gebhart/patrepeval huggingface dataset:
Autophagy regulates the processing of amino terminal huntingtin fragments (2003)

The N-terminus of mutant huntingtin (htt) has a polyglutamine expansion and forms neuronal aggregates in the brain of Huntington's disease (HD) patients. Htt expression in vitro activates autophagy, but it is unclear whether autophagic/lysosomal pathways process htt, especially N-terminal htt fragments. We explored the role of autophagy in htt processing in three cell lines, clonal striatal cells, PC12 cells and rodent embryonic cells lacking cathepsin D. Blocking autophagy raised levels of exogenously expressed htt1-287 or 1-969, reduced cell viability and increased the number of cells bearing mutant htt aggregates. Stimulating autophagy promoted htt degradation, including breakdown of caspase cleaved N-terminal htt fragments. Htt expression increased levels of the lysosomal enzyme cathepsin D by an autophagy-dependent pathway. Cells without cathepsin D accumulated more N-terminal htt fragments and cells with cathepsin D were more efficient in degrading wt htt than mutant htt in vitro. These results suggest that autophagy plays a critical role in the degradation of N-terminal htt. Altered processing of mutant htt by autophagy and cathepsin D may contribute to HD pathogenesis.
Multidrug resistance proteins (MRPs/ABCCs) in cancer chemotherapy and genetic diseases (2011)

The ATP-binding cassette (ABC) transporters are a superfamily of membrane proteins that are best known for their ability to transport a wide variety of exogenous and endogenous substances across membranes against a concentration gradient via ATP hydrolysis. There are seven subfamilies of human ABC transporters, one of the largest being the 'C' subfamily (gene symbol ABCC). Nine ABCC subfamily members, the so-called multidrug resistance proteins (MRPs) 1-9, have been implicated in mediating multidrug resistance in tumor cells to varying degrees as the efflux extrude chemotherapeutic compounds (or their metabolites) from malignant cells. Some of the MRPs are also known to either influence drug disposition in normal tissues or modulate the elimination of drugs (or their metabolites) via hepatobiliary or renal excretory pathways. In addition, the cellular efflux of physiologically important organic anions such as leukotriene C(4) and cAMP is mediated by one or more of the MRPs. Finally, mutations in several MRPs are associated with human genetic disorders. In this minireview, the current biochemical and physiological knowledge of MRP1-MRP9 in cancer chemotherapy and human genetic disease is summarized. The mutations in MRP2/ABCC2 leading to conjugated hyperbilirubinemia (Dubin-Johnson syndrome) and in MRP6/ABCC6 leading to the connective tissue disorder Pseudoxanthoma elasticum are also discussed.
The Broad Spectrum of Cytokine Gene Expression by Myoid Cells from the Human Marrow Microenvironment (1997)

Nontransformed stromal colony-derived cell lines (CDCLs) consist of a pure stromal cell population that differentiates following a vascular smooth muscle cell repertoire, and whose in vivo counterpart is that of myoid cells found in adult and fetal human bone marrow cords. We studied the cytokine expression by reverse-transcriptase polymerase chain reaction (RT-PCR) from pooled fast-growing clones from 10 different bone marrow samples. RT-PCR indicated that 30 cytokines (out of 42 studied) were expressed by CDCLs (20 after medium renewal and hydrocortisone renewal, three after addition of interleukin I beta (IL-1 beta) and seven in only part of the CDCL layers examined). The cytokines expressed comprised mediators known to be involved in the maintenance of early and late hematopoiesis (IL-1 alpha and IL-beta, IL-6, IL-7, IL-8, IL-11 and IL-13; colony-stimulating factors, thrombopoietin, erythropoietin, stem cell factor, fit 3-ligand, hepatocyte cell growth factor, tumor necrosis factor alpha, leukemia inhibitory factor, transforming growth factors beta 1 and beta 3; and macrophage inflammatory protein 1 alpha), angiogenic factors (fibroblast growth factors 1 and 2, vascular endothelial growth factor) and mediators whose usual target (and source) is the connective tissue-forming cells (platelet-derived growth factor A, epidermal growth factor, transforming growth factors alpha and beta 2, oncostatin M and insulin-like growth factor 1), or neuronal cells (nerve growth factor). The cytokines not expressed were lymphokines (IL-2, IL-3, IL-4, IL-5, IL-9, IL-10, and IL-12 and interferon gamma) or mediators synthesized by macrophages (inhibin, activin, platelet-derived growth factor B, and IL-1 receptor antagonist). This study complements the description of the phenotype of the myoid cells, confirming that these cells are the marrow connective tissue-forming cells; moreover, this work suggests that stromal control of hematopoiesis is multifactorial and that myoid cells are involved in the control of marrow angiogenesis and innervation.
Polarimetry in Capillary Dimensions (1996)

