gebhart/patrepeval huggingface dataset:
Elevated Expression of the Oncogene c-fms and Its Ligand, the Macrophage Colony-Stimulating Factor-1, in Cervical Cancer and the Role of Transforming Growth Factor-β1 in Inducing c-fms Expression (2007)

Cervical cancer is the third most common gynecologic cancer in the United States. The presence and possible involvement of several cytokines have been studied in cervical cancer; however, very little data, if any, are available on whether cervical tumors are responsive to stimulation by the macrophage colony-stimulating factor-1 (CSF-1). Given the involvement of c-fms and its ligand CSF-1 in gynecologic cancers, such as that of the uterus and the ovaries, we have examined the expression of c-fms and CSF-1 in cervical tumor (n = 17) and normal cervix (n = 8) samples. The data show that c-fms and its ligand are significantly higher in cervical carcinomas compared with normal samples. Immunohistochemistry not only showed that tumor cells expressed significantly higher levels of c-fms but also c-fms levels were markedly higher in tumor cells than tumor-associated stromal cells. Blocking c-fms activity in cervical cancer cells, which express CSF-1 and c-fms, resulted in increased apoptosis and decreased motility compared with control, suggesting that CSF-1/c-fms signaling may be involved in enhanced survival and possibly invasion by cervical cancer cells via an autocrine mechanism. Combined, the data show for the first time the induction of CSF-1 and c-fms in cervical carcinomas and suggest that c-fms activation may play a role in cervical carcinogenesis. Additionally, our data suggest that transforming growth factor-beta1 may be a factor in inducing the expression of c-fms in cervical cancer cells. The data suggest that c-fms may be a valuable therapeutic target in cervical cancer.
Tumor type M2pyruvate kinase expression in gastric cancer, colorectal cancer and controls (2004)

Tumor M(2)-PK has a higher sensitivity than markers CEA and CA72-4, and is a valuable tumor marker for the detection of gastrointestinal cancer.
Towards energy proportionality for large-scale latency-critical workloads (2014)

Reducing the energy footprint of warehouse-scale computer (WSC) systems is key to their affordability, yet difficult to achieve in practice. The lack of energy proportionality of typical WSC hardware and the fact that important workloads (such as search) require all servers to remain up regardless of traffic intensity renders existing power management techniques ineffective at reducing WSC energy use. We present PEGASUS, a feedback-based controller that significantly improves the energy proportionality of WSC systems, as demonstrated by a real implementation in a Google search cluster. PEGASUS uses request latency statistics to dynamically adjust server power management limits in a fine-grain manner, running each server just fast enough to meet global service-level latency objectives. In large cluster experiments, PEGASUS reduces power consumption by up to 20%. We also estimate that a distributed version of PEGASUS can nearly double these savings
Infrared imaging of subcutaneous veins (2004)

Imaging in the near-IR range (880-930 nm) provides relatively good contrast of subcutaneous veins, underscoring its value for diagnosis. This technique has the potential for the diagnosis of varicose veins with a diameter of 0.5-2 mm at a depth of 1-3 mm, guidance of venous access, podiatry, phlebotomy, injection sclerotherapy, and control of laser interstitial therapy.
If A1 is the Answer, What was the Question? An Edgy Na&#239;f's Retrospective on Promulgating the Trusted Computer Systems Evaluation Criteria (2005)

This paper provides an introspective retrospective on the history and development of the United States Department of Defense Trusted Computer System Evaluation Criteria (TCSEC). Known to many as the Orange Book, the TCSEC contained a distillation of what many researchers considered to be the soundest proven principles and practices for achieving graded degrees of sensitive information protection on multiuser computing systems. While its seven stated evaluation classes were explicitly directed to standalone computer systems, many of its authors contended that its principles would stand as adequate guidance for the design, implementation, assurance, evaluation and certification of other classes of computing applications including database management systems and networks. The account is a personal reminiscence of the author, and concludes with a subjective assessment of the TCSEC's validity in the face of its successor evaluation criteria.
An historical overview of the use of silver in wound management (2001)

