gebhart/patrepeval huggingface dataset:
Can chromatin conformation technologies bring light into human molecular pathology? (2015)

Regulation of gene expression in eukaryotes involves many complex processes, in which chromatin structure plays an important role. In addition to the epigenetic effects, such as DNA methylation and phosphorylation or histone modifications, gene expression is also controlled by the spatial organization of chromatin. For example, distant regulatory elements (enhancers, insulators) may come into direct physical interaction with target genes or other regulatory elements located in genomic regions of up to several hundred kilobases in size. Such long-range interactions result in the formation of chromatin loops. In the last several years, there has been a rapid increase in our knowledge of the spatial organization of chromatin in the nucleus through the chromosome conformation capture (3C) technology. Here we review and compare the original 3C and 3C-based methods including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), hi-resolution chromosome confomation capture (HiC). In this article, we discuss different aspects of how the nuclear organization of chromatin is associated with gene expression regulation and how this knowledge is useful in translational medicine and clinical applications. We demonstrate that the knowledge of the chromatin 3D organization may help understand the mechanisms of gene expression regulation of genes involved in the development of human diseases, such as CFTR (responsible for cystic fibrosis) or IGFBP3 (associated with breast cancer pathogenesis). Additionally, 3C-derivative methods have been also useful in the diagnosis of some leukemia subtypes.
Self-Assembly and Self-Metallization of Porphyrin Nanosheets (2007)

Square porphyrin nanosheets with uniform thickness (7−12 nm) and aspect ratios up to 100 have been synthesized for the first time using a reprecipitation method. They retain the photocatalytic activity of the precursor molecules and can be self-metallized with Pt, Pd, and Au. Their unique morphology, photocatalytic properties, and large surface areas suggest potential applications in photo- and electrocatalysis, sensing, as components for optoelectronic nanodevices, and solar energy capture and conversion.
Measles virus RNA is not detected in inflammatory bowel disease using hybrid capture and reverse transcription followed by the polymerase chain reaction (1998)

Recent epidemiological and immunohistochemical studies have indicated a possible link between measles virus and inflammatory bowel disease (IBD). The aim of this study was to use a sensitive and robust method for the detection of measles virus RNA in IBD and control clinical samples. Peripheral blood mononuclear cells and intestinal resection tissue from IBD and control patients were studied. Two methods were used to determine the presence of measles virus RNA: hybrid capture, using measles virus-specific oligonucleotides linked to paramagnetic solid-phase supports, was carried out on total cellular RNA to enrich for measles virus RNA sequences. Reverse transcription followed by the polymerase chain reaction (RT-PCR) using rTth DNA polymerase was employed for amplification of measles virus N-gene sequences amongst the enriched species. Total RNA was also used for RT-PCR of a housekeeping mRNA species to assess RNA quality. RT-PCR for another region of the measles genome (the haemagglutinin (H) gene) was also undertaken in order to confirm the results obtained using N-gene primers for analysis of these samples. None of the samples were positive for measles N- or H-gene RNA using RT-PCR. Positive control samples confirmed the sensitivity of the methods employed. These results show that either measles virus RNA was not present in the samples, or was present below the sensitivity limits known to have been achieved.
Resolution of Neurotoxicity and β-Cell Toxicity in an Islet Transplant Recipient following Substitution of Tacrolimus with MMF (2006)

Calcineurin inhibitors such as tacrolimus have well-recognized efficacy in organ transplantation but side effects of nephrotoxicity, neurotoxicity, and beta-cell toxicity that can be particularly detrimental in islet transplantation. Neuro- and nephrotoxicity have been demonstrated in multiple islet transplant recipients despite the relatively low serum maintenance levels typically used (3-5 ng/ml). We describe a single patient in whom symptoms and signs of neurotoxicity necessitated substitution of tacrolimus with mycophenolate mofetil (MMF), which resulted in complete symptom resolution over the subsequent 9 months. Concomitantly noted were an almost immediate improvement in glycemic control and an improved response to stimulation testing, suggesting remission of tacrolimus-induced beta-cell toxicity and insulin resistance. At 18 months post-"switch," 30 months posttransplant, the patient remains insulin independent with good glycemic control. The goal to remove calcineurin inhibitors from regimens of islet transplantation is a worthy one.
Human microparticles generated during sepsis in patients with critical illness are neutrophil-derived and modulate the immune response (2012)

