RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.

RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.

Exceptionally High O-H Bond Dissociation Free Energy of a Dicopper(II) µ-Hydroxo Complex and Insights into the Geometric and Electronic Structure Origins Thereof.

The strength of the relevant bonds in bond-making and bond-breaking processes can directly affect the overall efficiency of the process. Copper-oxygen sites are known to catalyze reactions with some of the most recalcitrant C-H bonds found in nature as quantified by the bond dissociation free energy (BDFE), yet only a handful of copper-bound O-H bond strengths have been defined. Equally important in the design of synthetic catalysts is an understanding of the geometric and electronic structure origins of these thermodynamic parameters. In this report, the BDFE(OH) of two dicopper-hydroxo complexes, {[LCu]2-(µ-OH)}3+ and {[LCu]2-(µ-OH)}4+ (L = tris(2-pyridylmethyl)amine), were measured. Two key observations were made: (i) the BDFE(OH)s of these complexes were exceptionally high at 103.4 and 91.7 kcal/mol, respectively, which are the highest condensed phase MO-H BDFEs to date and (ii) that the higher oxidation state had a lower BDFE(OH), which is counter to expectations based on known mononuclear BDFE(OH)s which increase with the oxidation state. To understand the origin of these thermodynamic values, the BDFE(OH)s were measured and analyzed for the mononuclear complexes [LCu(OH2)]1+ and [LCu(OH2)]2+ in the same ligand environment. This treatment revealed "dinuclear effects" that include contributions from rehybridization of the oxygen, mixed valency of the metals, magnetic exchange between the metals, and differences in solvation, which are general with respect to [M]2-OH complexes to varying degrees. These analyses are important because they provide a starting point for rationally tuning the thermodynamics of catalytic intermediates broadly and for understanding how copper active sites achieve activation of strong C-H bonds.

Development of an Open-Source Thermal Image Processing Software for Improving Irrigation Management in Potato Crops (Solanum tuberosum L.).

Accurate determination of plant water status is mandatory to optimize irrigation scheduling and thus maximize yield. Infrared thermography (IRT) can be used as a proxy for detecting stomatal closure as a measure of plant water stress. In this study, an open-source software (Thermal Image Processor (TIPCIP)) that includes image processing techniques such as thermal-visible image segmentation and morphological operations was developed to estimate the crop water stress index (CWSI) in potato crops. Results were compared to the CWSI derived from thermocouples where a high correlation was found ( r P e a r s o n = 0.84). To evaluate the effectiveness of the software, two experiments were implemented. TIPCIP-based canopy temperature was used to estimate CWSI throughout the growing season, in a humid environment. Two treatments with different irrigation timings were established based on CWSI thresholds: 0.4 (T2) and 0.7 (T3), and compared against a control (T1, irrigated when soil moisture achieved 70% of field capacity). As a result, T2 showed no significant reduction in fresh tuber yield (34.5 ± 3.72 and 44.3 ± 2.66 t ha - 1 ), allowing a total water saving of 341.6 ± 63.65 and 515.7 ± 37.73 m 3 ha - 1 in the first and second experiment, respectively. The findings have encouraged the initiation of experiments to automate the use of the CWSI for precision irrigation using either UAVs in large settings or by adapting TIPCIP to process data from smartphone-based IRT sensors for applications in smallholder settings.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

BACKGROUND: Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors and gene expression profiles. In the case of widely used model organisms, such as Escherichia coli K-12, the new knowledge gained from these approaches needs to be integrated with the legacy of accumulated knowledge from genetic and molecular biology experiments conducted in the pre-genomic era in order to attain the deepest level of understanding possible based on the available data. RESULTS: In this paper, we describe an expansion of RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization in E. coli K-12, to include the genome-wide dataset collections from 32 ChIP and 19 gSELEX publications, in addition to around 60 genome-wide expression profiles relevant to the functional significance of these datasets and used in their curation. Three essential features for the integration of this information coming from different methodological approaches are: first, a controlled vocabulary within an ontology for precisely defining growth conditions; second, the criteria to separate elements with enough evidence to consider them involved in gene regulation from isolated transcription factor binding sites without such support; and third, an expanded computational model supporting this knowledge. Altogether, this constitutes the basis for adequately gathering and enabling the comparisons and integration needed to manage and access such wealth of knowledge. CONCLUSIONS: This version 10.0 of RegulonDB is a first step toward what should become the unifying access point for current and future knowledge on gene regulation in E. coli K-12. Furthermore, this model platform and associated methodologies and criteria can be emulated for gathering knowledge on other microbial organisms.

