Miracle-dz/UniFAR-FTUs huggingface dataset:
High-dose methotrexate based chemotherapy with deferred radiation for treatment of newly diagnosed primary central nervous system lymphoma

The addition of high-dose methotrexate (HD-MTX) to whole-brain radiation therapy (WBRT) has improved the survival of patients with primary central nervous system lymphoma (PCNSL). However, combined therapy is associated with increased neurotoxicity. In an effort to limit this toxicity, we treated a series of non-immunocompromised patients with HDMVP, a HD-MTX based regimen, with deferral of WBRT until progression. Twenty-three patients were treated with the HDMVP regimen consisting of MTX, vincristine, and procarbazine. The mean age at diagnosis was 60.9 years (range 45–79 years). The overall response rate was 65% (14 complete responses and one partial response). For patients achieving an initial response with HDMVP the median response duration was 40.4 months (95% confidence interval [CI] 19.5–61.3). The median progression-free survival was 4.6 months (95% CI 0.0–20.4) and median overall survival was 41.4 months (95% CI 0.0–95.5). Fourteen patients received WBRT for relapsed or progressive disease. The conclusion of this trial is that HDVMP results in good initial response rates but only moderate disease control. Ultimately the majority of the patients in this series required WBRT for salvage treatment, potentially enabling a delay in treatment-associated neurotoxicity.
IEEE Std 1045-1992, IEEE Standard for Software Productivity Metrics

A consistent way to measure the elements that go into computing software productivity is deÞned. Software productivity metrics terminology are given to ensure an understanding of measurement data for both source code and document production. Although this standard prescribes measurements to characterize the software process, it does not establish software productivity norms, nor does it recommend productivity measurements as a method to evaluate software projects or software developers. This standard does not measure the quality of software. This standard does not claim to improve productivity, only to measure it. The goal of this standard is for a better understanding of the software process, which may lend insight to improving it.
On the Feasibility of Imaging Carbonatite-Hosted Rare Earth Element Deposits Using Remote Sensing

Rare earth elements (REEs) generate characteristic absorption features in visible to shortwave infrared (VNIR-SWIR) reflectance spectra. Neodymium (Nd) has among the most prominent absorption features of the REEs and thus represents a key pathfinder element for the REEs as a whole. Given that the world’s largest REE deposits are associated with carbonatites, we present spectral, petrographic, and geochemical data from a predominantly carbonatitic suite of rocks that we use to assess the feasibility of imaging REE deposits using remote sensing. Samples were selected to cover a wide range of extents and styles of REE mineralization, and encompass calcio-, ferro- and magnesio-carbonatites. REE ores from the Bayan Obo (China) and Mountain Pass (United States) mines, as well as REE-rich alkaline rocks from the Motzfeldt and Ilimaussaq intrusions in Greenland, were also included in the sample suite. The depth and area of Nd absorption features in spectra collected under laboratory conditions correlate positively with the Nd content of whole-rock samples. The wavelength of Nd absorption features is predominantly independent of sample lithology and mineralogy. Correlations are most reliable for the two absorption features centered at ~744 and ~802 nm that can be observed in samples containing as little as ~1,000 ppm Nd. By convolving laboratory spectra to the spectral response functions of a variety of remote sensing instruments we demonstrate that hyperspectral instruments with capabilities equivalent to the operational Airborne Visible-Infrared Imaging Spectrometer (AVIRIS) and planned Environmental Mapping and Analysis Program (EnMAP) systems have the spectral resolutions necessary to detect Nd absorption features, especially in high-grade samples with economically relevant REE accumulations (Nd > 30,000 ppm). Adding synthetic noise to convolved spectra indicates that correlations between Nd absorption area and whole-rock Nd content only remain robust when spectra have signal-to-noise ratios in excess of ~250:1. Although atmospheric interferences are modest across the wavelength intervals relevant for Nd detection, most REE-rich outcrops are too small to be detectable using satellite-based platforms with >30-m spatial resolutions. However, our results indicate that Nd absorption features should be identifiable in high-quality, airborne, hyperspectral datasets collected at meter-scale spatial resolutions. Future deployment of hyperspectral instruments on unmanned aerial vehicles could enable REE grade to be mapped at the centimeter scale across whole deposits.
Typing of Human Mycobacterium aviumIsolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

ABSTRACT All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern.
Accurate HLA Typing at High-Digit Resolution from NGS Data

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT. Keywords—Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.
The influences of stimulus wavelength and eccentricity on short‐wavelength pathway isolation in automated perimetry

