Miracle-dz/UniFAR-FTUs huggingface dataset:
Global reductions in seafloor biomass in response to climate change

Seafloor organisms are vital for healthy marine ecosystems, contributing to elemental cycling, benthic remineralization, and ultimately sequestration of carbon. Deep‐sea life is primarily reliant on the export flux of particulate organic carbon from the surface ocean for food, but most ocean biogeochemistry models predict global decreases in export flux resulting from 21st century anthropogenically induced warming. Here we show that decadal‐to‐century scale changes in carbon export associated with climate change lead to an estimated 5.2% decrease in future (2091–2100) global open ocean benthic biomass under RCP8.5 (reduction of 5.2 Mt C) compared with contemporary conditions (2006–2015). Our projections use multi‐model mean export flux estimates from eight fully coupled earth system models, which contributed to the Coupled Model Intercomparison Project Phase 5, that have been forced by high and low representative concentration pathways (RCP8.5 and 4.5, respectively). These export flux estimates are used in conjunction with published empirical relationships to predict changes in benthic biomass. The polar oceans and some upwelling areas may experience increases in benthic biomass, but most other regions show decreases, with up to 38% reductions in parts of the northeast Atlantic. Our analysis projects a future ocean with smaller sized infaunal benthos, potentially reducing energy transfer rates though benthic multicellular food webs. More than 80% of potential deep‐water biodiversity hotspots known around the world, including canyons, seamounts, and cold‐water coral reefs, are projected to experience negative changes in biomass. These major reductions in biomass may lead to widespread change in benthic ecosystems and the functions and services they provide.
Tikhonov regularisation in diffusion signal estimation

In diffusion magnetic resonance imaging, images sensitised to water diffusion are acquired by applying magnetic field gradients in different directions. In order to reduce the scanning time so that the procedure is clinically plausible, it is necessary to limit the number of directions, and thus the spatial and angular resolution of the image. Missing data is then reconstructed in the post-processing step. However, the measurement noise can be significant and affect adversely the reconstructed signal. An elegant way of dealing with this problem is to use regularisation during reconstruction. Depending on the strength of regularisation applied, it may lead to an under- or over-regularised solution. Previous works have established the L-curve analysis as a procedure for automatic selection of regularisation strength in diffusion signal reconstruction. In this paper the L-curve-based approach is compared with a recently proposed method based on ground truth validation.
Optimal Power Flow with Weighted chance constraints and general policies for generation control

Due to the increasing amount of electricity generated from renewable sources, uncertainty in power system operation will grow. This has implications for tools such as Optimal Power Flow (OPF), an optimization problem widely used in power system operations and planning, which should be adjusted to account for this uncertainty. One way to handle the uncertainty is to formulate a Chance Constrained OPF (CC-OPF) which limits the probability of constraint violation to a predefined value. However, existing CC-OPF formulations and solutions are not immune to drawbacks. On one hand, they only consider affine policies for generation control, which are not always realistic and may be sub-optimal. On the other hand, the standard CC-OPF formulations do not distinguish between large and small violations, although those might carry significantly different risk. In this paper, we introduce the Weighted CC-OPF (WCC-OPF) that can handle general control policies while preserving convexity and allowing for efficient computation. The weighted chance constraints account for the size of violations through a weighting function, which assigns a higher risk to a higher overloads. We prove that the problem remains convex for any convex weighting function, and for very general generation control policies. In a case study, we compare the performance of the new WCC-OPF and the standard CC-OPF and demonstrate that WCC-OPF effectively reduces the number of severe overloads. Furthermore, we compare an affine generation control policy with a more general policy, and show that the additional flexibility allow for a lower cost while maintaining the same level of risk.
The Effects of the Spatial Distribution of Direct Anthropogenic Aerosols Radiative Forcing on Atmospheric Circulation

