gebhart/patrepeval huggingface dataset:
Melanoma cell-cell interactions are mediated through heterophilic Mel-CAM/ligand adhesion. (1997)

Mel-cell adhesion molecule (CAM), also known as MUC18 and CD146, is a novel member of the immunoglobulin supergene family. Mel-CAM was first identified as an integral membrane glycoprotein in human melanoma and is also abundantly expressed by endothelial cells of various origins. In a previous study (I. M. Shih et al., Cancer Res., 54: 2514-2520, 1994), we showed that Mel-CAM is a cell-cell adhesion molecule with a possible role in melanoma invasion and metastasis. Here, we define the molecular mechanism responsible for cell-cell adhesion of Mel-CAM and demonstrate its role in melanoma-endothelial cell interactions. Most of human melanoma cells, including Mel-CAM-negative SBcl-2 cells, adhered to nitrocellulose-immobilized Mel-CAM produced by baculovirus recombinants. This adhesion can be blocked by full-length Mel-CAM or polyclonal antiserum against Mel-CAM. Adhesion is not affected by the presence of EDTA, truncated Mel-CAM extracellular domain, or heparan sulfate proteoglycan. In cell aggregation assays, Mel-CAM-negative SBcl-2 cells cluster with U937TM cells (U937 transfected with Mel-CAM cDNA) but not with control nontransfectants, suggesting that SBcl-2 cells express the ligand for Mel-CAM. SBcl-2 cells also form heterotypic aggregates with Mel-CAM-positive human endothelial cells but not with Mel-CAM-negative but ligand-positive smooth muscle cells. Taken together, our results show that Mel-CAM mediates cell-cell adhesion through heterophilic adhesion to an as yet unidentified ligand present on melanoma but not on endothelial cells. Thus, melanoma-endothelial interactions during metastasis may occur through this novel mechanism.
Maps of strength of positional signalling activity in the developing chick wing bud. (1985)

Tissue from the posterior margin of the developing limb bud, when grafted to the anterior margin, evokes the formation of a mirror-image limb duplication from the host tissue. We present maps of the spatial and temporal distribution of this signalling activity in the chick wing bud based on a bioassay that provides a quantitative measure of the completeness of the additional structures (the strength of activity index). Activity is first detected prior to the initial appearance of the limb primordium as early as Hamburger & Hamilton stage 14. It reaches a maximum during early outgrowth of the bud at stages 19 to 25. It then declines as the limb starts to differentiate into its final morphological pattern. The design of the experiment provides serendipitous data showing that two operators can consistently perform grafts with high reproducibility between them while variability between embryos is somewhat higher. The maps of activity are of particular practical value in precisely defining for the experimental embryologist and molecular biologist those positions and stages at which peak signalling activity resides.
Treatment of metastatic melanoma with an autologous tumor-cell vaccine: clinical and immunologic results in 64 patients. (1990)

We treated 64 patients with metastatic melanoma using a melanoma vaccine preceded by low-dose cyclophosphamide (CY), and monitored immunologic effects and antitumor activity. On day 0, the patients were given CY 300 mg/m2 intravenously. Three days later, they were injected intradermally with vaccine consisting of 10 to 25 x 10(6) autologous, enzymatically dissociated, cryopreserved, irradiated (25 Gy) tumor cells mixed with bacillus Calmette-Guérin (BCG). This treatment sequence was repeated every 28 days. Of 40 assessable patients with measurable metastases, five had responses, four complete and one partial, with a median duration of 10 months (7 to 84+ months). In six additional patients, we observed an antitumor response that seems to be peculiar to this vaccine therapy: the regression of metastatic lesions that appeared after the immunotherapy was begun. Delayed-type hypersensitivity (DTH) to autologous, mechanically dissociated melanoma cells that had not been exposed to extraneous antigens, such as enzymes or fetal calf serum, increased significantly following immunotherapy (day 0 v day 49, P less than .001; day 0 v day 161, P less than .001; day 0 v day 217, P = .021). Antitumor responses to the vaccine were strongly associated with DTH, as indicated by three observations: (1) eight of 10 patients who exhibited tumor regression had positive DTH, (2) in postsurgical adjuvant patients, there was a highly significant linear relationship (P less than .001) between the intensity of DTH to autologous melanoma cells and the time to recurrence of tumor, and (3) nine patients who developed DTH to the autologous melanoma cells in their original vaccine developed new metastases that failed to elicit DTH or elicited a much smaller response. In three cases, we were able to excise regressing tumors for histologic examination; such tumors were characterized by an intense infiltration of lymphocytes. This demonstration that an immune response to melanoma-associated antigens can be elicited in cancer-bearing patients provides some basis for optimism about the prospects for developing active immunotherapy that has practical therapeutic value.
Technologies for nanofluidic systems: top-down vs. bottom-up—a review (2005)

