Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of 12-Hour Creatinine Clearance and Estimated Glomerular Filtration Rate in Renal Transplant Recipients

Glomerular filtration rate (GFR) is an essential clinical assessment of renal function post-renal transplantation. Creatinine clearance (CrCl) measured over 12 h and estimated GFR (e-GFR) (calculated by the Modification of Diet in Renal Disease equation) were compared in 28 stable renal transplant recipients (RTRs). This single center study included 14 African American (AA) and 14 Caucasian (CC) recipients. The 12-h creatinine clearance (CrCl-12 h) was determined by monitored urine collection and by e-GFR on two occasions (two phases) separated by at least 2 weeks. Statistics included mixed model analysis of CrCl-12 h and e-GFR relative to race, phase, and difference between parameters. In the first phase, the e-GFR was higher in AA males (58.4 ± 14.8 mL/min) than the CC males (46.2 ± 10.2 mL/min) (p = 0.032), whereas the CrCl-12 h of AA males (70.8 ± 8.7 mL/min) and CC males (63.3 ± 21.7 mL/min) was not different (p = 0.740). During the second phase, the e-GFR in AA and CC RTRs was 55.4 ± 10.1 mL/min and 47.6 ± 10.7 mL/min (p = 0.117), respectively, whereas CrCl-12 h in AAs was 64.71 ± 17.9 mL/min and in CCs was 62.0 ± 14.9 mL/min (p = 1.000). The CrCl-12 h was higher than the e-GFR (p < 0.001) irrespective of race or phase. CrCl-12 h was not different on both occasions (p = 0.289) in all the patients. CrCl-12 h was consistently greater than e-GFR. The difference between these e-GFR estimates may have an importance in the care of RTRs.
Subpixel measurement of image features based on paraboloid surface fit

A digiuil image processing inspection system is under development at Oak Ridge National Laboratory that will locate image features on printed material and measure distances between them to accuracies of 0. 001 in. An algorithm has been developed for this system that can locate unique image features to subpixel accuracies. It is based on a least-squares fit of a paraboloid function to the surface generated by correlating a reference image feature against a test image search area. Normalizing the correlation surface makes the algorithm robust in the presence of illumination variations and local flaws. Subpixel accuracies of better than 1/16 of a pixel have been achieved using a variety of different reference image features.
Polyclonal Recipient nTregs Are Superior to Donor or Third-Party Tregs in the Induction of Transplantation Tolerance

Induction of donor-specific tolerance is still considered as the “Holy Grail” in transplantation medicine. The mixed chimerism approach is virtually the only tolerance approach that was successfully translated into the clinical setting. We have previously reported successful induction of chimerism and tolerance using cell therapy with recipient T regulatory cells (Tregs) to avoid cytotoxic recipient treatment. Treg therapy is limited by the availability of cells as large-scale expansion is time-consuming and associated with the risk of contamination with effector cells. Using a costimulation-blockade based bone marrow (BM) transplantation (BMT) model with Treg therapy instead of cytoreductive recipient treatment we aimed to determine the most potent Treg population for clinical translation. Here we show that CD4+CD25+ in vitro activated nTregs are superior to TGFβ induced iTregs in promoting the induction of chimerism and tolerance. Therapy with nTregs (but not iTregs) led to multilineage chimerism and donor-specific tolerance in mice receiving as few as 0.5 × 106 cells. Moreover, we show that only recipient Tregs, but not donor or third-party Tregs, had a beneficial effect on BM engraftment at the tested doses. Thus, recipient-type nTregs significantly improve chimerism and tolerance and might be the most potent Treg population for translation into the clinical setting.
ApoD, a glia‐derived apolipoprotein, is required for peripheral nerve functional integrity and a timely response to injury

