gebhart/patrepeval huggingface dataset:
Document image processing based on enhanced border following algorithm (2002)

An enhanced border-following algorithm and its application to document image processing is presented. Various kinds of components (characters, text lines, text blocks, figures, tables, etc.) in a document image can be flexibly segmented and extracted with a variable-size mask for border following instead of the conventional 3*3-size mask. An automatic document image structuring process to construct a multimedia document and a raster/geometric conversion method for the segmented graphic parts of the image. such as diagrams and tables, are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genetics of Actinorhodin Biosynthesis by Streptomyces coelicolor A3(2) (1979)

A series of 76 mutants of Streptomyces coelicolor A3(2) specifically blocked in the synthesis of the binaphthoquinone antibiotic actinorhodin were classified into seven phenotypic classes on the basis of antibiotic activity, accumulation of pigmented precursors or shunt products of actinorhodin biosynthesis, and cosynthesis of actinorhodin in pairwise combinations of mutants. The polarity of cosynthetic reactions, and other phenotypic properties, allowed six of the mutant classes to be arranged in the most probable linear sequence of biosynthetic blocks. One member of each mutant class was mapped unambigiguously to the chromosomal linkage map in the short segment between the hisD and guaA loci, suggesting that structural genes for actinorhodin biosynthesis may form an uninterrupted cluster of chromosomal genes.
High-Sensitivity C-Reactive Protein and Coronary Heart Disease in a General Population of Japanese (2008)

hs-CRP levels were clearly associated with future CHD events in a general population of Japanese. In Japanese populations, the hs-CRP cut-off point for high-risk of future development of CHD is likely to be >1.0 mg/L, which is much lower than that for Western populations.
A Catalyst for Efficient and Highly Enantioselective Hydrogenation of Aromatic, Heteroaromatic, and α,β-Unsaturated Ketones (2000)

PhanePhos-ruthenium-diamine complexes catalyze the asymmetric hydrogenation of a wide range of aromatic, heteroaromatic, and alpha, beta-unsaturated ketones with high activity and excellent enantioselectivity.
Identification of a Bordetella pertussis regulatory factor required for transcription of the pertussis toxin operon in Escherichia coli (1995)

Transcription of the pertussis toxin operon (ptx) is positively regulated in Bordetella pertussis by the bvgAS locus. However, a ptx-lacZ transcriptional fusion in Escherichia coli cannot be activated by bvgAS in trans. This suggests that an additional factor(s) is required for transcription of ptx. A gene encoding a Bvg accessory factor (Baf) was identified by its ability to activate an E. coli ptx-lacZ fusion in the presence of bvgAS. The expression of ptx-lacZ was decreased by the addition of 40 mM MgSO4, a compound that also modulates ptx expression in B. pertussis. Baf alone did not activate expression of an E. coli fhaB-lacZ fusion, nor did it increase expression of fhaB-lacZ in trans with bvgAS. The gene encoding Baf was localized, sequenced, and found to produce a novel 28-kDa protein. Sequences homologous to B. pertussis baf were identified in Bordetella bronchiseptica and Bordetella parapertussis but not in Bordetella avium. When an additional copy of baf was integrated into the chromosome of BC75, a B. pertussis mutant that produces a low level of pertussis toxin, pertussis toxin production was partially complemented in the cointegrate strain.
An evaluation of methodological issues in workflow management (1998)

Ankara : Department of Computer Engineering and Information Science and the Institute of Engineering and Science of Bilkent University, 1998.
WhereStore (2010)

In recent years, two major trends have changed the way mobile phones are used: smartphones have become a platform for applications, and 3G connectivity has turned them into ubiquitous Internet clients. Increasingly, applications on smartphones (such as document sharing, media players and map browsers) interact with the cloud as a backend for data storage and computation. We observe that, for many mobile applications, the specific data that is accessed depends on the current location of the user. For example, a restaurant recommendation application is often used to get information about nearby restaurants. In this paper, we present WhereStore, a location-based data store for smart-phones interacting with the cloud. It uses filtered replication along with each device's location history to distribute items between smartphones and the cloud. We discuss the challenges of designing such a system, relevant applications, and a specific design and prototype implementation.
Insulin binding and effects in isolated soleus muscle of lean and obese mice. (1978)

