gebhart/patrepeval huggingface dataset:
Peripheral blood T lymphocyte changes in multiple sclerosis: a marker of disease progression rather than of relapse? (1986)

A serial study of peripheral blood T lymphocytes in 27 patients with clinically definite multiple sclerosis and 11 healthy controls was carried out over a 12 month period. This showed that contrary to many previous reports, relapses were not consistently associated with reduced numbers of peripheral blood suppressor T lymphocytes or any other T cells. Persistently low T cells numbers, including both the helper and suppressor T cell subsets, were, however, associated with disease activity as measured by the development of increased disability during the course of the study. This was true both for the patients with relapsing/remitting disease and those with progressive disease. The importance of carrying out a serial study was emphasised by the consistent and significant differences that were detected between individuals in both the control and the patient groups. A serial study is the most reliable means by which clinical events can clearly be correlated with laboratory estimations. The association in this study between the development of increased disability and persistently low levels of peripheral blood T lymphocytes suggest that both may be related to the underlying disease process in multiple sclerosis.
A brief survey of program slicing (2005)

Program slicing is a technique to extract program parts with respect to some special computation. Since Weiser first proposed the notion of slicing in 1979, hundreds of papers have been presented in this area. Tens of variants of slicing have been studied, as well as algorithms to compute them. Different notions of slicing have different properties and different applications. These notions vary from Weiser's syntax-preserving static slicing to amorphous slicing which is not syntax-preserving, and the algorithms can be based on dataflow equations, information-flow relations or dependence graphs.Slicing was first-developed to facilitate debugging, but it is then found helpful in many aspects of the software development life cycle, including program debugging, software testing, software measurement, program comprehension, software maintenance, program parallelization and so on.Over the last two decades, several surveys on program slicing have been presented. However, most of them only reviewed parts of researches on program slicing or have now been out of date. People who are interested in program slicing need more information about the up to date researches. Our survey fills this gap. In this paper, we briefly review most of existing slicing techniques including static slicing, dynamic slicing and the latest slicing techniques. We also discuss the contribution of each work and compare the major difference between them. Researches on slicing are classified by the research hot spots such that people can be kept informed of the overall program slicing researches.
Identification of biomarkers in ductal carcinoma in situ of the breast with microinvasion (2008)

Compared with DCIS, DCIS-Mi is characterized by a slightly elevated cell proliferation capacity and enhanced apoptosis within the intraductal lesion, both of which are thought to promote the formation of cell necrotic foci. Furthermore, the differential expression of survivin may serve in deciding the response to therapy and may have some prognostic significance.
Time reversal of ultrasonic fields. Il. Experimental results (1992)

For pt.I see ibid., vol.39, no.5, p.555-66 (1992). A time-reversal mirror (TRM) is made of an array of transmit-receive transducers. The incident pressure field is sampled, digitized, stored, time-reversed and then re-emitted. This process can be used to focus, through inhomogeneous media, on a reflective target that may behave as an acoustic source after being insonified TRM experiments using a 64-channel prototype are described, and the results are given. Focusing experiments conducted on point targets through different aberrating media are described. The major result shows that the time-reversal focusing technique compensates for all the distortions whatever the TRM-aberrator distance. When the medium contains several targets, the authors show that the time-reversal process can be iterated in order to focus on the most reflective one. Lithotripsy applications are also discussed. Kidney stones are spatially extended targets and TRM experiments have been conducted on several kidney stones located behind inhomogeneous media. They show that the iterative TRM process is able to select one of the kidney stones and to focus on a small portion of it.
Results from an Integrated Safety Analysis of Urelumab, an Agonist Anti-CD137 Monoclonal Antibody (2016)

<b>Purpose:</b> Urelumab is an agonist antibody to CD137 with potential application as an immuno-oncology therapeutic. Data were analyzed to assess safety, tolerability, and pharmacodynamic activity of urelumab, including the dose selected for ongoing development in patients with advanced solid tumors and lymphoma.<b>Experimental Design:</b> A total of 346 patients with advanced cancers who had progressed after standard treatment received at least one dose of urelumab in one of three dose-escalation, monotherapy studies. Urelumab was administered at doses ranging from 0.1 to 15 mg/kg. Safety analyses included treatment-related and serious adverse events (AEs), as well as treatment-related AEs leading to discontinuation and death, with a focus on liver function test abnormalities and hepatic AEs.<b>Results:</b> Urelumab doses between 1 and 15 mg/kg given every 3 weeks resulted in a higher frequency of treatment-related AEs than 0.1 or 0.3 mg/kg every 3 weeks. Dose was the single most important factor contributing to transaminitis development, which was more frequent and severe at doses ≥1 mg/kg. At the MTD of 0.1 mg/kg every 3 weeks, urelumab was relatively well tolerated, with fatigue (16%) and nausea (13%) being the most common treatment-related AEs, and was associated with immunologic and pharmacodynamic activity demonstrated by the induction of IFN-inducible genes and cytokines.<b>Conclusions:</b> Integrated evaluation of urelumab safety data showed significant transaminitis was strongly associated with doses of ≥1 mg/kg. However, urelumab 0.1 mg/kg every 3 weeks was demonstrated to be safe, with pharmacodynamic activity supporting continued clinical evaluation of this dose as monotherapy and in combination with other immuno-oncology agents. <i>Clin Cancer Res; 23(8); 1929-36. ©2016 AACR</i>.
Comprehensive analysis of CpG islands in human chromosomes 21 and 22 (2002)

