gebhart/patrepeval huggingface dataset:
Pneumocystis jiroveci pneumonia and pneumomediastinum in an anti-TNFα naive patient with ulcerative colitis (2009)

We report the case of a 21-year-old man who was noted to have pneumomediastinum during an admission for an acute flare of ulcerative colitis. At that time, he was on maintenance treatment with azathioprine at a dose of 1.25 mg/kg per day, and had not received supplementary steroids for 9 mo. He had never received anti-tumor necrosis factor (TNF)alpha therapy. Shortly after apparently effective treatment with intravenous steroids and an increased dose of azathioprine, he developed worsening colitic and new respiratory symptoms, and was diagnosed with Pneumocystis jiroveci (carinii) pneumonia (PCP). Pneumomediastinum is rare in immunocompetent hosts, but is a recognized complication of PCP in human immunodeficiency virus (HIV) patients, although our patient's HIV test was negative. Treatment of PCP with co-trimoxazole resulted in resolution of both respiratory and gastrointestinal symptoms, without the need to increase the steroid dose. There is increasing vigilance for opportunistic infections in patients with inflammatory bowel disease following the advent of anti-TNFalpha therapy. This case emphasizes the importance of considering the possibility of such infections in all patients with inflammatory bowel disease, irrespective of the immunosuppressants they receive, and highlights the potential of steroid-responsive opportunistic infections to mimic worsening colitic symptoms in patients with ulcerative colitis.
Ocean bottom seismometers in the northern North Sea: Experience and preliminary results with the Statfjord OBS (1990)

Abstract The northern North Sea is one of the most seismically active regions of Northwest Europe, but offshore seismicity is difficult to study in detail because the severe environment places limits on options for deployment of near-field ocean bottom seismometers (OBS). The design of an OBS system deployed on the Statfjord oil field is presented, together with some results. Amplitude density spectra of ambient noise from two OBS installations are on average more than a factor of ten higher than the average of three onshore Western Norway Network (WNN) seismic stations. A theoretical detection threshold curve, based on background noise levels, is in close agreement with practical experience of detections at the Statfjord OBS and explains why only about 7 per cent of the events detected in the northern North Sea by the WNN are also detected on the Statfjord OBS. Comparison of earthquake source spectra, recorded on and off shore, reveal no evidence for either high attenuation or amplification in the Viking Graben. Earthquake focal depths in the central northern North Sea seem to be around 20 km.
Antitumor Immunity Induction by Intracellular Hyperthermia Using Magnetite Cationic Liposomes (1998)

Induction of antitumor immunity to T-9 rat glioma by intracellular hyperthermia using functional magnetic particles was investigated. Magnetite cationic liposomes (MCLs), which have a positive surface charge, were used as heating mediators for intracellular hyperthermia. Solid T-9 glioma tissues were formed subcutaneously on both femurs of female F344 rats, and MCLs were injected via a needle only into the left solid tumors (treatment side). The rats were then divided into two groups, which received no irradiation, or irradiation for 30 min given three times at 24-h intervals with an alternating magnetic field (118 kHz, 384 Oe). On the treatment side, the tumor tissue disappeared completely in many rats exposed to the magnetic field. The tumor tissue on the opposite side also disappeared completely, even though MCLs were not injected into the right solid tumors. To examine whether a long-lasting and tumor-specific immunity could be generated, the rats that had been cured by the hyperthermia treatment were rechallenged with T-9 cells 3 months later. After a period of transient growth, all tumors disappeared. Furthermore, immunocytochemical assay revealed that the immune response induced by the hyperthermia treatment was mediated by both CD8+ and CD4+ T cells and accompanied by a marked augmentation of tumor-selective cytotoxic T lymphocyte activity. These results suggest that our magnetic particles are potentially effective tools for hyperthermic treatment of solid tumors, because in addition to killing of the tumor cells by heat, a host immune response is induced.
The effect of fibroblast growth factor 8, isoform b, on the biology of prostate carcinoma cells and their interaction with stromal cells. (2000)

