gebhart/patrepeval huggingface dataset:
A structure-based approach to predicting in vitro transcription factor-DNA interaction (2013)

Summary form only given. Understanding the mechanism of transcriptional regulation remains to be an inspiring stage of molecular biology. Within the popular methods for modeling TFBS, position-specific weight matrix and k-mer based approaches have gained great success. However, both approaches fail to consider the structural properties of a binding site. Recently, a novel TFBS modeling and predicting approach is presented by Bauer et al. (2010), where the sequence-specific chemical and structural features of DNA are applied. However, the in vivo protein-DNA interactions observed in ChIP-chip assays, which were used in this study, are not necessarily direct, as some TFs tend to interact with DNAs extensively through other partners. Therefore, an evaluation on a proper in vitro dataset would be more appropriate to reveal the benefit of such physicochemical features in modeling TF-DNA interactions. Recently, in vitro protein-binding microarray experiment has greatly improved the understanding of transcription factor-DNA interaction. It is a high-throughput experiment used to measure the in vitro binding affinity of a given TF to the sequences on the probe array. Because typical confounding factors such as transcription co-factors present in ChIP-based experiments are eliminated, PBM data provide an excellent information source to develop structural models for TF-DNA interactions. On the other hand, directly mapping of the 3-mer or 4-mer based meta-features to the candidate DNA binding sequences as in their work may not reflect the TF-DNA binding nature, since a TFBS is usually an 8 to 12 base-pair. As a result, conventionally machine-learning algorithms, which rely on well-structured feature vector and label pairs, may not work well in modeling PBM data. In this paper we propose a novel approach to predicts in vitro transcription factor binding based on the structural properties of DNA using a so-called multiple-instance learning algorithm. Compared to conventional (single-instance based) learning algorithms, our multi-instance learning-based algorithm does not require the knowledge of the actual binding site within a candidate probe sequence, yet can still take full advantage of the physicochemical properties in modeling and predicting TF-DNA interactions. Evaluation on an in vitro protein binding microarray data of twenty mouse TFs shows that our new model performs significantly better than several k-mer or structure-based single-instance learning algorithms. It indicates that combining multi-instance learning and structural properties of DNA has promising potential for studying biological regulatory networks.
Derivatisation of 1,3,4,6-Tetra-<i>O</i>-Benzoyl-α-D-Fructofuranose at the Anomeric Site :<i>O</i>-Alkylation,<i>O</i>-Acylation,<i>O</i>-Arylation, Amination and Selenation Reactions (1992)

Abstract Treatment of D-fructose with benzoyl chloride gave either 1,2,3,4,6-penta-O-benzoyl-α-D-fructofuranose or 1,3,4,6-tetra-O-benzoyl-α-D-fructofuranose (lα) which with methanol, 2-nitrophenol, or 4-nitrophenol in the presence of the Mitsunobu reagents, diisopropyl azodicarboxylate and triphenylphosphine, gave the corresponding fructofuranosides in good yield; an analogous reaction with 4-methoxybenzylamine gave the corresponding D-fructo-furanosylamine. Alkylation with isopropyl alcohol or t-butyl alcohol was complicated by competition from transesterification and fructose disaccharide formation. There was little or no inversion in these reactions. The 2-O-acetyl derivative of 1 reacted with selenophenol and diethyl ether-boron trifluoride to give phenyl l-deoxy-3,4,6-tri-O-benzoyl-2-seleno-α,β-D-fructofuranose as a minor product and phenyl l,3,4,6-tetra-O-benzoyl-2-seleno-α,β-D-fructo-furanose which with tris(trimethylsilyl)silane and AIBN gave l,3,4,6-tetra-O-benzoyl-2,5-anhydro-D-mannitol and l,3,4,6-tetra-O-benzoyl-2,5-anhydro-D-glucitol. Treatment of the acetyl derivative of 1 with Me3SiN3 gave l,3,4,6-tetra-O-benzoyl-α,β-D-fructofuranosyl azide which was hydrogenated to afford the corresponding fructofuranosylamine. This compound rearranged to give N-benzoyl-1,4,6,-tri-O-benzoyl-β-D-fructofuranosylarnine
Biotransformation in Double-Phase Systems: Physiological Responses of <i>Pseudomonas putida</i> DOT-T1E to a Double Phase Made of Aliphatic Alcohols and Biosynthesis of Substituted Catechols (2004)