Microinterferometeric backscatter is employed to detect optically active molecules in capillary tubes. The capillary polarimetric detector (CPD) is based on the interaction between a polarized laser beam and a capillary tube. The simple optical configuration employs a He−Ne laser, a glass polarizing plate, a fused silica tube, and a CCD-based laser beam analyzer. Side illumination of the capillary produces a 360° fan of scattered light that contains two sets of high-contrast interference fringes. These light and dark spots are viewed on a flat plane in the direct backscatter configuration. It is shown that the modulation depth for the high-frequency component is sensitive to the polarization plane for the illumination source and facilitates the quantitative determination of optical activity for a fluid contained in a capillary. A 90° rotation of exciting plane-polarized light results in a depth of modulation change of ∼80% when unmodified capillaries ranging from 75 to 530 μm i.d. are employed. Signal interrogation in the CPD is based on quantifying the relative intensities (depth of modulation) of adjacent high-frequency interference fringes. Mandelic acid, [α]23 of −153°, is used as the optically active molecule and can be detected at a 2σ detection limit of 1.49 × 10-3 M within a probe volume of about 30 nL. This limit of detection corresponds to 44 pmol or 6.7 ng of mandelic acid. The folded optical arrangement is simple and can be miniaturized with low-cost components. Initial investigations suggest that the CPD can be employed for detection in capillary electrophoresis or for studying the onset and level of solute aggregation.
Modulation of prostaglandin I2 production from bovine aortic endothelial cells by serum amyloid A and its N-terminal tetradecapeptide. (1998)

The study was aimed to explore the possible involvement of the acute phase HDL apolipoprotein, serum amyloid A (SAA) in the regulation of PGI2 production by endothelial cells. This, in view of the recent detection of SAA mRNA in endothelial cells of human atherosclerotic lesions. Human SAA induces PGI2 formation in bovine aortic endothelial cells culture in a concentration relevant to moderate acute phase events. 50 micrograms/ml of purified human SAA increases PGI2 production from a mean basal level of 2,490 +/- 330 pg/ml by 1.80 +/- 0.1 fold (n = 10; p < 0.01). The PGI2 inducing activity resides apparently in the N-terminal, i.e. amino acid residues 1-14, of the SAA molecule, 50 micrograms/ml of the peptide induces 2.9 +/- 0.5 fold increase of PGI2 production (n = 4; p < 0.03). TNF and LPS each induce PGI2 production in a concentration and time dependent manner. TNF in concentration of 10 ng/ml induces, in the presence of calf serum, an increase of 24.9 +/- 2.3 fold (n = 4; p < 0.001) and LPS in concentration of 1 microgram/ml causes a 18.3 +/- 1.3 fold increase, (n = 4; p < 0.01). In serum-free cultures, only a 2.5 +/- 0.3 fold increase was detected by 10 ng/ml TNF (n = 4), and a 5.9 +/- 0.4 by 1 microgram/ml of LPS. Thus, serum has a strong effect on PGI2 induction. When 50 micrograms/ml SAA is coadministered with 1 ng/ml TNF it reduces the TNF-induction of PGI2 from 7.7 +/- 2.8 to 3.3 +/- 1.2 fold (n = 4; p < 0.01). SAA attenuates, as well, LPS-mediated activity, although in a less pronounced manner. Our finding suggest a potential physiological function for SAA in regulation of basal and cytokine-induced PGI2 production by vascular endothelium. The capacity of SAA to markedly moderate PGI2 induction by TNF and LPS suggest that it may play a role in defending against vessel damage, in cases of atherosclerosis, bacterial infection or septic shock. The induction of PGI2 by SAA through its N-terminal domain, which also exhibits an anti-platelet aggregation activity, suggests a potential therapeutical use for this peptide as an anti-hypertensive and an anti-aggregatory agent.
A defined growth medium for Clostridium difficile (1995)