Postfire nitrogen balance of Mediterranean shrublands: Direct combustion losses versus gaseous and leaching losses from the postfire soil mineral nitrogen flush.

Fire is a major factor controlling global carbon (C) and nitrogen (N) cycling. While direct C and N losses caused by combustion have been comparably well established, important knowledge gaps remain on postfire N losses. Here, we quantified both direct C and N combustion losses as well as postfire gaseous losses (N2 O, NO and N2 ) and N leaching after a high-intensity experimental fire in an old shrubland in central Spain. Combustion losses of C and N were 9.4 Mg C/ha and 129 kg N/ha, respectively, representing 66% and 58% of initial aboveground vegetation and litter stocks. Moreover, fire strongly increased soil mineral N concentrations by several magnitudes to a maximum of 44 kg N/ha 2 months after the fire, with N largely originating from dead soil microbes. Postfire soil emissions increased from 5.4 to 10.1 kg N ha-1  year-1 for N2 , from 1.1 to 1.9 kg N ha-1  year-1 for NO and from 0.05 to 0.2 kg N ha-1  year-1 for N2 O. Maximal leaching losses occurred 2 months after peak soil mineral N concentrations, but remained with 0.1 kg N ha-1  year-1 of minor importance for the postfire N mass balance. 15 N stable isotope labelling revealed that 33% of the mineral N produced by fire was incorporated in stable soil N pools, while the remainder was lost. Overall, our work reveals significant postfire N losses dominated by emissions of N2 that need to be considered when assessing fire effects on ecosystem N cycling and mass balance. We propose indirect N gas emissions factors for the first postfire year, equalling to 7.7% (N2 -N), 2.7% (NO-N) and 5.0% (N2 O-N) of the direct fire combustion losses of the respective N gas species.

Thermodynamics of a µ-oxo Dicopper(II) Complex for Hydrogen Atom Abstraction.

The mono-µ-hydroxo complex {[Cu(tmpa)]2-(µ-OH)}3+ (1) can undergo reversible deprotonation at -30 °C to yield {[Cu(tmpa)]2-(µ-O)}2+ (2). This species is basic with a pKa of 24.3. 2 is competent for concerted proton-electron transfer from TEMPOH, but is an intrinsically poor hydrogen atom abstractor (BDFE(OH) of 77.2 kcal/mol) based on kinetic and thermodynamic analyses. Nonetheless, DFT calculations experimentally calibrated against 2 reveal that [Cu2O]2+ is likely thermodynamically viable in copper-dependent methane monoxygenase enzymes.

Rate of Change of Initial Intrinsicoid Deflection Predicts Endocardial Versus Epicardial Ventricular Tachycardia.

BACKGROUND: Assessment of origin of ventricular tachycardias (VTs) arising from epicardial vs endocardial sites are largely challenged by the available criteria and etiology of cardiomyopathy. Current electrocardiographic (ECG) criteria based on 12-lead ECG have varying sensitivity and specificity based on site of origin and etiology of cardiomyopathy. OBJECTIVES: This study sought to test the hypothesis that epicardial VT has a slower initial rate of depolarization than endocardial VT. METHODS: We developed a method that takes advantage of the fact that electrical conduction is faster through the cardiac conduction system than the myocardium, and that the conduction system is primarily an endocardial structure. The technique calculated the rate of change in the initial VT depolarization from a signal-averaged 12-lead ECG. We hypothesized that the rate of change of depolarization in endocardial VT would be faster than epicardial. We assessed by applying this technique among 26 patients with VT in nonischemic cardiomyopathy patients. RESULTS: When comparing patients with VTs ablated using epicardial and endocardial approaches, the rate of change of depolarization was found to be significantly slower in epicardial (6.3 ± 3.1 mV/s vs 11.4 ± 3.7 mV/s; P < 0.05). Statistical significance was found when averaging all 12 ECG leads and the limb leads, but not the precordial leads. Follow up analysis by calculation of a receiver-operating characteristic curve demonstrated that this analysis provides a strong prediction if a VT is epicardial in origin (AUC range 0.72-0.88). Slower rate of change of depolarization had high sensitivity and specificity for prediction of epicardial VT. CONCLUSIONS: This study demonstrates that depolarization rate analysis is a potential technique to predict if a VT is epicardial in nature.

