gebhart/patrepeval huggingface dataset:
A clinicopathologic study of lymphoid neoplasias associated with human immunodeficiency virus infection in Italy (1991)

The clinicopathologic features of 45 human immunodeficiency virus (HIV)-infected patients (mainly intravenous drug users [IVDU]) with lymphoid neoplasias seen from September 1984 through July 1990 at an Italian cancer center are reviewed. Thirty-five had systemic non-Hodgkin's lymphoma (NHL), and ten had Hodgkin's disease (HD). Histologically, 27 NHL cases were intermediate grade (five cases) or high grade (22 cases, 14 of the small noncleaved cell type), according to the Working Formulation. Eight NHL cases, including four anaplastic large cell (ALC) BerH2 (CD30)-positive lymphomas, were in the miscellaneous group. Immunohistologic and/or gene rearrangement analysis showed the B-cell origin of 20 of the 24 NHL cases studied. At presentation, 71% of NHL patients had advanced stages (Stage III or IV), and 85% had extranodal disease (predominantly gastrointestinal tract and marrow). Of the 23 patients evaluable for treatment, only seven had a complete clinical response after lymphoma therapy; the median survival of 34 evaluable patients was 22 months after the diagnosis of NHL. Fifteen patients died; most deaths were attributable to progressive lymphoma and opportunistic infections. As with NHL, advanced disease, extranodal involvement, aggressive histologic findings, and poor response to therapy were also observed in patients with HD. This study shows that lymphoid neoplasias occurring in Italian IVDU with HIV infection and those previously reported in North American homosexual men with HIV infection share similar clinicopathologic features. However, some features such as the absence of history of Kaposi's sarcoma at diagnosis, the lack of detection of primary brain and rectal NHL, and the occurrence of B-cell ALC BerH2 (CD30)-positive NHL were observed uniquely in this series of patients.
Fluorescence Enhancement at Docking Sites of DNA-Directed Self-Assembled Nanoantennas (2012)

We introduce self-assembled nanoantennas to enhance the fluorescence intensity in a plasmonic hotspot of zeptoliter volume. The nanoantennas are prepared by attaching one or two gold nanoparticles (NPs) to DNA origami structures, which also incorporated docking sites for a single fluorescent dye next to one NP or in the gap between two NPs. We measured the dependence of the fluorescence enhancement on NP size and number and compare it to numerical simulations. A maximum of 117-fold fluorescence enhancement was obtained for a dye molecule positioned in the 23-nanometer gap between 100-nanometer gold NPs. Direct visualization of the binding and unbinding of short DNA strands, as well as the conformational dynamics of a DNA Holliday junction in the hotspot of the nanoantenna, show the compatibility with single-molecule assays.
Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly (2009)

Broad applications of zinc finger nuclease (ZFN) technology-which allows targeted genome editing-in research, medicine, and biotechnology are hampered by the lack of a convenient, rapid, and publicly available method for the synthesis of functional ZFNs. Here we describe an efficient and easy-to-practice modular-assembly method using publicly available zinc fingers to make ZFNs that can modify the DNA sequences of predetermined genomic sites in human cells. We synthesized and tested hundreds of ZFNs to target dozens of different sites in the human CCR5 gene-a co-receptor required for HIV infection-and found that many of these nucleases induced site-specific mutations in the CCR5 sequence. Because human cells that harbor CCR5 null mutations are functional and normal, these ZFNs might be used for (1) knocking out CCR5 to produce T-cells that are resistant to HIV infection in AIDS patients or (2) inserting therapeutic genes at "safe sites" in gene therapy applications.
ATP-Binding Cassette Cholesterol Transporters and Cardiovascular Disease (2006)