CpG islands are useful markers for genes in organisms containing 5-methylcytosine in their genomes. In addition, CpG islands located in the promoter regions of genes can play important roles in gene silencing during processes such as X-chromosome inactivation, imprinting, and silencing of intragenomic parasites. The generally accepted definition of what constitutes a CpG island was proposed in 1987 by Gardiner-Garden and Frommer [Gardiner-Garden, M. & Frommer, M. (1987) J. Mol. Biol. 196, 261-282] as being a 200-bp stretch of DNA with a C+G content of 50% and an observed CpG/expected CpG in excess of 0.6. Any definition of a CpG island is somewhat arbitrary, and this one, which was derived before the sequencing of mammalian genomes, will include many sequences that are not necessarily associated with controlling regions of genes but rather are associated with intragenomic parasites. We have therefore used the complete genomic sequences of human chromosomes 21 and 22 to examine the properties of CpG islands in different sequence classes by using a search algorithm that we have developed. Regions of DNA of greater than 500 bp with a G+C equal to or greater than 55% and observed CpG/expected CpG of 0.65 were more likely to be associated with the 5' regions of genes and this definition excluded most Alu-repetitive elements. We also used genome sequences to show strong CpG suppression in the human genome and slight suppression in Drosophila melanogaster and Saccharomyces cerevisiae. This finding is compatible with the recent detection of 5-methylcytosine in Drosophila, and might suggest that S. cerevisiae has, or once had, CpG methylation.
Clustering of DNA Sequences in Human Promoters (2004)

We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.
Unified View of Data (1976)

A data model, called the entity-relationship model, is proposed. This model incorporates some of the important semantic information about the real world. A special diagrammatic technique is introduced as a tool for database design. An example of database design and description using the model and the diagrammatic technique is given. Some implications for data integrity, information retrieval, and data manipulation are discussed. The entity-relationship model can be used as a basis for unification of different views of data: t,he network model, the relational model, and the entity set model. Semantic ambiguities in these models are analyzed. Possible ways to derive their views of data from the entity-relationship model are presented.
Four unique monoclonal antibodies to the putative receptor binding domain of erythropoietin inhibit the biological function of the hormone. (1992)

We have produced a series of monoclonal antibodies (MoAbs) to amino acid region 99-129 of human erythropoietin (Epo) that distinguish unique structural features within this putative receptor binding domain of the hormone. The MoAbs recognize denatured Epo with widely different sensitivities on a Western blot and differentially bind to native Epo in solution. In addition, three of the four MoAbs neutralize the biological activity of Epo in a concentration-dependent fashion in vitro. Neutralization was measured both by inhibition of Epo-induced differentiation in Rauscher murine erythroleukemia cells and by inhibition of Epo-induced proliferation in normal murine splenic erythroid precursors. Characterization of the structural epitopes recognized by each of these four reagent MoAbs should provide us with important information concerning the requirements for hormone-receptor interaction.
Studies on antihypertensive and antispasmodic activities of methanol extract of Acacia nilotica pods (1999)

A methanol extract of Acacia nilotica pods (AN) caused a dose-dependent (3-30 mg/kg) fall in arterial blood pressure. Treatment of animals with atropine abolished the vasodilator response of acetylcholine (ACh), whereas the antihypertensive effect of the plant extract remained unaltered. Phentolamine (an alpha-adrenergic blocker) abolished the vasoconstrictor effect of norepinephrine (NE), whereas pretreatment of the animal with AN, did not modify the NE response. These results indicate that the antihypertensive effect of plant extract is independent of muscarinic receptor stimulation or adrenoceptor blockade. In the in vitro studies, AN produced a dose-dependent (0.3-3.0 mg/mL) inhibitory effect on force and rate of spontaneous contractions in guinea-pig paired atria. Similarly, it inhibited the spontaneous contraction of rabbit jejunum in a concentration-dependent (0.1-3.0 mg/mL) manner. AN also inhibited K(+)-induced contractions in rabbit jejunum at a similar concentration range, which suggests that the antispasmodic action of AN is mediated through calcium channel blockade, and this may also be responsible for the blood pressure lowering effect of AN, observed in the in vivo studies.
The intraflagellar transport protein, IFT88, is essential for vertebrate photoreceptor assembly and maintenance (2002)

