Predicting forest attributes In southeast Alaska using artificial neural networks

Artificial neural network (ANN) methods are used to predict forest characteristics. The data source is the Southeast Alaska (SEAK) Grid Inventory, a ground survey compiled by the USDA Forest Service at several thousand sites. The main objective of this article is to predict characteristics at unsurveyed locations between grid sites. A secondary objective is to evaluate the relative performance of different ANNs. Data from the grid sites are used to train six ANNs: multilayer perceptron, fuzzy ARTMAP, probabilistic, generalized regression, radial basis function, and learning vector quantization. A classification and regression tree method is used for comparison. Topographic variables are used to construct models: latitude and longitude coordinates, elevation, slope, and aspect. The models classify three forest characteristics: crown closure, species land cover, and tree size/structure. Models are constructed using n-fold cross-validation. Predictive accuracy is calculated using a method that accounts for the influence of misclassification as well as measuring correct classifications. The probabilistic and generalized regression networks are found to be the most accurate. The predictions of the ANN models are compared with a classification of the Tongass national forest in southeast Alaska based on the interpretation of satellite imagery and are found to be of similar accuracy.

Vosaroxin and vosaroxin plus low-dose Ara-C (LDAC) vs low-dose Ara-C alone in older patients with acute myeloid leukemia

The development of new treatments for older patients with acute myeloid leukemia is an active area, but has met with limited success. Vosaroxin, a quinolone-derived intercalating agent has several properties that could prove beneficial. Initial clinical studies showed it to be well-tolerated in older patients with relapsed/refractory disease. In vitro data suggested synergy with cytarabine (Ara-C). To evaluate vosaroxin, we performed 2 randomized comparisons within the "Pick a Winner" program. A total of 104 patients were randomized to vosaroxin vs low-dose Ara-C (LDAC) and 104 to vosaroxin + LDAC vs LDAC. When comparing vosaroxin with LDAC, neither response rate (complete recovery [CR]/complete recovery with incomplete count recovery [CRi], 26% vs 30%; odds ratio [OR], 1.16 (0.49-2.72); P = .7) nor 12-month survival (12% vs 31%; hazard ratio [HR], 1.94 [1.26-3.00]; P = .003) showed benefit for vosaroxin. Likewise, in the vosaroxin + LDAC vs LDAC comparison, neither response rate (CR/CRi, 38% vs 34%; OR, 0.83 [0.37-1.84]; P = .6) nor survival (33% vs 37%; HR, 1.30 [0.81-2.07]; P = .3) was improved. A major reason for this lack of benefit was excess early mortality in the vosaroxin + LDAC arm, most obviously in the second month following randomization. At its first interim analysis, the Data Monitoring and Ethics Committee recommended closure of the vosaroxin-containing trial arms because a clinically relevant benefit was unlikely.

Probabilistic Planning in AgentSpeak using the POMDP framework.

AgentSpeak is a logic-based programming language, based on the Belief-Desire-Intention (BDI) paradigm, suitable for building complex agent-based systems. To limit the computational complexity, agents in AgentSpeak rely on a plan library to reduce the planning problem to the much simpler problem of plan selection. However, such a plan library is often inadequate when an agent is situated in an uncertain environment. In this paper, we propose the AgentSpeak+ framework, which extends AgentSpeak with a mechanism for probabilistic planning. The beliefs of an AgentSpeak+ agent are represented using epistemic states to allow an agent to reason about its uncertain observations and the uncertain effects of its actions. Each epistemic state consists of a POMDP, used to encode the agent’s knowledge of the environment, and its associated probability distribution (or belief state). In addition, the POMDP is used to select the optimal actions for achieving a given goal, even when facing uncertainty.

Modulation of intracellular calcium homeostasis blocks autophagosome formation

Cellular stress responses often involve elevation of cytosolic calcium levels, and this has been suggested to stimulate autophagy. Here, however, we demonstrated that agents that alter intracellular calcium ion homeostasis and induce ER stress-the calcium ionophore A23187 and the sarco/endoplasmic reticulum Ca (2+)-ATPase inhibitor thapsigargin (TG)-potently inhibit autophagy. This anti-autophagic effect occurred under both nutrient-rich and amino acid starvation conditions, and was reflected by a strong reduction in autophagic degradation of long-lived proteins. Furthermore, we found that the calcium-modulating agents inhibited autophagosome biogenesis at a step after the acquisition of WIPI1, but prior to the closure of the autophagosome. The latter was evident from the virtually complete inability of A23187- or TG-treated cells to sequester cytosolic lactate dehydrogenase. Moreover, we observed a decrease in both the number and size of starvation-induced EGFP-LC3 puncta as well as reduced numbers of mRFP-LC3 puncta in a tandem fluorescent mRFP-EGFP-LC3 cell line. The anti-autophagic effect of A23187 and TG was independent of ER stress, as chemical or siRNA-mediated inhibition of the unfolded protein response did not alter the ability of the calcium modulators to block autophagy. Finally, and remarkably, we found that the anti-autophagic activity of the calcium modulators did not require sustained or bulk changes in cytosolic calcium levels. In conclusion, we propose that local perturbations in intracellular calcium levels can exert inhibitory effects on autophagy at the stage of autophagosome expansion and closure.

