gebhart/patrepeval huggingface dataset:
A Prospective Longitudinal Study of BK Virus Infection in 104 Renal Transplant Recipients (2005)

BK virus (BKV) infection during the first year after renal transplantation was studied prospectively in 104 unselected consecutive patients. Viral DNA in urine (DNAuria) and plasma (DNAemia) samples was detected and quantified by real-time PCR. The noncoding control region (NCCR) of BKV isolates was sequenced. DNAuria and DNAemia occurred in 57% and 29% of patients, respectively. Three groups were defined, uninfected patients (group 1, n=45), patients with DNAuria (group 2, n=29) and patients with positive DNAemia (group 3, n=30). Active infection started within the first 3 months in 80% of patients. Cold ischemia duration over 24 h and the administration of tacrolimus were identified as significant risks factors for DNAuria, whereas it remains more frequently negative in patients receiving cyclosporine A. The risk for positive DNAemia was higher in patients with DNAuria (notably for viral load (VL)>4 log/mL) or treated with tacrolimus. No relationship was found with genetic variability in the NCCR sequence. Our data highlight the high frequency of active BKV infection after renal transplantation. Although high VL was detected in some patients, none developed a BKV nephropathy. A prospective follow-up of the whole population during the first year post renal transplantation is thus not useful to predict BKV disease.
OASIS: Online Active Semi-Supervised Learning (2011)

We consider a learning setting of importance to large scale machine learning: potentially unlimited data arrives sequentially, but only a small fraction of it is labeled. The learner cannot store the data; it should learn from both labeled and unlabeled data, and it may also request labels for some of the unlabeled items. This setting is frequently encountered in real-world applications and has the characteristics of online, semi-supervised, and active learning. Yet previous learning models fail to consider these characteristics jointly. We present OASIS, a Bayesian model for this learning setting. The main contributions of the model include the novel integration of a semi-supervised likelihood function, a sequential Monte Carlo scheme for efficient online Bayesian updating, and a posterior-reduction criterion for active learning. Encouraging results on both synthetic and real-world optical character recognition data demonstrate the synergy of these characteristics in OASIS.
Almacenamiento en dos sitios del Epiclásico: Xochicalco (Morelos) y Cacaxtla (Tlaxcala) (2012)

El almacenamiento es una estrategia económica que permite asegurar el aprovisionamiento para el futuro. Conforme las sociedades trascienden, sus necesidades van cambiando y van surgiendo los elementos necesarios para garantizar la integración económica de los sistemas políticos y el buen funcionamiento de las instituciones. Es el palacio, construcción monumental y de complejidad arquitectónica ubicada dentro del contexto urbano, un edificio multifuncional con acceso controlado y circulación restringida, que asegura la protección de lo almacenado y de lo administrado.Xochicalco, ciudad-Estado característica del periodo epiclásico, fue fundada alrededor del año 650 d.C. y abandonada y destruida para el 1000 d.C. Debido a su situación estratégica donde el acceso al agua estaba físicamente restringido, los constructores de la ciudad crearon un complejo sistema de recolección y almacenamiento de agua. En cuanto al almacenamiento de granos y alimentos, éste se realizaba en graneros dispuestos en la parte central de la ciudad, así como en grandes tinajas asociadas a las áreas de preparación de alimentos. Otros materiales y objetos de concha y piedra verde fueron almacenados y resguardados en edificios particulares denotando la importancia de los bienes almacenados.Por otra parte, Cacaxtla, sitio contemporáneo de Xochicalco, muestra elementos utilizados para el almacenamiento de diversos materiales y granos dentro del Gran Basamento, que es un ejemplo más de un edificio de carácter palaciego y que confirma lo que en cierta forma aquí se expone.
Affirming Church Activity, or Why the Church Is As True As the Gospel (1986)

Eugene England presented this paper, based on the first chapter of his book of essays, "Why the Church Is As True As the Gospel" (Bookcraft, 1986) at the AMCAP Convention in Salt Lake City, Utah, 3 October 1986. It is an expanded version of an essay first printed in Sunstone.
Modulation of host innate and adaptive immune defenses by cytomegalovirus: timing is everything (2010)