Approximately 10% of the photoreceptor outer segment (OS) is turned over each day, requiring large amounts of lipid and protein to be moved from the inner segment to the OS. Defects in intraphotoreceptor transport can lead to retinal degeneration and blindness. The transport mechanisms are unknown, but because the OS is a modified cilium, intraflagellar transport (IFT) is a candidate mechanism. IFT involves movement of large protein complexes along ciliary microtubules and is required for assembly and maintenance of cilia. We show that IFT particle proteins are localized to photoreceptor connecting cilia. We further find that mice with a mutation in the IFT particle protein gene, Tg737/IFT88, have abnormal OS development and retinal degeneration. Thus, IFT is important for assembly and maintenance of the vertebrate OS.
Parallel task execution in LANs and performance analysis (2002)

This paper analyzes the performance of local area networks (LANs) of workstations for distributed computing. Application programs are scheduled by the user workstation (master) for parallel execution in the idle or lightly loaded processors (slaves). Partial results are collected by the master station to synchronize the operation of slave nodes. A general speedup equation is derived to verify the measurement values. The sequential and parallel execution times and the performance degradation factors (scheduling, communication, TCP/IP communication overhead, and synchronization times) were measured for various network loads and sizes. Experimental and theoretical results show that the system performance is degraded mainly by the TCP/IP overhead (0.2 s), the network size, and the network load.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biofilm Forming Lactobacillus: New Challenges for the Development of Probiotics (2016)

Probiotics are live bacteria, generally administered in food, conferring beneficial effects to the host because they help to prevent or treat diseases, the majority of which are gastrointestinal. Numerous investigations have verified the beneficial effect of probiotic strains in biofilm form, including increased resistance to temperature, gastric pH and mechanical forces to that of their planktonic counterparts. In addition, the development of new encapsulation technologies, which have exploited the properties of biofilms in the creation of double coated capsules, has given origin to fourth generation probiotics. Up to now, reviews have focused on the detrimental effects of biofilms associated with pathogenic bacteria. Therefore, this work aims to amalgamate information describing the biofilms of Lactobacillus strains which are used as probiotics, particularly L. rhamnosus, L. plantarum, L. reuteri, and L. fermentum. Additionally, we have reviewed the development of probiotics using technology inspired by biofilms.
RalA Function in Dermal Fibroblasts Is Required for the Progression of Squamous Cell Carcinoma of the Skin (2010)

A large body of evidence has shown that stromal cells play a significant role in determining the fate of neighboring tumor cells through the secretion of various cytokines. How cytokine secretion by stromal cells is regulated in this context is poorly understood. In this study, we used a bioengineered human tissue model of skin squamous cell carcinoma progression to reveal that RalA function in dermal fibroblasts is required for tumor progression of neighboring neoplastic keratinocytes. This conclusion is based on the observations that suppression of RalA expression in dermal fibroblasts blocked tumorigenic keratinocytes from invading into the dermal compartment of engineered tissues and suppressed more advanced tumor progression after these tissues were transplanted onto the dorsum of mice. RalA executes this tumor-promoting function of dermal fibroblasts, at least in part, by mediating hepatocyte growth factor (HGF) secretion through its effector proteins, the Sec5 and Exo84 subunits of the exocyst complex. These findings reveal a new level of HGF regulation and highlight the RalA signaling cascade in dermal fibroblasts as a potential anticancer target.
Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence (1998)

The complete genome sequence of an organism contains information that has not been fully utilized in the current prediction methods of gene functions, which are based on piece-by-piece similarity searches of individual genes. We present here a method that utilizes a higher level information of molecular pathways to reconstruct a complete functional unit from a set of genes. Specifically, a genome-by-genome comparison is first made for identifying enzyme genes and assigning EC numbers, which is followed by the reconstruction of selected portions of the metabolic pathways by use of the reference biochemical knowledge. The completeness of the reconstructed pathway is an indicator of the correctness of the initial gene function assignment. This feature has become possible because of our efforts to computerize the current knowledge of metabolic pathways under the KEGG project. We found that the biosynthesis pathways of all 20 amino acids were completely reconstructed in Escherichia coli, Haemophilus influenzae, and Bacillus subtilis, and probably in Synechocystis and Saccharomyces cerevisiae as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases.
Chemoradiotherapy: Emerging treatment improvement strategies (2002)

