Miracle-dz/UniFAR-FTUs huggingface dataset:
FishMap: a community resource for zebrafish genomics.

An enormous amount of information on a genomics scale is available for zebrafish (Danio rerio), which is a well-studied model organism for human diseases. However, a majority of this annotation is scattered in obscure data sources. There have been limited efforts to present it on a unified and integrated platform, which would help to understand the biological processes in this organism better. FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. The datasets have been methodically collected from various resources and supplementary information of publications and mapped to the zebrafish genome. The data are organized into nine major sections, which include comparative genomics, mapping and sequencing, gene and gene predictions, expression and regulation, and variation and repeats. A number of unique sections have been incorporated, which include tracks on noncoding gene annotation, location of retrovirus/transposon integrations in the genome, and their flanking genomic sequences and novel transcripts. The datasets are linked to related data sources. FishMap is built on the Gbrowse, which is a part of the Generic Model Organism Database Consortium Project. The resource also features a Web-based BLAST server for sequence homology search and a gene ID converter that would enable users to sift through different interchangeable gene annotation identifier systems. The database is amenable to programmatic access through the Distributed Annotation System as well as BioMoby protocols, thus making it a central community resource that can be integrated with existing data mining and analysis workflows. We hope that FishMap would be an integral resource for community participation in zebrafish genomics. The resource is freely available at http://miracle.igib. res.in/fishmap, or at http://fishmap.igib. res.in.
Comparison of Iron Loss Models for Electrical Machines With Different Frequency Domain and Time Domain Methods for Excess Loss Prediction

The goal of this paper is to investigate the accuracy of modeling the excess loss in electrical steels using a time domain model with Bertotti's loss model parameters n0 and V0 fitted in the frequency domain. Three variants of iron loss models based on Bertotti's theory are compared for the prediction of iron losses under sinusoidal and non-sinusoidal flux conditions. The non-sinusoidal waveforms are based on the realistic time variation of the magnetic induction in the stator core of an electrical machine, obtained from a finite element-based machine model.
Towards the realization of clinical extracellular vesicle diagnostics: challenges and opportunities

Extracellular vesicles (EVs) have been intensively researched in the last decade. As a result, many reports have revealed that disease-associated EVs can indeed be used as novel diagnostic tools to serve as a noninvasive ‘liquid biopsy’. EVs are multi-molecular complexes and each molecule can be targeted for diagnostics. An increasing number of targetable molecules in EVs, such as miRNAs or proteins, have been identified and the accumulation of evidence will likely result in the identification of consensus EV markers. Also highlighted here are some advanced technologies that can be used as next generation assays. These technologies may overcome several challenges that continue to hinder the clinical use of EV diagnostics. A perspective is outlined for the potential contribution of EV research to develop diagnostic technologies for cancer and various other diseases.
Genetic predictors of response to treatment with citalopram in depression secondary to traumatic brain injury

Objectives: To determine which serotonergic system-related single nucleotide polymorphisms (SNPs) predicted variation in treatment response to citalopram in depression following a traumatic brain injury (TBI). Methods: Ninety (50 M/40 F, aged 39.9, SD = 18.0 years) post-TBI patients with a major depressive episode (MDE) were recruited into a 6-week open-label study of citalopram (20 mg/day). Six functional SNPs in genes related to the serotonergic system were examined: serotonin transporter (5HTTLPR including rs25531), 5HT1A C-(1019)G and 5HT2A T-(102)C, methylene tetrahydrofolate reductase (MTHFR) C-(677)T, brain-derived neurotrophic factor (BDNF) val66met and tryptophan hydroxylase-2 (TPH2) G-(703)T. Regression analyses were performed using the six SNPs as independent variables: Model 1 with response (percentage Hamilton Depression (HAMD) change from baseline to endpoint) as the dependent variable and Model 2 with adverse event index as the dependent variable (Bonferroni corrected p-value < 0.025). Results: MTHFR and BDNF SNPs predicted greater treatment response (R2= 0.098, F = 4.65, p = 0.013). The 5HTTLPR predicted greater occurrence of adverse events (R2= 0.069, F = 5.72, p = 0.020). Conclusion: Results suggest that polymorphisms in genes related to the serotonergic system may help predict short-term response to citalopram and tolerability to the medication in patients with MDE following a TBI.
Flash Crowd Detection Using Decoy Hyperlinks

