gebhart/patrepeval huggingface dataset:
Hypothermic Storage and Cryopreservation of Cartilage (1985)

Osteochondral autografts of femoral condyles in dogs were frozen at different cooling velocities after exposure to either glycerol or dimethyl sulfoxide to determine the freezing regimen best suited for preservation of intact cartilage. Autografts were also subjected to hypothermic storage in tissue culture media for ascertainment of how long they can be stored under these conditions. Autografts maintained in vitro under various conditions of storage were examined after transplantation. Autografts were chosen for this portion of the investigation in order to study the effects of storage uncomplicated by immunologic interactions. No differences were found between the cryoprotective actions of glycerol and dimethyl sulfoxide. The freezing rate that produced the least damage in the cartilage was 2°/min. Cartilage survived ten days of hypothermic storage in tissue culture medium. Allografts frozen by the standard method of glycerolization and cooling at l°/min were also studied. These showed eventual loss of chondrocytes and conversion of hyaline cartilage to fibrocartilage.
<i>Streptococcus agalactiae</i> GAPDH Is a Virulence-Associated Immunomodulatory Protein (2007)

Certain extracellular proteins produced by several pathogenic microorganisms interfere with the host immune system facilitating microbial colonization and were thus designated virulence-associated immunomodulatory proteins. In this study, a protein with B lymphocyte stimulatory activity was isolated from culture supernatants of Streptococcus agalactiae strain NEM316. This protein, with an apparent molecular mass of 45 kDa, was identified as GAPDH by N-terminal amino acid sequencing. The gapC gene was cloned and expressed in Escherichia coli for the production of a recombinant histidyl-tagged protein. The recombinant GAPDH (rGAPDH), purified in an enzymatically active form, induced in vitro an up-regulation of CD69 expression on B cells from normal and BCR transgenic mice. In addition, rGAPDH induced an increase in the numbers of total, but not of rGAPDH-specific, splenic Ig-secreting cells in C57BL/6 mice treated i.p. with this protein. These in vitro- and in vivo-elicited B cell responses suggest that the B cell stimulatory effect of rGAPDH is independent of BCR specificity. A S. agalactiae strain overexpressing GAPDH showed increased virulence as compared with the wild-type strain in C57BL/6 mice. This virulence was markedly reduced in IL-10-deficient and anti-rGAPDH antiserum-treated mice. These results suggest that IL-10 production, which was detected at higher concentrations in the serum of rGAPDH-treated mice, is important in determining the successfulness of the host colonization by S. agalactiae and they highlight the direct role of GAPDH in this process. Taken together, our data demonstrate that S. agalactiae GAPDH is a virulence-associated immunomodulatory protein.
The effect of Taurolidine on adherent and floating subpopulations of melanoma cells (2003)

The annual incidence of malignant melanoma is estimated at 10–12 per 100 000 inhabitants in countries of Central Europe and the US, with more recent estimates showing a dramatic upward trend. Taurolidine (Carter/Wallace, Cranberry, NJ) is a novel, potentially effective, antitumor chemotherapeutic agent. We hypothesized that Taurolidine could inhibit the growth, induce apoptosis, affect the cell cycle and change morphology of melanoma cells. We expected this process to be different in adherent and floating subpopulations that may be reflective of solid tumors and their metastases. Analysis of MNT-1 human and B16F10 murine melanoma cells showed that at 72 h the IC50 of Taurolidine was 25.4±3.3 μM for MNT-1 human melanoma cells and 30.9±3.6 μM for B16F10 murine melanoma cells. Taurolidine induced DNA fragmentation of melanoma cells in a dose-dependent manner. Taurolidine (75 and 100 μM) induced 52–97% Annexin-V binding (apoptosis), respectively. Evaluation of cell cycle after 72 h exposure to Taurolidine (0–100 μM) revealed that the percentage of melanoma cells in S phase increased from 27 to 40% in the adherent subpopulation and from 33 to 49% in the floating subpopulation. Phase contrast microscopy revealed a marked swelling of melanoma cells and decreasing cell numbers in adherent subpopulation starting at 24 h with 25 μM Taurolidine. Shrinkage of cells dominated at 75–100 μM Taurolidine. Using Cytospin assay in the floating population, we observed swelling of melanoma cells induced by 25–100 μM Taurolidine and appearance of giant (multinuclear) forms resulting from exposure to 75–100 μM Taurolidine. Some floating cells with normal morphology were observed with low concentrations of Taurolidine (0–25 μM). These data show that effects of Taurolidine may be different in adherent and floating subpopulations of melanoma cells. More importantly, floating subpopulations that may contain some viable melanoma cells, may be reflective of potential metastasis after treatment of solid tumors in vivo.
Activation of Arachidonic Acid‐Specific Phospholipase A<sub>2</sub> in Human Neuroblastoma Cells after Chronic Alcohol Exposure: Prevention by GM1 Ganglioside (1997)