To get some insight into the mechanisms of insulin resistance in obesity, insulin binding and biological effects were investigated in soleus muscles isolated from normal and obese mice. Basal and insulin-stimulated 2-deoxyglucose uptake were measured at the steady state of insulin binding. The results were consistent with the concept of spare receptors, i.e., maximal insulin effect was achieved when only about 20% of total receptors was occupied. When similar studies were applied to muscles of gold thioglucose obese or genetically obese (ob/ob) mice, and compared to lean controls: a) insulin binding was decreased; b) the insulin dose-response curve of 2-deoxyglucose uptake was shifted to the right; c) maximally insulin-stimulated 2-deoxyglucose uptake, glycolysis, and glycogen synthesis were markedly decreased. Insulin binding and effects returned toward normal after a 40-h fast in obese mice. These results point to two loci for the insulin resistance of skeletal muscle in obesity: 1) a decrease in the number of insulin receptors, which results in a diminished insulin sensitivity; and 2) one or more alterations beyond receptor that are responsible for the decreased responsiveness of the tissue to insulin and appear to play a major role in the insulin resistance of muscle in obesity.
Concordance of Human Immunodeficiency Virus Detection by Polymerase Chain Reaction and by Serologic Assays in a Dutch Cohort of Seronegative Homosexual Men (1992)

In three subgroups of a clinically and socially well defined group of Dutch homosexual men, the prevalence of human immunodeficiency virus type 1 (HIV-1) sequences in seronegative blood samples was studied using the polymerase chain reaction (PCR). In 19 seronegative partners of seropositive persons, no HIV-1 sequences were found by PCR in either early (1984/1985) or more recent (1987) samples. In 42 seronegative persons selected by their high risk for HIV-1 infection, none harbored HIV-1 sequences in either early (1985/1986) or late (1989) samples. In 15 people who seroconverted for HIV-1, only 2 samples collected 3 months before seroconversion were PCR-positive. These persons were also HIV antigen-positive at this time. These data suggest that a latent infection greater than 6 months does not occur and that the combination of HIV antibody and HIV antigen tests is appropriate and conclusive in most cases of HIV-1 infection.
RegulonDB: a database on transcriptional regulation in Escherichia coli (1998)

RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli , as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. The operon is the basic structure used in RegulonDB to describe the elements and properties of transcriptional regulation. The current version contains information around some 500 regulation mechanisms, essentially for sigma 70 promoters.
Inefficacy of Thalidomide on Rat Adjuvant-induced Arthritis and Lack of Arthrogenicity of Hansen Bacilli (1988)

ENLを抑制するクロファジミンがラットァジュバント関節炎を抑制したので,同じくENLを抑制するサリドマイドが当関節炎を抑制するか否かを調べた。当関節炎の誘起にヒト型結核菌の他にらい菌を用いその誘起能を調べた。オーストラリァ産の雌DAラットは雄SDラットと比べて格段に誘発応答性が優れ,ヒト型結核菌青山Bの0.05mgで充分に二次反応が誘発された。しかしらい菌はより大量の加熱死菌を投与しても二次反応を誘起せず,僅かに投与部位の右後肢足蹠に微少な一過性腫脹が検出されたのみだった。この結果は,らい菌だけでは免疫促進もまたそれに伴う副作用も生起しにくい事を示唆した。当関節炎の亜誘起量である3×107のヒト型結核菌青山Bを先行投与しておくと,充分な誘起量を再投与しても関節炎の誘発を認めなかった。雌DAラットに誘起された重篤な関節炎に対し,20mg/kgのクロファジミン投与は雄SDラットの際より若干弱いながら充分な抑制効果を示したが,10mg/kgのサリドマイド投与は抑制効果を示さなかった。これら結果に基づき,当関節炎はENL抑制用処方のスクリーニングのための実験動物モデルとして限界が在る事,ENLと当関節炎の矛盾点やサリドマイドのENL抑制機作の疑問点を討議した。
Excitation spectrum for ultrafast photogeneration of charged solitons in polyacetylene (2002)

