gebhart/patrepeval huggingface dataset:
TIMP-1 Alters Susceptibility to Carcinogenesis (2004)

Tissue inhibitors of metalloproteinases (TIMPs) are a family of multifunctional proteins known to possess a broad range of biological activities, including inhibition of metalloproteinase activity, regulation of proliferation and apoptosis of a variety of cell types, and, depending on the context, differential regulation of angiogenic and inflammatory responses. Elevated mRNA expression of TIMP family members correlates with malignancy and clinical outcome in many human cancer types; however, a protective role for TIMPs also has been observed in various mouse models of human cancer. In the current study, we found distinct spatial-temporal expression patterns for the mRNA of TIMP family members in a mouse model of epithelial carcinogenesis [i.e., keratin 14-human papillomavirus 16 (K14-HPV16) transgenic mice]. To test the hypothesis that elevated expression of TIMP-1 functionally regulates epithelial carcinogenesis, we introduced a human TIMP-1 transgene into K14-HPV16 transgenic mice and assessed neoplastic progression. Results from these studies suggest that TIMP-1 enhances tumorgenicity by potentiating keratinocyte hyperproliferation and appearance of chromosomal aberrations in premalignant cells, thereby increasing their risk to undergo malignant conversion. In addition, TIMP-1 inhibits tissue gelatinolytic activity in tumor stroma, affects stabilization of collagen fibrils, but does not inhibit malignant conversion of dysplasias into carcinomas or development of metastases. The combined implications of these studies suggest that TIMP-1 is an important contributor to epithelial neoplastic progression and supports the concept that TIMP-1 exerts differential regulation on tissues in a stage-dependent manner.
A brief summary of bridge networks (1940)

An outline classification of Bridge networks that may be of assistance to users of Bridges, students, and others interested in the subject
In‐hospital complications of autologous hematopoietic stem cell transplantation for lymphoid malignancies (2008)

Adverse events are both common and costly after auto HSCT. Strategies to minimize complications could significantly reduce not only morbidity and mortality but also the cost of the procedure. Administrative data can be profitably exploited to investigate outcomes in this population.
Mitochondrial Superoxide Dismutase (1973)

Mitochondria were isolated from chicken liver and were then separated into fractions containing the outer membrane, the soluble components of the intermembrane space, the inner membrane, and the soluble enzymes of the matrix space. The manganosuperoxide dismutase was found primarily in the matrix space whereas the cuprozinc superoxide dismutase, previously isolated from the cytosol, was found in the intermembrane space. No activity was associated with the membranous fractions. A strain of petite mutants of Saccharomyces cerevisiae which lacks mitochondrial DNA, was examined and found to contain both the mangano- and the cuprozinc types of superoxide dismutase. This result indicates that the manganoenzyme, although localized in the mitochondrial matrix, is actually made under the directions of the nuclear genome and that its biosynthesis therefore probably takes place in the cytosol.
Phage-Displayed Peptides as Developmental Agonists for <i>Phytophthora capsici</i> Zoospores (2002)

As part of its pathogenic life cycle, Phytophthora capsici disperses to plants through a motile zoospore stage. Molecules on the zoospore surface are involved in reception of environmental signals that direct preinfection behavior. We developed a phage display protocol to identify peptides that bind to the surface molecules of P. capsici zoospores in vitro. The selected phage-displayed peptides contained an abundance of polar amino acids and proline but were otherwise not conserved. About half of the selected phage that were tested concomitantly induced zoospore encystment in the absence of other signaling agents. A display phage was shown to bind to the zoospore but not to the cyst form of P. capsici. Two free peptides corresponding to active phage were similarly able to induce encystment of zoospores, indicating that their ability to serve as signaling ligands did not depend on their exact molecular context. Isolation and subsequent expression of peptides that act on pathogens could allow the identification of receptor molecules on the zoospore surface, in addition to forming the basis for a novel plant disease resistance strategy.
The Tumour Specific Pro-Apoptotic Factor Apoptin (Vp3) from Chicken Anaemia Virus (2004)