Human cytomegalovirus (HCMV) (HHV-5, a beta-herpesvirus) causes the vast majority of infection-related congenital birth defects, and can trigger severe disease in immune suppressed individuals. The high prevalence of societal infection, the establishment of lifelong persistence and the growing number of immune-related diseases where HCMV is touted as a potential promoter is slowly heightening public awareness to this virus. The millions of years of co-evolution between CMV and the immune system of its host provides for a unique opportunity to study immune defense strategies, and pathogen counterstrategies. Dissecting the timing of the cellular and molecular processes that regulate innate and adaptive immunity to this persistent virus has revealed a complex defense network that is shaped by CMV immune modulation, resulting in a finely tuned host-pathogen relationship.
Evaluation of the clinical value of the newly identified urine biomarker HIST1H4K for diagnosis and prognosis of prostate cancer in Bulgarian patients. (2014)

The results suggest that the promoter hypermethylation of HIST1H4K is rather due to aging than related to prostate carcinogenesis. To elucidate this observation analysis of larger samples is needed.
Lon Peptidase 1 (LONP1)-dependent Breakdown of Mitochondrial 5-Aminolevulinic Acid Synthase Protein by Heme in Human Liver Cells (2011)

5-Aminolevulinic acid synthase (ALAS-1) is the first rate controlling enzyme that controls cellular heme biosynthesis. Negative feedback regulation of ALAS-1 by the end product heme is well documented and provides the foundation for heme treatment of acute porphyrias, a group of diseases caused by genetic defects in the heme biosynthesis pathway and exacerbated by controlled up-regulation of ALAS-1. Heme is known to affect ALAS-1 activity by repressing gene transcription, accelerating mRNA degradation, and impeding pre-ALAS-1 mitochondrial translocation. In the current study, we examined the effect of heme on the rate of mature ALAS-1 protein turnover in human cells and tissues and explored the mediator involved in this new regulatory mechanism. We found that heme and other metalloporphyrins such as CoPP and CrPP decreased mitochondrial ALAS-1 protein through proteolysis. This degradative effect cannot be emulated by iron or free protoporphyrin, two major chemical components of the heme ring, and is independent of oxidative stress. Down-regulating the activity of mitochondrial LONP1, an ATP-dependent protease that controls the selective turnover of mitochondrial matrix proteins, with potent inhibitors and specific siRNA diminished the negative effect of heme on mitochondrial ALAS-1. Therefore, our data support the existence of a conserved heme feedback regulatory mechanism that functions on the mature form of ALAS-1 protein through the activity of a mitochondrial proteolytic system.
Automatic classification of Web queries using very large unlabeled query logs (2007)

Accurate topical classification of user queries allows for increased effectiveness and efficiency in general-purpose Web search systems. Such classification becomes critical if the system must route queries to a subset of topic-specific and resource-constrained back-end databases. Successful query classification poses a challenging problem, as Web queries are short, thus providing few features. This feature sparseness, coupled with the constantly changing distribution and vocabulary of queries, hinders traditional text classification. We attack this problem by combining multiple classifiers, including exact lookup and partial matching in databases of manually classified frequent queries, linear models trained by supervised learning, and a novel approach based on mining selectional preferences from a large unlabeled query log. Our approach classifies queries without using external sources of information, such as online Web directories or the contents of retrieved pages, making it viable for use in demanding operational environments, such as large-scale Web search services. We evaluate our approach using a large sample of queries from an operational Web search engine and show that our combined method increases recall by nearly 40% over the best single method while maintaining adequate precision. Additionally, we compare our results to those from the 2005 KDD Cup and find that we perform competitively despite our operational restrictions. This suggests it is possible to topically classify a significant portion of the query stream without requiring external sources of information, allowing for deployment in operationally restricted environments.
LipL32 Is an Extracellular Matrix-Interacting Protein of <i>Leptospira</i> spp. and <i>Pseudoalteromonas tunicata</i> (2008)

