gebhart/patrepeval huggingface dataset:
Hsp70 and Antifibrillogenic Peptides Promote Degradation and Inhibit Intracellular Aggregation of Amyloidogenic Light Chains (2001)

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its beta sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocated out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach.
On the decision regions of multilayer perceptrons (1990)

The capabilities of two-layer perceptrons are examined with respect to the geometric properties of the decision regions they are able to form. It is known that two-layer perceptrons can form decision regions which are nonconvex and even disconnected, though the extent of their capabilities in comparison to three-layer structures is not well understood. By relating the geometry of arrangements of hyperplanes to combinatorial properties of subsets hypercube vertices, certain facts concerning the decision regions of two-layer perceptrons are deduced, and examples of decision regions which can be realized by three-layer perceptrons but not by a two-layer form are constructed. The results indicate that the graduation in ability between two- and three-layer architectures is strict. The examples of nonconvex and disconnected decision regions illustrate that the two-layer perceptron is a more capable structure than was once supposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Real Time Zero-difference Ambiguities Fixing and Absolute RTK (2008)

Until recently it was believed that integer ambiguities could only be fixed on differenced measurements in order to remove biases. Recently Mercier and Laurichesse [2] have demonstrated that simple assumptions on bias stability are sufficient to fix integer ambiguities on zero-difference phase measurements. A solution for clocks over a regional network can then be computed using these unambiguous phase measurements and precise GPS satellites ephemerides (such as IGS products), giving integer phase clocks for the satellites. These clocks have an interesting property : they allow the positioning of an independent receiver using a PPP like method, with integer ambiguities properties on the phase residuals [1]. If this zero difference ambiguity fixing is performed in realtime, it becomes possible to compute RTK solutions with centimeter accuracy without using any close reference station. In this paper, we address real time issues of zero differenced ambiguity fixing, and we present a method for absolute RTK for dual-frequency receivers.
Choice of FACTS Device Control Inputs for Damping Interarea Oscillations (2004)

A method is proposed in this paper to select the input signals for both single and multiple flexible ac transmission system (FACTS) devices in small and large power systems. Different input-output controllability analyses are used to assess the most appropriate input signals (stabilizing signal) for the static var compensator (SVC), the static synchronous compensator (SSSC), and the unified power-flow controller (UPFC) for achieving good damping of interarea oscillations. The study presented in this paper is carried out on one small system with one FACTS device at a time; and one large system equipped with the SVC, the SSSC, and the UPFC.
Establishment of conditionally immortalized human glomerular mesangial cells in culture, with unique migratory properties (2011)

The aim of this study was to establish an immortalized human mesangial cell line similar to mesangial cells in vivo for use as a tool for understanding glomerular cell function. Mesangial cells were isolated from glomerular outgrowths from a normal human kidney, then retrovirally transfected with a temperature-sensitive SV40T antigen+human telomerase (hTERT). Mesangial cells exhibited features of compact cells with small bodies in a confluent monolayer at 33°C, but the cell shape changed to flat and stellate after 5 days in growth-restrictive conditions (37°C). Western blot and immunofluorescence analysis showed that podocyte markers (nephrin, CD2AP, podocin, Wilms' tumor-1) and an endothelial-specific molecule (VE-cadherin) were not detectable in this cell line, whereas markers characteristic of mesangial cells (α-SMA, fibronectin, and PDGFβ-R) were strongly expressed. In migration assays, a significant reduction in wound surface was observed in podocyte and endothelial cells as soon as 12 h (75 and 62%, respectively) and complete wound closure after 24 h. In contrast, no significant change was observed in mesangial cells after 12 h, and even after 48 h the wounds were not completely closed. Until now, conditionally immortalized podocyte and endothelial cell lines derived from mice and humans have been described, and this has greatly boosted research on glomerular physiology and pathology. We have established the first conditionally immortalized human glomerular mesangial cell line, which will be an important adjunct in studies of representative glomerular cells, as well as in coculture studies. Unexpectedly, mesangial cells' ability to migrate seems to be slower than for other glomerular cells, suggesting this line will demonstrate functional properties distinct from previously available mesangial cell cultures. This conditionally immortalized human mesangial cell line represents a new tool for the study of human mesangial cell biology in vitro.
Gastroparesis and functional dyspepsia: excerpts from the AGA/ANMS meeting (2010)

This manuscript reviews the advances in the understanding of the epidemiology, pathophysiology, diagnosis, and treatment of gastroparesis and functional dyspepsia as discussed at a recent conference sponsored by the American Gastroenterological Association (AGA) and the American Neurogastroenterology and Motility Society (ANMS). Particular focus is placed on discussing unmet needs and areas for future research.
Joint height estimation and semantic labeling of monocular aerial images with CNNS (2017)

