gebhart/patrepeval huggingface dataset:
A sweeping line algorithm based on two dimensional region search (2002)

The authors present a new plane-sweep algorithm which is based on several primitive functions of region query for a number of overlapped rectangles in 2-D space. A theorem proves that the presented algorithm can be built from any spatial data structure with region query functions. Experimental results presented show that this algorithm has been successfully implemented in C language based on two kinds of spatial data structures, the multiple storage quad tree and the quad list quad tree. This algorithm can be performed in a time complexity of O(N log N).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Quantification of the N-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples (2012)

Cells secrete a large number of proteins to communicate with their surroundings. Furthermore, plasma membrane proteins and intracellular proteins can be released into the extracellular space by regulated or non-regulated processes. Here, we profiled the supernatant of 11 cell lines that are representative of different stages of breast cancer development by specifically capturing N-glycosylated peptides using the N-glyco FASP technology. For accurate quantification we developed a super-SILAC mix from several labeled breast cancer cell lines and used it as an internal standard for all samples. In total, 1398 unique N-glycosylation sites were identified and quantified. Enriching for N-glycosylated peptides focused the analysis on classically secreted and membrane proteins. N-glycosylated secretome profiles correctly clustered the different cell lines to their respective cancer stage, suggesting that biologically relevant differences were detected. Five different profiles of glycoprotein dynamics during cancer development were detected, and they contained several proteins with known roles in breast cancer. We then used the super-SILAC mix in plasma, which led to the quantification of a large number of the previously identified N-glycopeptides in this important body fluid. The combination of quantifying the secretome of cancer cell lines and of human plasma with a super-SILAC approach appears to be a promising new approach for finding markers of disease.
FUZZINESS VS. PROBABILITY (1990)

Fuzziness is explored as an alternative to randomness for describing uncertainty. The new sets-as-points geometric view of fuzzy sets is developed. This view identifies a fuzzy set with a point in a unit hypercube and a nonfuzzy set with a vertex of the cube. Paradoxes of two-valued logic and set theory, such as Russell's paradox, correspond to the midpoint of the fuzzy cube. The fundamental questions of fuzzy theory—How fuzzy is a fuzzy set? How much is one fuzzy set a subset of another?—are answered geometrically with the Fuzzy Entropy Theorem, the Fuzzy Subsethood Theorem, and the Entropy-Subsethood Theorem. A new geometric proof of the Subsethood Theorem is given, a corollary of which is that the apparently probabilistic relative frequency nA /N turns out to be the deterministic subsethood S(X, A), the degree to which the sample space X is contained in its subset A. So the frequency of successful trials is viewed as the degree to which all trials are successful. Recent Bayesian polemics against fuzzy theory are examined in light of the new sets-as-points theorems.
Serological evidence of infection with Chlamydia pneumoniae is related to the severity of asthma (2000)

There is evidence that infection with Chlamydia pneumoniae is associated with asthma of recent onset and that it can influence the severity of asthma. This has led to the suggestion that macrolide antibiotics may be useful in the treatment of asthma in subjects infected with C. pneumoniae. This study examined the association between immunoglobulin (Ig)G and IgA titres to C. pneumoniae and the severity of asthma. IgG and IgA antibodies to C. pneumoniae were measured in 619 subjects with asthma (18-60 yrs), using the microimmunofluoresence method. Subjects were asked about their use of asthma medicines, symptoms, previous hospitalization for asthma, smoking status and age of onset of asthma. In subjects with IgG titres of > or =1:64 and/or IgA titres > or =1:16 (n=212), spirometry was performed and peak expiratory flow rate (PEFR) and symptoms were recorded twice daily for 4 weeks on a diary card. The use of high dose inhaled steroids was associated with an increase of 74.1% in the titre of IgG antibodies (p=0.04) and an increase of 70.6% in the titre of IgA antibodies (p=0.0001) when compared with the use of low dose inhaled steroids. There was an inverse association between IgG antibodies and forced expiratory volume in one second (FEV1) as a percentage of predicted in those subjects with elevated IgG and/or IgA (p=0.04). In this group IgA antibodies were also associated with a higher daytime symptom score (p=0.04). Higher titres of antibodies to Chlamydia pneumoniae appears to be associated with markers of asthma severity. This raises the possibility that chronic infection with Chlamydia pneumoniae leads to an increase in the severity of asthma. Studies aimed at eradicating chronic infection with Chlamydia pneumoniae are necessary to determine whether or not this is the case.
The type and effect discipline (2003)