Ultrafast photoinduced absorption by infrared-active vibrational modes is used to detect charged solitons in oriented trans-polyacetylene. Soliton pairs are photogenerated within \ensuremath{\sim}250 fs with quantum efficiencies $({\ensuremath{\varphi}}_{\mathrm{ch}})$ approaching unity. The excitation spectrum of ${\ensuremath{\varphi}}_{\mathrm{ch}}$ shows an onset at \ensuremath{\sim}1.0 eV with a weak photon energy dependence up to 4.7 eV. The results are consistent with the ultrafast soliton formation predicted by Su and Schrieffer and with the Su-Scrieffer-Heeger threshold of ${2E}_{g}/\ensuremath{\pi}$ for soliton pair production. The recombination dynamics of charged solitons is very fast (initial $\mathrm{decay}&lt;1\mathrm{ps})$ with a modest dependence on the pump photon energy.
Prevalent expression of the immunostimulatory MHC class I chain–related molecule is counteracted by shedding in prostate cancer (2004)

The MHC class I chain-related molecules (MICs) have previously been shown to be induced on most epithelial tumor cells. Engagement of MIC by the activating immune receptor NKG2D triggers NK cells and augments antigen-specific CTL anti-tumor immunity. The MIC-NKG2D system was proposed to participate in epithelial tumor immune surveillance. Paradoxically, studies suggest that tumors may evade MIC-NKG2Dmediated immunity by MIC shedding-induced impairment of effector cell function. Here we demonstrate the first evidence to our knowledge of a significant correlation of MIC shedding and deficiency in NK cell function with the grade of disease in prostate cancer. MIC is widely expressed in prostate carcinoma. The presence of surface target MIC, however, is counteracted by shedding. A significant increase in serum levels of soluble MIC (sMIC) and deficiency in NK cell function was shown in patients with advanced cancer. Finally, the deficiency in NK cell function can be overcome by treatment with IL-2 or IL-15 in vitro. Our results suggest that (a) deficiency in MIC-NKG2D immune surveillance may contribute to prostate cancer progression, (b) sMIC may be a novel biomarker for prostate cancer, and (c) using cytokines to restore MIC-NKG2D-mediated immunity may have clinical significance for prostate cancer in cell-based adaptive immunotherapy. Nonstandard abbreviations used: Gleason score(s) (GS); high-grade prostatic intraepithelial neoplasia (HGPIN); MHC class I chain-related molecule (MIC); phycoerythrin (PE); primary epithelial cell (PrEC); prostate-specific antigen (PSA); soluble MIC (sMIC); UL16-binding protein (ULBP).
In vivo effects of chicken myelomonocytic growth factor: delivery via a viral vector (1996)

We have constructed a recombinant fowlpox virus (FPV) that expresses chicken myelomonocytic growth factor (cMGF). Administration of this construct (fp/cMGF) to 1-day-old chicks resulted in a marked and sustained increase in the number of circulating blood monocytes compared with chicks infected with the parental FPV strain (fp/M3). Blood monocyte numbers were elevated within 4 days of fp/cMGF infection, reached maximal levels at day 9, and returned to normal levels by day 16. During the peak response, approximately 35% of blood leukocytes were monocytes, compared with 4 to 7% in uninfected control birds. Infection with fp/M3 also resulted in a detectable increase in monocyte numbers; however, the effect was less dramatic. Compared with fp/M3, fp/cMGF consistently induced two- to threefold higher monocyte numbers, and the period of monocytosis was longer (10 vs 5 days). No other specific changes in white blood cell populations were observed. Associated with the increase in the number of monocytes was an increase in their state of activation, as measured by the ability to produce nitric oxide (NO) and to phagocytose latex beads. Blood monocytes from birds infected with fp/cMGF produced about 6 times as much NO per cell compared with monocytes from fp/M3-infected birds. Monocytes from normal birds failed to produce detectable levels of NO. Furthermore, cMGF treatment specifically induced enhanced phagocytic activity in blood monocytes. Overall, these results indicate that viral vectors are suitable for the delivery of biologically active cytokines and that they allow an assessment of cytokine activities in vivo.
Engraftment of human hematopoietic stem cells is more efficient in female NOD/SCID/IL-2Rgc-null recipients (2010)

Repopulation of immunodeficient mice remains the primary method to assay human hematopoietic stem cells (HSCs). Here we report that female NOD/SCID/IL-2Rg(c)-null mice are far superior in detecting human HSCs (Lin(-)CD34(+)CD38(-)CD90(+)CD45RA(-)) compared with male recipients. When multiple HSCs were transplanted, female recipients displayed a trend (1.4-fold) toward higher levels of human chimerism (female vs male: injected femur, 44.4 +/- 9.3 vs 32.2 +/- 6.2; n = 12 females, n = 24 males; P = .1). Strikingly, this effect was dramatically amplified at limiting cell doses where female recipients had an approximately 11-fold higher chimerism from single HSCs (female vs male: injected femur, 8.1 +/- 2.7 vs 0.7 +/- 0.7; n = 28 females, n = 20 males; P < .001). Secondary transplantations from primary recipients indicate that females more efficiently support the self-renewal of human HSCs. Therefore, sex-associated factors play a pivotal role in the survival, proliferation, and self-renewal of human HSCs in the xenograft model, and recipient sex must be carefully monitored in the future design of experiments requiring human HSC assays.
Design of monolithically integrated GeSi electro-absorption modulators and photodetectors on a SOI platform (2007)

