Miracle-dz/UniFAR-FTUs huggingface dataset:
UC Irvine UC Irvine Previously Published Works Title Evolutionary algorithms and other metaheuristics in water resources : Current status , research challenges and future directions

The development and application of evolutionary algorithms (EAs) and other metaheuristics for the optimisation of water resources systems has been an active research field for over two decades. Research to date has emphasized algorithmic improvements and individual applications in specific areas (e.g. model calibration, water distribution systems, groundwater management, river-basin planning and management, etc.). However, there has been limited synthesis between shared problem traits, common EA challenges, and needed advances across major applications. This paper clarifies the current status and future research directions for better solving key water resources problems using EAs. Advances in understanding fitness landscape properties and their effects on algorithm performance are critical. Future EA-based applications to real-world problems require a fundamental shift of focus towards improving problem formulations, understanding general theoretic frameworks for problem decompositions, major advances in EA computational efficiency, and most importantly aiding real decision-making in complex, uncertain application contexts. © 2014 Elsevier Ltd. All rights reserved.
LESIONS MISTAKEN FOR MALIGNANT MELANOMA OF THE POSTERIOR UVEA. A CLINICOPATHOLOGIC ANALYSIS OF 100 CASES WITH OPHTHALMOSCOPICALLY VISIBLE LESIONS.

Enucleation of an eye that is erroneously thought to harbor a malignant melanoma is, in many cases, a tragic loss for the patient. History tends to repeat itself, and a lesion that has confused one ophthalmologist in the past is likely to confuse others in the future. A thoughtful analysis of eyes that have been enucleated because of such erroneous diagnoses should be helpful in reducing the frequency of these misfortunes in the future. Several attempts at such an analysis have been made in the past. 1-5 To obtain meaningful information, however, cases selected for this type of study must meet two major criteria: (1) the lesion must have been ophthalmoscopically visible, and (2) suspicion that the ophthalmoscopically visible lesion was due to a malignant melanoma must have been so great that enucleation was the result. The first criterion stems from the fact that many eyes that are clinically blind
Original Contribution Thiazolidinediones and Parkinson Disease : A Cohort Study

Thiazolidinediones, a class of medications indicated for the treatment of type 2 diabetes mellitus, reduce inflammation and have been shown to provide a therapeutic benefit in animal models of Parkinson disease. We examined the association between treatment with thiazolidinediones and the onset of Parkinson disease in older individuals. We performed a cohort study of 29,397 Medicare patients enrolled in state pharmaceutical benefits programs who initiated treatment with thiazolidinediones or sulfonylureas during the years 1997 through 2005 and had no prior diagnosis of Parkinson disease. New users of thiazolidinediones were propensity score matched to new users of sulfonylureas and followed to determine whether they were diagnosed with Parkinson disease. We used Cox proportional hazards models to compare time to diagnosis of Parkinson disease in the propensity score–matched populations. To assess the association with duration of use, we performed several analyses that required longer continuous use of medications. In the primary analysis, thiazolidinedione users had a hazard ratio for a diagnosis of Parkinson disease of 1.09 (95% confidence interval: 0.71, 1.66) when compared with sulfonylurea users. Increasing the duration-of-use requirements to 10 months did not substantially change the association; the hazard ratios ranged from 1.00 (95% confidence interval: 0.49, 2.05) to 1.17 (95% confidence interval: 0.60, 2.25). Thiazolidinedione use was not associated with a longer time to diagnosis of Parkinson disease than was sulfonylurea use, regardless of duration of exposure.
Systemic challenge with endotoxin stimulates corticotropin-releasing hormone and arginine vasopressin secretion into hypophyseal portal blood: coincidence with gonadotropin-releasing hormone suppression.