Human neuroblastoma cells were exposed to ethanol (EtOH; 100 mM) in culture for various time periods. It was found that chronic EtOH exposure increased the arachidonyl‐specific phospholipase A 2 (PLA 2 ) activity significantly in both cytosol (1.6‐fold) and membrane (2.2‐fold) fractions when 1‐palmitoyl‐2‐arachidonyl‐ sn ‐glycero‐3‐phosphocholine was used as a substrate. This arachidonyl‐specific PLA 2 activity progressively increased with increasing duration of EtOH exposure and reached peak level at 72‐hr EtOH exposure (chronic). A significant amount of the PLA 2 activity was associated with the membrane fraction. No significant difference in PLA 2 activity was observed when 1‐palmitoyl‐2 oleoyl or linoleoyl‐ sn ‐glycero‐3‐phosphocholine was used as a substrate. It was also found that co‐treatment of neuroblastoma cells with ganglioside GM1 reduced the EtOH‐induced activation of arachidonyl‐specific PLA 2 activity. The present results indicate that arachidonic acid‐specific PLA 2 may play a role in adaptation mechanism to chronic EtOH in cultured neuroblastoma cells. Ganglioside GM1, in part, may exert its neuroprotective effects by modulating arachidonyl‐specific PLA 2 activity in chronic EtOH‐exposed neuroblastoma cells.
Crosslinking density and resorption of dimethyl suberimidate-treated collagen (1997)

Collagen was purified from bovine Achilles tendon and crosslinked with dimethyl suberimidate (DMS) and glutaraldehyde (GTA). Under optimal conditions, the shrinkage temperature (Ts) was raised to 74 degrees C for collagen crosslinked with DMS and to 80 degrees C for those crosslinked with GTA. Crosslinking density measurements were done on the hydrothermally denatured collagen by the method based on the Flory-Rehner equation. GTA treatment was found to introduce more number of crosslinks than DMS. The maximum tension attained during heating (after shrinkage has occurred) was greater for GTA-treated collagen than for DMS and control. The control collagen membranes broke during heating (at 73 degrees C), while for the crosslinked membranes the tension kept on increasing up to 100 degrees C. The crosslinking density correlated well with the data determined from the in vitro and in vivo degradation studies. Uncrosslinked and DMS crosslinked collagen membranes were more susceptible to degradation by enzymes in vitro, while GTA-treated collagen was highly resistant to degradation. The biocompatibility of the collagen membranes was studied by subcutaneous implantation in rats. Uncrosslinked collagen membranes degraded within 14 days with the formation of granulation tissue. DMS crosslinked membranes degraded within 21 days and the area was replaced by numerous fibroblasts and newly formed collagen. No calcification was observed. For GTA-treated membranes, necrosis was observed after 7 days implantation and by 14 days the membrane had started to calcify.
Online event-driven subsequence matching over financial data streams (2004)

Subsequence similarity matching in time series databases is an important research area for many applications. This paper presents a new approximate approach for automatic online subsequence similarity matching over massive data streams. With a simultaneous on-line segmentation and pruning algorithm over the incoming stream, the resulting piecewise linear representation of the data stream features high sensitivity and accuracy. The similarity definition is based on a permutation followed by a metric distance function, which provides the similarity search with flexibility, sensitivity and scalability. Also, the metric-based indexing methods can be applied for speed-up. To reduce the system burden, the event-driven similarity search is performed only when there is a potential event. The query sequence is the most recent subsequence of piecewise data representation of the incoming stream which is automatically generated by the system. The retrieved results can be analyzed in different ways according to the requirements of specific applications. This paper discusses an application for future data movement prediction based on statistical information. Experiments on real stock data are performed. The correctness of trend predictions is used to evaluate the performance of subsequence similarity matching.
Novel Trisubstituted Benzimidazoles, Targeting <i>Mtb</i> FtsZ, as a New Class of Antitubercular Agents (2010)