The large uncertainty in estimating the global aerosol radiative forcing (ARF) is one of the major challenges the climate community faces for climate projection. While the global-mean ARF may affect global quantities such as surface temperature, its spatial distribution may result in local thermodynamical and, thus, dynamical changes. Future changes in aerosol emissions distribution could further modulate the atmospheric circulation. Here, the effects of the spatial distribution of the direct anthropogenic ARF are studied using an idealized global circulation model, forced by a range of estimated-ARF amplitudes, based on the Copernicus Atmosphere Monitoring Service data. The spatial distribution of the estimated-ARF is globally decomposed, and the effects of the different modes on the circulation are studied. The most dominant spatial distribution feature is the cooling of the Northern Hemisphere in comparison to the Southern Hemisphere. This induces a negative meridional temperature gradient around the equator, which modulates the mean fields in the tropics. The ITCZ weakens and shifts southward, and the Northern (Southern) Hemisphere Hadley cell strengthens (weakens). The localization of the ARF in the Northern Hemisphere midlatitudes shifts the subtropical jet poleward and strengthens both the eddy-driven jet and Ferrel cell, because of the weakening of high-latitude eddy fluxes. Finally, the larger aerosol concentration in Asia compared to North America results in an equatorial superrotating jet. Understanding the effects of the different modes on the general circulation may help elucidate the circulation’s future response to the projected changes in ARF distribution.
Improved Feature Selection by Incorporating Gene Similarity Into the LASSO

Personalized medicine is customizing treatments to a patientâs genetic profile, and it has the potential to revolutionize medical practice. An important process used in personalized medicine is gene expression profiling. Analyzing gene expression profiles is difficult, because there are usually few patients and thousands of genes. This leads to the curse of dimensionality. In order to combat this problem, some researchers suggest using prior knowledge to enhance feature selection for supervised learning algorithms. We propose an enhancement to the LASSO, a shrinkage and selection technique that induces parameter sparsity by penalizing a modelâs objective function. Our enhancement gives preference to the selection of genes that are involved in similar biological processes. We expect this to be the case because co-expressed genes are likely to be involved in related pathways. Our modified LASSO selects similar genes by penalizing interaction terms between genes. We devised a coordinate descent algorithm to minimize the corresponding objective function. To evaluate our method, we created simulation data where we compared our model to the standard LASSO model and an interaction LASSO model. Our model outperformed both the standard LASSO and the interaction model in terms of detecting important genes and gene interactions for a reasonable number of training samples. This preliminary study leads us to believe that our method has the potential compete with state of the art methods in gene expression analysis.
Tonic spasms are a common clinical manifestation in patients with neuromyelitis optica.

UNLABELLED Tonic spasms have been most commonly associated with multiple sclerosis. To date, few reports of series of patients with neuromyelitis optica and tonic spasms have been published. METHODS We analyzed the characteristics and frequency of tonic spasms in 19 subjects with neuromyelitis optica. Data was collected using a semi-structured questionnaire for tonic spasms, by both retrospectively reviewing medical records and performing clinical assessment. RESULTS All patients except one developed this symptom. The main triggering factors were sudden movements and emotional factors. Spasms were commonly associated to sensory disturbances and worsened during the acute phases of the disease. Carbamazepine was most commonly used to treat the symptom and patients showed good response to the drug. CONCLUSIONS Tonic spasms are a common clinical manifestation in patients with neuromyelitis optica.
Field Studies of Microbial Removal from Stormwater by Bioretention Cells with Fly-Ash Amendment

Microbial pollution in stormwater is a concern in urban areas across the U.S. and is a leading cause of water-quality impairment in the United States. This issue may be addressed through the use of best management practices (BMPs) and target limits for pathogenic indicator species. Bioretention is a commonly used low impact development strategy that addresses this growing pollution problem at the source. Bioretention removal efficiencies have been well studied when considering nutrients and heavy metals, but field-scale treatment data are limited for microbial indicators. The primary objective of this study was to quantify microbial removal by installed bioretention cells with fly-ash amended soils. Three bioretention cells in Grove, Oklahoma were monitored over one and a half years and the removal microbial efficiency was quantified. Overall, removal rates for E. coli, enterococci, and coliphage were highly variable, with mean and standard deviations for removals for each site respectively: E. coli 87%, 35%, and 43%; enterococci 97%, 95%, and 80%; and coliphage 38%, 75%, and 32%. The site with negative removal efficiency appears to have some groundwater intrusion during storm events. Based on this relatively limited data set, these fly-ash amended bioretention cells performed 49% better than those with a sand-only filter media layer currently reported in the literature. Based on this initial field study, it appears that fly-ash amended bioretention cells may be a viable option for enhanced microbial removal from stormwater runoff.
The role of the yolk syncytial layer in germ layer patterning in zebrafish.

