gebhart/patrepeval huggingface dataset:
Interval mapping of multiple quantitative trait loci. (1993)

The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple QTL models instead of the single QTL models (and no QTL models) used in interval mapping. However, the computational work involved with multiple QTL models is considerable when the number of QTLs is large. In this paper it is proposed to combine multiple linear regression methods with conventional interval mapping. This is achieved by fitting one QTL at a time in a given interval and simultaneously using (part of) the markers as cofactors to eliminate the effects of additional QTLs. It is shown that the proposed method combines the easy computation of the single QTL interval mapping method with much of the efficiency and accuracy of multiple QTL models.
Learning query intent from regularized click graphs (2008)

This work presents the use of click graphs in improving query intent classifiers, which are critical if vertical search and general-purpose search services are to be offered in a unified user interface. Previous works on query classification have primarily focused on improving feature representation of queries, e.g., by augmenting queries with search engine results. In this work, we investigate a completely orthogonal approach --- instead of enriching feature representation, we aim at drastically increasing the amounts of training data by semi-supervised learning with click graphs. Specifically, we infer class memberships of unlabeled queries from those of labeled ones according to their proximities in a click graph. Moreover, we regularize the learning with click graphs by content-based classification to avoid propagating erroneous labels. We demonstrate the effectiveness of our algorithms in two different applications, product intent and job intent classification. In both cases, we expand the training data with automatically labeled queries by over two orders of magnitude, leading to significant improvements in classification performance. An additional finding is that with a large amount of training data obtained in this fashion, classifiers using only query words/phrases as features can work remarkably well.
Aberrant activation of c-kit protects colon carcinoma cells against apoptosis and enhances their invasive potential. (2001)

Multiple genetic aberrations contribute to the development of biologically aggressive, clinically malignant colorectal carcinomas (CRCs). Some of these have been linked to inappropriate signaling through the tyrosine kinase moieties of growth factor receptors. We have described previously (G. Bellone et al., J. Cell. Physiol., 172: 1-11, 1997) that human CRCs overexpress both the receptor tyrosine kinase c-kit and its ligand, stem cell factor (SCF), relative to normal mucosa cells, thus establishing an autocrine c-kit-mediated loop. In addition, we noted that exogenous SCF contributes to anchorage-independent growth of HT-29 colon carcinoma cells in semisolid medium. Here, we investigated possible roles of the c-kit/SCF autocrine/paracrine system in survival and invasive capacity of DLD-1 colon carcinoma cells. We report that SCF was required for migration and invasion of DLD-1 cells through reconstituted basement membranes (Matrigel) and up-regulated gelatinase (matrix metalloproteinase-9) activity in DLD-1 cells. Furthermore, we describe that SCF supported survival of DLD-1 cells in growth factor-deprived conditions. These results suggest multiple roles of c-kit activation in support of the malignant phenotype of DLD-1 cells related to growth, survival, migration, and invasive potential.
The Proposed Inflammatory Pathophysiology of Rosacea: Implications for Treatment (2003)

The pathophysiology of the vascular and inflammatory stages of facial rosacea and proposes an underlying cause is reviewed. It can be argued that all the stigmata of rosacea are manifestations of an inflammatory process: neutrophilic dermatosis. For this reason, treatments that block neutrophil involvement in the development of rosacea, such as topical metronidazole and systemic antibodies, should be considered first-line therapy for all stages of the disease.
A SYNTHESIS OF ALANINE LABELED WITH HEAVY CARBON IN THE α POSITION (1949)

During a series of investigations on amino acid metabolism in Torulopsis yeast (1, 2) we required quantities of D-and n-alanine isotopically marked in position 2. The well known methods for obtaining alanine, e.g. from acetaldehyde by the Strecker method (3-5) or from acetic acid through acetyl cyanide and pyruvic acid (6), although theoretically capable of application in our case, were found to be unsuitable in view of the large number of steps involved and the low over-all yields.A new synthesis was, therefore, clearly indicated.For various reasons it seemed desirable to form the carboxyl group by an oxidation step at as late a stage as possible in the synthesis.With this end in view several routes were explored which aimed at the preparation of compounds of the type R'-C*H(NHz)-CH, where R = 2-furyl-or polyhydroxyphenyl.Oxidation of such compounds after appropriate protection of the amino group should give alanine derivatives labeled in position 2.This method of introducing a carboxyl group into a molecule has been described by several workers (7, 9.
In Vivo Pro-Apoptotic and Antitumor Efficacy of a c-Raf Antisense Phosphorothioate Oligonucleotide: Relationship to Tumor Size (2002)