We tested the hypothesis that systemic immune/inflammatory challenge (endotoxin) activates the neuroendocrine stress axis centrally by stimulating the secretion of CRH and arginine vasopressin (AVP) into hypophyseal portal blood. In addition, we examined the temporal association between this stimulation of the stress neuropeptides and the inhibition of pulsatile GnRH and LH secretion. Using alert, normally behaving ewes, hypophyseal portal and peripheral blood were sampled simultaneously at 10-min intervals for 14 h. Temperature was monitored remotely by telemetry at the same interval. Endotoxin (400 ng/kg, i.v. bolus) or saline as a control was injected after a 4-h baseline period. Portal blood was assayed for CRH, AVP, and GnRH, and peripheral blood was assayed for cortisol, progesterone, and LH. In controls, hypophyseal portal CRH and AVP remained just above or at assay sensitivity, and cortisol showed a regular rhythmic pattern unaffected by saline and typical of basal secretion. In contrast, endotoxin potently stimulated CRH and AVP secretion into portal blood, and cortisol and progesterone into peripheral blood. Both CRH and AVP generally rose and fell simultaneously, although the peak of the AVP response was approximately 10-fold greater than that of CRH. The AVP in portal blood was not due to recirculation of hormone secreted into the peripheral circulation by the posterior pituitary gland, because the AVP increase in peripheral blood was negligible relative to the marked increase in portal blood. The stimulation of CRH and AVP coincided with significant suppression of GnRH and LH pulsatile secretion in these same ewes and with the generation of fever. We conclude that endotoxin induces central activation of the neuroendocrine stress axis, stimulating both CRH and AVP release into the hypophyseal portal blood of conscious, normally behaving ewes. This response is temporally coupled to inhibition of pulsatile GnRH and LH release as well as with stimulation of adrenal cortisol and progesterone secretion and generation of fever.
Predicting Cisplatin-Induced Acute Kidney Injury by Urinary Neutrophil Gelatinase-Associated Lipocalin Excretion: A Pilot Prospective Case-Control Study

Background/Aims: Nephrotoxicity is the major limitation to cisplatin therapy for solid tumors. We aimed at evaluating whether early increases in serum/urine levels of neutrophil gelatinase-associated lipocalin (NGAL), a biomarker of tubular damage and regeneration, predict cisplatin-induced acute kidney injury (AKI). Methods: We compared changes in serum creatinine and serum/urine NGAL levels (ELISA assay) at 1 and 4 h and 1, 2, 3, 7 and 15 days after cisplatin infusion (70–80 mg/m2) versus baseline in 12 consecutive cancer patients (cases) with AKI (>25% serum creatinine increase vs. baseline) and 12 consecutive controls without AKI. Results: Baseline characteristics and posttreatment serum NGAL levels were similar in both groups. Urinary NGAL levels increased significantly more in cases than in controls at 1, 2, 3 and 15 days after cisplatin. The NGAL increase preceded AKI by 4.5 days and the NGAL increase at day 2 after cisplatin independently predicted AKI (p < 0.05). Six cases with residual kidney dysfunction at 15 days showed a trend to earlier and higher increase in urinary NGAL levels compared to cases with renal function recovery. Conclusion: An early increase in urinary NGAL excretion may help in identifying patients at risk of cisplatin-induced AKI who might benefit from innovative treatments to prevent cisplatin nephrotoxicity.
Microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence.

AIM To investigate the microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence. METHODS Forty-one specimens were obtained from esophageal cancer (EC) patients. Histopathological assessment identified 23 squamous cell carcinomas (SCC) and 18 adenocarcinomas (ADC), including only 8 ADC with Barrett esophageal columnar epithelium (metaplasia) and dysplasia adjacent to ADC. Paraffin-embedded normal squamous epithelium, Barrett esophageal columnar epithelium (metaplasia), dysplasia and esophageal tumor tissues were dissected from the surrounding tissues under microscopic guidance. DNA was extracted using proteinase K digestion buffer, and DNA was diluted at 1:100, 1:1000, 1:5000, 1:10000 and 1:50000, respectively. Seven microsatellite markers (D2S123, D3S1616, D3S1300, D5S346, D17S787, D18S58 and BATRII loci) were used in this study. Un-dilution and dilution polymerase chain reactions (PCR) were performed, and microsatellite analysis was carried out. RESULTS No statistically significant difference was found in microsatellite instability (MSI) and loss of heterozygosity (LOH) of un-diluted DNA between SCC and ADC. The levels of MSI and LOH were high in the metaplasia-dysplasia-adenocarcinoma sequence of diluted DNA. The more the diluted DNA was, the higher the rates of MSI and LOH were at the above 7 loci, especially at D3S1616, D5S346, D2S123, D3S1300 and D18S58 loci. CONCLUSION The sequence of metaplasia-dysplasia-adenocarcinoma is associated with microsatellite alterations, including MSI and LOH. The MSI and LOH may be the early genetic events during esophageal carcinogenesis, and genetic alterations at the D3S1616, D5S346 and D3S123 loci may play a role in the progress of microsatellite alterations.
Symmetric synaptic patterns between starburst amacrine cells and direction selective ganglion cells in the rabbit retina