This paper gives an overview of the most commonly used techniques for nanostructuring and nanochannel fabrication employed in nanofluidics. They are divided into two large categories: top-down and bottom-up methods. Top-down methods are based on patterning on large scale while reducing the lateral dimensions to the nanoscale. Bottom-up methods arrange atoms and molecules in nanostructures. Here, we review the advantages and disadvantages of those methods and give some future perspectives. It is concluded that technology in the region of 1-10 nm is lacking and potentially can be covered by using the pulsed-laser deposition method as a controlled way for thin film deposition (thickness of a few nanometers) and further structuring by the top-down method.
Impact of Agricultural Practices on the Zea mays L. Endophytic Community (2004)

Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community. We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments. Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L. Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability. No endophytic amplification product was obtained for type II methanotrophs. Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate. In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants. The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group. Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community. It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.
Min-Max Hash for Jaccard Similarity (2013)

Min-wise hash is a widely-used hashing method for scalable similarity search in terms of Jaccard similarity, while in practice it is necessary to compute many such hash functions for certain precision, leading to expensive computational cost. In this paper, we introduce an effective method, i.e. the min-max hash method, which significantly reduces the hashing time by half, yet it has a provably slightly smaller variance in estimating pair wise Jaccard similarity. In addition, the estimator of min-max hash only contains pair wise equality checking, thus it is especially suitable for approximate nearest neighbor search. Since min-max hash is equally simple as min-wise hash, many extensions based on min-wise hash can be easily adapted to min-max hash, and we show how to combine it with b-bit minwise hash. Experiments show that with the same length of hash code, min-max hash reduces the hashing time to half as much as that of min-wise hash, while achieving smaller mean squared error (MSE) in estimating pair wise Jaccard similarity, and better best approximate ratio (BAR) in approximate nearest neighbor search.
Plant molecular biology : essential techniques (1997)

Partial table of contents: Isolation of Proteins and Nucleic Acids. Analysis of Gene Expression: Gene Structure. Analysis of Gene Expression: Transcription. Analysis of Gene Expression: Protein Analysis. DNA Manipulation. Transformation, Transfection and Regeneration. Appendix. Indexes.
Improved Distance M-ary (d,k) Codes for High Density Recording (1994)

We consider the problem of coding for a high density recording channel. New recording media have been developed that support unsaturated, M-ary (M/spl ges/3) signaling. This paper is concerned with the analysis and design of M-ary runlength limited (RLL) codes for multi-amplitude, linear recording AWGN channels. The codes achieve the largest known coding density and have improved minimum distance over an ordinary Adler-Coppersmith-Hassner code designed via the state splitting algorithm. Comparisons are made with Ungerboeck-style trellis codes with comparable complexity. >
Synergy of syntax and morphology in automatic parsing of French language with a minimum of data feasibility study of the method (1986)

We intend to present in this paper a parsing method of French language whose particularities are: a multi-level approach: syntax and morphology working simultaneously, the use of string pattern matching and the absence of dictionary. We want here to evaluate the feasibility of the method rather than to present an operational system.
Nucleotide Sequence of Plasmid pAQ1 of Marine Cyanobacterium Synechococcus sp. PCC7002 (1998)