NDMPs are generated at the site of inflammation in patients with critical illness during sepsis. They have a divergent effect on the immune response by activating phagocytic cells and deactivating bystander cells. NDMPs may play an important role in regulating the inflammatory response to sepsis in patients with critical illness.
IN VIVO KINEMATIC ANALYSIS OF THE SPINE USING 3D MRI BONE-MARROW MODEL (2018)

Introduction Kinematics analyses of the spine have been recognized as an effective method for functional analysis of the spine. CT is suitable for obtaining bony geometry of the vertebrae but radiation is a clinical concern. MRI is noninvasive but it is difficult to detect bone edges especially at endplates and processes where soft tissues attach. Kinematics analyses require tracking of solid bodies; therefore, bony geometry is not always necessary for kinematics analysis of the spine. This study aimed to develop a reliable and robust method for kinematics analysis of the spine using an innovative MRI-based 3D bone-marrow model. Materials and Methods This IRB-approved study recruited 17 patients undergoing lumbar decompression surgery to treat a single-level symptomatic herniation as part of a clinical trial for a new dynamic stabilization device. T1 & T2 sagittal MRI scans were acquired as part of the pre-operative evaluation in three positions: supine and with the shoulders rotated 45° to the left and right to induce torsion of the lumbar spine. 3D bone-marrow models of L5 and S1 at the neutral and rotated positions were created by selecting a threshold level of the bone-marrow intensity at bone-marrow/bone interface. Validated 3D-3D registration techniques were used to track movements of L5 and S1. Segmental movements at L5/S1 during torsion were calculated. Results Bone-marrow models were created not only in the vertebral body but also in superior/inferior, transverse and spinous processes, pedicles and laminae. Segmental rotation (mean±SD) at L5/S1 was shown to be symmetric for both left and right motions (p=0.149; Left: 1.04°±0.93° and Right: 1.33°±0.80°). The range of motion recorded was: left [0.05°-3.70°] and right [0.35°-3.25°]. These values were equivalent to previously reported values of axial lumbar rotation measured by 3D CT lumbar models. Conclusions This study demonstrated feasibility of kinematic analyses using the 3D bone-marrow model created with clinical MRI. The bone-marrow model shows the bone-marrow/bone interface geometry –the internal structure of the vertebra rather than outside geometry usually used for kinematic analyses– that is easily and consistently detected due to its high-contrast interface MRI intensity, which does not require lengthy manual tracing of the bony contour. The bone-marrow model includes key elements of the vertebra including posterior elements and the 3D-3D registration technique used for 3D-CT model can be applied (Fig.1). This type of methodology can be used in the clinic to evaluate with sufficient accuracy subject-specific spinal kinematics without exposure to additional radiation. The MRI-based 3D bone-marrow model may also be useful for kinematic analyses of other major joints such as hip, knee, ankle and shoulder joints.
<i>Spathaspora arborariae</i>âsp. nov., a d-xylose-fermenting yeast species isolated from rotting wood in Brazil (2009)

Four strains of a new yeast species were isolated from rotting wood from two sites in an Atlantic Rain Forest and a Cerrado ecosystem in Brazil. The analysis of the sequences of the D1/D2 domains of the large-subunit rRNA gene showed that this species belongs to the Spathaspora clade. The new species ferments D-xylose efficiently and is related to Candida jeffriesii and Spathaspora passalidarum, both of which also ferment D-xylose. Similar to S. passalidarum, the new species produces unconjugated asci with a single greatly elongated ascospore with curved ends. The type strain of Spathaspora arborariae sp. nov. is UFMG-HM19.1A(T) (=CBS11463(T)=NRRL Y-48658(T)).
Microarray analysis after strenuous exercise in peripheral blood mononuclear cells of endurance horses (2010)

