placing biological parts on a canvas and by connecting them through 'wires' that enable flow of signal carriers, as it happens in electrical engineering. Our simulations of well-known synthetic circuits agree well with published computational and experimental results. AVAILABILITY: The code is available on request from the authors.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Using internet discussion of antimicrobial susceptibility databases for continuous quality improvement of the testing and management of antimicrobial resistance.

Accurate results from the world's microbiology laboratories are essential for care of patients, control of hospital and community infections, and global epidemiology. Yet those laboratories differ greatly in their access to supplies, published literature and standards, training courses, peer interaction, and mandated quality control. Because much of what is needed is information, new information technology should help. In particular, measurements of susceptibility to antimicrobial agents, now increasingly filed in electronic databases, exhibit many kinds of variances due both to test performance and to the diversity of bacteria and of their mechanisms of resistance. In industry, workers' ongoing evaluation of variances in measurements of performance has been the basis of management programs of continuous quality improvement. Examples suggest how collegial evaluation of variances in shared susceptibility test data might similarly improve quality not only of testing but also of other aspects of the management of antimicrobial resistance. Internet access is now making such ongoing evaluation and discussion increasingly possible in most parts of the world.

Role for anti-Müllerian hormone in congenital absence of the uterus and vagina.

Molecular genetic techniques were used to determine if mutations in the genes encoding anti-Müllerian hormone (AMH) (also known as Müllerian inhibiting substance (MIS)) and its receptor (AMHR) are commonly present in patients with congenital absence of the uterus and vagina (CAUV). Twenty-two CAUV patients and 96 control subjects from diverse ethnic groups were studied after obtaining informed consent. Genomic DNA samples prepared from leukocytes were digested separately with several different restriction enzymes, and the resultant fragments were analyzed for restriction fragment melting polymorphisms (RFMPs) by denaturing gradient gel electrophoresis (DGGE). Electrophoretic mobility of DNA fragments which were 200-700 base pairs in length was compared using polyacrylamide gels that included linear gradients of denaturing solvents designed to separate DNA fragments according to sequence-dependent variation in thermal stability. Two RFMPs were found in the AMH gene in both patients and normal control subjects. One RFMP in the AMHR gene was present at low frequencies in both patients and normal control subjects. No RFMPs specific to CAUV patients were found in either gene. Because no mutations or rare DNA sequence polymorphisms were detected in the AMH and the AMHR genes in this group of CAUV patients, it is unlikely that either gene commonly has an etiologic role in CAUV.

Ability of laboratories to detect emerging antimicrobial resistance: proficiency testing and quality control results from the World Health Organization's external quality assurance system for antimicrobial susceptibility testing.

The accuracy of antimicrobial susceptibility data submitted by microbiology laboratories to national and international surveillance systems has been debated for a number of years. To assess the accuracy of data submitted to the World Health Organization by users of the WHONET software, the Centers for Disease Control and Prevention distributed six bacterial isolates representing key antimicrobial-resistance phenotypes to approximately 130 laboratories, all but one of which were outside of the United States, for antimicrobial susceptibility testing as part of the World Health Organization's External Quality Assurance System for Antimicrobial Susceptibility Testing. Each laboratory also was asked to submit 10 consecutive quality control values for several key organism-drug combinations. Most laboratories were able to detect methicillin (oxacillin) resistance in Staphylococcus aureus, high-level vancomycin resistance in Enterococcus faecium, and resistance to extended-spectrum cephalosporins in Klebsiella pneumoniae. Many laboratories, particularly those using disk diffusion tests, had difficulty in recognizing reduced susceptibility to penicillin in an isolate of Streptococcus pneumoniae. The most difficult phenotype for laboratories to detect was reduced susceptibility to vancomycin in an isolate of Staphylococcus epidermidis. The proficiency testing challenge also included a request for biochemical identification of a gram-negative bacillus, which most laboratories recognized as Enterobacter cloacae. Although only a small subset of laboratories have submitted their quality control data, it is clear that many of these laboratories generate disk diffusion results for oxacillin when testing S. aureus ATCC 25923 and S. pneumoniae ATCC 49619 that are outside of the acceptable quality control range. The narrow quality control range for vancomycin also proved to be a challenge for many of the laboratories submitting data; approximately 27% of results were out of range. Thus, it is important to establish the proficiency of laboratories submitting data to surveillance systems in which the organisms are tested locally, particularly for penicillin resistance in pneumococci and glycopeptide resistance in staphylococci.

Dominant transmission of imperforate hymen.

OBJECTIVE: Imperforate hymen is an uncommon anomaly of the reproductive tract, occurring in approximately 0.1% of newborn females. The familial occurrence of imperforate hymen in a child, her mother, and her mother's monozygotic twin is reported. DESIGN: Case report. SETTING: Academic medical center. PATIENT(S): Three affected family members. MAIN OUTCOME MEASURE(S): Karyotype and pedigree analysis. RESULT(S): The proband, presenting with peritonitis, was evaluated at age 12 for imperforate hymen because this condition was diagnosed in her mother at age 14. At age 14, the mother's monozygotic twin was asymptomatic except for primary amenorrhea and was also demonstrated to have imperforate hymen. No other reproductive system abnormalities were known to be present in the remaining family members. Chromosomal structural analysis confirmed that the mother of the proband had no chromosomal abnormalities. CONCLUSION(S): The occurrence of imperforate hymen in two consecutive generations of a family is consistent with a dominant mode of transmission, either sex-linked or autosomal. Previously reported examples of siblings with imperforate hymen suggested a recessive mode of inheritance. Taken together, these cases suggest that imperforate hymen can be caused by mutations in several genes. This case highlights the importance of evaluating all family members of affected patients. Familial examples of other developmental anomalies of the female reproductive tract also suggest a multifactorial genetic etiology.