We have determined the complete nucleotide sequence of pAQ1, the smallest plasmid of the unicellular marine cyanobacterium Synechococcus sp. PCC7002. The plasmid consists of 4,809 bp and has at least four open reading frames that potentially encode polypeptides of 50 or more amino acids. We found that a palindromic element, the core sequence of which is G(G/A)CGATCGCC, is over-represented not only in plasmid pAQ1 but also in the accumulated cyanobacterial genomic sequences from Synechococcus sp. PCC6301, PCC7002, PCC7942, vulcanus and Synechocystis sp. PCC6803 within GenBank and EMBL databases. It suggests that this sequence might mediate gene rearrangement, thus increasing genetic diversity, since recombination events are frequent in cyanobacteria.
Inactivation of poliovirus. (1981)

Inactivation of Polioviruses has been studied extensively in the 1950s and 1960's. It was shown that, to a certain extent, the kinetics of inactivation depend on the viral structure with which the inactivating agents react. Polio-RNA will loose its capacity for multiplication after one hit of an appropriate agent, thus being inactivated in a first order reaction. Multiple hits on the viral protein are needed to render the virus non-proliferate, which is characterized by a second order reaction. Examples for both types of reaction are given. While the "classical" inactivating chemicals are still in use for poliovaccines, other RNA viruses have successfully been treated with other agents and experimentally yet different substances have been described. Aiming for the highest possible antigenicity, the least harmful procedure seems essential. Since the inactivation procedure includes factors other than chemicals, such as temperature, time, pH etc., they too are part of the discussion evaluating the benefits and the shortcomings of the various technologies.
The National Cancer Institute Phase I Study of 2′,3′-Dideoxyinosine Administration in Adults with AIDS or AIDS-Related Complex: Analysis of Activity and Toxicity Profiles (1990)

2',3'-Dideoxyinosine (didanosine; ddI) was administered to 37 adults with AIDS or AIDS-related complex in an escalating-dose phase I study. Groups of three or four patients received intravenous dosages of 0.4 mg/(kg.d) to 25.6 mg/(kg.d) divided into two or three daily doses for 2 weeks, followed by oral ddI at twice the intravenous dosages. When given with antacids, ddI was well absorbed by the oral route and penetrated into the cerebrospinal fluid. The patients had an increase in mean number of CD4+ cells from 114/mm3 at entry to 161/mm3 at week 6 (P = .00004). They also had an increase in the CD4+/CD8+ ratio and in total number of lymphocytes. Sixteen of 18 evaluable patients had a decrease in levels of human immunodeficiency virus p24 antigen by week 6 (P = .0034). Many patients reported increased energy and appetite and gained weight. Dose-limiting toxicities at high dosages were painful peripheral neuropathy and sporadic pancreatitis. However, dosages up to 9.6 mg/(kg.d) have been tolerated in patients for 11-14 months. Thus, ddI has activity against human immunodeficiency virus at dosages that can be tolerated for approximately 1 year. However, life-threatening pancreatitis is a possible complication even at low dosages, and the best ways to manage and avoid adverse effects are still under study.
Energy Conservation in Acetogenic Bacteria (2003)

The anaerobic way of life comprises a great metabolic diversity and, correspondingly, diversity of energy-generating mechanisms ([52][1]). The facultative anaerobes have a respiratory system that uses preferentially oxygen, but in the absence of oxygen and presence of alternative electron acceptors
Arrested spread of vesicular stomatitis virus infections in vitro depends on interferon‐mediated antiviral activity (2005)