Fibroblast growth factor 8, isoform b (FGF8b), has been implicated in the oncogenesis of the prostate and mammary epithelia. We examined whether overexpression of FGF8b in a weakly tumorigenic prostate carcinoma cell line, LNCaP, could alter the growth and tumorigenic properties of these cells. LNCaP cells were infected with a lentivirus vector carrying FGF8b cDNA and the green fluorescent protein (GFP) cDNA in the same construct, and the infected cell population was sorted on the basis of GFP protein expression. It was demonstrated that, in comparison with the cells transduced with GFP-vector alone, LNCaP cells with FGF8b-GFP expression manifested an increased growth rate, higher soft agar clonogenic efficiency, enhanced in vitro invasion, and increased in vivo tumorigenesis. Most strikingly, whereas parental or vector-control LNCaP cells failed to grow at all in an in vivo tumorigenesis/diaphragm invasion assay in nude mice, the cells overexpressing FGF8b proliferated as deposits of tumor cells on the diaphragm, frequently with indications of tumor cell invasion into the diaphragm. Coculturing of primary prostatic or non-prostatic stromal cells with the infected LNCaP cells led us to observe that: (a) stromal cells, irrespective of tissue origin, strongly suppressed LNCaP cell growth; (b) FGF8b producing LNCaP cells could partially evade the stromal inhibition, perhaps from the autocrine stimulatory effect of FGF8b; and (c) production of FGF8b in the coculture had a stimulatory effect on the proliferation of the stromal cells, prostatic or non-prostatic. This stimulation was not attributable to the direct action of FGF8b on stromal cells. Instead, it appears that epithelial-stromal cell-cell contact and some unknown soluble factors secreted by LNCaP cells upon stimulation of FGF8b are required for the maximal effect. Together, these results suggest that the growth rate and biological behavior of prostatic cancer cells can be altered to a more aggressive phenotype by up-regulation of FGF8b expression. These changes in phenotype also influence the interaction of the affected cells with stromal cells. The data obtained may have direct relevance to the progression of prostate cancer, recognizing that FGF8b is naturally overexpressed in advanced disease.
Platinum and PARP Inhibitor Resistance Due to Overexpression of MicroRNA-622 in BRCA1-Mutant Ovarian Cancer (2016)

High-grade serous ovarian carcinomas (HGSOCs) with BRCA1/2 mutations exhibit improved outcome and sensitivity to double-strand DNA break (DSB)-inducing agents (i.e., platinum and poly(ADP-ribose) polymerase inhibitors [PARPis]) due to an underlying defect in homologous recombination (HR). However, resistance to platinum and PARPis represents a significant barrier to the long-term survival of these patients. Although BRCA1/2-reversion mutations are a clinically validated resistance mechanism, they account for less than half of platinum-resistant BRCA1/2-mutated HGSOCs. We uncover a resistance mechanism by which a microRNA, miR-622, induces resistance to PARPis and platinum in BRCA1 mutant HGSOCs by targeting the Ku complex and restoring HR-mediated DSB repair. Physiologically, miR-622 inversely correlates with Ku expression during the cell cycle, suppressing non-homologous end-joining and facilitating HR-mediated DSB repair in S phase. Importantly, high expression of miR-622 in BRCA1-deficient HGSOCs is associated with worse outcome after platinum chemotherapy, indicating microRNA-mediated resistance through HR rescue.
Grouped signed power-of-two algorithms for low-complexity adaptive equalization (2005)

With increasing demand for higher data rate, modern communication systems have grown more complex. Equalization has become more and more important as it is effective in mitigating the multipath fading often occurred in high-data-rate communication systems. However, the implementation complexity of adaptive equalizers is usually too high for mobile communication applications. In this paper, a novel adaptive equalization algorithm and its low-complexity architecture are proposed. This algorithm employs a new grouped signed power-of-two (GSPT) number representation. The GSPT algorithm and several enhanced versions are simulated as adaptive equalizers in a phase-shift keying communication receiver for several practical channels and the GSPT-based equalizers perform as well as the least mean square (LMS) equalizer. Moreover, for comparison, two GSPT-based equalizers and two other equalizers are implemented in field-programmable gate arrays. The GSPT-based equalizers require only about 25%-30% of the hardware resources needed in the LMS equalizer. Also the GSPT-based equalizers are more than twice as fast as the LMS equalizer.
Selection and Preliminary Characterization of Temperature-Sensitive Mutants of Type 5 Adenovirus (1972)