Inputs from starburst amacrine cells (SACs) to ON‐OFF direction selective ganglion cells (DSGCs) in the rabbit retina are themselves directional. However, the synaptic asymmetry between SACs and DSGCs required for generating direction selectivity has been controversial. We investigated dendritic contacts and distribution of inhibitory synapses between SACs and their overlapped DSGCs. Double injection of SAC/DSGC pairs and quantitative analysis revealed no obvious asymmetry of dendritic contacts between SACs and DSGCs. Furthermore, examination of the inhibitory input pattern on the dendrites of DSGCs using antibodies against GABAA receptors also suggested an isotropic arrangement with the overlapping SACs in both the preferred and the null directions. Therefore, the presynaptic mechanism of direction selectivity upon DSGCs may not result from a simple asymmetric arrangement with overlapping SACs. Multiple layer interactions and sophisticated synaptic connections between SACs and DSGCs are necessary. J. Comp. Neurol. 508:175–183, 2008. © 2008 Wiley‐Liss, Inc.
Contraceptive self-efficacy and contraceptive knowledge of Hong Kong Chinese women with unplanned pregnancy.

AIM AND OBJECTIVES The purpose of this study was to explore contraceptive practice, the level of knowledge and self-efficacy of contraception among Chinese women with unplanned pregnancy and to determine the relationships between these variables. BACKGROUND The construct of self-efficacy can be employed as a theory to design a nursing intervention to prevent sexually active women from unplanned pregnancy. Only a few western studies have investigated the relationships between self-efficacy and contraception behaviour yet none targeted at the Chinese population. DESIGN Cross-sectional survey. METHODS This study employed a cross-sectional survey design. A convenience sample of 117 eligible Chinese females completed all the questionnaires, which included the Chinese version of the Contraceptive Self-efficacy Scale and Contraceptive Knowledge Scale. RESULTS The findings in this study suggested that younger, unmarried women at the lower income group, who adopted male condoms are at risk for unplanned pregnancy. The sample demonstrated an above medium level of knowledge and self-efficacy in contraception. However, no significant relationship was found between contraceptive self-efficacy and knowledge (p>0.05). CONCLUSIONS Contraceptive obstacles were revealed by participants' moderate level of contraceptive self-efficacy and contraceptive knowledge. The relationship between contraceptive knowledge of specific methods and contraceptive self-efficacy need further exploration in future studies. RELEVANCE TO CLINICAL PRACTICE The dominant use of male condoms by the sample of this study sheds light on future direction in the development of educational programmes and contraceptive promotion strategies appropriate for women with unplanned pregnancy.
Do general practitioners and psychiatrists agree about defining cure from depression ? The DEsCRIBE TM survey

Background: This study aimed to document the outcome dimensions that physicians see as important in defining cure from depression. The study also aimed to analyse physicians’ attitudes about depression and to find out whether they affect their prescribing practices and/or the outcome dimensions that they view as important in defining cure. Methods: A 51-item questionnaire based on six validated scales was used to rate the importance of several depression outcome dimensions. Physicians’ attitudes about depression were also assessed using the Depression Attitude Scale. Overall, 369 Belgian physicians (264 general practitioners [GPs]; 105 psychiatrists) participated in the DEsCRIBE survey. Results: GPs and psychiatrists strongly agreed that functioning and depressive symptomatology were most important in defining cure; anxious and somatic symptomatology was least important. GPs and psychiatrists differed in their attitudes about depression (p <0.001). Logistic regression revealed that the attitudes of GPs but not psychiatrists were significantly associated with their rates of antidepressant prescription (p < 0.001) and that certain attitudes predicted which outcome dimensions were seen as important in defining cure. Conclusions: Belgian GPs and psychiatrists strongly agreed on which criteria were important in defining cure from depression but differed in their attitudes about depression. The outcome dimensions that were considered important in defining cure were influenced by physicians’ attitudes this was more pronounced in GPs than in psychiatrists.
On the role of spectral resolution and classifier complexity in the analysis of hyperspectral images of forest areas