It is known that moderate physical activity may have beneficial effects on health, whereas strenuous effort induces a state resembling inflammation. The molecular mechanisms underlying the cellular response to exercise remain unclear, although it is clear that the immune system plays a key role. It has been hypothesized that the physio-pathological condition that develops in athletes subjected to heavy training is caused by derangement of cellular immune regulation. The purpose of the present study was to obtain information on endurance horse gene transcription under strenuous conditions and to identify candidate genes causing immune system derangement. We performed a wide gene expression scan, using microarray technology, on peripheral blood mononuclear cells of ten horses chosen from high-level participants in national and international endurance races. The use of three different timepoints revealed changes in gene expression when post-effort samples (T1, taken immediately after the race; and T2, taken 24 h after the race) were compared with basal sample (T0, at rest). Statistical analysis showed no differences in gene expression between T0 and T2 samples, indicating complete restoration of homeostasis by 24 h after racing, whereas T1 showed strong modulation of expression, affecting 132 genes (97 upregulated, 35 downregulated). Ingenuity pathway analysis revealed that the main mechanisms and biofunctions involved were significantly associated with immunological and inflammatory responses. Real-time PCR was performed on 26 gene products to validate the array data.
A Delaunay triangulation approach for segmenting clumps of nuclei (2009)

Cell-based fluorescence imaging assays have the potential to generate massive amount of data, which requires detailed quantitative analysis. Often, as a result of fixation, labeled nuclei overlap and create a clump of cells. However, it is important to quantify phenotypic read out on a cell-by-cell basis. In this paper, we propose a novel method for decomposing clumps of nuclei using high-level geometric constraints that are derived from low-level features of maximum curvature computed along the contour of each clump. Points of maximum curvature are used as vertices for Delaunay triangulation (DT), which provides a set of edge hypotheses for decomposing a clump of nuclei. Each hypothesis is subsequently tested against a constraint satisfaction network for a near optimum decomposition. The proposed method is compared with other traditional techniques such as the watershed method with/without markers. The experimental results show that our approach can overcome the deficiencies of the traditional methods and is very effective in separating severely touching nuclei.
Hybrid Skeletal-Surface Motion Graphs for Character Animation from 4D Performance Capture (2015)

We present a novel hybrid representation for character animation from 4D Performance Capture (4DPC) data which combines skeletal control with surface motion graphs. 4DPC data are temporally aligned 3D mesh sequence reconstructions of the dynamic surface shape and associated appearance from multiple-view video. The hybrid representation supports the production of novel surface sequences which satisfy constraints from user-specified key-frames or a target skeletal motion. Motion graph path optimisation concatenates fragments of 4DPC data to satisfy the constraints while maintaining plausible surface motion at transitions between sequences. Space-time editing of the mesh sequence using a learned part-based Laplacian surface deformation model is performed to match the target skeletal motion and transition between sequences. The approach is quantitatively evaluated for three 4DPC datasets with a variety of clothing styles. Results for key-frame animation demonstrate production of novel sequences that satisfy constraints on timing and position of less than 1% of the sequence duration and path length. Evaluation of motion-capture-driven animation over a corpus of 130 sequences shows that the synthesised motion accurately matches the target skeletal motion. The combination of skeletal control with the surface motion graph extends the range and style of motion which can be produced while maintaining the natural dynamics of shape and appearance from the captured performance.
Metabolism of Dehydroisoandrosterone and Androstenedione in Human Pulmonary Endothelial Cells in Culture* (1983)