Cancer is a growing problem for human health world-wide. Dramatic breakthroughs have increased our understanding of the molecular mechanisms involved in the process of tumorigenesis, allowing us to develop more refined anti-cancer treatments, expanding the repertoire of available anti-cancer drugs, and increasing the efficiency of their delivery to malignant cells. Nevertheless, even with improved understanding of the complex origins of cancer cells, there is a dearth of efficient and above all specific anti-cancer treatments. Apoptin (viral protein 3 - VP3), a gene product derived from the Chicken Anaemia Virus (CAV) represents a novel anti-cancer tool. It appears to have innate tumour-specific p53-independent, Bcl-2-enhanced pro-apoptotic activity, and hence may be of great utility in the endeavour to achieve specific and efficient elimination of cancer cells, particularly in cases of drug resistance through Bcl-2 overexpression/loss of p53 function etc. This review will examine the unique aspects of apoptin's properties, and in particular, its ability to localise specifically in the nucleus of transformed but not normal cells. The latter ability, importantly, appears to be integrally related to its tumour-specific pro-apoptotic action.
Clinicopathologic Features of Signet-ring Cell Carcinoma of the Colon and Rectum (2006)

はじめに: 大腸印環細胞癌は極めてまれで予後不良とされているが, 発生頻度が少ないためその特長は明らかでない. 方法: 2003年までのm癌を除いた大腸癌症例3,169例の中で, 印環細胞癌は7例であった. 分化型腺癌, 低分化腺癌および粘液癌と比較し, 予後および臨床病理組織学的検討を行った. 結果: 印環細胞癌において男女比は2: 5, 平均年齢は45.7歳, 占居部位は肛門管を含む直腸4例, 盲腸1例, S状結腸1例, 横行結腸1例であった. 肉眼型は, 潰瘍浸潤型4例, 腫瘤型2例であった. 壁深達度はいずれもss (a1) 以上の進行癌でリンパ節転移は6例中5例で陽性であった. 同時性腹膜転移を7例中3例に認めたが肝転移は認めなかった. 根治度A/Bの4例の再発形式は2例が局所再発, 1例がリンパ節再発, 1例が骨髄転移であった. 7例全例が術後3年以内に死亡しており平均生存日数は319.9日で, 低分化腺癌・粘液癌と比較しても予後は極めて不良であった. 分子生物学的検討においてmicrosatellite instabilityは6例中3例に陽性であった. 考察: 予後の向上のためには, 早期診断および最近の化学療法を含めた集学的治療が重要であると考えられた.
Methodology, biology and clinical applications of mesenchymal stem cells (2009)

Mesenchymal stem cells (MSCs) are adult stem cells able to give rise to mature mesenchymal cell types. Plastic-adherent cells are operationally defined as MSCs based on their ability to proliferate and differentiate into cells such as osteoblasts, adipocytes and chondrocytes. In the past ten years, cultured MSCs have been shown to exhibit great plasticity in culture, as they can differentiate into cells with ectodermal and endodermal characteristics, suggesting their use as a source of cells to treat different diseases. More recently, cultured MSCs were found to secrete various bioactive molecules that display anti-apoptotic, immunomodulatory, angiogenic, anti-scarring, and chemoattractant properties, providing a basis for their use as tools to create local regenerative environments in vivo. Whereas the properties of cultured MSCs have been studied for a long time, their exact location in vivo is slowly becoming apparent as evidence indicates that pericytes behave as stem cells throughout the organism. In this review, we discuss some aspects of MSC basic biology, the methodology involved in MSC culture, and some clinical and pre-clinical applications of cultured MSCs.
The preparation and some properties of chlorinated tung oil (1959)

Summary The chlorination of tung oil was investigated, and certain chlorinated products were screened as plasticizers for polyvinyl chloride resin. Chlorine readily added at low temperatures (0 to 20°C.) as well as at higher temperature (75°C.). The chlorination was highly selective for triene conjugation as the disappearance of triene closely paralleled the amount of chlorine added during early staged to chlorination. Considerable conjugated diene is formed as indicated by characteristic ultraviolet absorption in the diene region. In later stages of chlorination considerable substitution occurs as evidenced by the fact that products containing more than 40% of chlorine could readily be obtained. All the products were more or less unstable, evolving hydrogen chloride and darkening at room temperature. The chlorinated tung oils were screened as plasticizers, at the 30% level, for polyvinyl chloride by using butyl epoxystearate as a stabilizer. Products containing small proportions of chlorine (less than about 20%) were not compatible with polyvinyl chloride; products containing moderate amounts (about 30%) were compatible and had some plasticizing effect but decomposed excessively on milling. Those products containing the highest proportion of chlorine (more than 40%) were compatible and did not decompose on milling or molding. These highly chlronated tung oilslowered the milling temperature of polyvinyl chloride copolymer but showed little, if any, ability to product compositions which are flexible at room temperature.
<title>Application of laser generated ultrasonic pulses in diagnostics of residual stresses in welds</title> (2006)

