gebhart/patrepeval huggingface dataset:
HTLV-1 infections (2000)

Human T lymphotropic virus type 1 (HTLV-1) causes disabling and fatal diseases, yet there is no vaccine, no satisfactory treatment, and no means of assessing the risk of disease or prognosis in infected people. Recent research on the molecular virology and immunology of HTLV-1 shows the importance of the host's immune response in reducing the risk of these diseases, and is beginning to explain why some HTLV-1 infected people develop serious illnesses whereas most remain healthy life long carriers of the virus. These findings might be applicable to other persistent virus infections such as human immunodeficiency virus, hepatitis B, and hepatitis C.
The use of oliodeoxynucleotide probes in chaotrope-based hybridization solutions (1991)

Hybridization solutions containing chaotropes may be used to modulate the thermal stability (Tm or Td) of oligodeoxynucleotide (ODN) duplexes or hybrids over a 90 degrees C range. Modulation of Td allows formulation of hybridization solutions that permit ambient temperature hybridization using most combinations of probe length, probe composition, target type, and facilitates development of convenient and rapid assay formats. The conditions required to achieve ODN duplex fidelity, and optimal yields of hybridized product, are described for trichloroacetate, thiocyanate, guanidinium salts and other chaotropic salts. The effects of different solid supports on Td are described. Also, a method is presented that uses chaotropic compounds to reduce background arising from signal ODN probes in a sandwich assay hybridization format.
Pathophysiology of Acute Kidney Injury: Roles of Potential Inhibitors of Inflammation (2007)

The pathogenesis of acute kidney injury (AKI) is complex and varies to some extent based on the particular cause. Inflammation contributes to this pathophysiology in a variety of contexts. Inflammation can result in reduction in local blood flow to the outer medulla with adverse consequences on tubule function and viability. Both the innate and adaptive immune responses are important contributors. With ischemia/reperfusion endothelial cells upregulate a number of adhesion molecules which have counterreceptors on leukocytes. A number of vasoactive mediators that are released with injury, such as nitric oxide, may also affect leukocyte- endothelial interactions. Tubule epithelial cells generate proinflammatory and chemotactic cytokines. We and others have found that injection of mesenchymal stem (stromal) cells is protective against renal injury as assessed by serum creatinine measured 24 h after ischemia. The mechanism of such protection may be through intrarenal paracrine effects to decrease inflammation or by systemic immune modulation. Resolvins (Rv) and protectins (PD) have been identified as two newly identified families of naturally occurring n-3 fatty acid docosahexaenoic acid metabolites. In collaboration with Serhan et al. we recently reported that, in response to bilateral ischemia/reperfusion injury, mouse kidneys produce D series resolvins (RvDs) and PD1 [J Immunol 2006;177:5902-5911]. Administration of RvDs or PD1 to mice prior to, or subsequent to, ischemia resulted in a reduction in functional and morphological kidney injury. Understanding how these anti-inflammatory processes are regulated may provide insight into how we might intervene to facilitate and enhance them so that we might prevent or mitigate the devastating consequences of AKI.
An integrated laser blood flowmeter (2003)

We have constructed a very small and lightweight blood flowmeter using micromachining and surface mounting techniques for a wearable health monitoring system. The hybrid integrated structure of the optical system incorporates a InGaAsP-InP distributed feedback laser diode (DFB-LD) with a wavelength of 1310 nm, an edge-illuminated photodiode (PD) and a polyimide waveguide on silicon substrate (2 mm × 3 mm). This integrated flowmeter can be positioned directly on the tissue and permits real-time monitoring of capillary microcirculation. In-vivo measurements of blood perfusion in a finger confirm the feasibility of the blood flowmeter.
Functional Properties of Human Embryonic Stem Cell‐Derived Cardiomyocytes (2005)