Glial cells are a key element to the process of axonal regeneration, either promoting or inhibiting axonal growth. The study of glial derived factors induced by injury is important to understand the processes that allow or preclude regeneration, and can explain why the PNS has a remarkable ability to regenerate, while the CNS does not. In this work we focus on Apolipoprotein D (ApoD), a Lipocalin expressed by glial cells in the PNS and CNS. ApoD expression is strongly induced upon PNS injury, but its role has not been elucidated. Here we show that ApoD is required for: (1) the maintenance of peripheral nerve function and tissue homeostasis with age, and (2) an adequate and timely response to injury. We study crushed sciatic nerves at two ages using ApoD knock‐out and transgenic mice over‐expressing human ApoD. The lack of ApoD decreases motor nerve conduction velocity and the thickness of myelin sheath in intact nerves. Following injury, we analyze the functional recovery, the cellular processes, and the protein and mRNA expression profiles of a group of injury‐induced genes. ApoD helps to recover locomotor function after injury, promoting myelin clearance, and regulating the extent of angiogenesis and the number of macrophages recruited to the injury site. Axon regeneration and remyelination are delayed without ApoD and stimulated by excess ApoD. The mRNA and protein expression profiles reveal that ApoD is functionally connected in an age‐dependent manner to specific molecular programs triggered by injury. © 2010 Wiley‐Liss, Inc.
Concentration of Measure Inequalities in Information Theory, Communications, and Coding

Concentration inequalities have been the subject of exciting developments during the last two decades, and have been intensively studied and used as a powerful tool in various areas. These include convex geometry, functional analysis, statistical physics, mathematical statistics, pure and applied probability theory, information theory, theoretical computer science, learning theory, and dynamical systems. Concentration of Measure Inequalities in Information Theory, Communications, and Coding focuses on some of the key modern mathematical tools that are used for the derivation of concentration inequalities, on their links to information theory, and on their various applications to communications and coding. In addition to being a survey, this monograph also includes various new recent results derived by the authors. This third edition of the bestselling book introduces the reader to the martingale method and the Efron-Stein-Steele inequalities in completely new sections. A new application of lossless source coding with side information is described in detail. Finally, the references have been updated and ones included that have been published since the original publication. Concentration of Measure Inequalities in Information Theory, Communications, and Coding is essential reading for all researchers and scientists in information theory and coding.
Epigenetic Mechanisms in Penile Carcinoma

Penile carcinoma (PeCa) represents an important public health problem in poor and developing countries. Despite its unpredictable behavior and aggressive treatment, there have only been a few reports regarding its molecular data, especially epigenetic mechanisms. The functional diversity in different cell types is acquired by chromatin modifications, which are established by epigenetic regulatory mechanisms involving DNA methylation, histone acetylation, and miRNAs. Recent evidence indicates that the dysregulation in these processes can result in the development of several diseases, including cancer. Epigenetic alterations, such as the methylation of CpGs islands, may reveal candidates for the development of specific markers for cancer detection, diagnosis and prognosis. There are a few reports on the epigenetic alterations in PeCa, and most of these studies have only focused on alterations in specific genes in a limited number of cases. This review aims to provide an overview of the current knowledge of the epigenetic alterations in PeCa and the promising results in this field. The identification of epigenetically altered genes in PeCa is an important step in understanding the mechanisms involved in this unexplored disease.
Uraemia: an unrecognized driver of central neurohumoral dysfunction in chronic kidney disease?

Chronic kidney disease (CKD) carries a large cardiovascular burden in part due to hypertension and neurohumoral dysfunction – manifesting as sympathetic overactivity, baroreflex dysfunction and chronically elevated circulating vasopressin. Alterations within the central nervous system (CNS) are necessary for the expression of neurohumoral dysfunction in CKD; however, the underlying mechanisms are poorly defined. Uraemic toxins are a diverse group of compounds that accumulate as a direct result of renal disease and drive dysfunction in multiple organs, including the brain. Intensive haemodialysis improves both sympathetic overactivity and cardiac baroreflex sensitivity in renal failure patients, indicating that uraemic toxins participate in the maintenance of autonomic dysfunction in CKD. In rodents exposed to uraemia, immediate early gene expression analysis suggests upregulated activity of not only pre‐sympathetic but also vasopressin‐secretory nuclei. We outline several potential mechanisms by which uraemia might drive neurohumoral dysfunction in CKD. These include superoxide‐dependent effects on neural activity, depletion of nitric oxide and induction of low‐grade systemic inflammation. Recent evidence has highlighted superoxide production as an intermediate for the depolarizing effect of some uraemic toxins on neuronal cells. We provide preliminary data indicating augmented superoxide production within the hypothalamic paraventricular nucleus in the Lewis polycystic kidney rat, which might be important for mediating the neurohumoral dysfunction exhibited in this CKD model. We speculate that the uraemic state might serve to sensitize the central actions of other sympathoexcitatory factors, including renal afferent nerve inputs to the CNS and angiotensin II, by way of recruiting convergent superoxide‐dependent and pro‐inflammatory pathways.
Transport and translation of MBP mRNA is regulated differently by distinct hnRNP proteins