In this paper a novel method for detecting denial of service attacks (DoS) on web services are presented and evaluated by using decoy hyperlinks embedded in web pages. The decoys are hyperlinks without semantic information or are invisible to the human user, acting like traps for DoS attacks because a human user would never follow them. An attack on a web server is detected when such hyperlink is followed. This approach has significant advantages over other approaches like graphic Turing tests, it is transparent to the user, it can be used on general-purpose web sites and retains the web site's usability. The proposed method has been evaluated using real web sites and the results show false positive rates that are less than 10-4. A genetic algorithm is used for the optimum placement of the decoys using simulated web sites. The aspects of this new method are discussed and some experimental results are presented.
Cysteine modification of a specific repressor protein controls the translational status of nucleus-encoded LHCII mRNAs in Chlamydomonas

The cytosolic RNA-binding protein NAB1 represses translation of LHCII (light-harvesting complex of photosystem II) encoding mRNAs by sequestration into translationally silent mRNP complexes in the green alga Chlamydomonas reinhardtii. NAB1 contains 2 cysteine residues, Cys-181 and Cys-226, within its C-terminal RRM motif. Modification of these cysteines either by oxidation or by alkylation in vitro was accompanied by a decrease in RNA-binding affinity for the target mRNA sequence. To confirm the relevance of reversible NAB1 cysteine oxidation for the regulation of its activity in vivo, we replaced both cysteines with serines. All examined cysteine single and double mutants exhibited a reduced antenna at PSII caused by a perturbed NAB1 deactivation mechanism, with double mutations and Cys-226 single mutations causing a stronger and more distinctive phenotype compared with the Cys-181 mutation. Our data indicated that the responsible redox control mechanism is mediated by modification of single cysteines. Polysome analyses and RNA co-immunoprecipitation experiments demonstrated the interconnection of the NAB1 thiol state and its activity as a translation repressor in vivo. NAB1 is fully active in its dithiol state and is reversibly deactivated by modification of its cysteines. In summary, this work is an example that cytosolic translation of nucleus encoded photosynthetic genes is regulated via a reversible cysteine-based redox switch in a RNA-binding translation repressor protein.
Association Study of Adrenergic β3 Receptor (Trp64Arg) and G-Protein β3 Subunit Gene (C825T) Polymorphisms and Weight Change during Clozapine Treatment

Weight gain, a common adverse effect of clozapine, may impair health and affect patient compliance during treatment with this agent. The aim of this study was to investigate the relationship between genetic variants of the adrenergic β3 receptor (ADRB3) and the G-protein β3 subunit (GNB3) and clozapine-induced body weight change (BWC). Eighty-seven treatment-resistant schizophrenic patients were weighed before and after 4 months of clozapine treatment, with the subjects gaining an average of 2.6 kg in body weight. No statistically significant relationship was demonstrated for the investigated ADRB3 Trp64Arg and the GNB3 C825T polymorphisms in terms of BWC post-treatment, suggesting these two polymorphisms do not play a significant role in clozapine-induced BWC. Further exploration of other genetic variants implicated in clozapine-induced BWC is important, however, in order to predict and reduce clozapine-associated weight gain.
Comparison of modeled and reconstructed changes in forest cover through the past 8000 years