Regeneration of the diseased myocardium by cardiac cell transplantation is an attractive therapeutic modality. Yet, because the transplanted cardiomyocytes should functionally integrate within the diseased myocardium, it is preferable that their properties resemble those of the host. To determine the functional adaptability of human embryonic stem cell-derived cardiomyocytes (hESC-CM) to the host myocardium, the authors investigated the excitation-contraction (E-C) coupling and the responsiveness to common physiological stimuli. The main findings are: (1) hESC-CM readily respond to electrical pacing and generate corresponding [Ca(2+)](i) transients (measured by fura-2 fluorescence) and contractions (measured by video edge detector). (2) In contrast to the mature myocardium, hESC-CM display negative force-frequency relations. (3) The hESC-CM contraction is dependent on [Ca(2+)](o) and blocked by verapamil. (4) Surprisingly, ryanodine, the sarcoplasmic-endoplasmic reticulum Ca(2+)-ATPase inhibitor thapsigargin, and caffeine do not affect the [Ca(2+)](i) transient or contraction. Collectively, these results indicate that at the developmental stage of 45 to 60 days, the contraction is largely dependent on [Ca(2+)](o) rather than on sarcoplasmic reticulum (SR) Ca(2+) stores. The results show for the first time that the E-C coupling properties of hESC-CM differ from the adult myocardium, probably due to immature SR function. Based on these findings, genetic manipulation of hESC-CM toward the adult myocardium should be considered.
Nucleation and Growth of Oriented Ceramic Films onto Organic Interfaces (1996)

New materials synthetic methods are being investigated involving heterogeneous nucleation and growth of ceramic films from aqueous solutions onto surfaces modified with organic functional groups. Dense, nanocrystalline, iron hydroxide films were deposited onto sulfonated polystyrene and sulfonated self-assembling monolayers on oxidized silicon. (020) oriented goethite films were formed resulting in chains of edge-shared octahedra in the [001] direction lying parallel to the surface. Deposition amounts varied with pH primarily due to changes in solution supersaturation. The best films were formed when deposition occurred heterogeneously at supersaturations just below the critical supersaturation. Induction times decreased with increasing sulfonate site density due to a reduction in interfacial energy. Nucleation was initiated by binding of cationic species to sulfonate sites and hydrolysis and condensation reactions resulted in the growth and coalescence of crystallites.
Heat and Moisture Exchange Devices: Are They Doing What They Are Supposed to Do? (2004)

There is considerable variability in the in vivo performance of heat and moisture exchangers that have similar manufacturer specifications. These specifications, based on the International Standards Organization 9360 standard, which is measured in vitro, cannot be used to predict clinical performance.
Cutting Single-Wall Carbon Nanotubes through Fluorination (2002)

The fluorination of purified HiPco single-wall carbon nanotubes to a stoichiometry CFx (x ⩽ 0.2) followed by pyrolysis of the partially fluorinated nanotubes up to 1000 °C was found to have “cut” the nanotubes to a range of short lengths (average <50 nm). The pyrolysis process was monitored in-situ with TGA-FTIR. The fluorine was driven off the nanotube structure in the form of COF2 and CF4. The “cut” nanotubes have been characterized by Raman, ATR-IR, EDAX, and AFM measurements. Short bundles composed of strongly interacting individual nanotubes were found in the “cut” nanotube sample. The short lengths and specific reactivities should lead to novel applications for these nanotubes.
Fringe formation in speckle photography (1984)

The formation of Young fringes that are observed in speckle photography is discussed. Both the shape and the contrast of the fringes are derived by starting from the cross-correlation function of the light intensities to be recorded in a double-exposure specklegram. The effects of focusing and defocusing in specklegram recording on speckle displacement affecting the shape, as well as the origin of speckle decorrelation affecting the contrast, are discussed in detail. The degree of the decorrelation is shown to be given by the squared modulation transfer function of the imaging lens for a spatial frequency that is proportional to the speckle displacement at its pupil plane. These theoretical relations are verified by experiments performed for in-plane object translation combined with tilt.
Aorsin, a novel serine proteinase with trypsin-like specificity at acidic pH (2003)