LipL32 is the major outer membrane protein in pathogenic Leptospira. It is highly conserved throughout pathogenic species and is expressed in vivo during human infection. While these data suggest a role in pathogenesis, a function for LipL32 has not been defined. Outer membrane proteins of gram-negative bacteria are the first line of molecular interaction with the host, and many have been shown to bind host extracellular matrix (ECM). A search for leptospiral ECM-interacting proteins identified the major outer membrane protein, LipL32. To verify this finding, recombinant LipL32 was expressed in Escherichia coli and was found to bind Matrigel ECM and individual components of ECM, including laminin, collagen I, and collagen V. Likewise, an orthologous protein found in the genome of Pseudoalteromonas tunicata strain D2 was expressed and found to be functionally similar and immunologically cross-reactive. Lastly, binding activity was mapped to the C-terminal 72 amino acids. These studies show that LipL32 and an orthologous protein in P. tunicata are immunologically cross-reactive and function as ECM-interacting proteins via a conserved C-terminal region.
Regulated ATF5 loss-of-function in adult mice blocks formation and causes regression/eradication of gliomas (2011)

Glioblastomas are among the most incurable cancers. Our past findings indicated that glioblastoma cells, but not neurons or glia, require the transcription factor ATF5 (activating transcription factor 5) for survival. However, it was unknown whether interference with ATF5 function can prevent or promote regression/eradication of malignant gliomas in vivo. To address this issue, we created a mouse model by crossing a human glial fibrillary acidic protein (GFAP) promoter-tetracycline transactivator mouse line with tetracycline operon-dominant negative-ATF5 (d/n-ATF5) mice to establish bi-transgenic mice. In this model, d/n-ATF5 expression is controlled by doxycycline and the promoter for GFAP, a marker for stem/progenitor cells as well as gliomas. Endogenous gliomas were produced with high efficiency by retroviral delivery of platelet-derived growth factor (PDGF)-B and p53-short hairpin RNA (shRNA) in adult bi-transgenic mice in which expression of d/n-ATF5 was spatially and temporally regulated. Induction of d/n-ATF5 before delivery of PDGF-B/p53-shRNA virus greatly reduced the proportion of mice that formed tumors. Moreover, d/n-ATF5 induction after tumor formation led to regression/eradication of detectable gliomas without evident damage to normal brain cells in all 24 mice assessed.
Interpenetrating Polymer Networks as Innovative Drug Delivery Systems (2014)

Polymers have always been valuable excipients in conventional dosage forms, also have shown excellent performance into the parenteral arena, and are now capable of offering advanced and sophisticated functions such as controlled drug release and drug targeting. Advances in polymer science have led to the development of several novel drug delivery systems. Interpenetrating polymer networks (IPNs) have shown superior performances over the conventional individual polymers and, consequently, the ranges of applications have grown rapidly for such class of materials. The advanced properties of IPNs like swelling capacity, stability, biocompatibility, nontoxicity and biodegradability have attracted considerable attention in pharmaceutical field especially in delivering bioactive molecules to the target site. In the past few years various research reports on the IPN based delivery systems showed that these carriers have emerged as a novel carrier in controlled drug delivery. The present review encompasses IPNs, their types, method of synthesis, factors which affects the morphology of IPNs, extensively studied IPN based drug delivery systems, and some natural polymers widely used for IPNs.
Multinuclear NMR Spectroscopy Studies on NH&lt;sub&gt;4&lt;/sub&gt;Cl-Induced Metabolic Alterations and Detoxification Processes in Primary Astrocytes and Glioma Cells (1998)

Glutamine synthesis, the major pathway of ammonia detoxification, and the intracellular concentration of organic osmolytes in primary astrocytes and F98 glioma cells were investigated with multinuclear magnetic resonance spectroscopy. Acute exposure to ammonia (3 h incubation with NH4Cl) raised the concentration of glutamine and other amino acids, such as glutamate and aspartate, and decreased myo-inositol, hypotaurine, and taurine concentrations. The loss of these osmolytes was partially reversed by co-treatment with the glutamine synthetase inhibitor, methionine sulphoximine. Glutamate, the precursor of glutamine, is provided by stimulated anaplerotic flux via pyruvate carboxylase and glutamate dehydrogenase activity. Thus, the glutamine increase and myo-inositol decrease observed by in vivo magnetic resonance spectroscopy on patients with hepatic encephalopathy may be due to the disturbed osmoregulation in astrocytes caused by accumulation of glutamine and the subsequent loss of organic osmolytes.
1,2,3-Triazolylidenes as Versatile Abnormal Carbene Ligands for Late Transition Metals (2008)