A hallmark of atherosclerotic cardiovascular disease (CVD) is the accumulation of cholesterol in arterial macrophages. Factors that modulate circulating and tissue cholesterol levels have major impacts on initiation, progression, and regression of CVD. Four members of the ATP-binding cassette (ABC) transporter family play important roles in this modulation. ABCA1 and ABCG1 export excess cellular cholesterol into the HDL pathway and reduce cholesterol accumulation in macrophages. ABCG5 and ABCG8 form heterodimers that limit absorption of dietary sterols in the intestine and promote cholesterol elimination from the body through hepatobiliary secretion. All 4 transporters are induced by the same sterol-sensing nuclear receptor system. ABCA1 expression and activity are also highly regulated posttranscriptionally by diverse processes. ABCA1 mutations can cause a severe HDL-deficiency syndrome characterized by cholesterol deposition in tissue macrophages and prevalent atherosclerosis. ABCG5 or ABCG8 mutations can cause sitosterolemia, in which patients accumulate cholesterol and plant sterols in the circulation and develop premature CVD. Disrupting Abca1 or Abcg1 in mice promotes accumulation of excess cholesterol in macrophages, and manipulating mouse macrophage ABCA1 expression affects atherogenesis. Overexpressing ABCG5 and ABCG8 in mice attenuates diet-induced atherosclerosis in association with reduced circulating and liver cholesterol. Metabolites elevated in individuals with the metabolic syndrome and diabetes destabilize ABCA1 protein and inhibit transcription of all 4 transporters. Thus, impaired ABC cholesterol transporters might contribute to the enhanced atherogenesis associated with common inflammatory and metabolic disorders. Their beneficial effects on cholesterol homeostasis have made these transporters important new therapeutic targets for preventing and reversing CVD.
Spatial heterodyne spectroscopy: Modeling and interferogram processing (2013)

This work presents a radiometric model of a spatial heterodyne spectrometer (SHS) and a corresponding interferogram-processing algorithm for the calculation of calibrated spectral radiance measurements. The SHS relies on Fourier Transform Spectroscopy (FTS) principles, and shares design similarities with the Michelson Interferometer. The advantages of the SHS design, including the lack of moving parts, high throughput, and instantaneous spectral measurements, make it suitable as a field-deployable instrument. Operating in the long-wave infrared (LWIR), the imaging SHS design example included provides the capability of performing chemical detection based on reflectance and emissivity properties of surfaces of organic compounds. This LWIR SHS model takes into account the instruments entrance optics, interferometer, exit optics, and detection scheme to output realistic, interferometric data. The model serves as a tool to find the optimal SHS design parameters for the desired performance requirements and system application. It also assists in the data analysis and system characterization. The interferogram-processing algorithm performs flat-fielding and phase corrections as well as apodization before recovering the measured spectral radiance from the recorded interferogram via the Inverse Fourier Transform (IFT). The model and processing algorithm are tested with a variety of spectra and the results are comparable to those in the literature with a noise-equivalent change in temperature of 0.2K. These results demonstrate the model's validity and the algorithm's performance. Additional experiments show the algorithm's real-time processing capability, indicating the LWIR SHS system presented is feasible.
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature (2012)

This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
Chimeric anti-ganglioside GM2 antibody with antitumor activity. (1994)

Ganglioside GM2, which is one of the major gangliosides expressed on the cell surface of human tumors of neuroectodermal origin, has been focused on as a target molecule for passive immunotherapy. GM2 is thought to be one of the T-cell-independent antigens and to elicit only IgM antibody responses in rodents and humans. We have previously established two murine anti-GM2 monoclonal antibodies with high specificity and strong binding activity, KM696 and KM697, both of which are of the IgM class. Variable heavy and light chain complementary DNAs of these two murine monoclonal antibodies were cloned and used in the construction of mouse/human IgG1 chimeric antibodies, KM966 and KM967, respectively, in this study. One of the chimeric antibodies, KM966, retained strong and specific reactivity with GM2 and showed the similarity of the binding activity with tumor cell lines to that of the original murine monoclonal antibody. Indirect immunofluorescence staining of tumor cell lines with the chimeric KM966 revealed that the antigen was expressed in substantial amounts on pulmonary tumor cells and leukemia cells as well as neuroectodermal origin tumor cells. When human serum and human peripheral blood mononuclear cells were used as effectors in complement-dependent cytotoxicity and antibody-dependent cell-mediated cytotoxicity, respectively, chimeric KM966 was fully effective in killing GM2-expressing tumor cells. In addition, i.v. injection of chimeric KM966 markedly suppressed the establishment of human tumor xenografts in nude mice. Taken together, chimeric KM966 is the first antibody of the human IgG class to ganglioside GM2 and has strong antitumor activity both in vitro and in vivo. It is likely that chimeric KM966 will be a useful agent for passive immunotherapy of human cancer.
Co-culture with intestinal epithelial organoids allows efficient expansion and motility analysis of intraepithelial lymphocytes (2016)