Diagnostic performance on briefly presented digital pathology images

Background: Identifying new and more robust assessments of proficiency/expertise (finding new "biomarkers of expertise") in histopathology is desirable for many reasons. Advances in digital pathology permit new and innovative tests such as flash viewing tests and eye tracking and slide navigation analyses that would not be possible with a traditional microscope. The main purpose of this study was to examine the usefulness of time-restricted testing of expertise in histopathology using digital images.
Methods: 19 novices (undergraduate medical students), 18 intermediates (trainees), and 19 experts (consultants) were invited to give their opinion on 20 general histopathology cases after 1 s and 10 s viewing times. Differences in performance between groups were measured and the internal reliability of the test was calculated.
Results: There were highly significant differences in performance between the groups using the Fisher's least significant difference method for multiple comparisons. Differences between groups were consistently greater in the 10-s than the 1-s test. The Kuder-Richardson 20 internal reliability coefficients were very high for both tests: 0.905 for the 1-s test and 0.926 for the 10-s test. Consultants had levels of diagnostic accuracy of 72% at 1 s and 83% at 10 s.
Conclusions: Time-restricted tests using digital images have the potential to be extremely reliable tests of diagnostic proficiency in histopathology. A 10-s viewing test may be more reliable than a 1-s test. Over-reliance on "at a glance" diagnoses in histopathology is a potential source of medical error due to over-confidence bias and premature closure.

The single component geochemical map: Fact or fiction?

Single component geochemical maps are the most basic representation of spatial elemental distributions and commonly used in environmental and exploration geochemistry. However, the compositional nature of geochemical data imposes several limitations on how the data should be presented. The problems relate to the constant sum problem (closure), and the inherently multivariate relative information conveyed by compositional data. Well known is, for instance, the tendency of all heavy metals to show lower values in soils with significant contributions of diluting elements (e.g., the quartz dilution effect); or the contrary effect, apparent enrichment in many elements due to removal of potassium during weathering. The validity of classical single component maps is thus investigated, and reasonable alternatives that honour the compositional character of geochemical concentrations are presented. The first recommended such method relies on knowledge-driven log-ratios, chosen to highlight certain geochemical relations or to filter known artefacts (e.g. dilution with SiO2 or volatiles). This is similar to the classical normalisation approach to a single element. The second approach uses the (so called) log-contrasts, that employ suitable statistical methods (such as classification techniques, regression analysis, principal component analysis, clustering of variables, etc.) to extract potentially interesting geochemical summaries. The caution from this work is that if a compositional approach is not used, it becomes difficult to guarantee that any identified pattern, trend or anomaly is not an artefact of the constant sum constraint. In summary the authors recommend a chain of enquiry that involves searching for the appropriate statistical method that can answer the required geological or geochemical question whilst maintaining the integrity of the compositional nature of the data. The required log-ratio transformations should be applied followed by the chosen statistical method. Interpreting the results may require a closer working relationship between statisticians, data analysts and geochemists.

Semantics for possibilistic answer set programs: uncertain rules versus rules with uncertain conclusions

Although Answer Set Programming (ASP) is a powerful framework for declarative problem solving, it cannot in an intuitive way handle situations in which some rules are uncertain, or in which it is more important to satisfy some constraints than others. Possibilistic ASP (PASP) is a natural extension of ASP in which certainty weights are associated with each rule. In this paper we contrast two different views on interpreting the weights attached to rules. Under the first view, weights reflect the certainty with which we can conclude the head of a rule when its body is satisfied. Under the second view, weights reflect the certainty that a given rule restricts the considered epistemic states of an agent in a valid way, i.e. it is the certainty that the rule itself is correct. The first view gives rise to a set of weighted answer sets, whereas the second view gives rise to a weighted set of classical answer sets.