While silver and its compounds have been medically used for thousands of years, the recent research focus on this element has led to a resurgence in interest, particularly in the field of wound care product development. The increasing problems of antibiotic resistance, combined with concerns over the safety and toxicity of topical antiseptics, has highlighted the need for a safe agent which can be used to treat colonized and infected wounds effectively. Wounds, notably chronic wounds, can support a wide variety of microorganisms, many of which are pathogens, and act as a source for cross-infection. While systemic antibiotics are justifiably recognized as the first-line treatment of choice for chronic wounds with spreading cellulitis and infected wounds in ‘at risk’ patients, not all infected wounds merit this treatment. There is now a rationale for the judicious use of suitable topical antisepsis in certain colonized, critically colonized, and infected wounds. The increasing evidence available on products containing silver suggests that this element can fulfil a valuable role in wound care. This review of the history of silver as an antibacterial covers the mode of action of preparations containing silver and concludes with a focus on silver as a component of the modern wound management products: Arglaes, Acticoat, Actisorb Silver 220 and Avance.
Structure of the N-linked oligosaccharides that show the complete loss of alpha-1,6-polymannose outer chain from och1, och1 mnn1, and och1 mnn1 alg3 mutants of Saccharomyces cerevisiae. (1993)

The periplasmic invertase was purified from Saccharomyces cerevisiae och1::LEU2 disruptant cells (delta och1), which have a defect in elongation of the outer chain attached to the N-linked core oligosaccharides (Nakayama, K., Nagasu, T., Shimma, Y., Kuromatsu, J., and Jigami, Y. (1992) EMBO J. 11, 2511-2519). Structural analysis of the pyridylaminated (PA) neutral oligosaccharides released by hydrazinolysis and N-acetylation confirmed that the och1 mutation causes a complete loss of the alpha-1,6-polymannose outer chain, although the PA oligosaccharides (Man9GlcNAc2-PA and Man10GlcNAc2-PA), in which one or two alpha-1,3-linked mannose(s) attached to the endoplasmic reticulumn (ER)-form core oligosaccharide (Man8GlcNAc2) were also detected. Analysis of the delta och1 mnn1 strain oligosaccharides released from total cell mannoprotein revealed that the delta och1 mnn1 mutant eliminates the alpha-1,3-mannose attached to the core and accumulates predominantly a single ER-form oligosaccharide species (Man8GlcNAc2), suggesting a potential use of this strain as a host cell to produce glycoproteins containing mammalian high mannose type oligosaccharides. The delta och1 mnn1 alg3 mutants accumulated Man5GlcNAc2 and Man8GlcNAc2 in total cell mannoprotein, confirming the lack of outer chain addition to the incomplete corelike oligosaccharide and the leaky phenotype of the alg3 mutation. All the results suggest that the OCH1 gene encodes an alpha-1,6-mannosyltransferase that is functional in the initiation of alpha-1,6-polymannose outer chain addition to the N-linked core oligosaccharide (Man5GlcNAc2 and Man8GlcNAc2) in yeast.
Differential Requirements for Survival and Proliferation of CD8 Naïve or Memory T Cells (1997)

The requisite molecular interactions for CD8 T cell memory were determined by comparison of monoclonal naïve and memory CD8(+) T cells bearing the T cell receptor (TCR) for the HY antigen. Naïve T cells required only the right major histocompatibility complex (MHC) class I-restricting molecule to survive; to expand, they also needed antigen. In contrast, for survival, memory cells did not require the restricting MHC allele, but needed only a nonspecific class I; for expansion the correct class I, but not antigen, was required. Thus, maintenance of CD8 T cell memory still required TCR-MHC class I interactions, but memory T cells may have a lower functional activation threshold that facilitates secondary responses.
Synthetic routes to β, β‐diaryl‐α‐amino acids via nitrogen hetercycles (1964)

Abstract β, β‐Diphenylalanine and its ring‐substituted analogs are prepared from oxazolones, thiazolones, imidazolones, hydantoins, thiohydantoins, and piperazine 2,5‐diones by alkaline ring opening followed by acid cleavage of the N‐benzoyl group. The oxazolone approach, with its variations, offers the most advantageous route to these compounds. Several new amino acids are described.
Extended transient transfection by repeated delivery of in vitro-transcribed RNA (2008)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.
Without prior stimulation, tumor-associated lymphocytes from malignant effusions lyse autologous tumor cells in the presence of bispecific antibody HEA125xOKT3. (1999)