Reproducing the tree cover changes throughout the Holocene is a challenge for land surface–atmosphere models. Here, results of a transient Holocene simulation of the coupled climate–carbon cycle model, CLIMBER2-LPJ, driven by changes in orbital forcing, are compared with pollen data and pollen-based reconstructions for several regions of Eurasia in terms of changes in tree fraction. The decline in tree fraction in the high latitudes suggested by data and model simulations is driven by a decrease in summer temperature over the Holocene. The cooler and drier trend at the eastern side of the Eurasian continent, in Mongolia and China, also led to a decrease in tree cover in both model and data. In contrast, the Holocene trend towards a cooler climate in the continental interior (Kazakhstan) is accompanied by an increase in woody cover. There a relatively small reduction in precipitation was likely compensated by lower evapotranspiration in comparison to the monsoon-affected regions. In general the model-data comparison demonstrates that climate-driven changes during the Holocene result in a non-homogeneous pattern of tree cover change across the Eurasian continent. For the Eifel region in Germany, the model suggests a relatively moist and cool climate and dense tree cover. The Holzmaar pollen record agrees with the model for the intervals 8–3 ka and 1.7–1.3 ka BP, but suggests great reduction of the tree cover 3–2 ka and after 1.3 ka BP, when highly developed settlements and agriculture spread in the region.
Sugars from woody tissue photosynthesis reduce xylem vulnerability to cavitation.

Reassimilation of internal CO2 via woody tissue photosynthesis has a substantial effect on tree carbon income and wood production. However, little is known about its role in xylem vulnerability to cavitation and its implications in drought-driven tree mortality. Young trees of Populus nigra were subjected to light exclusion at the branch and stem levels. After 40 d, measurements of xylem water potential, diameter variation and acoustic emission (AE) were performed in detached branches to obtain acoustic vulnerability curves to cavitation following bench-top dehydration. Acoustic vulnerability curves and derived AE50 values (i.e. water potential at which 50% of cavitation-related acoustic emissions occur) differed significantly between light-excluded and control branches (AE50,light-excluded = -1.00 ± 0.13 MPa; AE50,control = -1.45 ± 0.09 MPa; P = 0.007) denoting higher vulnerability to cavitation in light-excluded trees. Woody tissue photosynthesis represents an alternative and immediate source of nonstructural carbohydrates (NSC) that confers lower xylem vulnerability to cavitation via sugar-mediated mechanisms. Embolism repair and xylem structural changes could not explain this observation as the amount of cumulative AE and basic wood density did not differ between treatments. We suggest that woody tissue assimilates might play a role in the synthesis of xylem surfactants for nanobubble stabilization under tension.
Diabetic Nephropathy and CKD—Analysis of Individual Patient Serum Creatinine Trajectories: A Forgotten Diagnostic Methodology for Diabetic CKD Prognostication and Prediction

Creatinine is produced in muscle metabolism as the end-product of creatine phosphate and is subsequently excreted principally by way of the kidneys, predominantly by glomerular filtration. Blood creatinine assays constitute the most common clinically relevant measure of renal function. The use of individual patient-level real-time serum creatinine trajectories provides a very attractive and tantalizing methodology in nephrology practice. Topics covered in this review include acute kidney injury (AKI) with its multifarious rainbow spectrum of renal outcomes; the stimulating vicissitudes of the diverse patterns of chronic kidney disease (CKD) to end-stage renal disease (ESRD) progression, including the syndrome of rapid onset end stage renal disease (SORO-ESRD); the syndrome of late onset renal failure from angiotensin blockade (LORFFAB); and post-operative AKI linked with the role of intra-operative hypotension in patients with diabetes mellitus and suspected diabetic nephropathy with CKD. We conclude that the study of individual patient-level serum creatinine trajectories, albeit a neglected and forgotten diagnostic methodology for diabetic CKD prognostication and prediction, is a most useful diagnostic tool, both in the short-term and in the long-term practice of nephrology. The analysis of serum creatinine trajectories, both in real time and retrospectively, indeed provides supplementary superior diagnostic and prognostic insights in the management of the nephrology patient.
Effect of Asphalt Fume Inhalation Exposure at Simulated Road Paving Conditions Prior to Bacterial Infection on Lung Defense Responses in Rats