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato.

Breeders have made important efforts to develop genotypes able to resist virus attacks in sweetpotato, a major crop providing food security and poverty alleviation to smallholder farmers in many regions of Sub-Saharan Africa, Asia and Latin America. However, a lack of accurate objective quantitative methods for this selection target in sweetpotato prevents a consistent and extensive assessment of large breeding populations. In this study, an approach to characterize and classify resistance in sweetpotato was established by assessing total yield loss and virus load after the infection of the three most common viruses (SPFMV, SPCSV, SPLCV). Twelve sweetpotato genotypes with contrasting reactions to virus infection were grown in the field under three different treatments: pre-infected by the three viruses, un-infected and protected from re-infection, and un-infected but exposed to natural infection. Virus loads were assessed using ELISA, (RT-)qPCR, and loop-mediated isothermal amplification (LAMP) methods, and also through multispectral reflectance and canopy temperature collected using an unmanned aerial vehicle. Total yield reduction compared to control and the arithmetic sum of (RT-)qPCR relative expression ratios were used to classify genotypes into four categories: resistant, tolerant, susceptible, and sensitives. Using 14 remote sensing predictors, machine learning algorithms were trained to classify all plots under the said categories. The study found that remotely sensed predictors were effective in discriminating the different virus response categories. The results suggest that using machine learning and remotely sensed data, further complemented by fast and sensitive LAMP assays to confirm results of predicted classifications could be used as a high throughput approach to support virus resistance phenotyping in sweetpotato breeding.

Thin 3D multiplication regions in plasmonically enhanced nanopillar avalanche detectors.

We demonstrate a nanopillar (NP) device structure for implementing plasmonically enhanced avalanche photodetector arrays with thin avalanche volumes (∼ 310 nm × 150 nm × 150 nm). A localized 3D electric field due to a core-shell PN junction in a NP acts as a multiplication region, while efficient light absorption takes place via surface plasmon polariton Bloch wave (SPP-BW) modes due to a self-aligned metal nanohole lattice. Avalanche gains of ∼216 at 730 nm at -12 V are obtained. We show through capacitance-voltage characterization, temperature-dependent breakdown measurements, and detailed device modeling that the avalanche region is on the order of the ionization path length, such that dead-space effects become significant. This work presents a clear path toward engineering dead space effects in thin 3D-confined multiplication regions for high performance avalanche detectors for applications in telecommunications, sensing and single photon detection.

Optic nerve hypoplasia and bilateral persistent fetal vasculature due to TUBA1A tubulinopathy.

PURPOSE: To describe a case of TUBA1A-associated optic nerve hypoplasia and persistent fetal vasculature. METHODS: Observational case report. RESULTS: A female, full term infant was found to have a Dandy-Walker malformation with cerebellar and brainstem hypoplasia, ventriculomegaly, and lissencephaly. Her ophthalmic exam was notable for persistent fetal vasculature, optic nerve hypoplasia, vitreous hemorrhage, and peripheral retinal non-perfusion. Subsequent genetic testing revealed a TUBA1A genetic variant. CONCLUSION: Persistent fetal vasculature, peripheral retinal vascular abnormalities, and optic nerve hypoplasia may be associated with TUBA1A variants. These patients should be carefully evaluated with dilated retinal exam and fluorescein angiography to detect retinal perfusion abnormalities requiring treatment.

Nerve Protection During Prostate Cryosurgery.

Cryosurgery is a minimally invasive approach to the treatment of focal prostate cancer (PCa). A major complication is the cryoinjury to the cavernous nerve in the neurovascular bundle (NVB). This nerve cryoinjury halts conduction of action potentials (APs) and can eventually result in erectile dysfunction and therefore diminished quality of life for the patient. Here, we propose the application of cryoprotective agents (CPA) to the regions of the nerves in the NVB, prior to prostate cryosurgery, to minimize non-recoverable loss of AP conduction. We modeled a cryosurgical procedure based on data taken during a clinical case and applied ex-vivo porcine phrenic nerves and rat sciatic nerve with temperature profile of NVB. The APs were measured before and after the CPA exposures and during 3 h of recovery. Comparisons of AP amplitude recovery with various CPA compositions reveal that certain CPAs (e.g., 5% DMSO + 7.5% Trehalose and 5% M22 for porcine and rat nerves, respectively) showed little or no toxicity and effective cryoprotection from freezing (on average 48% and 30% of recovered AP, respectively). In summary, we demonstrate that neural conduction can be preserved after exposure to freezing conditions if CPAs are properly selected and deployed onto the nerve.