Pseudomonas putida strain DOT-T1E is highly tolerant to organic solvents, with a logP(ow) (the logarithm of the partition coefficient of a solvent in a two-phase water-octanol system of > or =2.5. Solvent tolerant microorganisms can be exploited to develop double-phase (organic solvent and water) biotransformation systems in which toxic substrates or products are kept in the organic phase. We tested P. putida DOT-T1E tolerance to different aliphatic alcohols with a logP(ow) value between 2 and 4, such as decanol, nonanol, and octanol, which are potentially useful in biotransformations in double-phase systems in which compounds with a logP(ow) around 1.5 are produced. P. putida DOT-T1E responds to aliphatic alcohols as the second phase through cis-to-trans isomerization of unsaturated cis fatty acids and through efflux of these aliphatic alcohols via a series of pumps that also extrude aromatic hydrocarbons. These defense mechanisms allow P. putida DOT-T1E to survive well in the presence of high concentrations of the aliphatic alcohols, and growth with nonanol or decanol occurred at a high rate, whereas in the presence of an octanol double-phase growth was compromised. Our results support that the logP(ow) of aliphatic alcohols correlates with their toxic effects, as octanol (logP(ow) = 2.9) has more negative effects in P. putida cells than 1-nonanol (logP(ow) = 3.4) or 1-decanol (logP(ow) = 4). A P. putida DOT-T1E derivative bearing plasmid pWW0-xylE::Km transforms m-xylene (logP(ow) = 3.2) into 3-methylcatechol (logP(ow) = 1.8). The amount of 3-methylcatechol produced in an aliphatic alcohol/water bioreactor was 10- to 20-fold higher than in an aqueous medium, demonstrating the usefulness of double-phase systems for this particular biotransformation.
Reactivity of dorsal pedal vein of cattle to selected alkaloids associated with Acremonium coenophialum-infected fescue grass. (1989)

We determined the vasoconstrictive effects of selected ergot alkaloids, and a sample containing loline and its derivative alkaloids, on the isolated dorsal pedal vein of cattle, as a model system to study one of the toxic effects that result from cattle ingesting fescue forage infected with the endophytic fungus Acremonium coenophilalum. The ergot compounds ergotamine, ergosine, and agroclavine constricted this peripheral vein of cattle, but much less so than did the alpha-adrenergic agonist norepinephrine, which supports the ergots acting as partial agonists for these receptors. However, the sample of loline and loline-derivative alkaloids did not affect the dorsal pedal vein when given at concentrations similar to those of the ergot compounds. Loline and loline-derivative alkaloid sample at high concentrations partially inhibited norepinephrine-elicited vascular contraction, an effect that appeared to be unrelated to alpha-adrenoceptor activity. Thus, in the dorsal pedal vein model in cattle, the ergopeptide alkaloids were more venoconstrictive than were loline and its derivative alkaloids.
Salivary interleukin-8 levels in children suffering from Type 1 diabetes mellitus (2013)

An elevated salivary IL-8 level in subjects with Type 1 DM without concomitant periodontitis plays a major role in the development of diabetic micro and macroangiopathy and pathogenesis of atherosclerosis. Consequently, this may offer a basis for the assessment of risk, prophylaxis and treatment of diabetic complications.
Asphaltene Precipitation Inhibitors and Phase Behaviour Control for Bitumen Recovery by Solvent Injection (2014)