ABSTRACT In the developing nervous system, abundant synthesis of myelin basic protein (MBP) in oligodendrocytes is required for the formation of compact myelin sheaths around axons. The MBP mRNA is known to be transported into the processes of oligodendrocytes. However, knowledge of the regulatory mechanisms that ensure the tight temporal and spatial control of MBP translation within these processes is limited. Here, we have identified novel regions within the 3′-UTR of the MBP mRNA that are responsible for the regulation of its translation, and we have demonstrated that each of the mRNA-binding proteins heterogeneous nuclear ribonucleoprotein (hnRNP)-A2, hnRNP-K and hnRNP-E1 serve distinct functions to regulate controlled and localized protein synthesis. hnRNP-A2 is responsible for mRNA transport, not for translational inhibition. By contrast, hnRNP-K and hnRNP-E1 play opposing roles in the translational regulation of MBP mRNA. We have identified shared binding sites within the 3′-UTR, and show that translation is promoted by the exchange of inhibitory hnRNP-E1 for stimulatory hnRNP-K. We further show that this molecular switch in the MBP messenger RNA-ribonucleoprotein (mRNP) complex, which regulates the synthesis of MBP, is important for the normal growth and extension of myelin sheets.
Deposition and functionalization of thin films of carbon nanotubes using corona based electrostatic charge technique and their applications for gas detection

A new technique based on an electrostatic-force-directed-self- assembly has been developed to deposit thin films of multi-walled carbon nanotubes (MWCNTs) on thin dielectric wires of 8–10 mm length and 500 µm diameter using corona-charging technique. The same technique has also been developed to self-functionalize the nanotubes via acid-free dry route. Functionalization of the film was achieved in a few seconds. Infrared and Raman spectroscopic measurements confirmed grafting of the films with oxygenated functional groups. The electrostatically self-assembled films were used as sensors to detect gases such as NO2 and NH3 with high sensitivity and repeatability up to 100 ppm (parts per million). It was observed that resistance of the deposited films increased up to 9% when sensors were successively exposed to NH3 and decreased up to 6% with NO2 at room temperature. Recovery for the sensors was within few hours when exposed to NH3 and several hours for NO2 gas. The recovery was enhanced with UV exposure. It was realized that the corona based electrostatic self-assembly (CESA) pattering technique for batch fabrication of the sensors is fast, simple, low-cost, and required no specialized equipment. The technique also offers many technical advantages such as deposition at room temperature and self-functionalized CNT films for specific molecule detection.
Cognitive processes underlying lottery and sports gambling decisions: The role of stated probabilities and background knowledge

Two studies compared choice and underlying cognitive processes in equivalent decision tasks involving risk and uncertainty (lotteries versus sports gambles including displayed expert probability judgements). In sports gambles, background knowledge was triggered via information on team location, home or away. Otherwise, displayed risk information (stake, winnings, odds, and outcome probabilities) was controlled across gamble type. In a choice study, home win bets were chosen significantly more frequently than draws or away wins, compared to lottery equivalents. In a parallel study eliciting concurrent verbal protocols, participants made fewer evaluations of odds and probabilities, and more statements involving background knowledge in sports gambles. Furthermore, some sports gamble protocols indicated modifications of stated probabilities and decision strategies contingent on domain knowledge. It was concluded that stated probability revision and knowledge-based reasoning are key cognitive processes in sports gambling not normally applied in the lottery paradigms often employed in decision research.
Upregulation of Dendritic Arborization by N-acetyl-D-Glucosamine Kinase Is Not Dependent on Its Kinase Activity