The laser optoacoustic method is applied for nondestructive evaluation of residual stresses in metals. Theoretical background establishes the acoustoelasticity relationships between applied biaxial stresses and deviations of the longitudinal wave velocity in solids. The experimental technique bases on laser thermoptical excitation of nanosecond ultrasonic pulses on the surface of samples under study and their backward mode piezodetection with a high temporal resolution. The samples, produced from stainless steel, had thickness from 1.67 mm to 8.87 mm. Welds are made up by means of electronic beam overheating of the samples with different intensities of the beam. Plane distributions of relative longitudinal wave velocity deviations, produced by stresses, were obtained.
PRACTICAL EFFICIENCIES OF EXISTING SHORTEST-PATH ALGORITHMS AND A NEW BUCKET ALGORITHM (1984)

For the problem of finding the shortest paths from a prescribed vertex to the other vertices in a given network with nonnegative arc lengths, we investigate practical efficiencies of typical existing algorithms, i.e., the label-correcting method with a FIFO and that of a two-way sequence, and the label-setting method with a heap and that with a 1- or 2-level bucket system. We propose also a new method with a variable bucket system and compare it with those existing methods. Among the existing methods, the label-correcting method of a two-way sequence and the label-setting method with a I-level bucket system have been found efficient in most cases. The new proposed method is not only as efficient as those but it is also robust for a large variety of networks, so that it may be recommended for practical use.
Chemiluminescence of anthocyanins in the presence of acetaldehyde and <i>tert</i>‐butyl hydroperoxide (1995)

Light emission (chemiluminescence; CL) was observed in the reaction of anthocyanins with tert-butyl hydroperoxide (t-BuOOH) in the presence of acetaldehyde. The intensity of the CL of the anthocyanins was in the order of nasunin > rubrobrassicin > delphinidin > malvin = cyanidin > malvidin, indicating that glucosylation at C-3 and C-5 of the anthocyanin skeleton enhances the CL of the parent compound. CL intensity was enhanced at alkaline pH. The results suggest that the antioxidant effect of anthocyanins on lipid peroxidation, which is observed in the linoleic acid-beta-carotene-lipoxygenase system, is at least partly due to their strong reactivity with hydroperoxides.
Solid‐phase total synthesis of polymyxin B1 (1999)

The total solid-phase synthesis of polymyxin B1 (PMB1) has been achieved in 20% yield using the orthogonal protecting group N-1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl-(Dde). This report demonstrates that a complex peptide macrocycle can be synthesized in high yields using solid-phase synthesis. According to MS and HPLC, the synthetic peptide was identical to the naturally occurring antibiotic.
Predicting slippage and learning manipulation affordances through Gaussian Process regression (2013)

Object grasping is commonly followed by some form of object manipulation - either when using the grasped object as a tool or actively changing its position in the hand through in-hand manipulation to afford further interaction. In this process, slippage may occur due to inappropriate contact forces, various types of noise and/or due to the unexpected interaction or collision with the environment.
Successful Seventeen-Hour Preservation and Transplantation of Human-Cadaver Kidney (1968)

ORGAN preservation has been extensively studied for many years, but long-term storage of whole organs is still an unsolved problem. However, short-term preservation of organs such as the kidney would be a great advantage in a transplantation program in which cadaver organs are used. Because of encouraging results in our laboratory,1 we decided to attempt short-term preservation of a human-cadaver kidney. We were able to preserve such a kidney for 17 hours, followed by successful transplantation and function.Case ReportA 47-year-old Armenian became a resident of California in 1957. He had lived for 30 years in North Africa, where . . .
A control method to improve the efficiency of a soft-switching non-isolated bidirectional DC-DC converter for hybrid and plug-in electric vehicle applications (2014)