Weak and strong disjunction in possibilistic ASP

Possibilistic answer set programming (PASP) unites answer set programming (ASP) and possibilistic logic (PL) by associating certainty values with rules. The resulting framework allows to combine both non-monotonic reasoning and reasoning under uncertainty in a single framework. While PASP has been well-studied for possibilistic definite and possibilistic normal programs, we argue that the current semantics of possibilistic disjunctive programs are not entirely satisfactory. The problem is twofold. First, the treatment of negation-as-failure in existing approaches follows an all-or-nothing scheme that is hard to match with the graded notion of proof underlying PASP. Second, we advocate that the notion of disjunction can be interpreted in several ways. In particular, in addition to the view of ordinary ASP where disjunctions are used to induce a non-deterministic choice, the possibilistic setting naturally leads to a more epistemic view of disjunction. In this paper, we propose a semantics for possibilistic disjunctive programs, discussing both views on disjunction. Extending our earlier work, we interpret such programs as sets of constraints on possibility distributions, whose least specific solutions correspond to answer sets.

Novel system for distant assessment of cataract surgical quality in rural China

BACKGROUND: This study aims to assess the quality of various steps of manual small incision cataract surgery and predictors of quality, using video recordings.
DESIGN: This paper applies a retrospective study.
PARTICIPANTS: Fifty-two trainees participated in a hands-on small incision cataract surgery training programme at rural Chinese hospitals.
METHODS: Trainees provided one video each recorded by a tripod-mounted digital recorder after completing a one-week theoretical course and hands-on training monitored by expert trainers. Videos were graded by two different experts, using a 4-point scale developed by the International Council of Ophthalmology for each of 12 surgical steps and six global factors. Grades ranged from 2 (worst) to 5 (best), with a score of 0 if the step was performed by trainers.
MAIN OUTCOME MEASURES: Mean score for the performance of each cataract surgical step rated by trainers.
RESULTS: Videos and data were available for 49/52 trainees (94.2%, median age 38 years, 16.3% women and 77.5% completing > 50 training cases). The majority (53.1%, 26/49) had performed ≤ 50 cataract surgeries prior to training. Kappa was 0.57∼0.98 for the steps (mean 0.85). Poorest-rated steps were draping the surgical field (mean ± standard deviation = 3.27 ± 0.78), hydro-dissection (3.88 ± 1.22) and wound closure (3.92 ± 1.03), and top-rated steps were insertion of viscoelastic (4.96 ± 0.20) and anterior chamber entry (4.69 ± 0.74). In linear regression models, higher total score was associated with younger age (P = 0.015) and having performed >50 independent manual small incision cases (P = 0.039).
CONCLUSIONS: More training should be given to preoperative draping, which is poorly performed and crucial in preventing infection. Surgical experience improves ratings.© 2015 Royal Australian and New Zealand College of Ophthalmologists.

Phacoemulsification combined with posterior capsulorhexis and anterior vitrectomy in the management of malignant glaucoma in phakic eyes

Purpose: To describe sequential phacoemulsification-intraocular lens (IOL) implantation-posterior capsulorhexis-anterior vitrectomy in the management of phakic malignant glaucoma. Methods: Twenty consecutive patients (25 eyes) with phakic malignant glaucoma were enrolled at the Zhongshan Ophthalmic Center, Sun Yat-sen University. All patients underwent phacoemulsification, IOL implantation and posterior capsulorhexis together with anterior vitrectomy via a clear corneal paracentesis. Visual acuity, intraocular pressure (IOP), anterior chamber depth (ACD), surgical complications and medications required after the surgery were recorded. Results: After surgery, the mean LogMAR visual acuity and ACD increased significantly (visual acuity from -1.56 ± 1.17 to -0.54 ± 0.81, p < 0.001; ACD from 0.367 ± 0.397 mm to 2.390 ± 0.575 mm, p < 0.001), and mean IOP decreased significantly (from 39.6 ± 10.6 mm Hg to 14.5 ± 4.1 mmHg, p < 0.001). No serious perioperative complications occurred, and only five eyes required topical glaucoma medications after surgery. Conclusion: Combined phacoemulsification-IOL implantation-posterior capsulorhexis-anterior vitrectomy surgery is a safe and effective method for treating patients with phakic malignant glaucoma. © 2012 The Authors. Acta Ophthalmologica © 2012 Acta Ophthalmologica Scandinavica Foundation.

A proposed simple method for measurement in the anterior chamber angle: biometric gonioscopy

OBJECTIVE:

To design a system of gonioscopy that will allow greater interobserver reliability and more clearly defined screening cutoffs for angle closure than current systems while being simple to teach and technologically appropriate for use in rural Asia, where the prevalence of angle-closure glaucoma is highest.