The [3 + 2] cycloaddition of azides and acetylenes followed by nitrogen quaternization was applied for the generation of novel and highly modular triazolium salts. The selective substitution of the 1,3,4-substitution pattern presets such salts as precursors for a new class of abnormal carbene ligands, thus expanding the family of these high-impact ligands. Metalation of the triazolium salts is highly versatile and is illustrated by direct C-H bond activation as well as by applying a transmetalation protocol, thus providing access to Pd(II), Ru(II), Rh(I), and Ir(I) abnormal carbene complexes. The donor properties of these carbenes were analyzed by using Tolman electronic parameters and were found to be slightly stronger than those the most basic normal carbenes.
Enhancing the Spectral Sensitivity and Resolution of Interferometers Using Slow-Light Media (2007)

We demonstrate experimentally that the spectral sensitivity and resolution of an interferometer can be greatly enhanced by introducing a slow-light medium into it with an enhancement factor equal to the group index of the medium.
Quadrupole ion trap mass spectrometry of peptides (2008)

Biological mass spectrometry addresses the challenging unsolved structural issues surrounding biopolymers of fundamental importance to the biomedical sciences. Key to this discipline is the ability to extract useful information from complex peptide mixtures. Several approaches were developed to analyze peptides utilizing the unique capabilities of the quadrupole ion trap mass spectrometer. An external matrix-assisted laser desorption ionization source was constructed. Detection of peptides in the mid-femtomole range and of proteins in the low-femtomole range was reported. Singly-charged molecules with molecular weights in excess of 34,000 u were observed. Peptides generated by enzymatic digestion of the P protein of Sendai virus were separated by HPLC and the technique was successfully applied to locate phosphorylation sites. A hybrid quadrupole mass filter/quadrupole ion trap mass spectrometer was assembled. Peptide mixtures were separated by sequentially transmitting one value of m/z into the ion trap for mass analysis. The sequential injection technique served to significantly reduce space charge-induced suppression effects and improved resolution and fragmentation efficiency when compared to results obtained using an ion trap. A novel method of scanning afforded the ability to perform neutral loss experiments for the identification of phosphopeptides in a mixture. A long duty cycle, due to acquisition hardware, limited the utility of this approach for continuous ionization techniques. A low flowrate ionization source was constructed and interfaced to the hybrid and to an ion trap. A unique needle configuration provided a detection limit of 75 attomole of a peptide mixture infused into the source. A new type of liquid junction was developed to apply voltage to the sample consisting of a platinum wire inserted into the sidewall of a length of Teflon tubing. The junction was versatile, robust, and easy to use and performance compared well with other types of junctions. Capillary electrophoresis and hydrophobic membranes were used to separate peptide mixtures. Detection limits of the techniques were 1 femtomole and 10 femtomoles, respectively, for angiotensin. Differential release of peptides using step elutions from the hydrophobic membrane was demonstrated, providing a sensitive, high throughput means of mixture simplification prior to separation by capillary electrophoresis.
The <i>akuB</i> <sup>KU80</sup> Mutant Deficient for Nonhomologous End Joining Is a Powerful Tool for Analyzing Pathogenicity in <i>Aspergillus fumigatus</i> (2006)

To increase the frequency of homologous recombination, we inactivated the KU80 homologue in Aspergillus fumigatus (named akuB(KU80)). Homologous integration reached about 80% for both calcineurin A (calA) and polyketide synthase pksP (alb1) genes in the akuB(KU80) mutant to 3 and 5%, respectively, when using a wild-type A. fumigatus strain. Deletion of akuB(KU80) had no influence on pathogenicity in a low-dose murine infection model.
Glycomic Characterization of Prostate-Specific Antigen and Prostatic Acid Phosphatase in Prostate Cancer and Benign Disease Seminal Plasma Fluids (2009)

Prostate-specific antigen (PSA) and prostatic acid phosphatase (PAP) are glycoproteins secreted by prostate epithelial cells, and have a long clinical history of use as serum biomarkers of prostate cancers. These two proteins are present at significantly higher concentrations in seminal plasma, making this proximal fluid of the prostate a good source for purifying enough protein for characterization of prostate disease associated changes in glycan structures. With the use of seminal fluid samples representative of normal control, benign prostatic disease and prostate cancers, PAP and PSA were enriched by thiophilic absorption chromatography. Released N-linked glycan constituents from both proteins were analyzed by a combination of normal phase HPLC and MALDI-TOF spectrometry. For PSA, 40 putative glycoforms were determined, and 21 glycoforms were determined for PAP. PAP glycans were further analyzed with a hybrid triple quadrupole/linear ion trap mass spectrometer to assign specific glycoform classes to each of the three N-linked sites. The glycans identified in these studies will allow for more defined targeting of prostate disease-specific changes for PAP, PSA and other secreted prostatic glycoproteins.
Carotid sinus syndrome associated with carcinoma of the pyriform fossa. (1992)