A proteinase that hydrolyses clupeine and salmine at acidic pH, called aorsin, was found in the fungus Aspergillus oryzae. Purified aorsin also hydrolysed benzyloxycarbonyl-Arg-Arg-4-methylcoumaryl-7-amide optimally at pH 4.0. The specificity of aorsin appeared to require a basic residue at the P(1) position and to prefer paired basic residues. Aorsin activated plasminogen and converted trypsinogen to trypsin. The trypsin-like activity was inhibited strongly by antipain or leupeptin, but was not inhibited by any other standard inhibitors of peptidases. To identify the catalytic residues of aorsin, a gene was cloned and an expression system was established. The predicted mature protein of aorsin was 35% identical with the classical late-infantile neuronal ceroid lipofuscinosis protein CLN2p and was 24% identical with Pseudomonas serine-carboxyl proteinase, both of which are pepstatin-insensitive carboxyl proteinases. Several putative catalytic residues were mutated. The k (cat)/ K(m) values of the mutant enzymes Glu(86)-->Gln, Asp(211)-->Asn and Ser(354)-->Thr were 3-4 orders of magnitude lower and Asp(90)-->Asn was 21-fold lower than that of wild-type aorsin, indicating that the positions are important for catalysis. Aorsin is another of the S53 family serine-carboxyl proteinases that are not inhibited by pepstatin.
Skin collagen glycation, glycoxidation, and crosslinking are lower in subjects with long-term intensive versus conventional therapy of type 1 diabetes: relevance of glycated collagen products versus HbA1c as markers of diabetic complications. DCCT Skin Collagen Ancillary Study Group. Diabetes Control and Complications Trial. (1999)

The relationships between long-term intensive control of glycemia and indicators of skin collagen glycation (furosine), glycoxidation (pentosidine and N(epsilon)-[carboxymethyl]-lysine [CML]), and crosslinking (acid and pepsin solubility) were examined in 216 patients with type 1 diabetes from the primary prevention and secondary intervention cohorts of the Diabetes Control and Complications Trial. By comparison with conventional treatment, 5 years of intensive treatment was associated with 30-32% lower furosine, 9% lower pentosidine, 9-13% lower CML, 24% higher acid-soluble collagen, and 50% higher pepsin-soluble collagen. All of these differences were statistically significant in the subjects of the primary prevention cohort (P < 0.006-0.001) and also of the secondary intervention cohort (P < 0.015-0.001) with the exception of CML and acid-soluble collagen. Age- and duration-adjusted collagen variables were significantly associated with the HbA1c value nearest the biopsy and with cumulative prior HbA1c values. Multiple logistic regression analyses with six nonredundant collagen parameters as independent variables and various expressions of retinopathy, nephropathy, and neuropathy outcomes as dependent variables showed that the complications were significantly associated with the full set of collagen variables. Surprisingly, the percentage of total variance (R2) in complications explained by the collagen variables ranged from 19 to 36% with the intensive treatment and from 14 to 51% with conventional treatment. These associations generally remained significant even after adjustment for HbA1c, and, most unexpectedly, in conventionally treated subjects, glycated collagen was the parameter most consistently associated with diabetic complications. Continued monitoring of these subjects may determine whether glycation products in the skin, and especially the early Amadori product (furosine), have the potential to be predictors of the future risk of developing complications, and perhaps be even better predictors than glycated hemoglobin (HbA1c).
Secure routing for structured peer-to-peer overlay networks (2002)

Structured peer-to-peer overlay networks provide a substrate for the construction of large-scale, decentralized applications, including distributed storage, group communication, and content distribution. These overlays are highly resilient; they can route messages correctly even when a large fraction of the nodes crash or the network partitions. But current overlays are not secure; even a small fraction of malicious nodes can prevent correct message delivery throughout the overlay. This problem is particularly serious in open peer-to-peer systems, where many diverse, autonomous parties without preexisting trust relationships wish to pool their resources. This paper studies attacks aimed at preventing correct message delivery in structured peer-to-peer overlays and presents defenses to these attacks. We describe and evaluate techniques that allow nodes to join the overlay, to maintain routing state, and to forward messages securely in the presence of malicious nodes.
Evolution of WDM Optical IP Networks: A Cost and Energy Perspective (2009)

We review technologies and architectures for WDM optical IP networks from the viewpoint of capital expenditure and network energy consumption. We show how requirements of low cost and low energy consumption can influence the choice of switching technologies as well as the overall network architecture.
A scalable 32 Gb/s parallel data transceiver with on-chip timing calibration circuits (2002)