The type and effect discipline, a framework for reconstructing the principal type and the minimal effect of expressions in implicitly typed polymorphic functional languages that support imperative constructs, is introduced. The type and effect discipline outperforms other polymorphic type systems. Just as types abstract collections of concrete values, effects denote imperative operations on regions. Regions abstract sets of possibly aliased memory locations. Effects are used to control type generalization in the presence of imperative constructs while regions delimit observable side effects. The observable effects of an expression range over the regions that are free in its type environment and its type; effects related to local data structures can be discarded during type reconstruction. The type of an expression can be generalized with respect to the variables that are not free in the type environment or in the observable effect.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
HERITABILITY OF DENTAL CHARACTERS IN THE HOUSE MOUSE (1965)

The currently popular synthetic theory of evolution has been forged from data and concepts contributed by both the neontologist and the paleontologist. In general, however, the organisms and characters studied by the former have little in the way of an historical record, while the groups and organ-systems of paleontological interest have rather infrequently (e.g., Olson and Miller, 1958; Berry, 1964) been subjected to modern microevolutionary analyses. Change in the molar teeth of mammals is one of our best historical evidences of evolution. Although dental morphology has received considerable attention from students of Recent and fossil mammals, knowledge of the hereditary and environmental components of dental variation remains meager in spite of the potential value for studies of evolutionary mechanisms. Study of the variation in the dentition of extant rodents would seem to offer a particularly attractive opportunity to subject to genetical analysis characters which do possess a reasonable fossil record. Many, if not most, of the traits utilized by the systematist are of a quantitative, i.e., continuously varying, nature. In recent years a fundamental approach to such characters has been to partition their phenotypic variation into a number of causal categories (Falconer, 1960). The primary step is, of course, the identification of the relative contributions of the heredity and the environment. These, in turn, may be divided into a number of subclasses of causation. In a recent study (Bader and Lehmann, 1965) the hereditary and environmental components were estimated for three dental traits in the house mouse by appropriate comparisons of the phenotypic variation in wild, randombred, inbred, and hybrid populations. The present study is concerned primarily with the heritability of these characters. The heritability is the proportion of the total phenotypic variance due to genetic factors acting in an additive fashion, or it may be regarded as the reliability of the phenotype as an indicator of the breeding value of the individual and the population (Falconer, 1960). The total hereditary, or genotypic, variance includes both the additive and non-additive genetic fractions. Estimation of the heritability of a trait depends essentially upon the measurement of the degree of phenotypic resemblance among animals of known genetic relationship. The most commonly used methods are those of regression of offspring on one or both parents and fullor half-sib correlation. The relative merits of the various analyses are examined in detail by Falconer (1960, 1963). The method employed in the present study is that of the paternal half-sib analysis utilizing the hierarchal, or nested, analysis of variance. This design enables one to obtain an estimate of the heritability relatively free of non-additive genetic variance, to obtain an estimate of the non-heritable maternal effect, if any, and to make all measurements on one generation. It is more efficient, in the statistical sense, than the regression analysis when the heritability is low (Robertson, 1959a).
Operational Adequacy Studies of Power Systems With Wind Farms and Energy Storages (2012)

In a power system with high renewable power penetration, uncertain and intermittent characteristics of renewable energy resources become major concerns of system planning and operation. In such a power system, conventional thermal or hydro units have to be dispatched, shut down or started up more frequently to incorporate load, renewable resource variation and system failures. Slow ramp up (or down) of conventional units may cause energy shortage (or surplus) in power systems with high wind power penetration or in isolated micro grids with limited dispatchable capacity. This paper proposes a technique to evaluate operational reliability and energy utilization efficiency of power systems with high wind power penetration. The ramp rate of a conventional generator and energy storage system (ESS) are considered in the proposed technique. The effect of slow ramp-up rate or fast reduction of wind speed on system reliability is measured by the expected energy not supplied. A new index designated as the expected energy not used is proposed and formulated to represent energy surplus due to fast increase of wind speed and slow ramp down of conventional units. The IEEE-RTS is used to illustrate the applications of the proposed method.
Evaluation of PFBOA Method for the Determination of Aldehydes in Indoor Air Samples. (1997)