Abstract In situ bitumen recovery directly depends on the reduction of bitumen viscosity. Solvent injection is an alternative to thermal bitumen recovery by steam injection. Injection of solvents containing n-alkanes like butane, propane and naphtha may lead to asphaltene precipitation and deposition in the porous media and a possible negative effect on the ultimate oil recovery. Addition of an asphaltene inhibitor (stabilizer) to solvents is a way to prevent asphaltene precipitation and deposition in a reservoir. Efficiency of an asphaltene inhibitor depends on the characteristics of the inhibitor and bitumen properties.In addition to aromatic hydrocarbons, various natural and synthetic polar heteroatom species can be used as asphaltene inhibitors. Results of the study show that deasphalted bitumen is an effective asphaltene inhibitor and it is of the same strength as environmentally hazardous aromatic hydrocarbons. Resins prevent asphaltene precipitation and are similar to expensive synthetic inhibitors. Addition of less than 8 vol. % of resins to low boiling point n-alkanes provides total asphaltene stabilizationin the process of bitumen recovery. When n-alkanes are used as solvents, it is important to know the amount of precipitated asphaltenes in the reservoir. To obtain such data, an experimental study has been conducted to simulate bitumen recovery. A specially designed experimental set-up was used in the study. The experiments allowed a set of chemical additives to be selected to improve colloidal stability of asphaltenes in bitumen.
지령 30 집 기념호 : 학보 30 집 발간 기념 국제학술대회 발표논문 ; 시 (詩) 사 (詞) / 송사의 (宋詞) 아와 (雅) 속 (俗) - 염정사를 중심으로 - (1997)

宋人詞論中, 關於`雅?俗`的辨設점着重部빈. 宋人品評詞作家或者作品時, 重視雅俗造辨, 甚墓以`雅?俗`爲品評的依據. 其實, `雅?俗`不僅在宋詞, 也在全般中國文學爭議的問題. 組略地說, `雅`雌責族·士林文學約屬性, `俗`是 市井·鄕村文學的屬性, 雅化的詞是文人詞, 俗化的調是民間詞. 宋詞起源於唐五代民間詞, 宋代文人採取新興的民間詞, 把蛇精鍊成爲文人詞, 爲了理解宋詞的特色和發展情況, 應探討宋詞裏的`雅·俗`問題. 本文以艶情詞爲中心, 初步地探討了雅·俗`問題. `雅·俗`是作者·內容及語言三者互爲連關而表現出來的風格. 敦煌詞具有民間詞的特性, 就是通俗的語言, 直說○臆的表現, 內容反映着當時民間生活的面貌和情緖, 作者是當時各階層的一般人. 花間詞的作者都是當時知織階層的文人, 因此花間詞的語言比較情練與雅, 表現比較含蓄, 內容主要是男女艶情. 北宋初期的詞, 繼承了花間詞和民間詞的風格,雅俗竝存. 柳永詞和民間詞的關係흔密切, 他不避市井俗語, 作艶情俚詞, 沾染上市井氣, 帶有濃厚的色情味, 因此柳永遺受了士人責. 柳永詞從總體看, 是偏`俗`的, 但他把民問俗詞昇華爲雅俗共賞的作品, 這是他在宋詞上的功勞. 蘇軾開拓了新境地, 一洗綺羅向澤之態, 更新了天下之耳目, 促進了宋詞的士大夫化. 蘇軾創作了不少的艶情詞, 但他的艶情詞的風格淸新高雅, 與柳永不同. 周邦彦是婉約詞的高手, 深通音律, 精於格律, 善於融化詩句, 周詞被稱爲典雅詞·格律詞的典範. 北宋詞論中, 已有尊雅忌俗之風, 至南宋, 雅俗之辨更爲鮮明, 反俗主雅的主張更爲强烈. 宋詞到了姜鑛夔吳文英張炎之手, 完成了宋詞雅化的過程. 在這個適程中, 就出現了雅詞不爲市井所歌的現象, 雅詞遂漸衰微, 同南宋共命運, 終於滅亡了.
Medicinal Plants of Neterhat, Bihar, India (1994)