Inter-chip interconnect has become increasingly important due to the recent rapid development of switch fabric data network and symmetric multi-processing (SMP) server technologies. A high-speed parallel data transceiver megacell has low power, latency, and pin count for point-to-point interconnect between chips. Each macro includes a transmitter and a receiver. The aggregate bandwidth is 32 Gb/s, or 16 Gb/s in each direction. An on-chip timing calibration circuit performs data de-skewing and timing optimization. A transport layer handles error correction through the link. Low swing differential signaling further reduces noise and error probability, and therefore relaxes restrictions of board design. The entire macro is portable and scalable, and can be integrated with standard logic process. It also works well with standard packages such as EGA or QFP. Built-in self test (BIST) logic is implemented for product testing.
Synthèse et réactivité de nitro indazoles (1979)

Abstract La synthèse et les propriétés spectroscopiques en rmn de 44 dérivés nitrés de l'indazole dont 23 sont décrits pour la première fois, ont été étudiées. En fonction des rendements, on indique la meilleure voie d'accés aux dérivés halogénés méthyle's (halogénation avant ou après méthylation du nitro indazole). La réactivité' relative des différents sites du cycle vis à vis de l'agent électrophile est discutée.
Hox gene induction in the neural tube depends on three parameters: competence, signal supply and paralogue group (1997)

It has been previously shown that Hox gene expression in the rhombencephalon is controlled by environmental cues. Thus posterior transposition of anterior rhombomeres to the r7/8 level results in the activation of Hox genes of the four first paralog groups and in homeotic transformations of the neuroepithelial fate according to its position along the anteroposterior axis. We demonstrate here that although the anteroposterior levels of r2 to r6 express Hox genes they do not have inducing activity on more anterior territories. If transposed at the posterior rhombencephalon and trunk level, however, the same anterior regions are able to express Hox gene such as Hoxa-2, a-3 or b-4. We also provide evidence that these signals are transferred by two paths: one vertical, arising from the paraxial mesoderm, and one planar, travelling in the neural epithelium. The competence to express Hox genes extends up to the forebrain and midbrain but expression of Hox genes does not preclude Otx2 expression in these territories and results only in slight changes in their phenotypes. Similarly, rhombomeres transplanted to posterior truncal levels turned out to be able to express posterior genes of the first eight paralog groups to the exclusion of others located downstream in the Hox genes genomic clusters. This suggests that the neural tube is divided into large territories characterized by different Hox gene regulatory features.
Regulation by phosphorylation of the zinc finger protein KRC that binds the B motif and V(D)J recombination signal sequences (1999)

The DNA binding protein KRC (forkappaB binding andrecognitioncomponent of the V(D)J recombination signal sequence) belongs to a family of large zinc finger proteins that bind to the kappaB motif and contains two widely separated DNA binding structures. In addition to the kappaB motif, KRC fusion proteins bind to the signal sequences of V(D)J recombination to form highly ordered complexes. Here, we report that KRC may be regulated by post-translational modifications. Specific protein kinases present in the nucleus of pre-B cells phosphorylated a KRC fusion protein at tyrosine and serine residues. Such protein modifications increased DNA binding, thereby providing a mechanism by which KRC responds to signal transduction pathways. KRC is a substrate of epidermal growth factor receptor kinase and P34cdc2 kinase in vitro. Our results suggest that activation of the KRC family of transcription factors may provide a mechanism by which oncogenic tyrosine kinases regulate genes with kappaB-controlled gene regulatory elements.
Systemic gene therapy of murine melanoma using tissue specific expression of the HSVtk gene involves an immune component. (1994)

Previously we have demonstrated safe and effective transfer of the HSVtk cytotoxic gene to primary murine melanoma tumors by direct injection of plasmid and retroviral vectors in which the HSVtk gene is driven by the tissue-specific tyrosinase promoter. However, for general clinical application such forms of therapy should, ideally, be effective against disseminated metastases. We report here that the number of recently established lung metastases of B16 melanoma in C57BL mice treated with ganciclovir is reduced compared to controls after multiple i.v. administrations of high titer retroviral supernatant encoding the HSVtk gene, but not after administration of liposome-complexed plasmid DNA. Using polymerase chain reaction analysis, integration of the provirus was observed in metastasis-bearing lungs (4 of 6 mice) and in the spleens of some ganciclovir-treated animals (2 of 6 mice) but not in the testes, brain, heart, liver, or kidney. The reduction in the number of experimental metastases in C57BL mice exceeded the anticipated extent of transduction of tumor cells, which is indicative of a marked bystander effect. This magnitude of reduction was not observed in immunodeficient athymic mice, suggesting that the immune system plays some part in the bystander effect. In support of these data, we show that, whereas the parental tumor cells are only poorly immunogenic, an effective antitumor immune response is generated following the killing of neoplastic cells in vivo as a result of treatment with ganciclovir. These effects may be responsible for augmenting the efficacy of retroviral infection. The combination of local cell killing by the HSVtk/ganciclovir system and the induction of antitumor immunity suggests new opportunities for the design of vectors for the gene therapy of cancer.
Endogenous nitrogen oxides and bronchodilator S-nitrosothiols in human airways. (1993)