Asphalt fume inhalation has been suspected of affecting immune function in exposed workers. The objective of this study was to evaluate the effect of asphalt exposure on lung immune responses in rats using a bacterial infectivity model. Pathogen-free male Sprague-Dawley rats were exposed by inhalation to asphalt fumes (72.6 ± 4.95 mg/m3) or filtered air for 6 h/day for 5 days. One day after the final asphalt exposure, rats were intratracheally inoculated with 5 × 105 Listeria monocytogenes. At 0 (prior to bacterial inoculation), 3, and 7 days after L. monocytogenes instillation, the lungs of each animal were divided. Bronchoalveolar lavage (BAL) was performed on right lungs. The recovered BAL cells were then differentiated and counted, and alveolar macrophage (AM) function was determined. Albumin and lactate dehydrogenase (LDH), two indices of lung injury, were measured in the acellular BAL fluid. To assess bacterial clearance, the left lungs were removed, homogenized, and bacterial colony-forming units (CFUs) were counted. In addition, lung-draining lymph nodes were removed, and lymphocyte phenotype and lymphocyte-induced cytokine production were examined. Asphalt fume exposure did not cause lung injury or inflammation in rats in the absence of infection. Infection induced elevations in AMs, neutrophils (PMNs), albumin, and LDH. Importantly, no significant differences were seen when comparing the asphalt group with the air and nonexposed naive groups at any time before or after infection. Also, asphalt fume inhalation exposure did not affect the rate of pulmonary clearance of L. monocytogenes or AM production of reactive oxygen and nitrogen species. However, asphalt-related increases in lymphocyte secretion of interferon (IFN)-γ, interleukin (IL)-6, and IL-10 were observed at different times after bacterial infection, whereas the total number of lymph-node cells and the percentage of CD4+ and CD8+ cells were not significantly different among the treatment groups. Despite the asphalt-induced changes observed in lymphokine secretion, adaptive immune function seemed to function properly in lung defense against bacterial infection. Because innate nonspecific lung responses and pulmonary clearance of L. monocytogenes were unaffected by asphalt fume exposure, lung defenses were sufficient to control the infection. It was concluded that acute inhalation of asphalt fumes at a high concentration had a minimal effect on lung immune responses to infection in rats.
Noninvasive Polarimetric-Based Glucose Monitoring: An in Vivo Study

Background: Since 1990, there has been significant research devoted toward development of a noninvasive physiological glucose sensor. In this article, we report on the use of optical polarimetry for the noninvasive measurement of physiological glucose concentration in the anterior chamber of the eye of New Zealand white (NZW) rabbits. Method: Measurements were acquired using a custom-designed laser-based optical polarimetry system in a total of seven NZW rabbits anesthetized using an isoflurane-only anesthesia protocol. Aqueous humor-based polarimetric measurements were obtained by coupling light through the anterior chamber of the eye. Blood glucose levels were first stabilized and then altered with intravenous dextrose and insulin administration and measured every 3–5 min with a standard glucometer and intermittently with a YSI 2300 glucose analyzer. Acquired polarimetric glucose signals are calibrated to measured blood glucose concentration. Results: Based on a total of 41 data points, Clarke error grid analysis indicated 93% in zone A, 7% in zone B, and 0% in zones C and D, with reference concentrations between 93 and 521 mg/dl. Errors in prediction are shown to be related to gross movement of the rabbit during the procedures, incurring time-varying corneal birefringence effects that directly affect the measured polarimetric signal. These effects can be compensated for with appropriate design modifications. Conclusions: An optical polarimetry technique was used for in vivo physiological glucose monitoring. The technique demonstrated provides a basis for the development of a noninvasive polarimetric glucose monitor for home, personal, or hospital use.
Molecular Diversity of Methanogens in Fecal Samples From Captive Sumatran Orangutans (Pongo abelii)

Methane emissions have been previously detected from orangutans, but characterization of the diversity of methanogens in this species has yet to be completed. This preliminary study identified methanogen producing microorganims, also called methanogens, present in the feces from a colony of captive Sumatran orangutans at the Perth Zoo. All animals were housed in the same enclosure and were fed primarily a frugivorous diet. Methanogens were detected using a 16S rRNA gene clone library. A total of 207 clones were examined, revealing 37 different methanogen 16S rRNA sequences, or phylotypes. Of these, 31 phylotypes represented by 170 clones had 96.4–100% sequence identity to Methanosphaera stadtmanae, four phylotypes (32 clones) had 95.1–100% sequence identity to Methanobrevibacter smithii, while two phylotypes (five clones) had 95.9–97.7% sequence identity to Methanobacterium beijingense. Overall, five possible new species were identified from the clone library. This represents the first report of Msp. stadtmanae, a methanol utilizer, as the most predominant methanogen in the gastrointestinal tract of animals. This is likely due to the increased availability of methanol from the highly frugivorous diet of the orangutans. Further studies are warranted to properly assess the effects of frugivorous diets on the methanogen population. Am. J. Primatol. 74:408‐413, 2012. © 2012 Wiley Periodicals, Inc.
Elastic Properties of Lipid Bilayers: Theory and Possible Experiments