Libraries of novel trisubstituted benzimidazoles were created through rational drug design. A good number of these benzimidazoles exhibited promising MIC values in the range of 0.5-6 μg/mL (2-15 μM) for their antibacterial activity against Mtb H37Rv strain. Moreover, five of the lead compounds also exhibited excellent activity against clinical Mtb strains with different drug-resistance profiles. All lead compounds did not show appreciable cytotoxicity (IC(50) > 200 μM) against Vero cells, which inhibited Mtb FtsZ assembly in a dose dependent manner. The two lead compounds unexpectedly showed enhancement of the GTPase activity of Mtb FtsZ. The result strongly suggests that the increased GTPase activity destabilizes FtsZ assembly, leading to efficient inhibition of FtsZ polymerization and filament formation. The TEM and SEM analyses of Mtb FtsZ and Mtb cells, respectively, treated with a lead compound strongly suggest that lead benzimidazoles have a novel mechanism of action on the inhibition of Mtb FtsZ assembly and Z-ring formation.
Reduction in fertilization rate <i>in vitro</i> of oocytes from immature rats induced to superovulate (1984)

Immature female rats (65-70 g) were injected with 4 i.u. PMSG (control) or superovulated with 8, 16, 24 or 40 i.u. PMSG and were killed 68-70 h later, shortly after the normally expected time of ovulation. Oocytes were recovered from the oviducts and inseminated in vitro. After 18 h oocytes were counted and classed as degenerate or 1-cell. Mean numbers of oocytes recovered were 8.2, 26.8, 50.7, 38.7 and 38.5 for each dose of PMSG respectively. The 1-cell oocytes were assessed for sperm penetration of the vitellus and pronuclear development and later for development to the 2-cell stage. Fertilization rates at the 1-cell stage were 76.8, 62.9, 53.6, 52.2 and 44.5% for the rats treated with 4, 8, 16, 24 and 40 i.u. respectively (P less than 0.001). On average, 91% of fertilized 1-cell oocytes developed to the 2-cell stage and there was no difference between treatments in this respect. Significantly more of the unfertilized oocytes were degenerate in the rats treated with 24 or 40 i.u. PMSG (34.6 and 50.4%) than in those treated with 4, 8 or 16 i.u. (7.0, 13.9, and 7.5%) (P less than 0.001). When rats were killed 63-65 h after PMSG, just before the normally expected time of ovulation, some of the rats treated with 24 and 40 i.u. PMSG had partly ovulated: of the oocytes recovered from the oviducts only 12.3% (24 i.u.) and 26.6% (40 i.u.) were fertilized. These results demonstrate that proportionately fewer oocytes recovered from superovulated rats are competent to undergo in-vitro fertilization than are oocytes recovered from control rats.
Growth of Single Crystal Silicon Nanowires in Supercritical Solution from Tethered Gold Particles on a Silicon Substrate (2002)

Molecularly tethered gold (Au) nanocrystals with average diameter of 7 nm were used to grow single-crystal silicon (Si) nanowires on a substrate through a supercritical fluid−liquid−solid (sc-FLS) mechanism. Si wires were obtained by degrading diphenylsilane (DPS) in cyclohexane heated and pressurized well above its critical point (Tc = 281 °C; Pc = 4.1 MPa) and the Si/Au eutectic temperature (363 °C). Under these conditions, silicon dissolves in the gold nanocrystals and subsequently crystallizes in the form of wires. The nanowire diameter reflects the gold nanocrystal diameter, ranging from 5 to 30 nm, with lengths of several micrometers. Both batch and flow reactors were used. The flow reactor minimized the undesirable deposition of Si particulates formed in the bulk solution. Scanning electron microscopy (SEM) images of Si nanowires grown at a series of temperatures, reactor residence times, and Si precursor concentrations reveal that the wire growth kinetics influence nanowire morphology significantly and can be controlled effectively using a supercritical fluid flow reactor. A kinetic analysis of the process explains the dependence of the nanowire morphology on the reaction conditions qualitatively.
Preferential expression of a plant cystatin at nematode feeding sites confers resistance to <i>Meloidogyne incognita</i> and <i>Globodera pallida</i> (2003)