We aim to jointly estimate height and semantically label monocular aerial images. These two tasks are traditionally addressed separately in remote sensing, despite their strong correlation. Therefore, a model learning both height and classes jointly seems advantageous and so, we propose a multitask Convolutional Neural Network (CNN) architecture with two losses: one performing semantic labeling, and another predicting normalized Digital Surface Model (nDSM) from the pixel values. Since the nDSM/height information is used only in the second loss, there is no need to have a nDSM map at test time, and the model can estimate height automatically on new images. We test our proposed method on a set of sub-decimeter resolution images and show that our model equals the performances of two separate models, but at the cost of a single one.
Efficient Learning of Linear Separators under Bounded Noise (2015)

We study the learnability of linear separators in $\Re^d$ in the presence of bounded (a.k.a Massart) noise. This is a realistic generalization of the random classification noise model, where the adversary can flip each example $x$ with probability $η(x) \leq η$. We provide the first polynomial time algorithm that can learn linear separators to arbitrarily small excess error in this noise model under the uniform distribution over the unit ball in $\Re^d$, for some constant value of $η$. While widely studied in the statistical learning theory community in the context of getting faster convergence rates, computationally efficient algorithms in this model had remained elusive. Our work provides the first evidence that one can indeed design algorithms achieving arbitrarily small excess error in polynomial time under this realistic noise model and thus opens up a new and exciting line of research. We additionally provide lower bounds showing that popular algorithms such as hinge loss minimization and averaging cannot lead to arbitrarily small excess error under Massart noise, even under the uniform distribution. Our work instead, makes use of a margin based technique developed in the context of active learning. As a result, our algorithm is also an active learning algorithm with label complexity that is only a logarithmic the desired excess error $ε$.
Plasmids and stability of symbiotic properties of Rhizobium trifolii (1982)

A conjugal plasmid which encodes both peak nodulation genes and nitrogenase genes, and which is labeled with the transposon Tn5, was transferred to a wild-type Rhizobium trifolii strain to examine the stability and expression of the host range and fixation (Fix+) phenotypes. Transconjugates were isolated which were shown to initially form nitrogen-fixing nodules (Nod+ Fix+) on both clovers and peas. These hybrid strains were then repeatedly passaged through either pea or clover nodules or onto a solid agar medium to determine whether these broadened-host-range characteristics were stably maintained. An instability was noted in the capacity of some of these hybrids to form nitrogen-fixing nodules on all of the host plants used. The broadened nodulation ability was, however, more readily maintained. In some cases, the changes in the Nod+ Fix+ phenotype could be attributed to demonstrable changes in the plasmid profile of the hybrid strains, whereas in other cases no demonstrable plasmid alterations could be detected.
Molecularly Imprinted Polymers: Present and Future Prospective (2011)

Molecular Imprinting Technology (MIT) is a technique to design artificial receptors with a predetermined selectivity and specificity for a given analyte, which can be used as ideal materials in various application fields. Molecularly Imprinted Polymers (MIPs), the polymeric matrices obtained using the imprinting technology, are robust molecular recognition elements able to mimic natural recognition entities, such as antibodies and biological receptors, useful to separate and analyze complicated samples such as biological fluids and environmental samples. The scope of this review is to provide a general overview on MIPs field discussing first general aspects in MIP preparation and then dealing with various application aspects. This review aims to outline the molecularly imprinted process and present a summary of principal application fields of molecularly imprinted polymers, focusing on chemical sensing, separation science, drug delivery and catalysis. Some significant aspects about preparation and application of the molecular imprinting polymers with examples taken from the recent literature will be discussed. Theoretical and experimental parameters for MIPs design in terms of the interaction between template and polymer functionalities will be considered and synthesis methods for the improvement of MIP recognition properties will also be presented.
A Bacterial Signal Peptidase Enhances Processing of a Recombinant Single Chain Antibody Fragment in Insect Cells (1999)

The production of an antibody single chain fragment (scFv) in insect cells was accompanied by the formation of an insoluble intracellular precursor even with the inclusion of the bee melittin signal peptide. The presence of the precursor polypeptide suggests a limitation in the processing of the signal peptide so a baculovirus containing a signal peptidase from Bacillus subtilis (SipS) was constructed for expression studies. When the wild type SipS was coexpressed with scFv, preprocessed scFv fragments were no longer detected in insect cell lysates. Conversely, coexpression of scFv alone or with an inactive mutant SipS resulted in at least 30% of the intracellular polypeptide in an unprocessed form at 3 days post infection. Production of scFv in the medium was also enhanced in the presence of SipS; however, low secretion levels indicate the presence of a post-processing bottleneck.
Functional mapping of conserved, surface‐exposed charges of antibody variable domains (2002)