Hybrid energy storage system (HESS) can be adopted in hybrid, plug-in hybrid, and pure electric vehicles (HEV, PHEV, and EV), where a bidirectional DC-DC converter (BDC) is used to connect batteries and ultracapacitors. The efficiency improvement of the BDC is beneficial to increase the efficiency viability of HESS. Due to ZVS, high efficiency can be obtained at heavy load operations while the efficiency is low at light load operations mainly because of the conduction losses of the auxiliary circuits. These losses can be reduced by optimising the switching frequency. The relationship of efficiency and switching frequency are presented and discussed. A scaleddown 1 kW BDC prototype is built to verify the feasibility of the efficiency improvement. With the aim of achieving ZVS conditions and variable frequency control, the implementing method is proposed. The simulated results are also presented, which can validate the feasibility of the proposed control method.
Autoimmunity against type VII collagen in inflammatory bowel disease (2009)

Autoimmunity against type VII collagen, an adhesion molecule of the extracellular matrix in epithelial basement membranes, is causing the rare organ-specific epidermolysis bullosa acquisita (EBA). An intriguing association between EBA and inflammatory bowel disease (IBD) has been extensively documented over the last decades, but, because of the very low incidence of EBA, received little attention from physicians involved in the care of patients with IBD. More recently, autoantibodies against type VII collagen have been detected in up to 68% of IBD patients. Although these findings suggest that chronic intestinal inflammation in IBD predisposes for autoimmunity against type VII collagen, their relevance for the pathogenesis of both IBD and EBA is still unclear. In this review article, the main features of the association between IBD and EBA are presented and pathomechanistic hypotheses as well as future lines of investigation in this area are discussed. Future research should provide new pathomechanistic insights and will likely facilitate the development of more specific and effective immunotherapeutic strategies for both conditions.
Direct Noninvasive Assessment of Brain Metabolism during Increased Intracranial Pressure: Potential Therapeutic Vistas (1986)

Intracranial pressure was increased in cats by infusing 'mock' CSF intracranially, thus decreasing cerebral perfusion and oxygenation. The cats then randomly received either 50% O2 or 50% O2-5% CO2 by inhalation. As monitored by in vivo near-infrared spectroscopy (NIR), no improvement was noted after 50% O2 whereas 50% O2-5% CO2 resulted in increased perfusion, an oxidation of cytochrome a,a3, an increase in oxyhemoglobin, and reduced quantities of de-oxyhemoglobin (p less than 0.01) despite a further increase in intracranial pressure. The authors conclude that: NIR is a useful means of noninvasively and directly assessing brain metabolism and has advantages over simple ICP monitoring; and continued investigations of CO2 as a possible therapeutic modality after head injury appear warranted.
BUILDING A 3D REFERENCE MODEL FOR CANAL TUNNEL SURVEYING USING SONAR AND LASER SCANNING (2015)

Abstract. Maintaining canal tunnels is not only a matter of cultural and historical preservation, but also a commercial necessity and a security issue. This contribution adresses the problem of building a full 3D reference model of a canal tunnel by merging SONAR (for underwater data recording) and LASER data (for the above-water parts). Although both scanning devices produce point clouds, their properties are rather different. In particular, SONAR data are very noisy and their processing raises several issues related to the device capacities, the acquisition setup and the tubular shape of the tunnel. The proposed methodology relies on a denoising step by meshing, followed by the registration of SONAR data with the geo-referenced LASER data. Since there is no overlap between point clouds, a 3-step procedure is proposed to robustly estimate the registration parameters. In this paper, we report a first experimental survey, which concerned the entrance of a canal tunnel. The obtained results are promising and the analysis of the method raises several improvement directions that will help obtaining more accurate models, in a more automated fashion, in the limits of the involved technology.
Prolyl derivatives of enalapril as potential angiotensin converting enzyme inhibitors. (1988)

The synthesis of a new class of potential angiotensin converting enzyme (ACE) inhibitors, analogs of enalapril, is reported. In these molecules the C-terminal amino acidic sequence Ala-Pro of enalapril was replaced by the sequence Pro-Pro. The compounds were tested both in vitro and in vivo. They showed no in vivo activity but only a week in vitro inhibitory activity.
Cancer Metabolism: A Modeling Perspective (2015)