This novel co-culture method could serve as a unique tool to investigate the motility dynamics of IELs and their temporal and spatial interaction with IECs in vitro.
Quantitative RT-PCR: A Review of Current Methodologies (2003)

The powerful amplification potential of PCR has assured its use in the detection of low-abundance mRNA in cells and tissues. RT-PCR is currently the most sensitive technique available for mRNA detection and quantification. It can accurately quantify genes present at only a few hundred copies per sample, and has become the method of choice for the examination of gene expression. The technique consists of two parts: synthesis of cDNA from RNA by reverse transcription, and amplification of a specific cDNA by polymerase chain reaction (PCR). The method requires very little RNA and differs from Northern blotting because it is somewhat tolerant of degraded RNA, as long as the RNA is intact within the region of interest.
Automated reconstruction of urban house roofs from aerial imagery (2002)

In this paper, an approach for the automated reconstruction of urban house roofs from aerial images is proposed. We model a house roof as a set of planar polygonal patches, each of which is extracted by object related image segmentation and coplanar grouping. For object related Image segmentation we employ a region segmentation method by the distance transform. Coplanar grouping and polygonal patch formation is performed by selecting 3D line segments that are matched across different views using epipolar geometry and flight information. The algorithm has been applied to aerial images and the results show accurate reconstruction of urban house roofs.
Generalized arousal of mammalian central nervous system (2005)

A fundamental capacity of the mammalian CNS is becoming amenable to study with the techniques of functional genomics. Emphasized in this review are ascending connections from the medullary reticular formation and descending connections from the paraventricular nucleus of the hypothalamus. In particular, sex hormone effects on neurons allow us to relate generalized arousal to a specific form of arousal which is required for reproductive behaviors.
Regulation of dendritic cell numbers and maturation by lipopolysaccharide in vivo. (1996)

Dendritic cells (DC) are described as "nature's adjuvant," since they have the capacity to sensitize T cells in vivo upon first encounter with the antigen. The potent accessory properties of DC appear to develop sequentially. In particular, the ability to process antigens and to sensitize native T cells develops in sequence, a process termed "maturation" that is well described in vitro. Here, we obtain evidence for maturation in vivo in response to the bacterial product lipopolysaccharide (LPS). Before LPS treatment, many DC are found at the margin between the red and white pulp. These cells lack the M342 and DEC-205 markers, but process soluble proteins effectively. 6 h after LPS, DC with the M342 and DEC-205 markers are found in increased numbers in the T cell areas. These cells have a reduced capacity to process proteins, but show increases in the B7 costimulator and T cell stimulatory capacity. 48 h after LPS, the number of DC in the spleen is reduced markedly. We interpret these findings to mean that LPS can cause DC in the marginal zone to mature and to migrate into and then out of the T cell areas.
Post-Tuned Microstrip Antennas for Frequency-Agile and Polarization-Diverse Applications. (1981)