DESIGN:

Clinic-based validation and interobserver reliability trial.

PARTICIPANTS:

Study 1: 21 patients 18 years of age and older recruited from a university-based specialty glaucoma clinic; study 2: 32 patients 18 years of age and older recruited from the same clinic.

INTERVENTION:

In study 1, all participants underwent conventional gonioscopy by an experienced observer (GLS) using the Spaeth system and in the same eye also underwent Scheimpflug photography, ultrasonographic measurement of anterior chamber depth and axial length, automatic refraction, and biometric gonioscopy with measurement of the distance from iris insertion to Schwalbe's line using a reticule based in the slit-lamp ocular. In study 2, all participants underwent both conventional gonioscopy and biometric gonioscopy by an experienced gonioscopist (NGC) and a medical student with no previous training in gonioscopy (JK).

MAIN OUTCOME MEASURES:

Study 1: The association between biometric gonioscopy and conventional gonioscopy, Scheimpflug photography, and other factors known to correlate with the configuration of the angle. Study 2: Interobserver agreement using biometric gonioscopy compared to that obtained with conventional gonioscopy.

RESULTS:

In study 1, there was an independent, monotonic, statistically significant relationship between biometric gonioscopy and both Spaeth angle (P = 0.001, t test) and Spaeth insertion (P = 0.008, t test) grades. Biometric gonioscopy correctly identified six of six patients with occludable angles according to Spaeth criteria. Biometric gonioscopic grade was also significantly associated with the anterior chamber angle as measured by Scheimpflug photography (P = 0.005, t test). In study 2, the intraclass correlation coefficient between graders for biometric gonioscopy (0.97) was higher than for Spaeth angle grade (0.72) or Spaeth insertion grade (0.84).

CONCLUSION:

Biometric gonioscopy correlates well with other measures of the anterior chamber angle, shows a higher degree of interobserver reliability than conventional gonioscopy, and can readily be learned by an inexperienced observer.

Biometric gonioscopy and the effects of age, race, and sex on the anterior chamber angle.

AIM:

To utilise a novel method for making measurements in the anterior chamber in order to compare the anterior chamber angles of people of European, African, and east Asian descent aged 40 years and over.

METHODS:

A cross sectional study on 15 people of each sex from each decade from the 40s to the 70s, from each of three racial groups-black, white, and Chinese Singaporeans. Biometric gonioscopy (BG) utilises a slit lamp mounted reticule to make measurements from the apparent iris insertion to Schwalbe's line through a Goldmann one mirror goniolens. The main outcome measures were BG measurements of the anterior chamber angle as detailed above.

RESULTS:

There was no significant difference in angle measurement between black, white, and Chinese races in this study. However, at younger ages people of Chinese race appeared to have deeper angles than white or black people, whereas the angles of older Chinese were significantly narrower (p = 0.004 for the difference in slope of BG by age between Chinese and both black and white people).

CONCLUSION:

The failure to detect a difference in angle measurements between these groups was surprising, given the much higher prevalence of angle closure among Chinese. It appears that the overall apparent similarity of BG means between Chinese and Western populations may mask very different trends with age. The apparently more rapid decline in angle width measurements with age among Chinese may be due to the higher prevalence of cataract or "creeping angle closure." However, longitudinal inferences from cross sectional data are problematic, and this may represent a cohort phenomenon caused by the increasing prevalence of myopia in the younger Singaporean population.

Age, gender, biometry, refractive error, and the anterior chamber angle among Alaskan Eskimos.

BACKGROUND:

The prevalence of angle-closure glaucoma (ACG) is greater for Eskimos/Inuit than it is for any other ethnic group in the world. Although it has been suggested that this prevalence may be due to a population tendency toward shallower anterior chamber angles, available evidence for other populations such as Chinese with high rates of ACG has not consistently demonstrated such a tendency.

METHODS:

A reticule, slit-lamp, and standard Goldmann one-mirror goniolens were used to make measurements in the anterior chamber (AC) angle according to a previously reported protocol for biometric gonioscopy (BG) (Ophthalmology 1999;106:2161-7). Measurements were made in all four quadrants of one eye among 133 phakic Alaskan Eskimos aged 40 years and older. Automatic refraction, dilated examination of the anterior segment and optic nerve, and A-scan measurements of AC depth, lens thickness, and axial length were also carried out for all subjects.