Abstract A theory of the elasticity of lipid bilayers is proposed. Three types of strain, i. e. stretching, tilt and curvature, are distinguished and the associated stresses are identified. It is argued that in the case of vesicles (= closed bilayer films) the only elasticity controlling nonspherical shapes is that of curvature. Euler-Lagrange equations are derived for the shape in magnetic fields and under excess outside pressure. It is shown that magnetic fields can deform spherical vesicles into ellipsoids of revolution. Under excess outside pressure the spherical shape becomes unstable at a certain threshold pressure. Both effects can be influenced by a spontaneous curvature of the bilayer. Some possible experiments to determine the elastic properties are also discussed
Becoming centre: tourism placemaking and space production in two neighborhoods in Barcelona

Abstract Over the last decades Barcelona has experienced social and economic transformations brought by the conversion of peripheral urban neighborhoods into tourist attractions. In this sense urban tourism has been the latest chapter of spatial reorganization to sustain capitalism within the global neoliberal environment in the Catalan city. In addition, the urban commodification process has expanded into not only central and historical districts, but also more peripheral zones outside the tourist bubble. Those transformations signify a symbolic turn: they became part of the centre. Since the 1992 Olympic Games, Barcelona’s brand, both for the city and for tourism, has experienced an important promotion where the urban periphery has become both part of the centre, as well as part of its global city imagery through placemaking, public policy, and political decisions. In short, the steady inclusion of neighborhoods such as Vila de Gràcia and Poblenou into the tourist experience enhances the Barcelonan tourist imagery. The inclusion of new cultural icons and tourist attractions embody a slight spatial and symbolic turn to boost the city’s visitor activities. In order to facilitate an in-depth comprehension, the ethnographical approach has been taken.
Competing Speech Perception in Middle Age.

PURPOSE This research forum article summarizes research from our laboratory that assessed middle-aged adults' ability to understand speech in the presence of competing talkers. METHOD The performance of middle-aged adults on laboratory-based speech understanding tasks was compared to that of younger and older adults. RESULTS Decline in the ability to understand speech in complex listening environments can be demonstrated in midlife. The specific auditory and cognitive contributors to these problems have yet to be established. CONCLUSION There is evidence that the ability to understand a target speech message in the presence of competing speech messages changes relatively early in the aging process. The nature and impact of these changes warrant further investigation.
The Optimum Knee Flexion Angle for Skyline Radiography Is Thirty Degrees

There is wide variation in practice among orthopaedic surgeons regarding the use of skyline tangential patellar radiographs of the patellofemoral joint in patients with anterior knee pain. Various techniques are available for taking such radiographs and numerous radiologic parameters can be measured from them. There is no information as to which knee flexion angle is superior when taking skyline radiographs. The purpose of the current study was to compare the results of skyline radiographs taken at 30°, 50°, and 90° knee flexion. Sixty-seven knees were studied prospectively. All radiographs were made anonymous and then were studied in random order by two observers. Five recognized patellofemoral parameters were recorded. All the parameters studied were measured most reproducibly when measured from the radiograph taken at 30° knee flexion. The parameters were least reproducible when measured from the radiograph taken at 90° knee flexion. In terms of detecting abnormality of the parameters measured, the radiographs taken at 30° and 50° were similar. The radiograph taken at 90° knee flexion detected the fewest abnormalities. Skyline radiographic examination of the patellofemoral joint should be a mandatory part of the investigation of all knee problems. One radiograph, ideally taken at 30° knee flexion, offers the best means of assessing the patellofemoral joint. There is no benefit to requesting multiple images at different angles of knee flexion.