The capacity of endothelial cells from pulmonary arteries and veins to convert dehydroisoandrosterone (3 beta-hydroxy-5-androsten-17-one) and androstenedione to potent, biologically active steroids was investigated. The metabolites of [3H]dehydroisoandrosterone produced in pulmonary artery endothelial cells were androstenedione and 5-androstene-3 beta, 17 beta-diol. The metabolites isolated from incubation of pulmonary arterial cells with [3H]androstenedione were testosterone, 5 alpha-androstane-3,17-dione, 5 alpha-dihydrotestosterone (17 beta-hydroxy-5 alpha-androstan-3-one), isoandrosterone (3 beta-hydroxy-5 alpha-androstan-17-one), and androsterone. The products of [3H]androstenedione metabolism in human pulmonary venous cells were the same as those formed in arterial cells, and in addition, 5 alpha-androstane-3 alpha,17 beta-diol and 5 alpha-androstane-3 beta, 17 beta-diol were formed. The rates of metabolite formation from [3H]androstenedione in pulmonary arterial and venous endothelial cells were linear with incubation time up to 3 h. These findings suggest that the pulmonary endothelium is an important site for the metabolism of dehydroisoandrosterone and androstenedione in the human lung. Endothelial cells produce the same metabolites as human lung tissue, with the exception of hydroxylated steroids.
A new method for the deoxygenation of tertiary and secondary alcohols (1985)

S. C. Dolan and J. MacMillan, J. Chem. Soc., Chem. Commun., 1985, 1588 DOI: 10.1039/C39850001588
Opportunities for Combined Heat and Power in Data Centers (2009)

Data centers represent a rapidly growing and very energy intensive activity in commercial, educational, and government facilities. In the last five years the growth of this sector was the electric power equivalent to seven new coal-fired power plants. Data centers consume 1.5% of the total power in the U.S. Growth over the next five to ten years is expected to require a similar increase in power generation. This energy consumption is concentrated in buildings that are 10-40 times more energy intensive than a typical office building. The sheer size of the market, the concentrated energy consumption per facility, and the tendency of facilities to cluster in 'high-tech' centers all contribute to a potential power infrastructure crisis for the industry. Meeting the energy needs of data centers is a moving target. Computing power is advancing rapidly, which reduces the energy requirements for data centers. A lot of work is going into improving the computing power of servers and other processing equipment. However, this increase in computing power is increasing the power densities of this equipment. While fewer pieces of equipment may be needed to meet a given data processing load, the energy density of a facility designed to house this higher efficiency equipment will be as high as or higher than it is today. In other words, while the data center of the future may have the IT power of ten data centers of today, it is also going to have higher power requirements and higher power densities. This report analyzes the opportunities for CHP technologies to assist primary power in making the data center more cost-effective and energy efficient. Broader application of CHP will lower the demand for electricity from central stations and reduce the pressure on electric transmission and distribution infrastructure. This report is organized into the following sections: (1) Data Center Market Segmentation--the description of the overall size of the market, the size and types of facilities involved, and the geographic distribution. (2) Data Center Energy Use Trends--a discussion of energy use and expected energy growth and the typical energy consumption and uses in data centers. (3) CHP Applicability--Potential configurations, CHP case studies, applicable equipment, heat recovery opportunities (cooling), cost and performance benchmarks, and power reliability benefits (4) CHP Drivers and Hurdles--evaluation of user benefits, social benefits, market structural issues and attitudes toward CHP, and regulatory hurdles. (5) CHP Paths to Market--Discussion of technical needs, education, strategic partnerships needed to promote CHP in the IT community.
Distributed algorithms for computing shortest pairs of disjoint paths (1993)

Distributed algorithms for finding two disjoint paths of minimum total length from each node to a destination are presented. The algorithms have both node-disjoint and link-disjoint versions and provide each node with information sufficient to forward data on the disjoint paths. It is shown that this problem can be reduced to the problem of finding a minimal shortest path from each node to the destination in a modified network, and a distributed algorithm on the original network that simulates a shortest-paths algorithm running on the modified network is presented. The algorithm has a smaller space complexity than any previous distributed algorithm for the same problem, and a method for forwarding packets is presented that does not require any additional space complexity. A synchronous implementation of the algorithm is also presented and studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Combined communication and radio navigation system for small UAVs (2013)