N-acetylglucosamine kinase (GlcNAc kinase or NAGK; EC 2.7.1.59) is highly expressed and plays a critical role in the development of dendrites in brain neurons. In this study, the authors conducted structure-function analysis to verify the previously proposed 3D model structure of GlcNAc/ATP-bound NAGK. Three point NAGK mutants with different substrate binding capacities and reaction velocities were produced. Wild-type (WT) NAGK showed strong substrate preference for GlcNAc. Conversion of Cys143, which does not make direct hydrogen bonds with GlcNAc, to Ser (i.e., C143S) had the least affect on the enzymatic activity of NAGK. Conversion of Asn36, which plays a role in domain closure by making a hydrogen bond with GlcNAc, to Ala (i.e., N36A) mildly reduced NAGK enzyme activity. Conversion of Asp107, which makes hydrogen bonds with GlcNAc and would act as a proton acceptor during nucleophilic attack on the γ-phosphate of ATP, to Ala (i.e., D107A), caused a total loss in enzyme activity. The over-expression of EGFP-tagged WT or any of the mutant NAGKs in rat hippocampal neurons (DIV 5-9) increased dendritic architectural complexity. Finally, the overexpression of the small, but not of the large, domain of NAGK resulted in dendrite degeneration. Our data show the effect of structure on the functional aspects of NAGK, and in particular, that the small domain of NAGK, and not its NAGK kinase activity, plays a critical role in the upregulation of dendritogenesis.
Motion Objects Detection Based on Higher Order Statistics and HSV Color Space

For the inherent problem of the moving object segmentation based on the background subtraction criteria, the present paper proposes a novel shadow elimination algorithm based on HSV color space and the higher order statistics. The proposed algorithm can distinguish the changes occurring from background disturbing effects such as noise, shadows and illumination changes. It includes two stages: pre-detection of moving object and shadow elimination. Simulation experiment results show that the proposed algorithm cannot only eliminate the shadows of moving objects effectively, but can improve the accuracy of object detection. Moreover, our proposed algorithm is feasible for practical application due to setting parameters automatically.
Implementation Experience with Building an Object-oriented View Management System

Although views have been found to be important mechanisms for database systems, currently no commercially available OODBMS supports view management tools. There are many challenging problems related to view management that must be adressed in the context of object-oriented models: what features are required to support a view system, how to provide updatable views, and how to utilize the complexity of the object-oriented data model for view deenition (such as behavioral customization, view hierarchy manipulation , and incorporating virtual classes into a consistent global schema). We solve all of these problems in our implementation of the MultiView view management system, which supports updatable views on top of the GemStone OODBMS. The resulting system preserves the functionality of the underlying commercial OODBMS while adding view mechanisms and the features needed to support the view system. Our implementation is general purpose { we provide generic classes deened in Smalltalk that can easily be ported to other OODBMS systems. Program. We are also grateful for support from the 1993 NASA Graduate Student Researchers Program.
Overview of the TREC 2005 Enterprise Track

The goal of the enterprise track is to conduct experiments with enterprise data — intranet pages, email archives, document repositories — that reflect the experiences of users in real organisations, such that for example, an email ranking technique that is effective here would be a good choice for deployment in a real multi-user email search application. This involves both understanding user needs in enterprise search and development of appropriate IR techniques.
A Neuronal-specific Mammalian Homolog of theDrosophila Retinal Degeneration B Gene with Expression Restricted to the Retina and Dentate Gyrus