Previously, we have shown that a phosphorothioate antisense oligonucleotide (ODN) targeted against c-raf RNA (ISIS5132; cRaf-AS) induces apoptosis in human tumor cells. We now show that the same ODN also efficiently triggers apoptosis in human tumor xenografts in nu/nu mice. Although cRaf-AS showed a clearly inhibitory effect on the growth of established tumors (approximately 150 mm3) compared to a mismatched control ODN (MM), tumor progression was not prevented. This correlated with a partial refractoriness of the tumor to cRaf-AS-induced cell killing, which seemed to be due to an inhomogeneous and inefficient penetration of the ODN into the tumor tissue rather than cellular resistance. In agreement with this conclusion, we found that growth of small tumors (<50 mm3) was completely inhibited concomitantly with an accumulation of the ODN throughout the tumor. These data show that the cRaf-AS is a highly efficacious antitumor agent, provided accessibility into the tumor tissue is warranted, and suggest that PS-AS-ODN treatment may be particularly useful in an adjuvant setting.
Principles of Psychoneuroendocrinoimmunotherapy of Cancer (2011)

Recent advances in the knowledge of the mechanisms responsible for antitumor immunity have stimulated the elaboration of new cancer immunotherapeutic strategies. Moreover, more recent discoveries have demonstrated that immune responses are under a physiological modulatory control played by several neuroendocrine pathways, which explain the differences between the in vivo and in vitro immune responses. While until a few years ago the evaluation of the immune status of cancer patients was substantially established on the basis of clinical empirical criteria, recent discoveries of the antitumor cytokine network have allowed the biochemical bases of anticancer immunity to be defined, leading to new anticancer immunotherapeutic strategies, on the basis of patient neuroendocrine and neuroimmune status, in an attempt to correct the great number of cancer-related alterations on the basis of knowledge of the physiopathology of anticancer immunity. The rationale for cancer neuroimmunotherapy consists of the possibility to enhance the efficacy of the various immunotherapeutic strategies by a concomitant administration of antitumor cytokines (namely IL-2), in addition to neuroendocrine endogenous molecules (namely the pineal indole hormones), able to stimulate the anticancer immunoresponse by amplifying the anticancer reaction and/or by counteracting the generation of immunosuppressive events.
Potent and Selective Agonists of Sphingosine 1-Phosphate 1 (S1P1): Discovery and SAR of a Novel Isoxazole Based Series (2016)

Sphingosine 1-phosphate (S1P) is the endogenous ligand for the sphingosine 1-phosphate receptors (S1P1-5) and evokes a variety of cellular responses through their stimulation. The interaction of S1P with the S1P receptors plays a fundamental physiological role in a number of processes including vascular development and stabilization, lymphocyte migration, and proliferation. Agonism of S1P1, in particular, has been shown to play a significant role in lymphocyte trafficking from the thymus and secondary lymphoid organs, resulting in immunosuppression. This article will detail the discovery and SAR of a potent and selective series of isoxazole based full agonists of S1P1. Isoxazole 6d demonstrated impressive efficacy when administered orally in a rat model of arthritis and in a mouse experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis.
Site-Specific Cleavage of Human Chromosome 4 Mediated by Triple-Helix Formation (1991)

Direct physical isolation of specific DNA segments from the human genome is a necessary goal in human genetics. For testing whether triple-helix mediated enzymatic cleavage can liberate a specific segment of a human chromosome, the tip of human chromosome 4, which contains the entire candidate region for the Huntington's disease gene, was chosen as a target. A 16-base pyrimidine oligodeoxyribonucleotide was able to locate a 16-base pair purine target site within more than 10 gigabase pairs of genomic DNA and mediate the exact enzymatic cleavage at that site in more than 80 percent yield. The recognition motif is sufficiently generalizable that most cosmids should contain a sequence targetable by triple-helix formation. This method may facilitate the orchestrated dissection of human chromosomes from normal and affected individuals into megabase sized fragments and facilitate the isolation of candidate gene loci.
Hand Geometry: A New Approach for Feature Extraction (2006)