We present a design of monolithically integrated GeSi electroabsorption modulators and photodetectors for electronic-photonic integrated circuits on a silicon-on-insulator (SOI) platform. The GeSi electroabsorption modulator is based on the Franz-Keldysh effect, and the GeSi composition is chosen for optimal performance around 1550 nm. The designed modulator device is butt-coupled to Si(core)/SiO(2)(cladding) high index contrast waveguides, and has a predicted 3 dB bandwidth of >50 GHz and an extinction ratio of 10 dB. The same device structure can also be used for a waveguide-coupled photodetector with a predicted responsivity of > 1 A/W and a 3 dB bandwidth of > 35 GHz. Use of the same GeSi composition and device structure allows efficient monolithic process integration of the modulators and the photodetectors on an SOI platform.
Phosphorylation of the Goodpasture Antigen by Type A Protein Kinases (1995)

Collagen IV is the major component of basement membranes. The human alpha 3 chain of collagen IV contains an antigenic domain called the Goodpasture antigen that is the target for the circulating immunopathogenic antibodies present in patients with Goodpasture syndrome. Characteristically, the gene region encoding the Goodpasture antigen generates multiple alternative products that retain the antigen amino-terminal region with a five-residue motif (KRGDS). The serine therein appears to be the major in vitro cAMP-dependent protein kinase phosphorylation site in the isolated antigen and can be phosphorylated in vitro by two protein kinases of approximately 50 and 41 kDa associated with human kidney plasma membrane, suggesting that it can also be phosphorylated in vivo. Consistent with this, the Goodpasture antigen is isolated from human kidney in phosphorylated and non-phosphorylated forms and only the non-phosphorylated form is susceptible to phosphorylation in vitro. Since this motif is exclusive to the human alpha 3(IV) chain and includes the RGD cell adhesion motif, its phosphorylation might play a role in pathogenesis and influence cell attachment to basement membrane.
Toxicity and response criteria of the Eastern Cooperative Oncology Group (1982)

STANDARD CRITERIA FOR TOXICITY and for response to treatment are important prerequisites to the conduct of cancer trials. The Eastern Cooperative Oncology Group criteria for toxicity and response are presented to facilitate future reference and to encourage further standardization among those conducting clinical trials.
DNA methylation markers for early detection of women’s cancer: promise and challenges (2014)

Breast, ovarian and endometrial cancers cause significant morbidity and mortality. Despite the presence of existing screening, diagnostic and treatment modalities, they continue to pose considerable unsolved challenges. Overdiagnosis is a growing problem in breast cancer screening and neither screening nor early diagnosis of ovarian or endometrial cancer is currently possible. Moreover, treatment of the diversity of these cancers presenting in the clinic is not sufficiently personalized at present. Recent technological advances, including reduced representation bisulfite sequencing, methylation arrays, digital PCR, next-generation sequencing and advanced statistical data analysis, enable the analysis of methylation patterns in cell-free tumor DNA in serum/plasma. Ongoing work is bringing these methods together for the analysis of samples from large clinical trials, which have been collected well in advance of cancer diagnosis. These efforts pave the way for the development of a noninvasive method that would enable us to overcome existing challenges to personalized medicine.
Incorporating estuaries as a source or sink of sediment within assessments of coastline risk and adaptation to climate change (2012)