The aim of the study was to determine whether the suggested stimulus and background parameters employed in commercially available short‐wavelength sensitive perimetry (SWAP) are clinically appropriate. Threshold versus intensity curves were measured using a modified Humphrey Field Analyser. The reduction in background luminance was achieved using aperture stops in order to avoid changes in the chromaticity of the background. Short‐wavelength thresholds were determined for 440, 450 and 460 nm stimuli and were corrected for pre‐receptoral absorption. Short‐wavelength sensitive pathway isolation was approximately 1.5 log units and decreased with increases in eccentricity and in stimulus wavelength. It would seem that the use of a 450 nm narrowband stimulus filter would offer a compromise between both the physiological requirements and the physical properties of the stimulus. Such an approach would reduce some of the inherent between‐subject normal variability associated with SWAP.
Maintenance of the Flip Sequence Orientation of the Ears in the Parvoviral Left-End Hairpin Is a Nonessential Consequence of the Critical Asymmetry in the Hairpin Stem

ABSTRACT Parvoviral terminal hairpins are essential for viral DNA amplification but are also implicated in multiple additional steps in the viral life cycle. The palindromes at the two ends of the minute virus of mice (MVM) genome are dissimilar and are processed by different resolution mechanisms that selectively direct encapsidation of predominantly negative-sense progeny genomes and conserve a single Flip sequence orientation at the 3′ (left) end of such progeny. The sequence and predicted structure of these 3′ hairpins are highly conserved within the genus Parvovirus, exemplified by the 121-nucleotide left-end sequence of MVM, which folds into a Y-shaped hairpin containing small internal palindromes that form the “ears” of the Y. To explore the potential role(s) of this hairpin in the viral life cycle, we constructed infectious clones with the ear sequences either inverted, to give the antiparallel Flop orientation, or with multiple transversions, conserving their base composition but changing their sequence. These were compared with a “bubble” mutant, designed to activate the normally silent origin in the inboard arm of the hairpin, thus potentially rendering symmetric the otherwise asymmetric junction resolution mechanism that drives maintenance of Flip. This mutant exhibited a major defect in viral duplex and single-strand DNA replication, characterized by the accumulation of covalently closed turnaround forms of the left end, and was rapidly supplanted by revertants that restored asymmetry. In contrast, both sequence and orientation changes in the hairpin ears were tolerated, suggesting that maintaining the Flip orientation of these structures is a consequence of, but not the reason for, asymmetric left-end processing.
Different effects of glucose starvation on expression and stability of VEGF mRNA isoforms in murine ovarian cancer cells.

Vascular endothelial growth factor (VEGF) has been implicated as a potent regulator of angiogenesis in tumors, and its protein exists as at least five isoforms with distinct biologic activities and clinical significance. Tumors under metabolic stress conditions dramatically increase VEGF expression due to both increased transcription and decreased mRNA degradation. However, it is not known how stress conditions regulate expression of each VEGF isoform. Here, we report a novel Taqman real-time RT-PCR strategy for quantification of all murine VEGF isoforms and find that (1) glucose starvation dramatically up-regulates the mRNA level of all VEGF isoforms, with the three abundant isoforms, VEGF120, VEGF164, and VEGF188, increasing at a similar rate, while the rare isoform VEGF144 is more markedly up-regulated; (2) glucose starvation induces a significant increase of the relative abundance of VEGF144 mRNA, but not the more prevalent isoforms VEGF120, VEGF164, and VEGF188, compared to total VEGF; and (3) the stability of each isoform mRNA differs under the control conditions as well as glucose starvation. The latter significantly stabilizes mRNA of all VEGF isoforms at a different rate, with VEGF144 most significantly stabilized. Our results indicate that under metabolic stress conditions VEGF144 is the most dramatically up-regulated VEGF isoform, probably through mechanism(s) different from the three abundant VEGF isoforms.
Human immunodeficiency virus type 1 2-LTR circles reside in a nucleoprotein complex which is different from the preintegration complex

The preintegration complex of human immunodeficiency virus type 1 (HIV-1) is a large nucleoprotein complex containing viral nucleic acids in association with products of the viral gag and pol genes. One of these proteins, integrase, is absolutely required for the integration and formation of the provirus. Although HIV-1-specific 2-LTR circles from nuclei of HIV-1-infected cells were found to be associated within a high-molecular-weight nucleoprotein complex, antibodies to HIV-1 integrase failed to precipitate this form of viral DNA. This result indicates that circular forms of HIV-1 DNA are not associated with integrase. These viral DNA forms seem to exist in a context of a nucleoprotein complex that is different from a preintegration complex of HIV-1.
Spot size variation FCS in simulations of the 2D Ising model