Women suffering from advanced stage ovarian or mammary carcinoma frequently develop malignant ascites or pleural effusions consisting of tumor cells and tumor-associated lymphocytes (TALs). Locoregional immunotherapy with bispecific antibodies (bsAbs), which retarget T cells to tumor cells and induce their lysis, has been applied as an adjuvant treatment in the late stage of the disease. Until now, most of these therapies use peripheral blood mononuclear cells (PBMCs) as effector cells that have been stimulated and expanded ex vivo and loaded with bsAb before reinjection. Here we investigated whether TALs derived from malignant ascites or pleural effusions can be used as bsAb-guided effector cells without prior in vitro stimulation. For this we established a bsAb, HEA125xOKT3, which recognizes the epithelial antigen Egp34 on carcinoma cells and the CD3 molecule on T cells. BsAb HEA125xOKT3 induced lysis of various Egp34-expressing carcinoma lines by stimulated PBMCs. Optimal cytotoxicity was achieved at a bsAb concentration of 1 microg/ml. In three ovarian and two mammary carcinoma patients, we demonstrated efficient lytic activity of lymphocytes, isolated from malignant ascites or pleural effusion. Without prior stimulation, they lysed autologous tumor cells in the presence of bsAb HEA125xOKT3, indicating that they are already activated. Along this line, a subset of CD4+ and CD8+ unstimulated TALs expressed the early activation marker CD69. They are, however, negative for CD95, and only a small subpopulation of CD4+ TALs expresses CD25. OKT3/interleukin 2 stimulation of TALs increased the expression of activation markers on the CD4+ and CD8+ T-cell compartment. The activation markers CD69, CD25, CD95, and DR molecules are up-regulated on both T-cell types. However, lysis of autologous tumor cells by stimulated TALs is not significantly enhanced compared with unstimulated TALs. Our results may offer a novel and promising concept of adjuvant immunotherapy for ovarian and mammary carcinoma patients. Preactivation and expansion of PBMCs can be circumvented by exploring the cytotoxic capacity of unstimulated TALs in the presence of bsAbs in a locoregional therapeutic approach.
Saccharomyces cerevisiaecontains two discrete genes coding for the α-factor pheromone (1983)

Two genes, MF alpha 1 and MF alpha 2, coding for the alpha-factor in yeast Saccharomyces cerevisiae were identified by in situ colony hybridization of synthetic probes to a yeast genomic library. The probes were designed on the basis of the known amino acid sequence of the tridecapeptide alpha-pheromone. The nucleotide sequence revealed that the two genes, though similar in their overall structure, differ from each other in several striking ways. MF alpha 1 gene contains 4 copies of the coding sequence for the alpha-factor, which are separated by 24 nucleotides encoding the octapeptide Lys-Arg-Glu-Ala-Glu(or Asp)-Ala-Glu-Ala. The first alpha-factor coding block is preceded by a sequence for the hexapeptide Lys-Arg-Glu-Ala and 83 additional amino acids. MF alpha 2 gene contains coding sequences for two copies of the alpha-factor that differ from each other and from alpha-factor encoded by MF alpha 1 gene by a Gln leads to Asn and a Lys leads to Arg substitution. The first copy of the alpha-factor is preceded by a sequence coding for 87 amino acids which ends with Lys-Arg-Glu-Ala-Val-Ala-Asp-Ala. The coding blocks of the two copies of the pheromone are separated by the sequence for Lys-Arg-Glu-Ala-Asn-Ala-Asp-Ala. Thus, the alpha-factor can be derived from 2 different precursor proteins of 165 and 120 amino acids containing, respectively, 4 and 2 copies of the pheromone.
Purification and ex vivo expansion of postnatal human marrow mesodermal progenitor cells (2001)