Complex coastal landforms exhibit variable behaviour in response to sea-level rise. A proposed modelling framework that integrates shoreline changes associated with longterm recession, short-term variability and sea-level rise advocates that coastal risk assessment be undertaken within the context of a geomorphologically-based modelling framework whereby a coastline is subdivided into coastal compartments or cells, thereby recognising the sedimentary links between compartments. For example, the Narrabeen coastline includes bounding headland compartments, a bay compartment and an estuary compartment; and the behaviour of the coastline varies according to the response of each of these compartments to variable climatic and oceanic conditions. This approach is extended to other estuarine systems in southern NSW. Estuaries play an important role as a source or sink of sediment that varies widely in accordance with climatic and oceanic conditions. Accounting for the role of estuaries in coastline behaviour involves identifying the variable shorelines within estuaries; establishing the long-term estuarine shoreline behaviour and the response of shorelines to sea-level change; and integrating models that best represent the response of estuarine shorelines to climate change within the proposed integrated modelling framework for coastal risk assessment. Recognising the links between sedimentary sources and sinks and integrating models of estuarine behaviour with models of open coast behaviour will improve coastal risk assessment and provide greater confidence in adaptation options.
Using fault injection to increase software test coverage (2002)

During testing, it is nearly impossible to run all statements or branches of a program. It is especially difficult to test the code used to respond to exceptional conditions. This untested code, often the error recovery code, will tend to be an error prone part of a system. We show that test coverage can be increased through an "assertion violation" technique for injecting software faults during execution. Using our prototype tool, Visual C-Patrol (VCP), we were able to substantially increase test branch coverage in four software systems studied.
Activation of the STING Adaptor Attenuates Experimental Autoimmune Encephalitis (2014)

Cytosolic DNA sensing activates the stimulator of IFN genes (STING) adaptor to induce IFN type I (IFN-αβ) production. Constitutive DNA sensing to induce sustained STING activation incites tolerance breakdown, leading to autoimmunity. In this study, we show that systemic treatments with DNA nanoparticles (DNPs) induced potent immune regulatory responses via STING signaling that suppressed experimental autoimmune encephalitis (EAE) when administered to mice after immunization with myelin oligodendrocyte glycoprotein (MOG), at EAE onset, or at peak disease severity. DNP treatments attenuated infiltration of effector T cells into the CNS and suppressed innate and adaptive immune responses to myelin oligodendrocyte glycoprotein immunization in spleen. Therapeutic responses were not observed in mice treated with cargo DNA or cationic polymers alone, indicating that DNP uptake and cargo DNA sensing by cells with regulatory functions was essential for therapeutic responses to manifest. Intact STING and IFN-αβ receptor genes, but not IFN-γ receptor genes, were essential for therapeutic responses to DNPs to manifest. Treatments with cyclic diguanylate monophosphate to activate STING also delayed EAE onset and reduced disease severity. Therapeutic responses to DNPs were critically dependent on IDO enzyme activity in hematopoietic cells. Thus, DNPs and cyclic diguanylate monophosphate attenuate EAE by inducing dominant T cell regulatory responses via the STING/IFN-αβ/IDO pathway that suppress CNS-specific autoimmunity. These findings reveal dichotomous roles for the STING/IFN-αβ pathway in either stimulating or suppressing autoimmunity and identify STING-activating reagents as a novel class of immune modulatory drugs.
Circulating human mammary epithelial antigens in breast cancer. (1982)

Heterologous specific antisera against human mammary epithelial antigens (HME-Ags), which are present in the human milk fat globule membrane and breast epithelial cells, were used in a solid-phase radioimmunoassay to determine the presence of these antigens in the sera of patients with disseminated cancer of the breast and other organs. Breast cancer patients carry high levels of HME-Ags in their circulation, while patients with disseminated nonbreast cancer, as well as normal female controls, do not. A similar release of HME-Ags in the circulation was shown by us in a model system. To further corroborate these findings, a three-step procedure for the extraction and identification of HME-Ags from the sera was devised. In this analytical procedure, circulating HME-Ags are recovered on a solid phase carrying their corresponding antibody (anti-HME) and radioiodinated in situ. Later, the labeled HME-Ags are released from the solid phase and characterized by NaDodSO4 gel electrophoresis. With this procedure, HME-Ags were isolated from sera of breast cancer patients but not from sera of nonbreast cancer patients or of normal female controls. The extracted HME-Ags had molecular masses of 150,000, 70,000, and 46,000 daltons. To further support these findings, a monoclonal antibody, BLMRL-HMFG-Mc3, directed to the 46,000-dalton HME-Ag was also used to extract its corresponding antigen from sera. Breast cancer patient sera contained such antigen while the sera of the other patients and controls did not. This highly sensitive methodology offers a specific approach to breast cancer diagnosis as well as further insight into the nature of circulating antigens with a view to increasing our understanding of breast cancer biology.