Spot variation fluorescence correlation spectroscopy (svFCS) was developed to study the movement and organization of single molecules in plasma membranes. This experimental technique varies the size of an illumination area while measuring correlations in time using standard fluorescence correlation methods. Frequently, this data is interpreted using the assumption that correlation measurements reflect the dynamics of single molecule motions, and not motions of the average composition. Here, we explore how svFCS measurements report on the dynamics of components diffusing within simulations of a 2D Ising model with a conserved order parameter. Simulated correlation functions report on both the fast dynamics of single component mobility and the slower dynamics of the average composition. Over a range of simulation conditions, a conventional svFCS analysis suggests the presence of anomalous diffusion even though single molecule motions are nearly Brownian in these simulations. This misinterpretation is most significant when the surface density of the fluorescent label is elevated, therefore we suggest future measurements be made over a range of tracer densities. Some simulation conditions reproduce qualitative features of published svFCS experimental data. Overall, this work emphasizes the need to probe membranes using multiple complimentary experimental methodologies in order to draw conclusions regarding the nature of spatial and dynamical heterogeneity in these systems.
STUDIES ON THE EPIDEMIOLOGY OF ADVERSE DRUG REACTIONS. I. METHODS OF SURVEILLANCE.

OVER 13,000 drugs are listed in the Physicians' Desk Reference . 1 Although some vary in compounding, preparation, or brand name, the number of different drugs is staggering. No drug is completely harmless, even when used correctly, and all may produce adverse reactions. With rare exceptions, however, the exact incidence of adverse reactions to any of the drugs is not known. Based on sporadic reports of such reactions, and drawing from experience and observations, the physician empirically evaluates risks and hopes to avoid serious adverse drug reactions in his patients. Nevertheless, drugs do occasionally produce severe illness and death. Most often, adverse drug reactions are not severe, but the predictability of seriousness usually is not possible, and when reactions occur they are unexpected. The circumstances and factors predisposing patients to reactions, for the most part, are undefined. Previous observations suggest that certain individuals or certain diseases may be associated with increased
Modelling the insulation displacement process-Results of a Finite-Element Model study-

When considering the atmosphere of continuously growing pressure on time and costs in all areas of industry, it is clear that numerical simulations will increasingly dominate the development phase. In the final analysis, numerical methods will increase product and development quality and reduce the time and costs associated with testing. This trend has also become established in the field of connector design - and in this field in particular. The classic problems with regard to mechanical and thermal stability of contact carriers, the electrical and thermal stability of contact elements as well as their mutual coupling (multiphysics) are successfully processed with the help of the finite element method (FEM). This method has also lately been used to influence both the insulation displacement process as well as the design of the cutting elements (for the corresponding connectors). Within the context of this contribution to the conference, we will first offer a short overview of insulation displacement technology before we will discuss methods to predict the properties of IDT- connections during the development and the pre-production phase. The work presented here was focussed on the application of reasonable simulation approaches. The simulation results gained will be summarised and discussed comprehensively, including the general problems arising, in order to better understand the insulation displacement process and to deduce improved modelling approaches, which will be necessary to simulate IDT-connections both qualitatively and quantitatively in a correct manner. The simulation results will be compared with the metrologically determined values in order to describe the possibilities as well as the limits that the various model approaches have to offer. Furthermore first approaches for stranded wires and an example of use will be presented.
High-Selectivity and Miniaturized Filtering Wilkinson Power Dividers Integrated With Multimode Resonators

This paper presents two filtering Wilkinson power dividers (FWPDs) with high selectivity and miniature size. A multimode resonator is used to replace a quarter-wavelength transmission line in a conventional Wilkinson power divider, and then the resonator-based FWPD is capable of splitting power and selecting frequency simultaneously. Two tri-mode resonators and two quad-mode resonators are applied to design a single- and a dual-band FWPD, respectively. Characteristics of the tri- and quad-mode resonators are analyzed, and the equivalent circuits of the proposed single- and dual-band FWPDs are presented. The input port matching and filtering response are explained by the even-mode equivalent circuit, while the output port matching and isolation characteristics can be investigated by the odd-mode equivalent circuit. Moreover, the magnetic source-load coupling introduces multiple transmission zeros to improve the frequency selectivity. All measured results are in good agreement with the full-wave simulation results.
Long-Term Land Subsidence Monitoring of Beijing (China) Using the Small Baseline Subset (SBAS) Technique