Minimal requirements of amino acids and vitamins were determined in chemically defined medium for five strains of Clostridium difficile. Cysteine, isoleucine, leucine, proline, tryptophan and valine were essential amino acids for growth of C. difficile. Arginine, glycine, histidine, methionine and threonine enhanced growth. Biotin, pantothenate and pyridoxine were essential vitamins. A defined medium containing the minimal requirements of amino acids and vitamins produced a rapid and heavy growth which was comparable to that in modified brain heart infusion, a complex medium. Adenine was able to substitute for glycine and threonine, suggesting that the two amino acids may be utilized as precursors of purine nucleotides. The defined medium developed here will assist physiological and biochemical studies on C. difficile.
Whispering-gallery-mode microring laser using a conjugated polymer (1998)

We observed laser emission in whispering gallery modes using a microring composed of a semiconducting polymer poly[2,5-bis-(2′-ethylhexyloxy)-p-phenylenevinylene coated on an etched fiber under transient and quasisteady-state pumping conditions. The threshold for laser oscillation was 1 mJ/cm2 (0.1 MW/cm2) and 30 μJ/cm2 (300 MW/cm2) for nanosecond and femtosecond excitation, respectively. The laser output showed superlinear dependence on the excitation energy above the threshold. The demonstration of lasing under quasisteady-state pumping shows the possibility to develop electrically pumped polymer lasers.
Left ventricular diastolic pressure-volume relations in rats with healed myocardial infarction. Effects on systolic function. (1981)

To determine the effects of healed myocardial infarction on the diastolic compliance of the left ventricle, we studied 36 rats 26 days after left coronary artery ligation. Peak cardiac output and stroke volume were measured under ether anesthesia during volume loading, and peak left ventricular developed pressure was determined during occlusion of the ascending aorta. During a slow infusion of saline into the potassium-arrested left ventricle, diastolic pressure and volume were measured continuously over the pressure range -5 to 30 mm Hg. Infarct size was determined by planimetry of serial sections taken from each heart at 1-mm intervals from apex to base. In rats with healed infarcts, left ventricular volume was increased in proportion to infarct size and the diastolic pressure-volume relationship was shifted so that at pressures below 2.5 mm Hg volume was increased, resulting in an increased ventricular compliance in this low pressure range. Above this pressure, the slopes of the pressure-volume curves were similar in rats with and without infarctions. Peak cardiac output and pressure-generating capacity were impaired in proportion to infarct size. This impairment of cardiac performance correlated with the infarct size-related increase in diastolic volume, which served to offset the reduction in flow generating capacity caused by systolic dysfunction, while contributing directly to the impairment of pressure generating capacity.
Sustained Impairment of IFN-γ Secretion in Suppressed HIV-Infected Patients Despite Mature NK Cell Recovery: Evidence for a Defective Reconstitution of Innate Immunity (2002)

The impairment of NK cell functions in the course of HIV infection contributes to a decreased resistance against HIV and other pathogens. We analyzed the proportion of mature and immature NK cell subsets, and measured subsets of IFN-gamma and TNF-alpha-producing NK and T cells in viremic or therapy-suppressed HIV-infected subjects, and noninfected control donors. Viremic HIV(+) individuals had significantly lower proportions of mature CD3(-)/CD161(+)/CD56(+) NK cells and of IFN-gamma-producing NK cells compared with noninfected donors, independent of CD4(+) T cell counts. HIV-infected subjects with undetectable viral load recovered mature CD3(-)/CD161(+)/CD56(+) NK cells and cytotoxicity against tumor (K562) and HSV-infected target cells to percentages comparable with those of uninfected individuals, but their NK cells remained impaired in their ability to produce IFN-gamma. In parallel to these ex vivo findings, in vitro NK cell differentiation of CD34-positive cord blood precursors in the presence of R5 or X4 HIV-1 resulted in the production of NK cells with a normal mature phenotype, but lacking the ability to produce IFN-gamma, whereas coculture of uninfected PBMC with HIV failed to affect mature NK cell properties or IFN-gamma secretion. Altogether, our findings support the hypothesis that mature NK cell phenotype may be uncoupled from some mature functions following highly active antiretroviral therapy-mediated suppression of HIV-1, and indicate that relevant innate immune functions of NK cell subsets may remain altered despite effective viral suppression following antiretroviral treatment.
Stem Cells: Hype and Reality (2002)