Remote sensing hyperspectral sensors are important and powerful instruments for addressing land-cover classification problems, as they permit a detailed characterization of the spectral behavior of the considered information classes. However, the processing of hyperspectral data is particularly complex both from the theoretical viewpoint (e.g. problems related to the Hughes phenomenon [1]) and from the computational perspective. In this context, despite many investigations have been presented in the literature on feature reduction and feature extraction in hyperspectral data, only few studies analyzed the role of the spectral resolution on the classification accuracy in different application domains. In this paper, we present an empirical study aimed at understanding the relationships among spectral resolution, classifier complexity, and classification accuracy obtained with hyperspectral sensors in classification of forest areas. On the basis of this study, important conclusions can be derived on the choice of the spectral resolution of hyperspectral sensors for forest applications, also in relation to the complexity of the adopted classification methodology. These conclusions can be exploited both in the context of the design of hyperspectral sensors (or for programming spectral channels of the available instruments) and in the phase of development of classification system for hyperspectral data.
Effect of n-3 long chain polyunsaturated fatty acids during the perinatal period on later body composition

A systematic review to identify studies reporting the effects of n-3 long chain polyunsaturated fatty acids (LCPUFA) intake, during pregnancy and postnatally, on infants and young children's body composition was performed. A structured search strategy was performed in the MEDLINE (PubMed), EMBASE, and LILACS databases. Inclusion and exclusion criteria were defined according to the research question. Only those studies addressing the relationship between n-3 LCPUFA exposure during the perinatal period and later adiposity measured in terms of weight, height, body mass index (BMI), skinfold thickness and/or circumferences were included regardless of the study design. Studies quality was scored and were thereafter categorised into those reporting on maternal intake of n-3 LCPUFA during pregnancy or lactation (6 publications) or on infant's n-3 LCPUFA intake (7 publications). Two studies showed inverse associations between maternal n-3 LCPUFA intake and children's later body composition (lower adiposity, BMI or body weight), two showed direct associations and no effects were observed in the remaining two studies. Among those studies focusing on n-3 LCPUFA intake through enriched infant formulas; three observed no effect on later body composition and two showed higher weight and adiposity with increased amounts of n-3 LCPUFA. Reversely, in two studies weight and fat mass decreased. In conclusion, reported body composition differences in infants and young children were not clearly explained by perinatal n-3 LCPUFA intake via supplemented formulas, breastfeeding or maternal intakes of n-3 LCPUFA during pregnancy and lactation. Associated operational mechanisms including n-3 LCPUFA doses and sources applied are not sufficiently explained and therefore no conclusions could be made.
Heterogeneity of lipopolysaccharides from Pseudomonas aeruginosa: analysis of lipopolysaccharide chain length