Concurrent chemoradiotherapy, using standard chemotherapeutic agents, has emerged as an effective treatment for advanced cancer, but unfortunately at the expense of considerable increase in normal tissue toxicity. There are a number of potential emerging treatment strategies to further improve chemoradiotherapy. One consists of using newer chemotherapeutic drugs, which in preclinical studies are potent enhancers of tumor radioresponse. Another approach consists of targeting EGFR or COX-2 with selective inhibitors of these molecules.
The Early Holocene occupation of north-central Anatolia between 10,000 and 6,000 BC cal: investigating an archaeologicalterra incognita (2008)

Abstract This paper investigates why we lack convincing evidence for human activities in north-central Anatolia for the period between 10,000 and 6,000 BC cal. This paucity of data can be contrasted with substantial evidence for Neolithic communities in south-central Anatolia from about 8,500 BC cal, and of earlier hunter-gatherer communities in that region. This difference in our data is especially problematic because in terms of ecology both regions appear to be broadly similar. In this paper this enigmatic paucity of evidence for the Early Holocene occupation of north-central Anatolia will be scrutinised. In particular, this entails a discussion of the existing discourse on the paucity of evidence and an evaluation of the three types of argument that have been put forward to explain it: first, that the region was not occupied because of unfavourable ecological conditions; second, that the practices of Early Holocene groups in north-central Anatolia have left an insubstantial archaeological record; and, third, that the paucity of evidence is best explained by a combination of the factors of site preservation, site visibility and research intensity. Finally, a research strategy will be proposed for the future investigation of the Early Holocene occupation of north-central Anatolia.
Rapid 3-D screening with seismic terrain: deepwater Gulf of Mexico examples (2001)

What is a seismic terrain? A spectacular aerial view of surface outcrop terrain (Figure 1) shows the plunge of an anticline rimmed with flatirons. The field geologist can ascertain, at a glance, the dip and frequency of bedding and can gain an immediate sense of underlying structure. This experience is very similar to that gained by viewing a 3-D seismic terrain generated from time-slice instantaneous phase (Figure 2). Creating a seismic terrain map or 3-D visualization is a simple technique done with little or no interpretation other than extracting phase data and transforming them into two-way time. This technique allows geologists and geophysicists to routinely view the seismic volume in a realistic terrainlike display. This shortens the evaluation time for large 3-D surveys by quickly drawing attention to structurally prospective areas.
Efficient Synthesis of Doxorubicin Melanotransferrin p97 Conjugates Through SMCC Linker (2004)

Abstract Doxorubicin–succinimidyl 4‐[N‐maleimidomethyl]cyclohexane‐1‐carboxylate (SMCC) 3, prepared by treating doxorubicin (1) with SMCC 2, is treated with 2‐mercaptoacetic acid to give doxorubicin–SMCC–sulfo‐acetic acid 5. Treating with benzotriazol‐1‐yl‐N,N,N′,N‐tetramethyluronium tetrafluoroborate (BTTU), the carboxy group of 5 is activated, and reacts efficiently with the amino group of melanotransferrin p97 to afford the expected doxorubicin‐p97 conjugate 6, which is a potential agent capable to cross the blood–brain barrier (BBB) to treat brain tumors. Keywords: DoxorubicinBlood–brain barrierMelanotransferrinVector‐mediated approachSMCC linkerBioconjugate Acknowledgments We are grateful to Albany Molecular Research Inc for the preparation of some of the starting materials, Ms. Grace Laliberte, Dr. Pascale Tiger, Dr. Malcolm Kennard, Dr. Gavin Arthur for help discussions and part of analytic work.
Fine-Grain Adaptive Compression in Dynamically Variable Networks (2005)

Despite voluminous previous research on adaptive compression, we found significant challenges when attempting to fully utilize both network bandwidth and CPU. We describe the fine-grain (FG) mixing strategy that compresses and sends as much data as possible, and then uses any remaining bandwidth to send uncompressed packets. Experimental measurements show that FG mixing achieves significant gains in effective throughput, particularly at higher network bandwidths. However, non-trivial interactions between system components and layers (e.g., compression algorithms and middleware settings such as block size and buffer size) have significant impact on the overall system performance. Finally, the trade-offs and performance profiles of FG mixing are measured, observed, and found to be consistent over a wide range of combinations of compression algorithms (GZIP, LZO, BZ1P2), workload compression ratios (from 1 to 4), and network bandwidth (from 0 to 400 Mbps)