This update discusses what is known regarding embryonic and adult tissue-derived pluripotent stem cells, including the mechanisms underlying self-renewal without senescence, differentiation in multiple cell types both in vitro and in vivo, and future potential clinical uses of such stem cells. In Section I, Dr. Lansdorp reviews the structure and function of telomerase, the enzyme that restores telomeric ends of chromosomes upon cell division, highly present in embryonic stem cells but not adult stem cells. He discusses the structure and function of telomerase and signaling pathways activated by the enzyme, with special emphasis on normal and leukemic hematopoietic stem cells. In Section II, Dr. Pera reviews the present understanding of mammalian pluripotent embryonic stem cells. He discusses the concept of pluripotentiality in its embryonic context, derivation of stem cells from embryonic or fetal tissue, the basic properties of the stem cells, and methods to produce specific types of differentiated cell from stem cells. He examines the potential applications of stem cells in research and medicine and some of the barriers that must be crossed to achieve these goals. In Section III, Dr. Verfaillie reviews the present understanding of pluripotency of adult stem cells. She discusses the concept of stem cell plasticity, a term used to describe the greater potency described by several investigators of adult tissue-derived stem cells, critically reviews the published studies demonstrating stem cell plasticity, and possible mechanisms underlying such plasticity, and examines the possible role of pluripotent adult stem cells in research and medicine.
Improving DNN speaker independence with I-vector inputs (2014)

We propose providing additional utterance-level features as inputs to a deep neural network (DNN) to facilitate speaker, channel and background normalization. Modifications of the basic algorithm are developed which result in significant reductions in word error rates (WERs). The algorithms are shown to combine well with speaker adaptation by backpropagation, resulting in a 9% relative WER reduction. We address implementation of the algorithm for a streaming task.
Total-body radiation suppression of the clearance of phenylalanine ammonia-lyase from mouse plasma. (1978)

The ever-increasing necessity to miniaturize smooth torque rotary actuators has placed severe constraints on the current slotless permanent-magnet technology. These constraints are mainly the consequence of the relatively large effective magnetic airgap which limits the achievable magnetic loading and, therefore, the torque density of slotless permanent-magnet rotary actuators. Further, the miniaturization has to be achieved at ever-decreasing costs and, therefore, it would be advantageous to implement solid back irons. However this, even at reduced magnetic loading, still results in considerable eddy-current losses. Therefore, a careful selection of the various actuator dimensions and most appropriate soft magnetic laminated or solid material is a prerequisite for applications that require smooth speed and torque characteristic. This paper will identify the influence of various parameters of the slotless permanent-magnet actuator on the eddy-current loss in the back iron using both 2-D and 3-D finite-element analysis.
Active and Passive Immunization with rHyr1p-N Protects Mice against Hematogenously Disseminated Candidiasis (2011)

We previously reported that Candida albicans cell surface protein Hyr1 encodes a phagocyte killing resistance factor and active vaccination with a recombinant N-terminus of Hyr1 protein (rHyr1p-N), significantly protects immunocompetent mice from disseminated candidiasis. Here we report the marked efficacy of rHyr1p-N vaccine on improving the survival and reducing the fungal burden of disseminated candidiasis in both immunocompetent and immunocompromised mice using the FDA-approved adjuvant, alum. Importantly, we also show that pooled rabbit anti-Hyr1p polyclonal antibodies raised against 8 different peptide regions of rHyr1p-N protected mice in a hematogenously disseminated candidiasis model, raising the possibility of developing a successful passive immunotherapy strategy to treat this disease. Our data suggest that the rabbit anti-Hyr1p antibodies directly neutralized the Hyr1p virulence function, rather than enhanced opsonophagocytosis for subsequent killing by neutrophil in vitro. Finally, the rHyr1p-N vaccine was protective against non-albicans Candida spp. These preclinical data demonstrate that rHyr1p-N is likely to be a novel target for developing both active and passive immunization strategies against Candida infections.
The Impact of Continuous Pulse Oximetry Monitoring on Intensive Care Unit Admissions from a Postsurgical Care Floor (2006)