This work presents a complete control access system based on the hand geometry, a hardware key and a vital sign detector. The circuitry reads the hardware key and the heartbeat in order to confirm the identity of the author given by the analysis of the hand image. The presented system distinguish itself from other similar biometric systems mainly because of the feature extraction process which is based on the analysis of the curvature profile of the image, making the system invariant to the rotation and translation of the hand. This makes unnecessary the use of any kind of restriction devices such as pins or pegs to position the hand. FAR rates as low as 0.8% were obtained by the use of simple weighted geometric features on a database of more than 360 hand images.
Properties of polymer electrolytes composed of poly(ethylene oxide) and ionic liquids according to hard and soft acids and bases theory (2011)

We investigated the miscibility of 12 different ionic liquids (ILs) with poly(ethylene oxide) (PEO) under excess salt conditions, using hard and soft, acids and bases (HSAB) theory. The hardness of the component ions of a series of ILs was estimated from the energy calculation of their HOMO and LUMO. ILs composed of relatively hard acids, such as imidazolium cation, and soft bases such as bis(trifluoromethanesulfonyl)imide anion, displayed excellent miscibility with PEO regardless of mixing ratio. Good miscibility implies that the ions strongly interact with PEO chains, and accordingly the ionic conductivity decreased with increasing PEO content. On the other hand, the same ionic conductivity was found regardless of mixing ratio when ILs composed of soft acid and soft base such as N ‐methyl‐ N ‐butylpyrrolidinium bis(trifluoromethanesulfonyl)imide was mixed with PEO. These data suggest that high ionic conductivity should be supported by the micro‐phase separation of polymers and ionic liquids. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Purification and characterization of a beta-1,3-glucan binding protein from plasma of the crayfish Pacifastacus leniusculus. (1990)

The plasma of the crayfish Pacifastacus leniusculus contains a protein which is able to bind to laminarin (a soluble beta-1,3-glucan) and which has been isolated by two independent methods, affinity precipitation with a beta-1,3-glucan or immunoaffinity chromatography. The purified beta-1,3-glucan binding protein was homogenous as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It is a monomeric glycoprotein with a molecular mass of approximately 100,000 Da and an isoelectric point of approximately 5.0. Amino acid analysis showed a very high similarity with the amino acid composition of beta-1,3-glucan binding proteins recently purified from two insects, the cockroach Blaberus craniifer and the silkworm Bombyx mori. The N-terminal amino acid sequence was determined to be: H2N-Asp-Ala-Gly-X-Ala-Ser-Leu-Val-Thr-Asn-Phe-Asn-Ser-Ala-Lys-Leu-X-X-Ly s--- Using monospecific rabbit polyclonal antibodies, the presence of this protein has also been shown within the blood cells. The purified beta-1,3-glucan binding protein did not show any peptidase or phenoloxidase activity but was able to enhance the activation of hemocyte-derived peptidase and prophenoloxidase only in the presence of the beta-1,3-glucan, laminarin, whereas mannan, dextran (alpha-glucan), or cellulose (beta-1,4-glucan) incubated with the beta-1,3-glucan binding protein had no effect on these enzyme activities. The beta-1,3-glucan binding protein could only be affinity-precipitated from crayfish plasma by the beta-1,3-glucans laminarin or curdlan (an insoluble beta-1,3-glucan), while mannan or dextran did not bind to the beta-1,3-glucan binding protein. No hemagglutinating activity of the purified beta-1,3-glucan binding protein could be detected.
Eph-B2/Ephrin-B2 Interaction Plays a Major Role in the Adhesion and Proliferation of Waldenstrom's Macroglobulinemia (2011)

Ephrin-B2/Eph-B2 axis regulates adhesion, proliferation, cell cycle, and tumor progression in vivo through the interaction of WM with the cells in the bone marrow microenvironment.
Cow's Milk Formula as a Cause of Infantile Colic: A Double-Blind Study (1982)