A technique is investigated for controlling the operating frequency and polarization of microstrip antennas. The control is achieved by the placement of shorting posts at appropriate locations within the antenna's boundaries. By changing the number and locations of the posts, the operating frequency can be tuned over a 1.5-to-1 range, and the polarization can be changed from horizontal to vertical, right-hand circular, or left-hand circular. All these changes are obtained without significantly altering the input impedance or radiation patterns of the antenna and without increasing the complexity of the external microwave feed network. Also, the frequency and polarization can be electronically controlled by the use of microwave switching diodes for the shorting posts. Antennas that have two feeds and operate simultaneously in two orthogonal polarizations have been constructed with the capability to switch between linear and circular polarizations. Also, a thin, frequency-scanned array has been built with the frequency-agile microstrip elements. (Author)
The composition of the cell wall of Aspergillus niger (1965)

1. The cell-wall composition of Aspergillus niger has been investigated. Analysis shows the presence of six sugars, glucose, galactose, mannose, arabinose, glucosamine and galactosamine, all in the d-configuration, except that a small amount of l-galactose may be present. Sixteen common amino acids are also present. 2. The wall consists chiefly of neutral carbohydrate (73-83%) and hexosamine (9-13%), with smaller amounts of lipid (2-7%), protein (0.5-2.5%) and phosphorus (less than 0.1%). The acetyl content (3.0-3.4%) corresponds to 1.0mole/mole of hexosamine nitrogen. 3. A fractionation of the cell-wall complex was achieved, with or without a preliminary phenol extraction, by using n-sodium hydroxide. Though this caused some degradation, 30-60% of the wall could be solubilized (depending on the preparation). Analyses on several fractions suggest that fractionation procedures bring about some separation of components although not in a clear-cut fashion. 4. Cell-wall preparations were shown to yield a fraction having [alpha](D) approx. +240 degrees (in n-sodium hydroxide) and consisting largely of glucose. This was separated into two subfractions, one of which had [alpha](D)+281 degrees (in n-sodium hydroxide) and had properties resembling the polysaccharide nigeran; the other had [alpha](D) +231 degrees (in n-sodium hydroxide). It is suggested that nigeran is a cell-wall component.
Artificial neural networks for automatic ECG analysis (1998)

The analysis of ECGs can benefit from the wide availability of computing technology. This paper presents some results achieved by carrying out the classification tasks of equipment integrating the most common features of the ECG analysis: arrhythmia, myocardial ischemia, chronic alterations. Several ANN architectures are implemented, tested, and compared with competing alternatives. The approach, structure, and learning algorithm of ANNs are designed according to the features of each particular classification task. The trade-off between the time consuming training of ANNs and their performance is also explored. Data pre- and post-processing efforts for system performance are critically tested. The crucial role of these efforts for the reduction of input space dimensions, for a more significant description of the input features, and for improving new or ambiguous event processing is also documented. Finally, algorithm assessment is done on data coming from available ECG databases.
A novel cell-permeable antioxidant peptide decreases renal tubular apoptosis and damage in unilateral ureteral obstruction (2008)

Unilateral ureteral obstruction (UUO) is characterized by decreases in renal function, increased interstitial fibrosis, tubular apoptosis, and cellular infiltration. It has been suggested that inhibition of tubular apoptosis may protect against renal damage in obstruction. We have recently developed a series of peptides which are concentrated in the inner mitochondrial membrane and prevent cell death. These peptides are also active in vivo, in myocardial infraction, ischemic brain injury, and amyotrophic lateral sclerosis models. We therefore used SS-31, a prototype of these peptides, and assessed its effects on renal damage and oxidative stress in a 14-day obstruction model. SS-31 (1 or 3 mg/kg) or saline was given 1 day before and throughout the 14 days of obstruction. Kidneys were harvested and assessed for apoptosis (terminal transferase-dUTP-nick-end labeling, caspase 3 expression), fibrosis (trichrome staining), macrophage infiltration, fibroblast expression (immunoperoxidase), and oxidative damage (8-OH deoxyguanosine and heme oxygenase-1 expression), cytokines, and signaling pathways (transforming growth factor-beta, CCR-1, p38-MAPK, NF-kappaB). SS-31 significantly attenuated the effects of obstruction on all aspects of renal damage which were examined, with both the 1 and 3 mg/kg doses showing efficacy. We noted increased oxidative stress in obstruction, which was also attenuated by SS-31 treatment. Signaling via NF-kappaB and p38 MAPK pathways were both affected by SS-31 treatment. This study provides a proof of concept that peptides which protect mitochondria in vitro can provide protection from renal damage in a UUO model. The mechanism by which protection is afforded requires further studies both in vitro and in vivo.
Randomized polysomnography study of gabapentin enacarbil in subjects with restless legs syndrome (2011)