RESULTS:

Both central and peripheral AC measurements for the Eskimo subjects were significantly lower than those previously reported by us for Chinese, blacks, and whites under the identical protocol. Eskimos also seemed to have somewhat more hyperopia. There were no differences in biometric measurements between men and women in this Eskimo population. Angle measurements by BG seemed to decline more rapidly over life among Eskimos and Chinese than blacks or whites. Although there was a significant apparent decrease in AC depth, increase in lens thickness, and increase in hyperopia with age among Eskimos, all of these trends seemed to reverse in the seventh decade and beyond.

CONCLUSIONS:

Eskimos do seem to have shallower ACs than do other racial groups. Measurements of the AC angle seem to decline more rapidly over life among Eskimos than among blacks or whites, a phenomenon also observed by us among Chinese, another group with high ACG prevalence. This apparent more rapid decline may be due to a cohort effect with higher prevalence of myopia and resulting wider angles among younger Eskimos and Chinese.

Pupil constriction can alter the accuracy of dark room provocative test.

BACKGROUND: Primary angle-closure glaucoma (PACG) is a major cause of visual morbidity in East Asia. Dark-room provocative test (DRPT) has been used to determine which narrow angles have the risk to develop angle closure. However, the accuracy of DRPT might be altered because that after emerging from the dark room, the configuration of the angle is affected by the light of the slit-lamp and the appositionally closed angle reopens. The aim of this study was to examine the pupillary diameter in different light conditions and use it as a parameter to assess the accuracy of dark-room provocative test. METHODS: Patients with suspected primary angle-closure glaucoma undergoing DRPT were recruited. The anterior chamber angle was examined by anterior segment optical coherence tomography under the following conditions: (1) in standard room illumination; (2) after short-term dark-adaptation and (3) after DRPT. Mean values of pupil size and numbers of appositionally closed angle under different conditions were compared. RESULTS: A total of 47 eyes of 47 patients were analyzed. The pupil size after DRPT was smaller than that after short-term dark-adaptation (P < 0.001) and smaller than that in standard room illumination (P = 0.026). The numbers of appositionally closed angles after short-term dark-adaptation were significantly larger than those after DRPT (P < 0.001). There was no significant difference between the numbers of appositionally closed angles in standard room illumination and after DRPT (P = 0.157). CONCLUSIONS: Constriction of pupil size immediately after prolonged dark room provocative test may lead to change in the angle configuration, which may lead to false negative results. We suggest a modified protocol of recording intraocular pressure immediately after DRPT and performing gonioscopy following short-term dark adaptation to improve the accuracy of angle closure assessment.

INVESTIGATING THE ROLE OF NOX NADPH OXIDASE SIGNALLING IN CELL MIGRATION AND ANGIOGENESIS OF ENDOTHELIAL COLONY-FORMING CELLS

Introduction. Endothelial colony-forming cells (ECFCs) hold great cytotherapeutic potential for ischaemic disease. Emerging evidence supports a key role for NADPH oxidases in underlying angiogenic processes of these and other endothelial cells. Aims. To study the influence of Nox NADPH oxidases on the pro-angiogenic function of ECFCs. Methods. Human ECFCs isolated from umbilical cord blood were treated with pro-oxidant PMA and assessed in vitro, both under basal conditions and after siRNA knockdown of Nox4, a key endothelial NADPH oxidase isoform, alongside primary mature human aortic endothelial cells (HAoECs) for comparison, using an established scratch-wound assay as the functional end-point. Results. PMA (500nM for 8h) increased cell migration (control 18.6±2.8, PMA 32.7±6.6% wound closure; n=6, P<0.05) in a superoxide-dependent manner, as indicated by attenuation of this effect in the presence of PEG-SOD. Although HAoEC migration in response to PMA also tended to increase, this did not reach statistical significance. Notably, cell migration at 16h was reduced by Nox4 knockdown in ECFCs (control siRNA 53.4±3.5, Nox4 siRNA 35.1±4.9% closure; n=3, P<0.05), but not in HAoECs, whilst the pro-migratory effect of PMA in ECFCs was potentiated after Nox4 knockdown (control siRNA 53.4±3.5, +PMA 61.5±3.2% closure; n=3, P=NS; Nox4 siRNA 35.1±4.9, +PMA 53.0±4.9% closure; n=3, P<0.05). Conclusion. ECFC migration is enhanced by low concentrations of superoxide, to a greater extent compared to mature endothelial cells, and appears to be at least partly dependent upon NADPH oxidase, including a specific role for Nox4. Although, the precise contribution of endothelial Nox NADPH oxidases isoforms remains to be determined, it is clear that these findings may have significant implications for potential ECFC-based therapies for ischaemic disease, which is associated with an oxidative microenvironment.