In a programme to study tribal medicines, particularly for diseases for which the modern medical system has no effective treatment, localities on the Neterhat Plateau and adjoining areas were surveyed. Visits were made in different seasons, four times in two years, and tribal “herbalists” or individuals having medical knowledge of the local flora and living in the area were interviewed. Data on the medicinal uses of 105 plants species were gathered, of which 46 were recorded as new.
Intrusion analysis with deep packet inspection: Increasing efficiency of packet based investigations (2011)

Cloud computing's distributed architecture helps ensure service resilience and robustness. However, cloud architectures also increase dynamic data communications which inherently increases security risks. Examination of industry practice has revealed that increased data volume, as a result of increased communication, diminishes the efficiency of deep packet inspections (DPI). DPI is essential in protecting the cloud against malicious threats such as web exploits, zeroday attacks, data exfiltration, and malware based botnets. In this paper, we evaluate the effectiveness of a new utility that was developed to improve retrospective packet analysis which was tested against actual data center traffic from a large regional Internet Access Provider providing cloud services. Blitzdump is a lightning fast network data packet capture utility developed to improve network intrusion detection through deep packet inspection analysis. Implementation results indicate it outperformed existing techniques, in terms of query function performance, that ultimately improved efficiency in query responses by up to 6000%. Blitzdump reduces security risks by increasing the technical performance of intrusion detection to improve the security practitioner's productivity and effectiveness.
Experience and Understanding (1990)

To ask about W. H. Hudson's understanding of nature, and existence in general, is to ask such questions as: How does Hudson approach existence? What is the foundation or basis of his perceptual and interpretative awareness? In what ways does existence appear in Hudson's writings? These are some of the issues I will be attempting to deal with. Specifically, I will be fastening upon the notion of attention, in relation to an 'open', engaged, empathetic or participative mode of understanding. Attention occurs from a given, finite standpoint, involving a particularised horizon; and it is directed towards an understanding of existence in terms of its various modalities of being. This is not a simple procedure where the beings and things of existence — whatever they may be — are revealed totally, transparently, within an act of knowing: rather there are always layers, depths, degrees, shifting perspectives of illumination, and the process of understanding is an open-ended response to an essentially mysterious alterity. Beyond this, Hudson's reading of natural and existential details is ultimately directed towards the disclosure of the spiritual or supernatural.KeywordsParticipative ModeBlue ButterflyGreen EnclosureStanding MotionlessFleet StreetThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
The apelinergic system as an alternative to catecholamines in low-output septic shock (2018)

Catecholamines, in concert with fluid resuscitation, have long been recommended in the management of septic shock. However, not all patients respond positively and controversy surrounding the efficacy-to-safety profile of catecholamines has emerged, trending toward decatecholaminization. Contextually, it is time to re-examine the "maintaining blood pressure" paradigm by identifying safer and life-saving alternatives. We put in perspective the emerging and growing knowledge on a promising alternative avenue: the apelinergic system. This target exhibits invaluable pleiotropic properties, including inodilator activity, cardio-renal protection, and control of fluid homeostasis. Taken together, its effects are expected to be greatly beneficial for patients in septic shock.
Histomorphologic and immunophenotypic spectrum of primary gastro‐intestinal B‐Cell lymphomas (1991)