室内空気中アルデヒド類の測定におけるPFBOA法の有用性を2, 4-ジニトロフェニルヒドラジン法と比較することにより検討した。両方法により新築マンションの密閉状態での室内アルデヒド濃度を測定した。PFBOA法により得られた測定値はDNPH法によって得られた値とよく一致した。即ち, PFBOA法による測定値はホルムアルデヒドが31.2ppb, アセトアルデヒドが13.lppbであった。一方, DNPH法による測定値は, ホルムアルデヒドが30.8ppb, アセトアルデヒドが11.5ppbであった。DNPH法はGC-MSにより測定することができるが, その定量限界は, PFBOA法の定量限界よりも高い。それ故, PFBOA法は室内空気試料のアルデヒド類の測定に有用であることが認められた。室内空気試料中のアルデヒド濃度の削減効果についても検討した。換気はアルデヒド濃度を減少する効果があった。
Automatic ultrasound determination of thermal coagulation front during laser tissue heating (1999)

Thermal therapies using laser, microwaves, radio frequency radiation, and high intensity focused ultrasound have shown great promise for minimally invasive treatment of benign and malignant lesions. To treat tissue effectively and safely, techniques that could monitor the advancement of coagulation front during treatment are highly desirable. This paper presents a noninvasive ultrasound technique for automatically determining the propagation of coagulation damage front during laser tissue heating. The basic assumption underlying this technique is that when coagulation is taking place in a tissue, owing to thermally induced structure changes in tissue, the waveform of echo signal scattered from that treated region should be changing accordingly. We first track echoes scattered from many small tissue regions during heating using a cross-correlation echo-tracking technique. We then use the waveform-change information to determine the position of coagulation front via an automatic calculation procedure. To test our technique, we carried out 35 experiments in which we irradiated fresh canine liver samples with a Nd:YAG laser (1064-nm wavelength) at various light fluence (62 to 167 W/cm(2)) and exposure time (20 to 350 s). A 13-mm diameter 10-MHz broadband single-element spherical focused ultrasound transducer was used to detect the thermal coagulation front. The root mean square difference between ultrasonically and visually determined coagulation depths was 0.77 mm. This good agreement between visually inspected and ultrasonically determined coagulation depths shows the potential of our technique for monitoring coagulative tissue damage during thermal therapy.
Proteomic biomarkers of adverse pregnancy outcome in preterm birth: a theranostics opportunity (2007)

Biomedical research is evolving rapidly to address biological systems, such as molecular pathways integrated into complex networks. Tools for molecular discoveries are evolving to address old challenges and create new opportunities. Despite considerable financial and research effort combined with a variety of interventions, the rate of preterm birth has steadily increased to reach a high of 12.7%. Disappointingly, each year, 4.5 million premature infants are born in the USA alone. Although the etiology of most preterm births remains unknown, several distinct pathophysiological pathways are involved in triggering the syndrome, such as myometrial stretching, oxidative stress, decidual hemorrhage and infection. Novel research and diagnostic applications stemming from opportunities presented by the advances of genomics and proteomics begin to impact on clinical diagnosis, vaccine development, drug discovery and unique therapies in a modern diagnostic–therapeutic framework – part of the new scientific field of ‘theranostics.’ This review critically explores a number of newly discovered biomarkers that may potentially revolutionize the diagnosis and treatment of women at risk of preterm parturition.
Polymer-Stabilized Orthoconic Antiferroelectric Liquid Crystals (2006)