Continuous pulse oximetry (CPOX) has the potential to increase vigilance and decrease pulmonary complications and thus decrease intensive care unit (ICU) admissions. In a randomized nonblinded study of 1219 subjects we compared the effects of CPOX and standard monitoring on the rate of transfer to an ICU from a 33-bed postcardiothoracic surgery care floor. There was no difference in the rate of ICU readmission between the CPOX and standard monitor groups. Despite older age and comorbidity, estimated cost to time of censoring (enrollment to completion of the study) was less in the monitored patients who required ICU transfer than in the unmonitored patients who required ICU transfer (mean estimated cost difference of 28,195 dollars; P = 0.04). Use of CPOX altered the reasons that patients were transferred to an ICU but did not affect the rate of transfer. The duration, and thus estimated cost, of ICU stay was significantly less in the CPOX-monitored group. The potential for CPOX to allow for early intervention, or perhaps prevention of pulmonary complications, needs to be explored. Routine CPOX monitoring did not reduce transfer to ICU, mortality, or overall estimated cost of hospitalization, and it is unclear if there is any real benefit from the application of this technology in patients on a general care floor who are recovering from cardiothoracic surgery.
Mining Search Query Logs for Spoken Language Understanding (2012)

In a spoken dialog system that can handle natural conversation between a human and a machine, spoken language understanding (SLU) is a crucial component aiming at capturing the key semantic components of utterances. Building a robust SLU system is a challenging task due to variability in the usage of language, need for labeled data, and requirements to expand to new domains (movies, travel, finance, etc.). In this paper, we survey recent research on bootstrapping or improving SLU systems by using information mined or extracted from web search query logs, which include (natural language) queries entered by users as well as the links (web sites) they click on. We focus on learning methods that help unveiling hidden information in search query logs via implicit crowd-sourcing. 1
HfOx based vertical resistive random access memory for cost-effective 3D cross-point architecture without cell selector (2012)

Double-layer stacked HfOx vertical RRAM is demonstrated for 3D cross-point architecture using a cost-effective fabrication process. Electrode/oxide interface engineering using TiON layer results in non-linear I-V suitable for the selector-less array. The fabricated HfOx vertical RRAM shows excellent performances such as reset current (<;50μA), switching speed (~50ns), switching endurance (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> cycles), half-selected read disturbance immunity (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> cycles), retention (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> s @125 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sup> C). Moreover, a unique write/read scheme is proposed for 3D cross-point architecture. Analysis shows that for such 3D selector-less array, a large R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> (~100kΩ) from the non-linear I-V helps reduce the sneak path current, and a low interconnect resistance using metal planes as word lines reduces the undesirable voltage drop on the interconnect. As a conservative estimate, simulation shows that Mb-scale array without cell selector is achievable.
Modular Assembly of Furotropones and Benzofurotropones, and Study of Their Physicochemical Properties (2015)

A rapid and straightforward synthesis of a novel series of furo[2,3-d]tropones (or cyclohepta[b]furan-6-ones) has been developed starting from readily and commercially available materials. Directed α-lithiation of furan-3-carboxaldehydes and subsequent reaction with a variety of aldehydes efficiently provide, in one step, access to 3-formyl-2-furylcarbinols, which are otherwise only accessible with difficulty. The 3-formyl-2-furylcarbinols are further elaborated in two steps to the synthesis of furo[2,3-d]tropones in good yields via sequential bismuth(III)chloride-catalyzed furfurylation and an unusual base promoted cyclization strategy. Thus, diverse polysubstituted furotropones and benzofurotropones can be rapidly assembled. This methodology thereby offers a potential approach for the synthesis of several bioactive natural products containing cyclohepta[b]furan core and also for the buildup of complex molecular architectures through higher order cycloaddition reactions of tropones. Further, the new chromophores have been found to possess promising fluorescence properties. Selective fluorogenic sensing behavior of furotropones toward Fe(3+) ions has also been elucidated.