It is here reported that mesenchymal stem cells known to give rise to limb-bud mesoderm can, at the single-cell level, also differentiate into cells of visceral mesoderm and can be expanded extensively by means of clinically applicable methods. These cells were named mesodermal progenitor cells (MPCs). MPCs were selected by depleting bone marrow mononuclear cells from more than 30 healthy human donors of CD45(+)/glycophorin-A (GlyA)(+) cells. Cells were cultured on fibronectin with epidermal growth factor and platelet-derived growth factor BB and 2% or less fetal calf serum. It was found that 1/5 x 10(3) CD45(-)GlyA(-) cells, or 1/10(6) bone marrow mononuclear cells, gave rise to clusters of small adherent cells. Cell-doubling time was 48 to 72 hours, and cells have been expanded in culture for more than 60 cell doublings. MPCs are CD34(-), CD44(low), CD45(-), CD117 (cKit)(-), class I-HLA(-), and HLA-DR(-). MPCs differentiated into cells of limb-bud mesoderm (osteoblasts, chondrocytes, adipocytes, stroma cells, and skeletal myoblasts) as well as visceral mesoderm (endothelial cells). Retroviral marking was used to definitively prove that single MPCs can differentiate into cells of limb bud and visceral mesoderm. Thus, MPCs that proliferate without obvious senescence under clinically applicable conditions and differentiate at the single-cell level not only into mesenchymal cells but also cells of visceral mesoderm may be an ideal source of stem cells for treatment of genetic or degenerative disorders affecting cells of mesodermal origin.
Polysialylation: from bacteria to brains (1992)

Journal Article Polysialylation: from bacteria to brains Get access Frederic A. Troy Frederic A. Troy Department of Biological Chemistry, University of California School of MedicineDavis, CA 95616-8365, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Glycobiology, Volume 2, Issue 1, February 1992, Pages 5–23, https://doi.org/10.1093/glycob/2.1.5 Published: 01 February 1992 Article history Received: 29 October 1991 Accepted: 05 November 1991 Published: 01 February 1992
Budget-Aware Deep Semantic Video Segmentation (2017)

In this work, we study a poorly understood trade-off between accuracy and runtime costs for deep semantic video segmentation. While recent work has demonstrated advantages of learning to speed-up deep activity detection, it is not clear if similar advantages will hold for our very different segmentation loss function, which is defined over individual pixels across the frames. In deep video segmentation, the most time consuming step represents the application of a CNN to every frame for assigning class labels to every pixel, typically taking 6-9 times of the video footage. This motivates our new budget-aware framework that learns to optimally select a small subset of frames for pixelwise labeling by a CNN, and then efficiently interpolates the obtained segmentations to yet unprocessed frames. This interpolation may use either a simple optical-flow guided mapping of pixel labels, or another significantly less complex and thus faster CNN. We formalize the frame selection as a Markov Decision Process, and specify a Long Short-Term Memory (LSTM) network to model a policy for selecting the frames. For training the LSTM, we develop a policy-gradient reinforcement-learning approach for approximating the gradient of our non-decomposable and non-differentiable objective. Evaluation on two benchmark video datasets show that our new framework is able to significantly reduce computation time, and maintain competitive video segmentation accuracy under varying budgets.
Stable, Crystalline Acenedithiophenes with up to Seven Linearly Fused Rings (2004)

[structure: see text] We report the synthesis of a series of crystalline acenedithiophenes with up to seven linearly fused rings and silylethynyl substituents. These functional groups are designed to both improve solubility and enhance cofacial interactions in the solid. We discuss the crystal packing of these materials, as well as their physical properties such as oxidation potential, UV-vis absorption, fluorescence emission, and decomposition pathways.
Cellular and molecular mechanisms of memory T-cell survival (2009)

Long-term maintenance of the memory T-cell response is the hallmark of immune protection and, hence, constitutes one of the most important objectives of vaccine-development strategies. Persistent memory T cells, developed after vaccination or microbial infections, ensure the generation of an antimicrobial response upon re-exposure to the pathogen through rapid clonal proliferation and activation of effector functions. However, in the context of many pathogen infections, these memory T cells fail to persist and die. In this review, we will highlight recent exciting findings in studies of memory T cells, their generation, their lineage relationships and their survival pathways; indeed, survival of memory T cells and maintenance of their functionality are key features of the immune response in its quest to control disease progression and in the development of vaccines to persistent microbial infections.
TCP-Splitter: A TCP/IP flow monitor in reconfigurable hardware (2003)

TCP/IP is the most commonly-used protocol on the Internet. It provides a reliable transport for nearly all applications that utilize a network. These include Web browsers, FTP, Telnet, Secure Shell and other applications. New types of routers require the examination of TCP/IP flows transiting this networking equipment. This paper describes TCP-Splitter, a reconfigurable hardware based solution for analyzing and processing TCP/IP flows at multi-gigabit line rates. A consistent byte stream is delivered to a client application for every TCP/IP connection processed by TCP-Splitter. In order to maintain a design that is lightweight, efficient, and able to process a nearly unlimited number of flows at gigabit line rates, the system uses a non-passive flow processing algorithm.
Separate genes encode functionally equivalent ADP/ATP carrier proteins in Saccharomyces cerevisiae. Isolation and analysis of AAC2. (1988)