Eight temperature-sensitive (ts) mutants that replicate normally at 32 C but poorly, if at all, at 39.5 C have been isolated from mutagenized stocks of a wild-type strain of type 5 adenovirus. Three mutagens were employed: nitrous acid, hydroxylamine, and nitrosoguanidine. Ts mutants were isolated from mutagenized viral stocks with frequencies between 0.01 and 0.1%. All eight mutants had reversion frequencies of 10(-5) or less. Complementation experiments in doubly infected cultures at the nonpermissive temperature separated the mutants into three nonoverlapping complementation groups. Complementation yields ranged from a 2.3- to a 3,000-fold increase over the sums of the yields from the two singly infected controls. Genetic recombination was also demonstrated; approximate recombination frequencies ranged from 0.1 to 15%. Preliminary biochemical and immunological characterization of the mutants indicated that: (i) the single mutant in complementation group I did not replicate its deoxyribonucleic acid (DNA) or synthesize late proteins at the nonpermissive temperature but did inhibit host DNA synthesis to 25% of an uninfected control; (ii) the four group II mutants replicated viral DNA, shut off host DNA synthesis, synthesized penton base and fiber, but did not synthesize immunologically detectable hexon; the three mutants in complementation group III synthesized viral DNA, shut off host DNA synthesis, and made immunologically reactive capsid proteins (hexon, penton base, and fiber).
Using branch handling hardware to support profile-driven optimization (1994)

Profile-based optimizations can be used for instruction scheduling, loop scheduling, data preloading, function in-lining, and instruction cache performance enhancement. However, these techniques have not been embraced by software vendors because programs instrumented for profiling run 2–30 times slower, an awkward compile-run-recompile sequence is required, and a test input suite must be collected and validated for each program. This paper proposes using existing branch handling hardware to generate profile information in real time. Techniques are presented for both one-level and two-level branch hardware organizations. The approach produces high accuracy with small slowdown in execution (0.4%–4.6%). This allows a program to be profiled while it is used, eliminating the need for a test input suite. This practically removes the inconvenience of profiling. With contemporary processors driven increasingly by compiler support, hardware-based profiling is important for high-performance systems.
Multiflow optical transponder for efficient multilayer optical networking (2012)

Growing concerns regarding the scalability of current optical networks as well as IP-based networks are driving two important trends. One trend is a shift from the current rigid optical networks to spectrally efficient elastic optical networks with a flexible bandwidth and adaptive channel spacing. The other trend is IP traffic offloading to a lower layer yielding benefits that are potentially cost-effective and power-efficient. This article presents a novel multiflow optical transponder (OTP) that enables more efficient IP optical networking. A multiflow OTP allows client data flows that arrive from a single client interface to be mapped to multiple optical flows. In cooperation with the emerging spectrally efficient elastic optical path networking technology, multiflow OTPs can provide multiple optical connections from a single OTP to multiple OTPs. IP traffic offloading to an elastic optical path layer architecture and the effect of introducing multiflow OTPs (i.e., the potential reduction in the number of router interfaces and considerable potential for cost savings) are discussed. These benefits are brought about by increasing the number of directly connected router pairs while keeping router-to-optical-node interconnections simple. A novel optical virtual private line service based on multiflow OTPs that supports multiple optical connections from a single customer site to multiple customer sites with capacity adjustment is also discussed.
Role of cytokines and testosterone in regulating lean body mass and resting energy expenditure in HIV-infected men (2002)

Although catastrophic weight loss is no longer common in HIV-infected men, we hypothesized that a more gradual process of cachexia [loss of lean body mass (LBM) without severe weight loss, often accompanied by elevated resting energy expenditure (REE)] is still common and is driven by excessive production of the catabolic cytokines tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 beta (IL-1 beta). We performed a longitudinal analysis of an ongoing cohort study of nutritional status in 172 men with HIV infection. LBM loss of >1 kg occurred in 35% of the cohort, and LBM loss of >5% occurred in 12.2% over 8 mo of observation, but classical wasting (loss of approximately 10% of weight) was rare (2%). Both TNF-alpha (-150 g LBM. ng(-1) x ml(-1), P < 0.02) and IL-1 beta production (-130 g LBM x ng(-1) x ml(-1), P < 0.01) by peripheral blood mononuclear cells predicted loss of LBM. A rise in REE of >200 kcal/day was found in 17.7% of the subjects regardless of weight change. IL-1 beta (+9 kcal/day per ng/ml, P < 0.002) and TNF-alpha (+10 kcal/day per ng/ml, P < 0.02) production predicted Delta REE. Serum free testosterone was inversely associated with TNF-alpha production and was not an independent predictor of either Delta LBM or Delta REE after adjustment for cytokine production. Even though weight loss was rare in this cohort of patients treated with highly active antiretroviral therapy, loss of LBM was common and was driven by catabolic cytokines and not by inadequate dietary intake or hypogonadism.
Peak Power Reduction In Ofdm Systems Using Dynamic Constellation Shaping (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Class prediction and discovery using gene microarray andproteomics mass spectroscopy data: curses, caveats, cautions (2003)