Mutations in the Drosophila retinal degeneration B (rdgB) gene cause a rapid loss of the electrophysiological light response and subsequent light-enhanced photoreceptor degeneration. The rdgB gene encodes a protein with an N-terminal phosphatidylinositol transfer protein domain, a large C-terminal segment, and several hydrophobic regions thought to multiply span the subrhabdomeric cisternal membrane. A mammalian rdgB homolog (m-rdgB1) was previously identified and shown to exhibit widespread tissue distribution and functionally rescue theDrosophila rdgB mutant phenotypes. We describe a second mammalian rdgB homolog (m-rdgB2) that possesses 46% amino acid identity to Drosophila RdgB and 56% identity to M-RdgB1. M-RdgB2 possesses a neuronal-specific expression pattern, with high levels in the retina and the dentate gyrus mossy fibers and dendritic field. Using M-RdgB2-specific antibodies and subcellular fractionation, we demonstrate that M-RdgB2 is not an integral membrane protein but is stably associated with a particulate fraction through protein–protein interactions. Although transgenic expression of M-RdgB2 in rdgB2 null mutant flies suppressed the retinal degeneration, it failed to fully restore the electrophysiological light response. Because transgenic expression of M-RdgB2 does not restore the wild-type phenotype tordgB2 mutant flies to the same extent as M-RdgB1, functional differences likely exist between the two M-RdgB homologs.
Time Scales of Hydrometeor Development Simulated in a Bin Microphysics Model Show the Marshall Palmer Parameterization is Consistent with Observations

The resolution of global climate models (GCMs), and even many cloud-resolving models (CRMs), is not high enough to simulate the large range of spatiotemporal scales over which cloud processes occur. The very small-scale processes of cloud condensation nuclei activation, condensation, and collision-coalescence, are sub-grid and must be parameterized. The Marshall Palmer (MP) parameterization of hydrometeor size distribution is one such parameterization widely used in a range of model types including: CRMs, GCMs, and multi-scale modeling frameworks. The MP parameterization is evaluated here using a bin microphysics model, which simulates the evolution of the droplet size distribution in a rising air parcel under warm cloud conditions. The primary metric of evaluation is time scale; it is examined whether the time required to grow droplets from dry aerosol to rain is consistent with observed cloud lifetimes. It is shown that the hydrometeor concentration described by the MP parameterization develops in a realistic timeframe, but the size distribution is quite different from that developed in the bin microphysics model. These results are discussed in light of the limitations they imply for globalscale simulations. 10 −4 10 −3 10 −2 10 −1 10 0 10 1 10 2 10 3 10 4 10 −10 10 −5 10 0 10 5 Diameter (μm) d N /d D ( c m − 3 μ m − 1 ) ⇒ Hydrometeor Range Aerosol Range Figure 1. This figure shows the number concentration size distribution ranges for dry aerosols and hydrometeors. Both axes are in log scale indicating the large range over which these particles are spread. The aerosol range is from Hoppel et al. (1990) and the hydrometeor concentration has been calculated from the MP parameterization. 2This work was completed by G. J. Kooperman as part of SIO217d term projects created and advised by Lynn Russell, using a model created by Grabowski and Wang (2009), with programming help from Piotr Flatau and writing help from anonymous reviewers. The submitted work is not yet suitable for citation. Please contact G. J. Kooperman, Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Drive Dept. 0224, La Jolla, CA 92093-0224, gkooperm@ucsd.edu to receive an update on these results. Copyright 2009 by the American Geophysical Union. 0148-0227/09/$9.00
Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE

The strains of Thermus thermophilus that contain the nitrate respiration conjugative element (NCE) replace their aerobic respiratory chain by an anaerobic counterpart made of the Nrc‐NADH dehydrogenase and the Nar‐nitrate reductase in response to nitrate and oxygen depletion. This replacement depends on DnrS and DnrT, two homologues to sensory transcription factors encoded in a bicistronic operon by the NCE. DnrS is an oxygen‐sensitive protein required in vivo to activate transcription on its own dnr promoter and on that of the nar operon, but not required for the expression of the nrc operon. In contrast, DnrT is required for the transcription of these three operons and also for the repression of nqo, the operon that encodes the major respiratory NADH dehydrogenase expressed during aerobic growth. Thermophilic in vitro assays revealed that low DnrT concentrations allows the recruitment of the T. thermophilus RNA polymerase σA holoenzyme to the nrc promoter and its transcription, whereas higher DnrT concentrations are required to repress transcription on the nqo promoter. In conclusion, our data show a complex autoinducible mechanism by which DnrT functions as the transcriptional switch that allows the NCE to take the control of the respiratory metabolism of its host during adaptation to anaerobic growth.