Genetic and biochemical analysis of Saccharomyces cerevisiae containing a disruption of the nuclear gene (AAC1) encoding the mitochondrial ADP/ATP carrier has revealed a second gene for this protein. The second gene, designated AAC2, has been isolated by genetic complementation and sequenced. AAC2 contains a 954-base pair open reading frame coding for a protein of 318 amino acids which is highly homologous to the AAC1 gene product except that it is nine amino acids longer at the NH2 terminus. The two yeast genes are highly conserved at the level of DNA and protein and share identity with the ADP/ATP carriers from other organisms. Both genes complement an ADP/ATP carrier defect (op1 or pet9). However, the newly isolated gene AAC2 need be present only in one or two copies while the previously isolated AAC1 gene must be present in multiple copies to support growth dependent on a functional carrier protein. This gene dosage-dependent complementation combined with the high degree of conservation suggest that these two functionally equivalent genes may be differentially expressed.
Preparation and characterization of a collagen/chitosan/heparin matrix for an implantable bioartificial liver (2005)

A new type of collagen/chitosan/heparin matrix, fabricated by gelation of collagen/ chitosan with heparin sodium containing ammonia, was produced to construct livers by tissue engineering and regenerative engineering. The obtained collagen/chitosan/heparin matrix was found to be highly porous, swelled rapidly in PBS solution and was stable in vitro for at least 60 days in collagenase/lysozyme containing buffered aqueous solution (PBS, pH 7.4) at 37 degrees C. The collagen/chitosan/heparin matrix resulted in a superior blood compatibility compared to the ammonia-treated collagen and collagen/chitosan matrices. The morphology and behavior of the cells on the collagen/chitosan/heparin membrane were found to be similar to those on the collagen membrane but different from those on the collagen/chitosan membrane. Hepatocytes cultured on the collagen/chitosan/heparin matrices exhibited highest urea and triglyceride secretion functions 25 days post seeding. These results suggest that this collagen/chitosan/heparin matrix is a potential candidate for liver tissue engineering.
Automated DNA purification and amplification from blood-stained cards using a robotic workstation. (1995)

A new method for the purification of DNA on blood-stained cards was developed. This method was implemented into a high-throughput automated system using a Biomek 1000 robotic workstation. In addition, the processes of DNA purification and amplification were coupled into a completely automated and uninterrupted prototype system, and the resultant PCR products generated by this system were subjected to automated desalting for capillary electrophoresis analysis.
NELL-1 in the treatment of osteoporotic bone loss (2015)

NELL-1 is a secreted, osteoinductive protein whose expression rheostatically controls skeletal ossification. Overexpression of NELL-1 results in craniosynostosis in humans and mice, whereas lack of Nell-1 expression is associated with skeletal undermineralization. Here we show that Nell-1-haploinsufficient mice have normal skeletal development but undergo age-related osteoporosis, characterized by a reduction in osteoblast:osteoclast (OB:OC) ratio and increased bone fragility. Recombinant NELL-1 binds to integrin β1 and consequently induces Wnt/β-catenin signalling, associated with increased OB differentiation and inhibition of OC-directed bone resorption. Systemic delivery of NELL-1 to mice with gonadectomy-induced osteoporosis results in improved bone mineral density. When extended to a large animal model, local delivery of NELL-1 to osteoporotic sheep spine leads to significant increase in bone formation. Altogether, these findings suggest that NELL-1 deficiency plays a role in osteoporosis and demonstrate the potential utility of NELL-1 as a combination anabolic/antiosteoclastic therapeutic for bone loss.
Self-written waveguide on a VCSEL-emitting window using a photomask transfer method (2006)

This study is focused on a self-written waveguide (SWW) fabricated using a new photomask transfer method. With the proposed photomask transfer method, an SWW array was successfully fabricated on vertical-cavity surface-emitting laser (VCSEL) diode-emitting windows. It was found that the output power of a VCSEL having the SWW increased as compared to that of VCSEL without the SWW. We have confirmed that the optical output is independent of the placement of the emitting window inside the SWW. Optical coupling between an SWW and a graded-index multimode fiber was also demonstrated