A Multiscale Computational Model of Skeletal Muscle Electroporation Validated Using In Situ Porcine Experiments.

OBJECTIVE: The goal of our study was to determine the importance of electric field orientation in an anisotropic muscle tissue for the extent of irreversible electroporation damage by means of an experimentally validated mathematical model. METHODS: Electrical pulses were delivered to porcine skeletal muscle in vivo by inserting needle electrodes so that the electric field was applied in direction either parallel or perpendicular to the direction of the muscle fibres. Triphenyl tetrazolium chloride staining was used to determine the shape of the lesions. Next, we used a single cell model to determine the cell-level conductivity during electroporation, and then generalised the calculated conductivity changes to the bulk tissue. Finally, we compared the experimental lesions with the calculated field strength distributions using the Sørensen-Dice similarity coefficient to find the contours of the electric field strength threshold beyond which irreversible damage is thought to occur. RESULTS: Lesions in the parallel group were consistently smaller and narrower than lesions in the perpendicular group. The determined irreversible threshold of electroporation for the selected pulse protocol was 193.4 V/cm with a standard deviation of 42.1 V/cm, and was not dependent on field orientation. CONCLUSION: Muscle anisotropy is of significant importance when considering electric field distribution in electroporation applications. SIGNIFICANCE: The paper presents an important advancement in building up from the current understanding of single cell electroporation to an in silico multiscale model of bulk muscle tissue. The model accounts for anisotropic electrical conductivity and has been validated through experiments in vivo.

The Ocular Trauma Score Underestimates Visual Recovery for the Most Severe Open-Globe Injuries.

PURPOSE: To compare visual outcomes after open-globe injury (OGI) with those predicted by the Ocular Trauma Score (OTS), and to investigate the effect of treatment with pars plana vitrectomy (PPV). DESIGN: Retrospective cohort study. SUBJECTS: Patients presenting with OGI to an academic United States ophthalmology department from 2017 to 2020. METHODS: Best-corrected visual acuity (VA) measurements at the most recent follow-up were compared with final VA predicted by the OTS, based on preoperative injury characteristics. The most recently measured VA of patients treated with PPV during initial OGI repair (primary PPV group) was compared with patients treated with PPV after initial OGI repair (secondary PPV group) and patients never treated with PPV (No PPV group). MAIN OUTCOME MEASURES: Best-corrected VA in the injured eye at last follow-up; secondary outcome measures included the occurrence of vitreous hemorrhage at any time, occurrence of retinal detachment at any time, rates of additional surgery, and rates of enucleation. RESULTS: One-hundred and thirty-three subjects with OGI were identified and analyzed. The overall rate of PPV was 32%. Predictors of worse VA at last follow-up included older age (P = 0.047) and worse presenting VA (P < 0.001). Visual acuity outcomes for eyes in OTS categories 2 to 5 did not significantly differ from OTS predictions. However, eyes in OTS category 1 had a higher likelihood of last follow-up VA of light perception (LP) to hand motion (46% in the study cohort vs. 15% predicted by the OTS, P = 0.004) and a lower likelihood of no LP (33% vs. 74%, P < 0.001). The secondary PPV group had the worst VA at presentation among the 3 groups (P = 0.016), but VA at last follow-up did not significantly differ between the study groups (P = 0.338). CONCLUSIONS: The most severe OGIs (i.e., OTS category 1) had better visual outcomes than predicted by the published OTS expectations, and secondary PPV was associated with significant visual improvement despite poor prognostic predictions. Evaluation by a vitreoretinal surgeon should be considered for all patients with severe OGI, especially those in OTS category 1. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

Risk Factors for Fibrous Ingrowth in Eyes Requiring Primary Keratoplasty.