The expression patterns of three promoters preferentially active in the roots of Arabidopsis thaliana have been investigated in transgenic potato plants in response to plant parasitic nematode infection. Promoter regions from the three genes, TUB-1, ARSK1 and RPL16A were linked to the GUS reporter gene and histochemical staining was used to localize expression in potato roots in response to infection with both the potato cyst nematode, Globodera pallida and the root-knot nematode, Meloidogyne incognita. All three promoters directed GUS expression chiefly in root tissue and were strongly up-regulated in the galls induced by feeding M. incognita. Less activity was associated with the syncytial feeding cells of the cyst nematode, although the ARSK1 promoter was highly active in the syncytia of G. pallida infecting soil grown plants. Transgenic potato lines that expressed the cystatin OcIDeltaD86 under the control of the three promoters were evaluated for resistance against Globodera sp. in a field trial and against M. incognita in containment. Resistance to Globodera of 70 +/- 4% was achieved with the best line using the ARSK1 promoter with no associated yield penalty. The highest level of partial resistance achieved against M. incognita was 67 +/- 9% using the TUB-1 promoter. In both cases this was comparable to the level of resistance achieved using the constitutive cauliflower mosaic virus 35S (CaMV35S) promoter. The results establish the potential for limiting transgene expression in crop plants whilst maintaining efficacy of the nematode defence.
Lymphocytes produce IL-1beta in response to Fcgamma receptor cross-linking: effects on parenchymal cell IL-8 release. (1998)

Neutrophils mediate tissue injury in response to immune complexes, although the factors that induce their recruitment are incompletely understood. We have reported that lymphocytes may be important regulators of monocyte and macrophage IL-8 release in the presence of immobilized IgG. Since tissue parenchymal cells are important local producers of IL-8 but are not directly stimulated by FcgammaR cross-linking, we hypothesized that lymphocytes may also regulate parenchymal IL-8 release. Supernatants from lymphocytes incubated on immobilized IgG induced primary human fibroblasts and human mesangial cells to produce IL-8 (17 +/- 3.5 and 44 +/- 8 ng/ml, respectively). Fibroblast and mesangial cell IL-8 mRNA levels were similarly increased by the conditioned lymphocyte supernatant. Immobilized anti-human FcgammaRIII, but not FcgammaRI or FcgammaRII Abs, could stimulate this IL-8-inducing activity in lymphocytes, suggesting that FcgammaRIII-bearing lymphocytes were responsible. Supernatants from lymphocytes incubated on immobilized IgG contained 2.2 +/- 0.8 ng/ml of IL-1beta, while enriched monocyte preparations from the same donors incubated on immobilized IgG released only 0.1 +/- 0.04 ng/ml of IL-1beta (p = 0.05). Consistent with the identification of IL-1beta as the lymphocyte factor, fibroblast or mesangial cell IL-8 release induced by the IgG-stimulated lymphocyte supernatants was inhibited by 1) the combination of IL-1R antagonist and soluble type II IL-1R, 2) an IL-1-converting enzyme inhibitor, or 3) anti-IL-1beta but not preimmune Abs. These data suggest that targeted deposits of IgG can stimulate FcgammaRIII-bearing lymphocytes to produce IL-1beta, which induces parenchymal cell IL-8 release.
Optimal clock synchronization in networks (2009)

Having access to an accurate time is a vital building block in all networks; in wireless sensor networks even more so, because wireless media access or data fusion may depend on it. Starting out with a novel analysis, we show that orthodox clock synchronization algorithms make fundamental mistakes. The state-of-the-art clock synchronization algorithm FTSP exhibits an error that grows exponentially with the size of the network, for instance. Since the involved parameters are small, the error only becomes visible in midsize networks of about 10--20 nodes. In contrast, we present PulseSync, a new clock synchronization algorithm that is asymptotically optimal. We evaluate PulseSync on a Mica2 testbed, and by simulation on larger networks. On a 20 node network, the prototype implementation of PulseSync outperforms FTSP by a factor of 5. Theory and simulation show that for larger networks, PulseSync offers an accuracy which is several orders of magnitude better than FTSP. To round off the presentation, we investigate several optimization issues, e.g. media access and local skew.
Content-boosted matrix factorization for recommender systems (2011)

The Netflix prize has rejuvenated a widespread interest in the matrix factorization approach for collaborative filtering. We describe a simple algorithm for incorporating content information directly into this approach. We present experimental evidence using recipe data to show that this not only improves recommendation accuracy but also provides useful insights about the contents themselves that are otherwise unavailable.
Size & Regional Distribution of Financial Behavior Patterns in Spain (2010)