In order to compare primary gastro-intestinal (GI) B-cell lymphomas histomorphologically and immunophenotypically with orthologous steps of B-cell differentiation within the mucosa-associated lymphoid tissue (MALT) of the GI tract, a comprehensive panel of well characterized leucocyte differentiation antigens was composed. It comprised immunoglobulin constituents CD5, CD10, CD11c, CD20, CD23, CD24, CD30, CDw32, CD38, CD39, CDw75, CD76, and vimentin. These antigens yield characteristic immunoprofiles for the following B-cell compartments of the MALT, per se closely linked to cytologically distinct B-cell phenotypes: mantle zone (MZ), extrafollicular compartment (EF), follicle center (FC), and plasma-cell compartment (PC). An unselected series of 31 MALT B lymphomas (13 of low and 18 of high grade malignancy) was classified histologically in routine preparations and subsequently characterized immunohistochemically using fresh frozen tissue, monoclonal antibodies (MAbs) against the antigen panel listed above, and an indirect immunoperoxidase method. The final classification considered both morphology and immunoprofile of tumor cells. Ten tumors were "typical" in both respects: 2 closely corresponded to MZ, 5 to EF, 2 to FC and 1 to PC. The remaining 21 cases were characterized as "atypical" because of anaplastic cytology and/or abnormal co-expression and/or loss of antigens. A hybrid EF/FC phenotype was most frequently observed together with centrocyte-like or centrocytic anaplastic cytology of tumor cells. We conclude that MALT B-cell neoplasia comprises a broad spectrum of histo- and immunophenotypes ranging from well differentiated forms closely mimicking normal B-cell development to highly abnormal tumors which cannot be subclassified.
Mefluidide as an Enhancing Agent for Postemergence Broadleaf Herbicides in Soybeans (<i>Glycine max</i>) (1987)

In field studies, mefluidide { N -[2,4-dimethyl-5-[[(trifluoromethyl)sulfonyl] amino] phenyl] acetamide} was most effective as an enhancing agent for bentazon [3-(1-methylethyl)-(1 H )-2,1,3-benzothiadiazin-4(3 H )-one 2,2-dioxide] and/or acifluorfen {5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid} when applied as a tank mixture compared to sequential applications. The influence of mefluidide rate on weed control was not consistent. Additives improved the control of several weed species evaluated, but mefluidide generally was only equal to petroleum oil concentrate (phytobland petroleum oil plus emulsifiers in an 83:17 ratio) as an enhancing agent for bentazon and/or acifluorfen.
Clinical Pharmacokinetics of Pregabalin in Healthy Volunteers (2010)

Pregabalin has shown clinical efficacy for treatment of neuropathic pain syndromes, partial seizures, and anxiety disorders. Five studies in healthy volunteers are performed to investigate single‐ and multiple‐dose pharmacokinetics of pregabalin. Pregabalin is rapidly absorbed following oral administration, with peak plasma concentrations occurring between 0.7 and 1.3 hours. Pregabalin oral bioavailability is approximately 90% and is independent of dose and frequency of administration. Food reduces the rate of pregabalin absorption, resulting in lower and delayed maximum plasma concentrations, yet the extent of drug absorption is unaffected, suggesting that pregabalin may be administered without regard to meals. Pregabalin elimination half‐life is approximately 6 hours and steady state is achieved within 1 to 2 days of repeated administration. Corrected for oral bioavailability, pregabalin plasma clearance is essentially equivalent to renal clearance, indicating that pregabalin undergoes negligible nonrenal elimination. Pregabalin demonstrates desirable, predictable pharmacokinetic properties that suggest ease of use. Because pregabalin is eliminated renally, renal function affects its pharmacokinetics.
Update on optimized purification and characterization of natural milk allergens (2008)

Highly purified allergens namely cow's milk alpha-lactalbumin (ALA). (Bos d 4), beta-lactoglobulin (BLG) (Bos d 5) and casein (Bos d 8) and goat's milk casein were prepared from the raw milk from a single animal with a known genetic background. Consequently the natural isoforms are limited, constant and characterized. Purification included selective precipitations and chromatographical steps. Characterization of structure and allergenic activity assessment of milk allergens were carried out using physicochemical and immunochemical methods. Taken together data demonstrated the absence of impurities and of contamination by other milk allergens in each preparation. NMR and circular dichroism analyses confirmed the native conformation and proper folding of ALA and BLG and the expected absence of folding of bovine and caprine casein. Enzyme immuno assays confirmed the native conformation of BLG and the purity and immunoreactivity of all the proteins. The allergenic activity, e. g. the IgE binding capacity, of purified proteins was identical as that of those proteins when present in milk. The purified proteins also demonstrated the ability to provoke the degranulation of humanized rat basophilic leukaemia cells. All the data thus confirm the purity, identity, structural conformation and functionality of the prepared milk allergens.
Qwerty-like 3x4 keypad layouts for mobile phone (2005)