PURPOSE: The aim of this study was to define risks for corneal transplantation associated with fibrous ingrowth among first-time transplant recipients. METHODS: We performed a retrospective case-control study of patients with a histopathologic diagnosis of fibrous ingrowth between 2002 and 2019. Patients with fibrous ingrowth from a first corneal specimen were included. Those with incomplete records were excluded. A 1:2 case-control ratio was used. Controls were matched using surgical indication, surgery year, transplantation method, sex, and age. RESULTS: Seventy-eight eyes (76 patients) were included and matched with 160 control eyes. The incidence of fibrous ingrowth found on a first corneal transplant was 0.6% per year. The most common keratoplasty indications were pseudophakic corneal edema (n = 25, 32%) and aphakic corneal edema (n = 15, 19%). Cases were more likely to have a history of ocular trauma (odds ratio [OR], 2.94; 95% CI, 1.30-6.30; P = 0.007), uveitis (OR, 2.73; 95% CI, 1.12-6.63; P = 0.022), retinal detachment or previous retinal surgery (OR, 2.40; 95% CI, 1.34-4.30; P = 0.003), glaucoma tube-shunt surgery (OR, 2.70; 95% CI, 1.29-5.65; P = 0.007), aphakia (OR, 3.02; 95% CI, 1.61-5.67; P = 0.0004), or iris derangement (OR, 10.52; 95% CI, 5.45-20.30; P <0.0001). A multivariate logistic regression model using iris derangement, history of ocular trauma, history of uveitis, and history of cataract surgery demonstrated 81% sensitivity and 66% specificity in predicting presence of fibrous ingrowth. CONCLUSIONS: A history of ocular trauma, uveitis, retinal detachment or previous retinal surgery, glaucoma tube-shunt surgery, aphakia, and iris derangement are risks for detecting fibrous ingrowth among first-time keratoplasty recipients. Patients with these conditions should be monitored closely for corneal decompensation.

Development and Implementation of an Acute Kidney Injury Remote Patient Monitoring Program: Research Letter.

Acute kidney injury (AKI) survivors have a dynamic posthospital course which warrants close monitoring. Remote patient monitoring (RPM) could be used to improve quality and efficiency of AKI survivor care. Objective: The objective of this report was to describe the development and preliminary feasibility of an AKI RPM program launched in October 2021. Setting: Academic medical center. Patients: Patients enrolled in the AKI RPM program were those who experienced AKI during a hospitalization and underwent nephrology consultation. Measurements/Methods: At enrollment, patients were provided with home monitoring technology and underwent weekly laboratory assessments. Nurses evaluated the data daily and adhered to prespecified protocols for management and escalation of care if needed. Results: Twenty patients were enrolled in AKI RPM in the first 5 months. Median duration of program participation was 36 (31, 40) days. Eight patients (40%) experienced an unplanned readmission, or an emergency department visit, half (N = 4) of which were attributed to AKI and related circumstances. Of the 9 postgraduation survey respondents, all were satisfied with the RPM program and 89% would recommend RPM to other patients with similar health conditions. Limitations: Acute kidney injury RPM was made possible by the existing infrastructure in our integrated health system and the robust resources available in the Mayo Clinic Center for Digital Health. Such infrastructure may not be universally available which could limit scale and generalizability of such a program. Conclusions: Remote patient monitoring can offer a unique opportunity to bridge the care transition from hospital to home and increase access to quality care for the AKI survivors.

Les survivants d'un épisode d'insuffisance rénale aiguë (IRA) ont un parcours post-hospitalier dynamique qui justifie une surveillance étroite. La télésurveillance des patients (TSP) pourrait être employée pour améliorer la qualité et l'efficacité des soins pour les survivants de l'IRA. Objectif: L'objectif de ce rapport était de décrire le développement et la faisabilité préliminaire d'un programme de TSP-IRA (télésurveillance des patients atteints d'IRA) en octobre 2021. Cadre: Centre médical universitaire. Sujets: Les patients inscrits au programme de TSP-IRA étaient des patients qui avaient vécu un épisode d'IRA lors d'une hospitalisation et obtenu une consultation en néphrologie. Mesures et méthodologie: Au moment de l'inclusion, les patients ont reçu un dispositif de surveillance à domicile et se sont soumis à des évaluations de laboratoire hebdomadaires. Les infirmières ont évalué les données quotidiennement et ont respecté des protocoles prédéfinis pour la gestion et l'escalade des soins si nécessaire. Résultats: Vingt patients ont été inclus dans le programme de TSP-IRA au cours des cinq premiers mois. La durée médiane de participation au programme était de 36 (31, 40) jours. Huit patients (40%) ont dû être réadmis de façon non planifiée ou ont dû faire une visite aux urgences; pour la moitié d'entre eux (N = 4) en raison de l'IRA et de circonstances connexes. Parmi les neuf répondants qui ont répondu au sondage à la complétion du programme, tous se sont dits satisfaits du programme de TSP et 89% le recommanderaient à d'autres patients ayant des problèmes de santé similaires. Limites: Le programme de TSP-IRA a été rendu possible grâce à l'infrastructure existante dans notre système de santé intégré et aux ressources robustes disponibles au Mayo Clinic Center for Digital Health. Une telle infrastructure n'est peut-être pas universellement disponible, ce qui pourrait limiter l'ampleur et la généralisabilité d'un tel programme. Conclusion: La TSP peut offrir une occasion unique de faciliter la transition des soins entre l'hôpital et le domicile et d'accroître l'accès à des soins de qualité pour les survivants d'un épisode d'IRA.