Using very simple classifiers, we show for several publicly available microarray and proteomics datasets how these curses influence classification outcomes. In particular, even if the sample per feature ratio is increased to the recommended 5-10 by feature extraction/reduction methods, dataset sparsity can render any classification result statistically suspect. In addition, several 'optimal' feature sets are typically identifiable for sparse datasets, all producing perfect classification results, both for the training and independent validation sets. This non-uniqueness leads to interpretational difficulties and casts doubt on the biological relevance of any of these 'optimal' feature sets. We suggest an approach to assess the relative quality of apparently equally good classifiers.
PDZ Domain Recognition: Insight from Human Tax-Interacting Protein 1 (TIP-1) Interaction with Target Proteins (2015)

Cellular signaling is primarily directed via protein-protein interactions. PDZ (PSD-95/Discs large/ZO-1 homologous) domains are well known protein-protein interaction modules involved in various key signaling pathways. Human Tax-interacting protein 1 (TIP-1), also known as glutaminase interaction protein (GIP), is a Class I PDZ domain protein that recognizes the consensus binding motif X-S/T-X-V/I/L-COOH of the C-terminus of its target proteins. We recently reported that TIP-1 not only interacts via the C-terminus of its target partner proteins but also recognizes an internal motif defined by the consensus sequence S/T-X-V/L-D in the target protein. Identification of new target partners containing either a C-terminal or internal recognition motif has rapidly expanded the TIP-1 protein interaction network. TIP-1 being composed solely of a single PDZ domain is unique among PDZ containing proteins. Since it is involved in many important signaling pathways, it is a possible target for drug design. In this mini review, we have discussed human TIP-1, its structure, mechanism of function, its interactions with target proteins containing different recognition motifs, and its involvement in human diseases. Understanding the molecular mechanisms of TIP-1 interactions with distinct target partners and their role in human diseases will be useful for designing novel therapeutics.
Structure, biochemistry, and assembly of epithelial tight junctions (1987)

The zonula occludens (ZO), also referred to as the tight junction, forms the barrier to the diffusion of molecules and ions across the epithelial cell layer through the paracellular space. The level of electrical resistance of the paracellular pathway seems to depend on the number of strands in the ZO observed by freeze-fracture electron microscopy (EM). The ZO also forms the boundary between the compositionally distinct apical and basolateral plasma membrane domains because it is a barrier to the lateral diffusion of lipids and membrane proteins that reside in the extracytoplasmic leaflet of the membrane bilayer. In contrast to its appearance in transmission EM, the tight junction is not a fusion between the outer membrane leaflets of neighboring cells. Rather it consists of protein molecules, including the newly discovered protein ZO-1 and probably others, which bring the plasma membranes into extremely close apposition so as to occlude the extracellular space. Very little is known about the assembly of tight junctions, but several kinds of evidence suggest that they are very dynamic structures. Other elements of the epithelial junctional complex including the zonula adherens (ZA), the Ca2+-dependent cell adhesion molecule uvomorulin, or L-CAM, and actin filaments of the cytoskeleton may participate in the assembly of the ZO.
T-Cell Function and Migration — Two Sides of the Same Coin (2000)

Since the pioneering work of Gowans and colleagues in the 1960s,1,2 much progress has been made in understanding the pivotal role of cell migration in immunity. We now have considerable knowledge of the way in which specialized leukocytes are channeled to distinct target tissues in immune responses and inflammation (Figure 1). This review will concentrate on the migration of T cells, which are at the heart of most adaptive immune responses.Since T cells respond to pathogens only on direct contact with pathogen-derived antigen, they must migrate to sites where antigen is found. The T-cell receptor recognizes a peptide . . .
Magnetic properties of carbon structures (2004)