Most computer users are accustomed to the QWERTY keyboard layout. This study was started from the hypothesis that a user's skill in a QWERTY keyboard may be transferred to a 3x4 keypad environment. In order to test the hypothesis, we designed an experiment where users are instructed to type a series of sentences on a "blank" keypad after they were informed that the underlying layout is either QWERTY-like or ABC-type (alphabetical). We observed a more localized layout of typed characters over keys in the QWERTY-like case than in the ABC case. Encouraged by the results, we carried out a series of experiments in order to compare a QWERTY-like layout and an ABC-type layout, and obtained consistently better learning curves and better final typing speeds with a QWERTY-like keypad. As an effort to explain the results, we carried out an eye-gaze analysis for the two cases, and the results are presented.
Multimedia Terminal Adapter (MTA) Management Information Base for PacketCable- and IPCablecom-Compliant Devices (2006)

This memo defines a portion of the Management Information Base (MIB) for use with network management protocols in the Internet community. In particular, it defines a basic set of managed objects for Simple Network Management Protocol (SNMP)-based management of PacketCableand IPCablecom-compliant Multimedia Terminal Adapter devices. Table of Contents IPCDN MTA MIB December 2006 CODEC, COder-DECoder A Coder-DECoder is a hardware or software component used in audio/video systems to convert an analog signal to digital, and then (possibly) to compress it so that lower bandwidth telecommunications channels can be used. The signal is decompressed and converted (decoded) back to analog output by a compatible CODEC at the receiving end.
Plant Genetic Engineering (2012)

Acknowledgments 1. Introduction J. H. Dodds 2. Isolation and culture of plant protoplasts J. H. Dodds 3. Fusion of plant protoplasts J. H. Dodds 4. Isolated cell organelles and subprotoplasts: their roles in somatic cell genetics H. Lorz 5. Agrobacterium as a vector system for the introduction of genes into plants L. Herrera-Estrella, M. De Blocck, P. Zambryski, M. van Montagu and J. Schell 6. Viruses as vectors for plant genes R. Hull 7. Some possibilities for genetic engineering of Rubisco H. J. Newbury 8. Genetic engineering of seed proteins: current and potential applications R. R. D. Croy and J. A. Gatehouse 9. Applications of genetic engineering to agriculture M. G. K. Jones Author index Subject index.
Current perpendicular magnetoresistances of NiFeCo and NiFe “Permalloys” (2000)

Measurements are presented of the 4.2 K current perpendicular specific resistances (area times resistance) and magnetoresistances of a series of Ni66Fe13Co21=Py′-based symmetric exchange-biased spin valves and Py′–Co hybrid spin valves. The behaviors of both kinds of Py′-based spin valves are similar to those for comparable Ni84Fe16=Py-based spin valves. The low temperature giant magnetoresistive parameters of Py′ must, thus, be similar to those for Py, suggesting that Py′ should be a viable alternative to Py for technological uses.
THE INTERACTION OF DIALECT AND STYLE IN URBAN AMERICAN ENGLISH<sup>1</sup> (1971)

The largely unexplained relationship between stylistic variation and dialect differentiation in urban American English is discussed in terms of five current assumptions made by socio‐linguists in recent years. Implications of such assumptions are drawn for language use and language development in inner city schools. Three general guidelines emerge: (i) it is desirable for teachers to encourage the natural development of more formal dialect variants for all of their students with full acceptance of the validity of the less formal dialects that all children use; (ii) teachers should be trained to understand and to accept the informal styles used by all of the students they encounter; and (iii) urban Americans should be encouraged to recognize the emergence of dialect differences in inter‐ethnic communication for what they, in fact, are: an indication of developing friendship and informality.