The complex processes of antimicrobial resistance and the information needed to manage them.

Wide use of a succession of different manufactured antimicrobial agents during the past 60 years has prompted the eventual emergence and progressive spread through the world's interconnecting bacterial populations of a growing variety of genes expressing resistance to those agents. The complex processes that spread and link resistance genes into different distributions at different times and places are driven by antimicrobial selection and by contagion. Management of resistance by reducing selection and contagion in a coordinated way requires better information. Most of the information about the spread of resistance exists in laboratory files of isolates at medical centers, and the information about patient antimicrobial use is found in pharmacy files at the same centers. Putting these in a combined database at each center would give a valuable tool to each center's antimicrobial resistance management team. Merging such databases from multiple centers would provide a public health resource for benchmarking, overview surveillance, and general resistometrics.

Learning to listen: serendipitous outcomes of a research training experience.

Experience gained in a qualitative research-training project led a group of clinical nurse specialists to discover the value of using research interview strategies in their clinical work. Clinical interviews, designed to garner data sufficient to decide on interventions, narrow the focus of the interviewer to information deemed relevant to that end. Research interview strategies involve a temporary suspension of the search for intervention, encourage a full description of the respondent's story and experience, and emphasise really listening to that story. In this case it is the respondent who decides what the story is and what information is relevant. This leads the interviewer to a fuller understanding of the context and perceptions of the respondent. The understanding and knowledge thus obtained comprise a better foundation for devising interventions which are individualised and specific to the individual and family.

Effect of coupling on volume-regulatory response of ciliary epithelial cells suggests mechanism for secretion.

The ciliary epithelium of the eye secretes the aqueous humor. It is a double epithelium arranged so that the apical surfaces of the nonpigmented ciliary epithelial (NPCE) and pigmented ciliary epithelial (PCE) cells face each other and the basolateral membranes face the inside of the eye and the blood, respectively. We have investigated the volume responses of both single cells and coupled pairs from this tissue to osmotic challenge. Both NPCE and PCE cells undergo regulatory volume increase (RVI) and decrease (RVD) when exposed to hyper- and hyposmotic solution, respectively. In hyposmotic solution single cells swell and return to their original volumes within approximately 3 min. In nonpigmented cells RVD could be inhibited by blockers of volume-activated Cl- channels [tamoxifen (100%) > quinidine (87%) > DIDS (84%) > 5-nitro-2-(3-phenylpropylamino)benzoic acid (80%) > SITS (58%)] and K+ channels [Ba2+ (31%)]. However, in PCE cells these inhibitors and additionally tetraethylammonium and Gd3+ were without effect. Only bumetanide, an inhibitor of Na+-K+-2Cl- cotransport, was found to have any effect on RVD in PCE cells. NPCE-PCE cell coupled pairs also underwent RVD, but with altered kinetics. The onset of RVD of the PCE cell in a pair occurred approximately 80 s before that of the NPCE cell, and the peak swell was reduced. This is consistent with fluid movement from the PCE to the NPCE cell. The effect of the volume-activated Cl- channel inhibitor tamoxifen was to eliminate this difference in the times of onset of RVD in coupled cell pairs and to inhibit RVD in both the NPCE and PCE cells partially. On the basis of these observations we suggest that fluid is transferred from the PCE to the NPCE cell in coupled pairs during cell swelling and the subsequent RVD. Furthermore, we speculate that reciprocal RVI-RVD could underlie aqueous humor secretion.

Dephosphorylation activates the purified plant plasma membrane H+-ATPase--possible function of phosphothreonine residues in a mechanism not involving the regulatory C-terminal domain of the enzyme.

The plasma membrane H+-ATPase was purified from tobacco cells (line BY-2). After solubilization by lysophosphatidylcholine followed by separation on a glycerol gradient, a fraction with a high specific activity of 9 micromol ATP x min(-1) x mg protein(-1) was obtained, in which the H+-ATPase polypeptide represented at least 80% of the protein. The incubation of this fraction in the presence of alkaline phosphatase increased H+-ATPase activity by 40%, in a manner consistent with dephosphorylation of the enzyme itself. The hydrolytic activity of the solubilized enzyme and its proton translocating activity, after reconstitution into proteoliposomes, were stimulated to the same extent. Alkaline phosphatase treatment was also accompanied by a 92% decrease in the H+-ATPase phosphothreonine content, whereas the phosphoserine residues were almost unaffected. The dephosphorylation induced a slight decrease of the affinity of the enzyme towards ATP. The purified enzyme was not activated by lysophosphatidylcholine addition nor by trypsin-mediated proteolysis, two treatments reported to release the inhibitory control by the C-terminal domain of the H+-ATPase and to increase the affinity of the enzyme towards ATP. Based on these results, the regulatory phosphorylation evoked by alkaline phosphatase most likely differs from the autoinhibitory control of the H+-ATPase by its C-terminal domain.

Surveillance of antimicrobial resistance: the WHONET program.

Genes expressing resistance to each antimicrobial agent emerged after each agent became widely used. More than a hundred such genes now spread selectively through global networks of populations of bacteria in humans or animals treated with those agents. Information to monitor and manage this spread exists in the susceptibility test results of tens of thousands of laboratories around the world. The comparability of those results is uncertain, however, and their storage in paper files or in computer files with diverse codes and formats has made them inaccessible for analysis. The WHONET program puts each laboratory's data into a common code and file format at that laboratory, either by serving as or by translating from its own computer reporting system. It then enables each medical center to analyze its files in ways that help it monitor and manage resistance locally and to merge them with files of other centers for collaborative national or global surveillance of resistance.