The role of cow's milk in infantile colic in formula-fed infants was estimated in a double-blind study. Sixty colicky infants were given a cow's milk-containing formula (Enfamil) and a cow's milk-free formula based on soy (ProSobee). Eleven infants (18%) were free of symptoms while receiving soy formula. Symptoms of 32 infants (53%) were unchanged or worse when they were fed cow's milk formula and soy formula, but symptoms disappeared when they were fed a formula containing hydrolyzed casein (Nutramigen). Symptoms of 17 infants (29%) could not be related to the diet; these infants were permitted to continue on a cow's milk-based formula. A challenge with cow's milk-based formula after one month (at approximately age 3 months) produced symptoms of infantile colic in 22 infants (36%). At age 6 months, a challenge with cow's milk was positive in 11 infants (18%) with epidermal and gastrointestinal symptoms. Eight infants (13%) at 12 months of age and five infants (8%) at 16 months of age were still intolerant to cow's milk. Cow's milk seems to be a major cause of infantile colic in formula-fed infants. A dietary treatment is suggested for moderate or severe forms of the colic. Cow's milk protein intolerance is common later in infancy in these infants.
Long‐Term Organ Culture of Large Numbers of Human Fetal Pancreata: Analysis of Their Insulin Secretion (1987)

Cultured human fetal pancreas has been transplanted into diabetic man in an attempt to cure the metabolic disorder. However, the capacity of large numbers of these organs to secrete insulin in organ culture has not been reported previously. This report sets out the characteristics of 321 human fetal pancreases of gestational age 12-20 weeks obtained over a period of 34 months, 295 of these being maintained in organ culture. Average insulin secretion was constant at 2.22 +/- 0.35 mU/plate/day over a 90-day period, the maximal duration of culture possible. Explants were lost because of infection or reduced insulin secretion. Practical guidelines for obtaining and maintaining viable explants in culture were established as follows: Insulin secretion had to be greater than 0.1 mU/plate/day. Secretory rates of this order were associated with a positive insulinogenic response to theophylline. Prostaglandin induction, suction curettage, and hysterotomy were equally suitable as methods of termination of pregnancy. The pancreas had to be obtained within 4 hours of termination of pregnancy. The tissue had to be diced into explants within a further 4 hours.
Identification of a New Scaffold for Hsp90 C-Terminal Inhibition (2013)

Inhibition of Hsp90 C-terminal function is an advantageous therapeutic paradigm for the treatment of cancer. Currently, the majority of Hsp90 C-terminal inhibitors are derived from novobiocin, a natural product traditionally used as an antibiotic. Assisted by molecular docking studies, a scaffold containing a biphenyl moiety in lieu of the coumarin ring system found in novobiocin was identified for development of new Hsp90 C-terminal inhibitors. Initial structure-activity studies led to derivatives that manifest good antiproliferative activity against two breast cancer cell lines through Hsp90 inhibition. This platform serves as a scaffold upon which new Hsp90 C-terminal inhibitors can be readily assembled for further investigation.
Propagation Characteristics of Guided Modes in a Solid Dielectric Pyramidal Horn (2012)

An analytical theory has been developed for finding out the modal characteristics of a solid dielectric pyramidal horn. The dispersion characteristics have been solved numerically by varying various parameters, such as, axial length, flare angle and relative dielectric constant of the horn to investigate the modal characteristics which is crucial to include or avoid higher order modes in dielectric horn antenna design.
A weighted overlap-add method of short-time Fourier analysis/Synthesis (1980)

In this correspondence we present a new structure and a simplified interpretation of short-time Fourier synthesis using synthesis windows. We show that this approach can be interpreted as a modification of the overlap-add method where we inverse the Fourier transform and window by the synthesis window prior to overlap-adding. This simplified interpretation results in a more efficient structure for short-time synthesis when a synthesis window is desired. In addition, we show how this structure can be used for analysis/synthesis applications which require different analysis and synthesis rates, such as time compression or expansion.
Plasma proteins in a standardised skin mini-erosion (I): permeability changes as a function of time (2002)