Recent discoveries suggesting essential bioactivities of nitric oxide (NO.) in the lung are difficult to reconcile with the established pulmonary cytotoxicity of this common air pollutant. These conflicting observations suggest that metabolic intermediaries may exist in the lung to modulate the bioactivity and toxicity of NO.. We report that S-nitrosothiols (RS-NO), predominantly the adduct with glutathione, are present at nano- to micromolar concentrations in the airways of normal subjects and that their levels vary in different human pathophysiologic states. These endogenous RS-NO are long-lived, potent relaxants of human airways under physiological O2 concentrations. Moreover, RS-NO form in high concentrations upon administration of NO. gas. Nitrite (10-20 microM) is found in airway lining fluid in concentrations linearly proportional to leukocyte counts, suggestive of local NO. metabolism. NO. itself was not detected either free in solution or in complexes with transition metals. These observations may provide insight into the means by which NO. is packaged in biological systems to preserve its bioactivity and limit its potential O2-dependent toxicity and suggest an important role for NO. in regulation of airway luminal homeostasis.
Versatile Approach To Encoding Combinatorial Organic Syntheses Using Chemically Robust Secondary Amine Tags (1996)

Encoded combinatorial organic synthesis has recently emerged as a powerful tool for the discovery of biologically active compounds from complex chemical libraries. This report describes a new encoding methodology that uses chemically robust secondary amines as tags. These amines are incorporated into an N-[(dialkylcarbamoyl)methyl]glycine-coding oligomer through simple chemistry that is compatible with a wide range of polymer-supported transformations useful in combinatorial synthesis. In the decoding process acidic hydrolysis of the tagging polymer regenerates the secondary amines, which after dansylation are resolved and detected at sub-picomole levels by reversed-phase HPLC. The versatility of this strategy is demonstrated here by encoded syntheses of members of several representative heterocyclic compound classes, including beta-lactams, 4-thiazolidinones, and pyrrolidines.
Clostridium perfringens enterotoxin binds to the second extracellular loop of claudin‐3, a tight junction integral membrane protein (2000)

Claudins (claudin-1 to -18) with four transmembrane domains and two extracellular loops constitute tight junction strands. The peptide toxin Clostridium perfringens enterotoxin (CPE) has been shown to bind to claudin-3 and -4, but not to claudin-1 or -2. We constructed claudin-1/claudin-3 chimeric molecules and found that the second extracellular loop of claudin-3 conferred CPE sensitivity on L fibroblasts. Furthermore, overlay analyses revealed that the second extracellular loop of claudin-3 specifically bound to CPE at the K(a) value of 1.0x10(8) M(-1). We concluded that the second extracellular loop is the site through which claudin-3 interacts with CPE on the cell surface.
The Role of Fluorine Termination in the Chemical Stability of HF-Treated Si Surfaces (1990)

The principal role of silicon-fluorine bonds in the chemical nature of HF-etched Si surfaces has been investigated by angle-resolved X-ray photoelectron spectroscopy. The native oxide growth thickness and the fluorine coverage have been systematically measured as functions of HF concentration, pure water rinse time, air or N 2 +O 2 gas exposure time and gas phase H 2 O concentration. It is shown that the native oxide growth is strongly suppressed by the existence of Si-F bonds of about 0.12 monolayers on the surface. This is explained by a model in which Si-F bonds chemically stabilize the surface reactive sites such as atomic steps as supported by the result of the layer-by-layer oxidation of Si.