Lipopolysaccharide (LPS) from smooth strains of Pseudomonas aeruginosa 503, PAZ1, PAO1715, PAO1716, and Z61 was fractionated by gel filtration chromatography. LPS samples from the first four strains, all PAO1 derivatives, separated into three major size populations, whereas LPS from strain Z61, a Pac K799/WT mutant strain, separated into two size populations. When column fractions were applied to sodium dodecyl sulfate-polyacrylamide gels in their order of elution, molecules of decreasing size were resolved, and the ladder of molecules with different-length O antigens formed a diagonal across the gel. The LPS from the PAO1 derivatives contained two distinct sets of bands, distinguished on the gels as two sets of diagonals. The set of bands with the faster mobility, the B bands, was found in column fractions comprising the three major amino sugar-containing peaks. In the sample from strain 503, a fourth minor peak which contained B bands was resolved. The slower-moving set of bands, the A bands, were recovered in a minor peak. LPS from strain Z61 contained only one set of bands, with the higher-molecular-weight molecules eluting from the column in a volume similar to that of the B bands of the PAO1 strains. Analysis of the fractions of LPS from all strains indicated that less than 8% of the LPS molecules had a long, attached O antigen. Analysis of the peak that contained mainly A bands indicated a lack of reactive amino sugar and phosphate, although heptose and 2-keto-3-deoxyoctulosonic acid were detected. Reaction of isolated fractions with monoclonal antibody specific for the PAO1 O-antigen side chain indicated that only the B bands from the PAO1 strains were antigenically reactive. The bands from strain Z61 showed no reactivity. The data suggest that the A and B bands from the PAO1 strains are antigenically distinct. We propose that PAO1 strains synthesize two types of molecules that are antigenically different.
Suppression of Corticosteroid Production in the Dog by Monase

Summary Clinical toxicity encountered with 3-(2-aminobutyl)-indole acetate (Monase) has included syncope and hypotension. Hence the effects of this compound on adre-nocortical function were studied. A sharp decrease in adrenocortical steroid output of dogs under pentobarbital anesthesia was seen shortly after intravenous injection of this compound. Doses of 5 mg/kg and 10 mg/kg were used. Adrenal venous blood levels of 17-hydroxycorticosteroids returned to normal at 1-2 hours after drug administration. ACTH infusion as well as ether anesthesia prevented this corticosteroid depressant action. After hypophysectomy, Monase did not alter the increased corticosteroid secretion induced by exogenous ACTH. The data suggest that the pharmacologic action of Monase in reducing 17-hydroxycorticosteroid secretion in intact dogs is a result of suppression either of formation or release of ACTH in dogs under pentobarbital anesthesia. The able assistance of Mr. Donald L. Barber is gratefully acknowledged. We wish to thank the Upjohn Co., Kalamazoo, Mich. , for generous supplies of Monase.
Membrane fusion: what may transpire at the atomic level

Target membrane proteins, SNAP-25 and syntaxin (t-SNARE), and secretory vesicle- associated membrane protein (v-SNARE), are part of the conserved protein complex involved in fusion of opposing bilayers in biological systems in the presence of calcium. It is known that SNARE interaction allows opposing bilayers to come close within a distance of approximately 3 A, enabling calcium to drive membrane fusion. To understand the possible mechanism of membrane fusion at the atomic level, X-ray diffraction studies and light scattering measurements were performed in SNARE-reconstituted liposomes. Our study demonstrates that if t-SNARE vesicles and v-SNARE vesicles are allowed to interact prior to calcium addition, membrane fusion fails to occur. These studies suggest that hydrated calcium ions are too large (∼ 6 A) to fit between the space in SNARE-apposed bilayers, and therefore unable to induce membrane fusion. However in the presence of calcium, t-SNARE vesicles interact with v-SNARE vesicles, allowing the formation of calcium-phosphate bridges between the opposing bilayers, resulting in the expulsion of water due to disruption of the water shell around the calcium ion, enabling lipid mixing and membrane fusion.
The use of soluble protein structures in modeling helical proteins in a layered membrane

Major advances have been made in the prediction of soluble protein structures, led by the knowledge-based modeling methods that extract useful structural trends from known protein structures and incorporate them into scoring functions. The same cannot be reported for the class of transmembrane proteins, primarily due to the lack of high-resolution structural data for transmembrane proteins, which render many of the knowledge-based method unreliable or invalid. We have developed a method that harnesses the vast structural knowledge available in soluble protein data for use in the modeling of transmembrane proteins. At the core of the method, a set of transmembrane protein decoy sets that allow us to filter and train features recognized from soluble proteins for transmembrane protein modeling into a set of scoring functions. We have demonstrated that structures of soluble proteins can provide significant insight into transmembrane protein structures. A complementary novel two-stage modeling/selection process that mimics the two-stage helical membrane protein folding was developed. Combined with the scoring function, the method was successfully applied to model 5 transmembrane proteins. The root mean square deviations of the predicted models ranged from 5.0 to 8.8 Å to the native structures.