We assessed the efficacy and tolerability of gabapentin enacarbil in the treatment of moderate to severe primary restless legs syndrome and associated sleep disturbance. This was a multicenter, randomized, double-blind, placebo-controlled, 2-period crossover polysomnography study of gabapentin enacarbil 1200 mg or placebo taken once daily. Subjects were randomized 1:1 to a sequence of gabapentin enacarbil:placebo or placebo:gabapentin enacarbil, receiving each treatment for 4 weeks. The primary end point was the mean change from baseline at weeks 4 and 10 (4/10) last observation carried forward in wake time during sleep. The key secondary end point was the mean change from baseline at weeks 4/10 last observation carried forward in periodic limb movements associated with arousal per hour of sleep. Tolerability assessments included adverse events. One hundred thirty-six subjects were randomized (gabapentin enacarbil:placebo, 67; placebo:gabapentin enacarbil, 69), and 114 (gabapentin enacarbil:placebo, 53; placebo:gabapentin enacarbil, 61) completed the study. Gabapentin enacarbil 1200 mg significantly reduced wake time during sleep (mean change from baseline [adjusted mean treatment difference]: -26.0 minutes; P < .0001) and periodic limb movements associated with arousal per hour of sleep (adjusted mean treatment difference: -3.1 periodic limb movements with arousal/hour; P = .002) compared with placebo at weeks 4/10 last observation carried forward. The most commonly reported adverse events were dizziness (gabapentin enacarbil 20%, placebo 2%) and somnolence (gabapentin enacarbil 13%, placebo 2%). Gabapentin enacarbil 1200 mg once daily significantly reduces restless legs syndrome-associated sleep disturbance and periodic limb movements associated with arousal per hour of sleep and is generally well tolerated in adults with moderate to severe primary restless legs syndrome.
Extreme tunability in aluminum doped Zinc Oxide plasmonic materials for near-infrared applications (2014)

Plasmonic materials (PMs), featuring large static or dynamic tunability, have significant impact on the optical properties due to their potential for applications in transformation optics, telecommunications, energy, and biomedical areas. Among PMs, the carrier concentration and mobility are two tunable parameters, which control the plasma frequency of a metal. Here, we report on large static and dynamic tunability in wavelengths up to 640 nm in Al-doped ZnO based transparent conducting degenerate semiconductors by controlling both thickness and applied voltages. This extreme tunability is ascribed to an increase in carrier concentration with increasing thickness as well as voltage-induced thermal effects that eventually diminish the carrier concentration and mobility due to complex chemical transformations in the multilayer growth process. These observations could pave the way for optical manipulation of this class of materials for potential transformative applications.
Paget-Schroetter Syndrome (2013)

Paget-Schroetter is a rare diagnosis in the general population; however, it is more common in younger, physically active individuals. Clinicians must be familiar with the symptoms, physical examination, and initial imaging and treatment to expedite care and prevent possible life-threatening complications. Urgent referral to a regional specialist may improve the opportunity for thrombolysis to restore blood flow through the subclavian vein and to decrease the chance of pulmonary embolus, recurrent thrombosis, or need for vein grafting, as well as to improve the time to return to full activity (athletics and/or manual labor).