Horizontally surface-stabilized orthoconic antiferroelectric liquid crystals (OAFLCs) provide excellent contrast electrooptic switching. However, in very thin cells the bulk relaxation to the anticlinic state tends to be slow because the synclinic state is upheld by the surfaces. In cells thin enough to accomplish a surface-stabilized state of today's short-pitch OAFLC mixtures, the field-induced synclinic (ferroelectric) states often become metastable making the corresponding bright electrooptic state prevail for long times after the electric field is switched off. Fast relaxation is then achieved by specially designed waveforms. By introducing a polymer network formed by in-situ photopolymerization of a small concentration of a commercial reactive monomer dissolved in the OAFLC, we have succeded to drastically reduce the time for relaxation from the synclinic to the anticlinic state after switching off the field down to about 3 milliseconds at room temperature, without the use of any tailored electronic waveforms. The relaxation time of the polymer stabilized OAFLCs (PS-OAFLCs) is thus shorter than in todays nematic liquid crystal displays, which make PS-OAFLCs attractive for use in future high-contrast, blur-free displays.
Detection and identification of mycobacteria in formalin-fixed, paraffin-embedded tissues by nested PCR and restriction enzyme analysis (1996)

A novel assay based on a nested PCR and restriction enzyme analysis of the PCR products was developed for the rapid detection and identification of Mycobacterium bovis and M. avium-M. intracellulare species in formalin-fixed, paraffin-embedded tissue (PET) specimens. On the basis of the nucleotide sequence data obtained in the present study, general nested primers were constructed to amplify a 424-bp segment of the gene encoding the 65-kDa surface antigen of mycobacteria. The nested PCR assay proved to be highly sensitive, since as little as 5 to 10 fg of extracted mycobacterial DNA was detected. The safety of the assay as a routine method for the diagnosis of M. bovis and M. avium-M. intracellulare in PET specimens was provided by taking various precautions. In order to prevent false positivity, specific tools and procedures were applied. To detect false-negative results and assess the efficiency of the PCR, an internal standard molecule of amplification was constructed. The digestion of the amplicons with the restriction endonuclease Sau96-I allowed the identification of M. bovis and M. avium-M. intracellulare in a large number of clinical specimens. The present results indicate that PCR combined with an internal control of amplification and restriction enzyme analysis of the amplicons provides a rapid, sensitive, and reliable method for routine diagnostic laboratories to detect and identify M. bovis and M. avium-M. intracellulare in PET specimens.
Intramolecular Cyclisation of Phenolic Oximes, III.A Synthesis of <i>cis‐cis</i>‐Aerothionin (1978)

Abstract Cis‐cis ‐aerothionin has been synthesised by oxidative cyclisation of the diphenolic dioxime 4 with 2,4,4,6‐tetrabromocyclohexa‐2,5‐dienone followed by reduction with sodium tetrahydroborate. Certain methyl ethers react with cold pyridine giving misleading results when this solvent is used for 1 H‐NMR spectroscopy.
Efficient frequency-domain realization of robust generalized, sidelobe cancellers (2002)

This paper deals with hands-free acoustical front-ends for human/machine interaction in competing talker situations using efficient frequency-domain implementations of a robust generalized sidelobe canceller (GSC). A new scheme is devised which leads to a factor of three of computational savings. The GSC tracking behavior is not impaired as the block lengths are kept sufficiently small.
The nuclear orphan receptor TR4 promotes proliferation of myeloid progenitor cells. (2001)

Nuclear receptors represent key regulators in cell proliferation, differentiation, and development. Here we demonstrate that the nuclear orphan receptor TR4 is highly expressed in hematopoietic cells and tissues and have analyzed the impact of TR4 in this cell compartment. We show that TR4, when ectopically expressed in bone marrow cells via retrovirus vector, promotes proliferation of myeloid progenitor cells. Cells represent promyelocytes as judged by morphological features, expression of cell surface molecules, and specific markers like Mim-1 and CAAT/enhancer binding protein beta. We also demonstrate that the growth promoting activity of TR4 is not exclusively dependent on its association with DNA, because expression of a mutated TR4 version devoid of its DNA binding domain exhibits a similar proliferative potential as wild-type TR4. In conclusion, these data position the orphan receptor TR4 as an important regulator of myeloid progenitor cell proliferation and development.
In vitro analysis of boron-10 uptake and neutron beam design for boron neutron capture synovectomy (1996)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1996.
Nonlinear MMSE interference cancellation for asynchronous CDMA channels with convolutional coding (2003)