Formation of the three germ layers requires a series of inductive events during early embryogenesis. Studies in zebrafish indicate that the source of these inductive signals may be the extra-embryonic yolk syncytial layer (YSL). The characterization of genes encoding the nodal-related factor, Squint, and homeodomain protein, Bozozok, both of which are expressed in the YSL, suggested that the YSL has a role in mesendoderm induction. However, these genes, and a second nodal-related factor, cyclops, are also expressed in the overlying marginal blastomeres, raising the possibility that the marginal blastomeres can induce mesendodermal genes independently of the YSL. We have developed a novel technique to study signaling from the YSL in which we specifically eliminate RNAs in the YSL, thus addressing the in vivo requirement of RNA-derived signals from this region in mesendoderm induction. We show that injection of RNase into the yolk cell after the 1K cell stage (3 hours) effectively eliminates YSL transcripts without affecting ubiquitously expressed genes in the blastoderm. We also present data that indicate the stability of existing proteins in the YSL is unaffected by RNase injection. Using this technique, we show that RNA in the YSL is required for the formation of ventrolateral mesendoderm and induction of the nodal-related genes in the ventrolateral marginal blastomeres, revealing the presence of an unidentified inducing signal released from the YSL. We also demonstrate that the dorsal mesoderm can be induced independently of signals from the YSL and present evidence that this is due to the stabilization of (&bgr;)-catenin in the dorsal marginal blastomeres. Our results demonstrate that germ layer formation and patterning in zebrafish uses a combination of YSL-dependent and -independent inductive events.
Design and implementation of QoS measurement and network diagnosing framework for IP multicast in advanced collaborative environment

The access grid for collaborative environment exploits IP multicast. Although the IP multicast is quite a promising technology, it faces lots of challenges such as unreliable data transport and unstable network infrastructure. As a first step to achieve reliability and stability in IP multicast, it is essential to monitor and debug multicast networks. In this paper we introduce MMag, a user-oriented multicast monitoring tool for the access grid. The MMag provides both application and network level monitoring facilities to assess delivery statistics and to diagnose multicast problems. The implementation has been tested and will support access grid operators with a simple yet extensive view of multicast performance.
Interactive cross-detector analysis of vortical flow data

In this paper we discuss the application of multiple linked views for advanced vortex investigation in flow data. Local feature detectors and additional measures integrate into an interactive flow feature detection system based on multiple linked views. We discuss how linking and brushing of derived feature information can lead to increased performance in interactive feature analysis. In a case study we demonstrate how the possibility to integrate the information of multiple detectors leads to sound understanding of vortex type features. Enhanced credibility and combined advantages of several detectors can be achieved by uniting the results of multiple feature detectors in multiple coordinated views.
Demographic and Seizure Variables, But Not Hypnotizability or Dissociation, Differentiated Psychogenic from Organic Seizures

Abstract Early detection and differential diagnosis of psychogenic non-epileptic seizures (PNES) and epileptic seizures (ES) is a major clinical issue in comprehensive epilepsy centers. Using blind conditions with patients with PNES (N= 10) and ES (N= 31) before diagnosis, we tested the hypotheses that individuals with PNES would exhibit significantly greater dissociativity, hypnotizability, absorption, and history of early abuse than ES patients. Although PNES patients tended to show greater dissociative phenomena, only the last of our hypotheses was fully supported. Although absorption did not discriminate between the two diagnostic groups, it was significantly higher among those reporting early abuse. A logistic regression analysis using scores on dissociation, hypnotizability and absorption showed them to be poor predictors of diagnosis; however, other analyses revealed that female gender, reports of multiple trauma incidents lasting months or years, initial seizure onset in late teens or twenties, and daily seizure attacks significantly differentiated PNES from ES patients. Thus, demographic and seizure variables proved to be much better predictors of diagnosis than psychological dimensions often associated with PNES.
Minimising Disruption Caused by Online FPS Game Server Discovery in a Wireless Network

A key part of First Person Shooter network gaming is the game server discovery phase. Whilst probing for suitable servers from a wireless network, a large burst of network traffic is generated, potentially leading to detrimental effects on network capacity available to other wireless users. This can be minimised using an optimised algorithm to order the discovery probes and subsequently terminate the discovery process early. In this paper we explore further modifications to a previously proposed algorithm and examine its efficacy in further reducing the probe time/traffic during the server discovery phase. We show that it is possible to further reduce the overall discovery process duration by up to 13% while still presenting all suitable servers to the user for selection.
Increased Glyburide Clearance in the Pregnant Mouse Model