A quantitative understanding of the innate immune response will enable its recruitment against emerging, poorly characterized, or weaponized viral pathogens. To gain insights into how the innate responses can limit viral spread, we used quantitative focal infections to study how the spread of recombinant vesicular stomatitis viruses (VSV) on baby hamster kidney (BHK) and delayed brain tumor (DBT) cell monolayers is affected by innate cellular antiviral responses. We observed that rates of infection spread correlated with one-step growth rankings for four ectopic VSV strains: N1, N2, N3, and N4. However, this correlation was lost for M51R, a recombinant VSV mutant that lacks the ability to shut-off host gene expression. In BHK cells, M51R spread at two-thirds the rate of the recombinant control virus, XK3.1, even though their one-step growth was comparable. In DBT cells, M51R infections failed to spread beyond the site of inoculation. Addition of anti-interferon antibody restored M51R spread and one-step growth to wild-type levels. Interestingly, the antibody enhanced the spread of wild-type virus but not its growth. These results suggest that while the rate of viral spread generally correlates with the rate of viral growth, the induction of cellular antiviral activities can be in some cases, the overriding factor in both spread and growth. In summary, focal infections enabled us to visualize and quantify how viral spread was inhibited by cellular antiviral activities. This study demonstrates a mechanism for quantifying how innate cellular responses can mitigate infection spread in vitro.
Phase III Trial of Bevacizumab in Combination With Gemcitabine and Erlotinib in Patients With Metastatic Pancreatic Cancer (2009)

The primary objective was not met. The addition of bevacizumab to gemcitabine-erlotinib did not lead to a statistically significant improvement in OS in patients with metastatic pancreatic cancer. PFS, however, was significantly longer in the bevacizumab group compared with placebo. No unexpected safety events were observed from adding bevacizumab to gemcitabine-erlotinib.
Impedance of thin semiconductor films in low electric field (1983)

Impedance and admittance of a thin semiconductor film in the direction perpendicular to the film is calculated as a function of the sample length, doping, and temperature for voltages smaller than the thermal voltage. The calculation is based on the approximate solution of the Boltzmann equation in the relaxation time approximation. When the sample length is smaller than the mean free path, the conductance becomes independent of the sample length. In this limit the inductive susceptance is proportional to the sample length. When the sample length becomes comparable to the mean free path, the inductive susceptance reaches the maximum value, and then decreases. Our calculation shows that for high mobility GaAs samples at 77 K, the size effect may be important for films thinner than 5 μm. The results of the calculation are interpreted in the frame of a simple equivalent circuit which includes the bulk resistance, in series with the resistance due to the finiteness of the sample length, in series with the inductance L due to the inertia effect of the carrier transport, and all in parallel with the geometric capacitance C. The sample inductance L is approximately equal to (ω2pC)−1 where ωp is the plasma frequency. This simple model agrees fairly well with the results of the numerical calculation. The calculation, based on the model demonstrates that the predicted effects can be observed for realistic values of the contact resistance.
Oncogene Amplification During Tumorigenesis of Established Rat Fibroblasts Reversibly Transformed by Activated Human ras Oncogenes (1986)

Normal rat fibroblasts of the established cell line Rat 4 were cotransformed with activated human ras oncogenes and with a cloned chicken thymidine kinase (tk) gene. Linkage between tk and ras genes allowed the isolation of oncogene deletion revertants and of cell clones showing varying degrees of malignant phenotype. Southern and Northern experiments in concert with tumorigenicity assays show that the malignant transformation of these cells by mutant ras oncogenes is a gradual but reversible process that depends on the relative abundance of oncogene sequences and their corresponding transcripts. We also show that moderate amplification of a c-K-ras oncogene in these cells results in a clear increase in their tumorigenicity and that the mutant gene present in low copy numbers in cultured cells undergoes amplification in the corresponding in vivo induced tumors.
The Use of Collagen Membrane Barriers in Conjunction With Combined Demineralized Bone‐Collagen Gel Implants in Human Infrabony Defects (1990)