The relationship between the financial behaviour of firms and some business risk factors have been
thoroughly researched during decades. Our paper tries to draw a dynamic two-dimensional map of
companies using a broad number of accounting ratios during a period of seven years based on regional and
size characteristics. The intention is to explain financial behaviour for a subsequent comparative
classification of businesses. For small and medium sized firms, accounting ratios are not just the only data
available, but the best suitable building blocks to our research. In order to reduce input dimensionality
without losing information, we use two methodologies: the Principal Components Analysis, and correlation
analysis. Finally, we also use the whole data set of variables with the intention to see if there are outstanding
differences in the final results. Subsequently, the companies are sorted out by size and geographical /
political areas or regions, using a neural net model called Self-Organizing Maps. We also use a cluster
model as a benchmark. The model allows us to visualize dynamically some traits by means of mapping n
variables in two dimensions: We can classify firms in groups, see which variables determine each group,
monitor the evolution of firms in terms of group selection, and determine the fittest group in terms of financial
ratios and the firms within it. Finally, we also see no outstanding differences between the Principal
Component Analysis (PCA) model and the whole data set, whereas the model without high correlation
variables shows a weaker stability. Although this analysis represents a step forward for the right valuation of
the Spanish small and mid-size firm network, its applicability covers not only more dimensions, but any other
country with clear-cut differentiated political regions. The data has been taken from the Spanish Register of
Business Names, being the raw material the annual accounting books and records, covering the years 1998-
2004, both included
Network intrusion detection: evasion, traffic normalization, and end-to-end protocol semantics (2001)

A fundamental problem for network intrusion detection systems is the ability of a skilled attacker to evade detection by exploiting ambiguities in the traffic stream as seen by the monitor. We discuss the viability of addressing this problem by introducing a new network forwarding element called a traffic normalizer. The normalizer sits directly in the path of traffic into a site and patches up the packet stream to eliminate potential ambiguities before the traffic is seen by the monitor, removing evasion opportunities. We examine a number of tradeoffs in designing a normalizer, emphasizing the important question of the degree to which normalizations undermine end-to-end protocol semantics. We discuss the key practical issues of “cold start ” and attacks on the normalizer, and develop a methodology for systematically examining the ambiguities present in a protocol based on walking the protocol’s header. We then present norm, a publicly available user-level implementation of a normalizer that can normalize a TCP traffic stream at 100,000 pkts/sec in memory-to-memory copies, suggesting that a kernel implementation using PC hardware could keep pace with a bidirectional 100 Mbps link with sufficient headroom to weather a high-speed flooding attack of small packets.
Charge transfer efficiency in hybrid bulk heterojunction composites (2004)

On the basis of recently published electrochemical measurements, the charge transfer efficiency within CdSe nanocrystal/conducting polymer heterojunction composites was investigated by means of luminescence interaction strength. It was found that poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene] and poly-9-vinylcarbazole luminescence was not totally quenched by nanocrystals, whereas poly-3-octylthiophene and polyvinylpyrrolidone was completely quenched. In case of poly-3-hexylthiophene, the nanocrystal luminescence was quenched. The results are in complete agreement with the electrochemical findings and thus, the CdSe nanocrystal/Polyvinylpyrrolidone composite should be a promising material for electroluminescent devices.
3D Motion and reconstruction of coronary networks (1992)

This paper describes an original method combining spatial and temporal features for the 3D reconstruction of coronary arteries from two X-ray views. Motion estimation is performed along the vessel centerlines in the two images by means of an optical flow based method. Centerline tracking and matching is carried out through epipolar constraints. This scheme allows to process automatically these two overall image sequences. Its effectiveness has been demonstrated on real data and the results are discussed in terms of expected benefits and potential limitations.
Blood Transfusion (1997)

Blood transfusion is an early consistent risk factor for postinjury MOF, independent of other indexes of shock.
Renal Prostacyclin Biosynthesis in a Baboon Model of Shiga Toxin Mediated Hemolytic Uremic Syndrome (2002)

Renal PGI(2) biosynthesis appears to be affected by the dose and rate of Stx administration, and the timing of LPS infusion. PGI(2) does not protect our primate model from developing HUS.