Unmanned aerial vehicle systems are in a rapid spread not only in the military but in civilian application areas as well. The safety of these systems is more important when those are flying over civilized areas and leave the restricted flight territories. Two main areas are playing a key role in UAV safety: navigation and supervision. Most of the systems are using GPS sensors to navigate and COTS radio communication system for communication. When GPS system is jammed or the sensor fails the aircrafts have to use alternate navigation method. One solution is radio navigation. Our idea is a proprietary radio communication system which uses software defined radio technology for low power, long range communication and by the aid of multi antenna radio direction finding it can also assist the navigation system by supplying directional and distance information. In our paper we present the system concepts and suggested communication and radio navigation method.
A Pilot Phase II Study of Capecitabine in Advanced or Recurrent Gastric Cancer (2003)

Capecitabine was suggested to be safe and effective in the treatment of advanced or recurrent gastric cancer. Further phase II studies of capecitabine on a large scale are warranted.
Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV. (2012)

This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.
A Novel Src Homology 2 Domain-containing Molecule, Src-like Adapter Protein-2 (SLAP-2), Which Negatively Regulates T Cell Receptor Signaling (2002)

We have cloned a novel adapter protein containing Src homology 2 and Src homology 3 domains similar to the Src family of tyrosine kinases. This molecule lacks a catalytic tyrosine kinase domain and is related to a previously identified protein, Src-like adapter protein (SLAP), and is therefore designated SLAP-2. Northern blot analysis indicates that SLAP-2 is predominantly expressed in the immune system. Jurkat T cells express SLAP-2 protein and overexpression of SLAP-2 in these cells negatively regulates T cell receptor signaling as assessed by interleukin-2 promoter or NF-AT promoter reporter constructs. Mutational analysis revealed that an intact SH2 domain of SLAP-2 is essential for this inhibitory effect, whereas mutation of the SH3 domain alone has no effect. This inhibitory effect is upstream of the activation of Ras and increase of intracellular calcium levels, as no inhibition was observed when the cells were activated by phorbol ester plus ionomycin. SLAP-2 interacts with Cbl in vivo in a phosphorylation independent manner and with ZAP-70 and T cell receptor zeta chain upon T cell receptor activation. Finally, we show that the mutation of a predicted myristoylation site within the NH(2)-terminal of SLAP-2 is essential for its inhibitory effect. This report therefore implicates SLAP and SLAP-2 as a family of adapter proteins that negatively regulate T cell receptor signaling.
Learning to Hash with Binary Deep Neural Network (2016)

This work proposes deep network models and learning algorithms for unsupervised and supervised binary hashing. Our novel network design constrains one hidden layer to directly output the binary codes. This addresses a challenging issue in some previous works: optimizing non-smooth objective functions due to binarization. Moreover, we incorporate independence and balance properties in the direct and strict forms in the learning. Furthermore, we include similarity preserving property in our objective function. Our resulting optimization with these binary, independence, and balance constraints is difficult to solve. We propose to attack it with alternating optimization and careful relaxation. Experimental results on three benchmark datasets show that our proposed methods compare favorably with the state of the art.
Cytotoxic and Protein Kinase Inhibiting Nakijiquinones and Nakijiquinols from the Sponge <i>Dactylospongia metachromia</i> (2014)

Chemical investigation of the sponge Dactylospongia metachromia afforded five new sesquiterpene aminoquinones (1-5), two new sesquiterpene benzoxazoles (6 and 7), the known analogue 18-hydroxy-5-epi-hyrtiophenol (8), and a known glycerolipid. The structures of all compounds were unambiguously elucidated by one- and two-dimensional NMR and by MS analyses, as well as by comparison with the literature. Compounds 1-5 showed potent cytotoxicity against the mouse lymphoma cell line L5178Y with IC50 values ranging from 1.1 to 3.7 μM. When tested in vitro for their inhibitory potential against 16 different protein kinases, compounds 5, 6, and 8 exhibited the strongest inhibitory activity against ALK, FAK, IGF1-R, SRC, VEGF-R2, Aurora-B, MET wt, and NEK6 kinases (IC50 0.97-8.62 μM).