The present study evaluated the clinical efficacy of a combined graft of autolysed antigen-extracted allogeneic (AAA) bone and microfibrillar collagen (Zyderm) covered with a resorbable collagen membrane in human infrabony defects. The results were compared at 1 year with debrided controls, AAA bone grafts alone, combined AAA bone-collagen grafts (without membrane), and debrided defects covered only with collagen membranes. Ten adult patients having moderate periodontitis and one or more radiographically detectable angular defects probing 6 mm to 7 mm in each quadrant were included. Preoperative measurements of clinical attachment, probing depth, and recession were taken and compared at 1 year following surgery. Measurements at the time of surgery and at 1 year re-entry evaluated osseous defect fill and crestal changes. Each patient received the 5 treatment modalities. Treatment results per patient were used for a series of 2-way analyses of variance. When a significant difference was found, a Student-Newman-Keuls multiple range test was used to determine which treatments were statistically different (0.05 probability level) from each other. All treatment modalities showed improvement over the debrided controls. Similar advantages to using bone-collagen grafts with and without membranes were found in reducing probing depths and gaining new attachment. Significant differences were found when comparing the multifaceted bone graft collagen-membrane technique to all others in achieving superior defect fill. Ninety three percent of all defects treated resulted in 50% or greater fill.
Trajectory prediction of traffic agents at urban intersections through learned interactions (2017)

To navigate a complex urban environment, it is essential for autonomous vehicles to make educated assumptions and accurate predictions of the movement of other traffic agents. Beyond single object tracking, this task involves understanding behavior of other participants and predicting their trajectories. In this paper, we present a data-driven approach to learn the behavior of traffic agents at an intersection by observing several episodes of real-life scenarios captured through a static camera. We develop a feed-forward artificial neural network called the influence-network, which can simultaneously reason over the influence that agents and the environment have on each other. We compare it to an extension of popularly used Dynamic Bayesian Network. Based on data captured at a busy city intersection, we show that our model can predict trajectories of different classes of traffic agents with improved accuracy, and capture higher-level agent behavior.
The Transcription Factor MTF-1 Mediates Metal Regulation of the Mouse ZnT1 Gene (2000)

Metal regulation of the mouse zinc transporter (ZnT)-1 gene was examined in cultured cells and in the developing conceptus. Zinc or cadmium treatment of cell lines rapidly (3 h) and dramatically (about 12-fold) induced ZnT1 mRNA levels. In cells incubated in medium supplemented with Chelex-treated fetal bovine serum, to remove metal ions, levels of ZnT1 mRNA were reduced, and induction of this message in response to zinc or cadmium was accentuated (up to 31-fold induction). Changes in ZnT1 gene expression in these experiments paralleled those of metallothionein I (MT-I). Inhibition of RNA synthesis blocked metal induction of ZnT1 and MT-I mRNAs, whereas inhibition of protein synthesis did not. Metal response element-binding transcription factor (MTF)-1 mediates metal regulation of the metallothionein I gene. In vitro DNA-binding assays demonstrated that mouse MTF-1 can bind avidly to the two metal-response element sequences found in the ZnT1 promoter. Using mouse embryo fibroblasts with homozygous deletions of the MTF-1 gene, it was shown that this transcription factor is essential for basal as well as metal (zinc and cadmium) regulation of the ZnT1 gene in these cells. In vivo, ZnT1 mRNA was abundant in the midgestation visceral yolk sac and placenta. Dietary zinc deficiency during pregnancy down-regulated ZnT1 and MT-I mRNA levels (4-5-fold and >20-fold, respectively) in the visceral yolk sac, but had little effect on these mRNAs in the placenta. Homozygous knockout of the MTF-1 gene in transgenic mice also led to a 4-6-fold reduction in ZnT1 mRNA levels and a loss of MT-I mRNA in the visceral yolk sac. These results suggest that MTF-1 mediates the response to metal ions of both the ZnT1 and the MT-I genes the visceral yolk sac. Overall, these studies suggest that MTF-1 directly coordinates the regulation of genes involved in zinc homeostasis and protection against metal toxicity.