A trellis-based algorithm is derived in this paper for nonlinear MMSE estimation of convolutionally encoded signals in asynchronous CDMA channels with random spreading. Iterative nonlinear MMSE multiuser detection, proposed by the authors earlier for uncoded systems, is extended to forward error-correcting (FEC) coded CDMA systems by employing this algorithm. The resulting receiver is a Turbo-like combined FEC decoder and multiuser detector whose complexity is linear in the number of users. The proposed trellis-based estimation algorithm has the same order of complexity in the number of states of the FEC code as the Viterbi algorithm for optimal decoding of convolutional codes. Simulation results indicate that the proposed cancellation scheme can offer substantial improvement in performance over three other schemes in terms of cancellation error, capacity increase and tolerance to deep fades.
Plugging into Proteins: Poisoning Protein Function by a Hydrophobic Nanoparticle (2010)

Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the nanoparticle toxicity and other risks involved with these nanoparticles to human health. In this study, we use large-scale molecular dynamics simulations to study the interaction between several proteins (WW domains) and carbon nanotubes (one form of hydrophobic nanoparticles). We have found that the carbon nanotube can plug into the hydrophobic core of proteins to form stable complexes. This plugging of nanotubes disrupts and blocks the active sites of WW domains from binding to the corresponding ligands, thus leading to the loss of the original function of the proteins. The key to this observation is the hydrophobic interaction between the nanoparticle and the hydrophobic residues, particularly tryptophans, in the core of the domain. We believe that these findings might provide a novel route to the nanoparticle toxicity on the molecular level for the hydrophobic nanoparticles.
The ionic basis of chemotaxis. Separate cation requirements for neutrophil orientation and locomotion in a gradient of chemotactic peptide. (1980)

The behavior of cells undergoing chemotaxis may be analyzed in terms of their orientation, a static characteristic, and of their locomotion. We have examined the extracellular divalent cation requirements for orientation and locomotion of rabbit polymorphonuclear leukocytes (neutrophils) in a gradient of the chemotactic peptide N-formyl-methionyl-leu-cyl-phenylalanine (F-Met-Leu-Phe) using the chemotaxis chamber recently developed by Zigmond. This chamber allows direct observation of cells attached to glass coverslips as they move up a gradient of chemotactic agent established across a 1-mm bridge. The orientation of neutrophils in the direction of the gradient was equally efficient whether cells and F-Met-Leu-Phe were suspended in merium supplemented with both Ca2+ and Mg2+ (complete medium), with Mg2+ but not Ca2+ (by simple omission of Ca2+ or by addition of EGTA), or with nonsupplemented medium (by omission of Ca2+ and Mg2+ or by addition of EDTA). These data confirm and extend Zigmond's earlier observation that exogenous divalent cations are not required for polymorphonuclear leukocyte orientation toward the chemotactic peptide. In contrast, cell locomotion, determined by linking the chemotaxis chamber to a time-lapse videocassette recorder and TV monitor, is markedly affected by the medium's content of divalent cations. Cells suspended in medium supplemented with Mg2+ but not calcium (by omission or chelation) or in nonsupplemented medium moved on the average 25% more rapidly than cells in complete Ca2+ and Mg2+ medium. Although the simple omission of Mg2+ does not prevent chemotaxis, chelation of Mg2+ in the medium completely abolishes leukocyte locomotion. Addition of varying concentrations of Mg2+ to the buffer in the presence of EDTA established that cell movement is fully restored by Mg2+ concentrations in the range of 3 X 10(-9) M, concentrations easily attained in the absence of added Mg2+. It was concluded that neither Ca2+ nor Mg2+ is needed for orientation in response to F-Met-Leu-Phe. However, low levels of exogenous Mg2+ but not Ca2+ are required for effective locomotion of neutrophils in the Zigmond changer. This result contrasts with data obtained in the Boyden chamber, where exogenous Ca2+ is considered essential for maximum chemotactic response.