Magnetic properties of the main allotropic modifications of carbon (diamond, graphite, nanographite, nanotubes, and fullerenes) are described. Properties of nanocarbon are considered from the standpoint of the interrelation between structural imperfection and magnetic ordering. Experimental data on high-temperature ferromagnetism in carbon structures and some theoretical models of magnetic carbon are reported.
N-acetyl-4-S-cysteaminylphenol as a new type of depigmenting agent for the melanoderma of patients with melasma (1991)

<h3>• Background and Design.—</h3> Melasma is a difficult medical problem to treat. Hydroquinone is administered to many patients, but it is unstable and local irritation and dermatitis may develop after a prolonged use at a high concentration. This study introduces a new depigmenting agent,<i>N</i>-acetyl-4-S-cysteaminylphenol, for better management of melanoderma in patients with melasma. <h3>Results.—</h3> Our study, based on a retrospective observation of 12 patients using 4% N-acetyl-4-S-cysteaminylphenol in oil-in-water emulsion, showed a complete loss (8%), a marked improvement (66%), or a moderate improvement (25%) of melasma lesions. Visible changes of melanoderma can be seen in 2 to 4 weeks after daily topical application. This depigmentation was associated with a decrease in the number of functioning melanocytes and in the number of melanosomes transferred to keratinocytes.<i>N</i>-acetyl-4-S-cysteaminylphenol is the tyrosinase substrate, and, on exposure to tyrosinase, it formed a melanin-like pigment. <h3>Conclusions.—</h3> A phenolic thioether,<i>N</i>-acetyl-4-S-cysteaminylphenol, is a new type of depigmenting agent for the better management of melasma. It is much more stable and less irritating to the skin than hydroquinone, and it is specific to melanin-synthesizing cells. (<i>Arch Dermatol.</i>1991;127:1528-1534)
Serotype-specific epitope(s) present on the VP8 subunit of rotavirus VP4 protein (1991)

cDNA clones representing the VP8 and VP5 subunits of VP4 of symptomatic human rotavirus strain KU (VP7 serotype 1 and VP4 serotype 1A) or DS-1 (VP7 serotype 2 and VP4 serotype 1B) or asymptomatic human rotavirus strain 1076 (VP7 serotype 2 and VP4 serotype 2) were constructed and inserted into the pGEMEX-1 plasmid and expressed in Escherichia coli. Immunization of guinea pigs with the VP8 or VP5 protein of each strain induced antibodies that neutralized the rotavirus from which the VP4 subunits were derived. In a previous study (M. Gorziglia, G. Larralde, A.Z. Kapikian, and R. M. Chanock, Proc. Natl. Acad. Sci. USA 87:7155-7159, 1990), three distinct serotypes and one subtype of VP4 outer capsid protein were identified among 17 human rotavirus strains that had previously been assigned to five distinct VP7 serotypes. The results obtained by cross-immunoprecipitation and by neutralization assay with antisera to the VP8- and VP5-expressed proteins suggest that the VP8 subunit of VP4 contains the major antigenic site(s) responsible for serotype-specific neutralization of rotavirus via VP4, whereas the VP5 subunit of VP4 is responsible for much of the cross-reactivity observed among strains that belong to different VP4 serotypes.
Anti-neutrophil cytoplasm antibodies in Wegener's granulomatosis recognize an elastinolytic enzyme. (1990)

The target antigen of anti-neutrophil cytoplasm antibodies (ACPA; also known as ANCA) was isolated by affinity chromatography from supernatants of human neutrophils, stimulated with phorbol ester to induce degranulation. Sequence analysis of the antigen revealed 17 NH2-terminal amino acids (IVGGHEAQPHIRPIYMA), which have considerable sequence homology with known serine proteinases. Investigation of the enzymatic activity showed that the antigen is a neutral serine proteinase that is able to cleave elastin. Since the molecular weight of the antigen, its substrate specificity, and its inhibitor profile reported in this study are identical with those reported recently for proteinase 3, we conclude that ACPA are most probably directed against proteinase 3.