Advanced techniques of multi-temporal InSAR (MT-InSAR) represent a valuable tool in ground subsidence studies allowing remote investigation of the behavior of mass movements in long time intervals by using large datasets of SAR images covering the same area and acquired at different epochs. Beijing is susceptible to subsidence, producing undesirable environmental impacts and affecting dense population. Excessive groundwater withdrawal is thought to be the primary cause of land subsidence, and rapid urbanization and economic development, mass construction of skyscrapers, highways and underground engineering facilities (e.g., subway) are also contributing factors. In this paper, a spatial–temporal analysis of the land subsidence in Beijing was performed using one of the MT-InSAR techniques, referred to as Small Baseline Subset (SBAS). This technique allows monitoring the temporal evolution of a deformation phenomenon, via the generation of mean deformation velocity maps and displacement time series from a data set of acquired SAR images. 52 C-band ENVISAT ASAR images acquired from June 2003 to August 2010 were used to produce a linear deformation rate map and to derive time series of ground deformation. The results show that there are three large subsidence funnels within this study area, which separately located in Balizhuang-Dajiaoting in Chaoyang district, Wangjing-Laiguangying Chaoyang district, Gaoliying Shunyi district. The maximum settlement center is Wangsiying-Tongzhou along the Beijing express; the subsidence velocity exceeds 110 mm/y in the LOS direction. In particular, we compared the achieved results with leveling measurements that are assumed as reference. The estimated long-term subsidence results obtained by SBAS approach agree well with the development of the over-exploitation of ground water, indicating that SBAS techniques is adequate for the retrieval of land subsidence in Beijing from multi-temporal SAR data.
Three Stages of a Biofilm Community Developing at the Liquid-Liquid Interface between Polychlorinated Biphenyls and Water

ABSTRACT Soil contaminated with polychlorinated biphenyls (PCB) was used as an inoculum to grow a complex biofilm community on PCB oil (Aroclor 1242) on a substratum (Permanox). The biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (SSCP), amplicons of the 16S rRNA genes, and chemical analyses of the PCB congeners. SSCP analysis of the young biofilm revealed a rather diverse microbial community with species of the genera Herbaspirillum and Bradyrhizobium as dominant members. The biofilm developing on the PCB droplets displayed pronounced stages of PCB degradation and biofilm development not described before from pure-culture experiments. The first step was the colonization of the substratum while the PCB oil was hardly populated. When a certain density of bacteria was reached on the Permanox, the PCB was colonized, but soon the degradation of the congeners was markedly reduced and many cells were damaged, as seen by LIVE/DEAD staining. Finally, the biofilm formed aggregates and invaded the PCB oil, showing lower numbers of damaged cells than before and a dramatic increase in PCB degradation. This sequence of biofilm formation is understood as a maturation process prior to PCB oil colonization. This is followed by a thin biofilm on the PCB droplet, an aggregation process forming pockets in the PCB, and finally an invasion of the biofilm into the PCB oil. Only the mature biofilm showed degradation of pentachlorinated PCB congeners, which may be reductively dechlorinated and the resulting trichlorobiphenyls then aerobically metabolized.
A LoCATe‐based visual place recognition system for mobile robotics and GPGPUs

In this paper, a novel visual Place Recognition approach is evaluated based on a visual vocabulary of the Color and Edge Directivity Descriptor (CEDD) to address the loop closure detection task. Even though CEDD was initially designed so as to globally describe the color and texture information of an input image addressing Image Indexing and Retrieval tasks, its scalability on characterizing single feature points has already been proven. Thus, instead of using CEDD as a global descriptor, we adopt a bottom‐up approach and use its localized version, Local Color And Texture dEscriptor, as an input to a state‐of‐the‐art visual Place Recognition technique based on Visual Word Vectors. Also, we use a parallel execution pipeline based on a previous work of ours using the well established General Purpose Graphics Processing Unit (GPGPU) computing. Our experiments show that the usage of CEDD as a local descriptor produces high accuracy visual Place Recognition results, while the parallelization used allows for a real‐time implementation even in the case of a low‐cost mobile device.
nterspecies difference in liver-specific functions and biotransformation of estosterone of primary rat, porcine and human hepatocyte in an organotypical andwich culture

Interspecies difference is an important issue in toxicology research. We compared the potential in vitro metabolism of human, porcine and rat hepatocytes over 2 weeks in culture in an organotypical culture model which reflects the in vivo situation. All three species show similar LDH-rates. Albumin measurements showed that rat cells are about twice as active as human and porcine hepatocytes. The ethoxyresorufin-O-deethylase (EROD) activity of the rat hepatocytes is with about 14 U/106 cells distinctly higher than those of porcine and human cells (1.8 and 0.5 U/106 cells respectively), furthermore, the activity of the rat EROD increases slightly during the prolonged time in culture, whereas those of porcine and human enzymes slightly decrease. Concerning ethoxycoumarin-O-deethylase (ECOD), the rimary porcine hepatocytes estosterone iotransformation lbumin etabolites YP activity etabolism enzyme activities are found to be in three different ranges where rat cells show the highest activity with 66 U/106 cells, porcine hepatocytes exhibit an activity of about 23 U/106 cells, and human activity is lowest with 0.7 U/106 cells. All three species show a similar decreasing trend of ECOD during the period of study. Regarding the biotransformation of testosterone, human and porcine liver cells form three major metabolites whereas rat cells form a mixture of all measured metabolites. Hence, in vitro metabolism using porcine hepatocytes would be much more scientific sense than one using rat hepatocytes since the uch metabolic pathways are m