Tumor cells alter their metabolism to maintain unregulated cellular proliferation and survival, but this transformation leaves them reliant on constant supply of nutrients and energy. In addition to the widely studied dysregulated glucose metabolism to fuel tumor cell growth, accumulating evidences suggest that utilization of amino acids and lipids contributes significantly to cancer cell metabolism. Also recent progresses in our understanding of carcinogenesis have revealed that cancer is a complex disease and cannot be understood through simple investigation of genetic mutations of cancerous cells. Cancer cells present in complex tumor tissues communicate with the surrounding microenvironment and develop traits which promote their growth, survival, and metastasis. Decoding the full scope and targeting dysregulated metabolic pathways that support neoplastic transformations and their preservation requires both the advancement of experimental technologies for more comprehensive measurement of omics as well as the advancement of robust computational methods for accurate analysis of the generated data. Here, we review cancer-associated reprogramming of metabolism and highlight the capability of genome-scale metabolic modeling approaches in perceiving a system-level perspective of cancer metabolism and in detecting novel selective drug targets.
A novel small molecule inhibitor of deubiquitylating enzyme USP14 and UCHL5 induces apoptosis in multiple myeloma and overcomes bortezomib resistance (2013)

Proteasome inhibitors have demonstrated that targeting protein degradation is effective therapy in multiple myeloma (MM). Here we show that deubiquitylating enzymes (DUBs) USP14 and UCHL5 are more highly expressed in MM cells than in normal plasma cells. USP14 and UCHL5 short interfering RNA knockdown decreases MM cell viability. A novel 19S regulatory particle inhibitor b-AP15 selectively blocks deubiquitylating activity of USP14 and UCHL5 without inhibiting proteasome activity. b-AP15 decreases viability in MM cell lines and patient MM cells, inhibits proliferation of MM cells even in the presence of bone marrow stroma cells, and overcomes bortezomib resistance. Anti-MM activity of b-AP15 is associated with growth arrest via downregulation of CDC25C, CDC2, and cyclin B1 as well as induction of caspase-dependent apoptosis and activation of unfolded protein response. In vivo studies using distinct human MM xenograft models show that b-AP15 is well tolerated, inhibits tumor growth, and prolongs survival. Combining b-AP15 with suberoylanilide hydroxamic acid, lenalidomide, or dexamethasone induces synergistic anti-MM activity. Our preclinical data showing efficacy of b-AP15 in MM disease models validates targeting DUBs in the ubiquitin proteasomal cascade to overcome proteasome inhibitor resistance and provides the framework for clinical evaluation of USP14/UCHL5 inhibitors to improve patient outcome in MM.
Collective Learning From Diverse Datasets for Entity Typing in the Wild (2018)

Entity typing (ET) is the problem of assigning labels to given entity mentions in a sentence. Existing works for ET require knowledge about the domain and target label set for a given test instance. ET in the absence of such knowledge is a novel problem that we address as ET in the wild. We hypothesize that the solution to this problem is to build supervised models that generalize better on the ET task as a whole, rather than a specific dataset. In this direction, we propose a Collective Learning Framework (CLF), which enables learning from diverse datasets in a unified way. The CLF first creates a unified hierarchical label set (UHLS) and a label mapping by aggregating label information from all available datasets. Then it builds a single neural network classifier using UHLS, label mapping, and a partial loss function. The single classifier predicts the finest possible label across all available domains even though these labels may not be present in any domain-specific dataset. We also propose a set of evaluation schemes and metrics to evaluate the performance of models in this novel problem. Extensive experimentation on seven diverse real-world datasets demonstrates the efficacy of our CLF.
Trends and Perspectives in Image and Video Coding (2004)

The objective of the paper is to provide an overview on recent trends and future perspectives in image and video coding. Here, I review the rapid development in the field during the past 40 years and outline current state-of-the art strategies for coding images and videos. These and other coding algorithms are discussed in the context of international JPEG, JPEG 2000, MPEG-1/2/4, and H.261/3/4 standards. Novel techniques targeted at achieving higher compression gains, error robustness, and network/device adaptability are described and discussed.