Glyburide (GLB) is an oral sulfonylurea, commonly used for the treatment of gestational diabetes mellitus. It has been reported that the clearance of GLB in pregnant women is significantly higher than that in nonpregnant women. The molecular mechanism by which pregnancy increases the clearance of GLB is not known, but it may be caused by increased CYP3A activity. Because liver tissue from pregnant women is not readily available, in the present study, we investigated the mechanism of such pregnancy-related changes in GLB disposition in a mouse model. We demonstrated that the systemic clearance of GLB in pregnant mice was increased approximately 2-fold (p < 0.01) compared with nonpregnant mice, a magnitude of change similar to that observed in the clinical study. Plasma protein binding of GLB in mice was not altered by pregnancy. The half-life of GLB depletion in hepatic S-9 fractions of pregnant mice was significantly shorter than that of nonpregnant mice. Moreover, GLB depletion was markedly inhibited by ketoconazole, a potent inhibitor of mouse Cyp3a, suggesting that GLB metabolism in mice is primarily mediated by hepatic Cyp3a. These data suggest that the increased systemic clearance of GLB in pregnant mice is likely caused by an increase in hepatic Cyp3a activity during pregnancy, and they provide a basis for further mechanistic understanding and analysis of pregnancy-induced alterations in the disposition of GLB and drugs that are predominantly and extensively metabolized by CYP3A/Cyp3a.
Normal fasting plasma glucose levels and type 2 diabetes in young men.

BACKGROUND The normal fasting plasma glucose level was recently defined as less than 100 mg per deciliter (5.55 mmol per liter). Whether higher fasting plasma glucose levels within this range independently predict type 2 diabetes in young adults is unclear. METHODS We obtained blood measurements, data from physical examinations, and medical and lifestyle information from men in the Israel Defense Forces who were 26 to 45 years of age. RESULTS A total of 208 incident cases of type 2 diabetes occurred during 74,309 person-years of follow-up (from 1992 through 2004) among 13,163 subjects who had baseline fasting plasma glucose levels of less than 100 mg per deciliter. A multivariate model, adjusted for age, family history of diabetes, body-mass index, physical-activity level, smoking status, and serum triglyceride levels, revealed a progressively increased risk of type 2 diabetes in men with fasting plasma glucose levels of 87 mg per deciliter (4.83 mmol per liter) or more, as compared with those whose levels were in the bottom quintile (less than 81 mg per deciliter [4.5 mmol per liter], P for trend <0.001). In multivariate models, men with serum triglyceride levels of 150 mg per deciliter (1.69 mmol per liter) or more, combined with fasting plasma glucose levels of 91 to 99 mg per deciliter (5.05 to 5.50 mmol per liter), had a hazard ratio of 8.23 (95 percent confidence interval, 3.6 to 19.0) for diabetes, as compared with men with a combined triglyceride level of less than 150 mg per deciliter and fasting glucose levels of less than 86 mg per deciliter (4.77 mmol per liter). The joint effect of a body-mass index (the weight in kilograms divided by the square of the height in meters) of 30 or more and a fasting plasma glucose level of 91 to 99 mg per deciliter resulted in a hazard ratio of 8.29 (95 percent confidence interval, 3.8 to 17.8), as compared with a body-mass index of less than 25 and a fasting plasma glucose level of less than 86 mg per deciliter. CONCLUSIONS Higher fasting plasma glucose levels within the normoglycemic range constitute an independent risk factor for type 2 diabetes among young men, and such levels may help, along with body-mass index and triglyceride levels, to identify apparently healthy men at increased risk for diabetes.
Role of Active Site Rigidity in Activity: MD Simulation and Fluorescence Study on a Lipase Mutant

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
Multi-variate probit analysis.

SUMMARY This paper is concerned with the situation in which samples from a population of biological organisms are exposed to a stimulus at various levels, the effect on the organisms being manifested in terms of the observable quantal responses of two or more separate physiological systems. A method of analysis is put forward, based upon the notion that each organism may be characterised by a tolerance vector, the components of which correspond to the reaction of the various physiological systems. In this way, it is possible to assess the relation between the responses of the different systems in terms of the correlation structure of the components of the tolerance vector, as well as the dosage-response relation for each separate system. The problems of estimation and hypothesis testing are discussed and the proposed methods are illustrated by a study of the prevalence of respiratory symptoms in a human population.