The results indicate that fluid sampled at 0 h after forming the erosion represents dermal IF before the full onset of inflammation. From 24 h onward, the sampled fluid reflects a steady state of increased permeability induced by inflammation. This technique is promising as a tool for clinically sampling substances that are freely distributed in the body and as a model for studying inflammation and vascular permeability.
HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity (2013)

These findings imply that the development of CrNA might depend on specific characteristics of early Env. Env signatures that correlate with the induction of CrNA might be relevant for the design of effective HIV-1 vaccines.
New thermal wave aspects on burn evaluation of skin subjected to instantaneous heating (1999)

Comparative studies on the well-known Pennes' equation and the newly developed thermal wave model of bioheat transfer (TWMBT) were performed to investigate the wave like behaviors of bioheat transfer occurred in thermal injury of biological bodies. The one-dimensional TWMBT in a finite medium was solved using separation of variables and the analytical solution showed distinctive wave behaviors of bioheat transfer in skin subjected to instantaneous heating. The finite difference method was used to simulate and study practical problems involved in burn injuries in which skin was stratified as three layers with various thermal physical properties. Deviations between the TWMBT and the traditional Pennes' equation imply that, for high flux heating with extremely short duration (i.e., flash fire), the TWMBT which accounts for finite thermal wave propagation may provide realistic predictions on burn evaluation. A general heat flux criterion has been established to determine when the thermal wave propagation dominates the principal heat transfer process and the TWMBT can be used for tissue temperature prediction and burn evaluation. A preliminary interpretation on the mechanisms of the wave like behaviors of heat transfer in living tissues was conducted. The application of thermal wave theory can also be possibly extended to other medical problems which involve instantaneous heating or cooling.
Updates and Incremental Validation of XML Documents (2003)

We consider the incremental validation of updates on XML documents. When a valid XML document (i.e., one satisfying some constraints) is updated, it has to be verified that the new document still conforms to the imposed constraints. Incremental validation of updates leads to significant savings on computing time when compared to brute-force validation of an updated document from scratch. This paper introduces a correct and complete set of update operations that can be integrated in an XML manipulation language. Indeed, any document generated by a composition of our update operations is valid, and, every valid document can be generated by a composition of our update operations (from the empty document). To accept an update, the validity of the result is checked first (without any change on the original document). Validation tests are performed incrementally, i.e., only the validity of the part of the document directly affected by the update is checked. Changes to the original document are effectively performed only when the update is accepted. 1
Level of reactive oxygen species induced by p21WAF(1)/CIP(1) is critical for the determination of cell fate (2009)

p21(WAF(1)/)(CIP(1)) is a well-known cell cycle regulatory protein which is overexpressed in several cancer cell lines, and known to determine cell fate. We generated three recombinant adenovirus vectors that expressed either the full-length p21 (Ad-p21F), a p21 mutant with a deletion of the C-terminal proliferative cell nuclear antigen (PCNA) binding domain (Ad-p21N), or a p21 mutant with a deletion of the N-terminal cyclin-dependent kinase binding domain (Ad-p21C). We transfected these vectors into five cancer cell lines. Premature senescence was induced in all of the lines only following transfection with Ad-p21N and Ad-p21F. In addition, apoptosis was also induced in LoVo and HCT116 cells that harbored wild-type p53 and the reactive oxygen species (ROS) level was higher than in senescent cells. Finally, the induction of apoptosis was inhibited by using siRNA to downregulate p53. This observation implies that there is a feedback signaling loop involving p21/ROS/p53 in apoptotic responses. It appears to be, at least in part, driven by high levels of p21 protein. Next, we investigated the cell death effect of endogenous p21 protein on cell fate using sodium butyrate (NaB). Treatment with 1 mM NaB or 2 to 5 mM NaB induced senescence or apoptosis, respectively. The level of intracellular ROS in 5 mM NaB treated cells was 2-fold higher, compared with that in 1 mM NaB treated cells. We also demonstrated that DNA damage response signals including ataxia telangiectasia mutated, gammaH2AX, and p38 MAPK were involved in NaB-induced cell death. The magnitude of intracellular ROS levels in response to p21 elicited either senescence or apoptosis in the cancer cell lines.