A patient who developed syncope due to carotid sinus syndrome is described. The patient was suffering from carcinoma of the pyriform fossa for the past one year and received radiotherapy in the region of the neck for the same. Demand pacing was ineffective in alleviating syncopal episodes. The patient responded to oral administration of an anticholinergic (belladonna) and a sympathomimectic agent (orciprenaline).
Successful autologous transplantation of blood stem cells mobilized with recombinant human granulocyte-macrophage colony-stimulating factor. (1990)

We investigated the effect of recombinant human granulocyte-macrophage colony-stimulating factor (rhuGM-CSF) on the pool of circulating hemopoietic progenitor cells in 11 patients with hematological malignancies of nonmyeloid origin and 1 patient with sarcoma. These patients were eligible for autologous blood stem cell transplantation rather than autologous bone marrow transplantation because sufficient marrow aspirates could not be performed due to damage at the usual sites of bone marrow harvest by previous chemo- and/or radiotherapy. Recombinant human GM-CSF was given as continuous i.v. infusion via central venous line for a median time of 11.5 days (range 5-22 days), during which a median number of six aphereses were performed. In comparison to the pretreatment level the median increase in the number of granulocyte-macrophage colony-forming units (CFU-GM)/ml of peripheral blood was 8.5-fold. In all 12 patients a median decrease of the platelet count of 21% (range 7%-67%) was observed during rhuGM-CSF treatment prior to the start of the apheresis procedures. Six patients were treated with a myeloablative conditioning therapy consisting of total body irradiation and/or high-dose polychemotherapy followed by autografting with blood stem cells. Five of them achieved a sustained engraftment. Recombinant human GM-CSF proved to be highly efficient in increasing the number of circulating progenitor cells in these patients with severely compromised hemopoiesis. Blood stem cells harvested under a rhuGM-CSF treatment are capable of restoring hemopoiesis in man after a myeloablative pretransplant therapy.
EMT-associated up-regulation of L1CAM provides insights into L1CAM-mediated integrin signalling and NF-κB activation (2012)

Expression of L1 cell adhesion molecule (L1CAM) is associated with poor prognosis in a variety of human carcinomas including breast, ovarian and pancreatic ductal adenocarcinoma (PDAC). Recently we reported that L1CAM induces sustained nuclear factor kappa B (NF-κB) activation by augmenting the autocrine production of interleukin 1 beta (IL-1β), a process dependent on interaction of L1CAM with integrins. In the present study, we demonstrate that transforming growth factor β1 (TGF-β1) treatment of breast carcinoma (MDA-MB231) and PDAC (BxPc3) cell lines induces an EMT (epithelial to mesenchymal transition)-like phenotype and leads to the expression of L1CAM. In MDA-MB231 cells, up-regulation of L1CAM augmented expression of IL-1β and NF-κB activation, which was reversed by depletion of L1CAM, L1CAM-binding membrane cytoskeleton linker protein ezrin, β1-integrin or focal adhesion kinase (FAK). Over-expression of L1CAM not only induced NF-κB activation but also mediated the phosphorylation of FAK and Src. Phosphorylation was not induced in cells expressing a mutant form of L1CAM (L1-RGE) devoid of the integrin-binding site. FAK- and Src-phosphorylation were inhibited by knock-down of various components of the integrin signalling pathway such as β1- and α5-integrins, integrin-linked kinase (ILK), FAK and the phosphoinositide 3-kinase (PI3K) subunit p110β. In summary, these results reveal that during EMT, L1CAM promotes IL-1β expression through a process dependent on integrin signalling and supports a motile and invasive tumour cell phenotype. We also identify important novel downstream effector molecules of the L1CAM-integrin signalling crosstalk that help to understand the molecular mechanisms underlying L1CAM-promoted tumour progression.