Multiplication theory for dynamically biased avalanche photodiodes: new limits for gain bandwidth product.

Novel theory is developed for the avalanche multiplication process in avalanche photodiodes (APDs) under time-varying reverse-biasing conditions. Integral equations are derived characterizing the statistics of the multiplication factor and the impulse-response function of APDs, as well as their breakdown probability, all under the assumption that the electric field driving the avalanche process is time varying and spatially nonuniform. Numerical calculations generated by the model predict that by using a bit-synchronous sinusoidal biasing scheme to operate the APD in an optical receiver, the pulse-integrated gain-bandwidth product can be improved by a factor of 5 compared to the same APD operating under the conventional static biasing. The bit-synchronized periodic modulation of the electric field in the multiplication region serves to (1) produce large avalanche multiplication factors with suppressed avalanche durations for photons arriving in the early phase of each optical pulse; and (2) generate low avalanche gains and very short avalanche durations for photons arriving in the latter part of each optical pulse. These two factors can work together to reduce intersymbol interference in optical receivers without sacrificing sensitivity.

New perspective on passively quenched single photon avalanche diodes: effect of feedback on impact ionization.

Single-photon avalanche diodes (SPADs) are primary devices in photon counting systems used in quantum cryptography, time resolved spectroscopy and photon counting optical communication. SPADs convert each photo-generated electron hole pair to a measurable current via an avalanche of impact ionizations. In this paper, a stochastically self-regulating avalanche model for passively quenched SPADs is presented. The model predicts, in qualitative agreement with experiments, three important phenomena that traditional models are unable to predict. These are: (1) an oscillatory behavior of the persistent avalanche current; (2) an exponential (memoryless) decay of the probability density function of the stochastic quenching time of the persistent avalanche current; and (3) a fast collapse of the avalanche current, under strong feedback conditions, preventing the development of a persistent avalanche current. The model specifically captures the effect of the load's feedback on the stochastic avalanche multiplication, an effect believed to be key in breaking today's counting rate barrier in the 1.55-µm detection window.

Modifying rainfall patterns in a Mediterranean shrubland: system design, plant responses, and experimental burning.

Global warming is projected to increase the frequency and intensity of droughts in the Mediterranean region, as well as the occurrence of large fires. Understanding the interactions between drought, fire and plant responses is therefore important. In this study, we present an experiment in which rainfall patterns were modified to simulate various levels of drought in a Mediterranean shrubland of central Spain dominated by Cistus ladanifer, Erica arborea and Phillyrea angustifolia. A system composed of automatic rainout shelters with an irrigation facility was used. It was designed to be applied in vegetation 2 m tall, treat relatively large areas (36 m2), and be quickly dismantled to perform experimental burning and reassembled back again. Twenty plots were subjected to four rainfall treatments from early spring: natural rainfall, long-term average rainfall (2 months drought), moderate drought (25% reduction from long-term rainfall, 5 months drought) and severe drought (45% reduction, 7 months drought). The plots were burned in late summer, without interfering with rainfall manipulations. Results indicated that rainfall manipulations caused differences in soil moisture among treatments, leading to reduced water availability and growth of C. ladanifer and E. arborea in the drought treatments. However, P. angustifolia was not affected by the manipulations. Rainout shelters had a negligible impact on plot microenvironment. Experimental burns were of high fire intensity, without differences among treatments. Our system provides a tool to study the combined effects of drought and fire on vegetation, which is important to assess the threats posed by climate change in Mediterranean environments.