Surface-exposed charges can affect protein structure, stability and solubility as well as the kinetics of both the folding process and interaction with binding partners. We have investigated the influence on kinetic interaction parameters of 14 conserved, surface-exposed charges located away from the paratope in the variable domains of two antibodies of different specificity. We found that conserved, surface-exposed, charged framework residues are asymmetrically distributed on opposite faces of both VH and VL domains. Some of the charges play a critical role in protein folding and stability. While electrostatic forces within or close to the binding interface can be used to optimize the association rate, we confirmed the predicted minor effects of charge modifications remote from the binding site. They had no effect on the dissociation rate parameter. Our study demonstrates the role of residues remote from the interaction site in the recognition function as well as the limited effect of surface charge modifications in antibody fragments on kinetic interaction parameters.
A new register file access architecture for software pipelining in VLIW processors (2005)

This paper presents a novel architecture of register files that combines the local register files and the global register file for clustered VLIW (Very Long Instruction Word) processors. The communication between function units through global register file will be more efficient. The concept of associate register is introduced for this architecture. This makes it possible to write a result to two destination registers in one operation, which can efficiently speed up the software pipelining.
Thoughts on Carolyn Gallaher’s On the Fault Line (2015)

Not available
Prediction of Coronary Heart Disease Using Risk Factor Categories (1998)

Recommended guidelines of blood pressure, total cholesterol, and LDL cholesterol effectively predict CHD risk in a middle-aged white population sample. A simple coronary disease prediction algorithm was developed using categorical variables, which allows physicians to predict multivariate CHD risk in patients without overt CHD.
Natural and Induced CD4+CD25+ Cells Educate CD4+CD25− Cells to Develop Suppressive Activity: The Role of IL-2, TGF-β, and IL-10 (2004)

Thymus-derived, natural CD4(+)CD25(+) regulatory T cells can educate peripheral CD4(+)CD25(-) cells to develop suppressive activity by poorly understood mechanisms. TGF-beta has IL-2-dependent costimulatory effects on alloactivated naive, human CD4(+) T cells and induces them ex vivo to become potent contact-dependent, cytokine-independent suppressor cells. In this study, we report that CD4(+)CD25(+) cells are the targets of the costimulatory effects of IL-2 and TGF-beta. These cells do not divide, but, instead, greatly increase the numbers of CD4(+)CD25(-) cells that become CD25(+) cytokine-independent suppressor cells. These CD4(+)CD25(+) regulatory cells, in turn, induce other alloactivated CD4(+)CD25(-) cells to become potent suppressor cells by mechanisms that, surprisingly, require both cell contact and TGF-beta and IL-10. The suppressive effects of these secondary CD4(+)CD25(+) cells depend upon TGF-beta and IL-10. Moreover, both the naive CD4(+) cells induced by IL-2 and TGF-beta to become suppressor cells, and the subsequent CD4(+)CD25(-) cells educated by them to become suppressors express FoxP3. We suggest that the long-term effects of adoptively transferred natural-like CD4(+)CD25(+) regulatory cells induced ex vivo are due to their ability to generate new cytokine-producing CD4(+) regulatory T cells in vivo.
Potent inhibition of CYP2D6 by haloperidol metabolites: stereoselective inhibition by reduced haloperidol (2001)

The principal metabolites of haloperidol inhibit CYP2D6, suggesting that they might contribute to the inhibitory effects of the drug. Reduced haloperidol seems to inhibit CYP2D6 activity in an enantioselective manner with the physiologically occurring S(-) enantiomer being more potent.
Role of oxidized low density lipoprotein in atherogenesis. (1991)

Evidence to support an important role of oxidative modification in mediating the atherogenicity of LDL continues to grow. New hypotheses suggest mechanisms by which Ox-LDL or products of Ox-LDL can affect many components of the atherogenic process, including vasomotor properties and thrombosis, as well as lesion initiation and progression itself. These ideas suggest new approaches, that in combination with lowering of plasma cholesterol, could lead to the prevention of atherosclerosis and its complications.
Growth inhibition and induction of apoptosis in acute myeloid leukemia cells by new indolinone derivatives targeting fibroblast growth factor, platelet-derived growth factor, and vascular endothelial growth factor receptors (2006)

In acute myeloid leukemia (AML), receptor tyrosine kinase ligands promote growth and survival and contribute to AML-associated marrow neoangiogenesis. We have tested simultaneous inhibition of vascular endothelial growth factor, fibroblast growth factor, and platelet-derived growth factor receptor signaling by novel indolinone derivatives using 14 myeloid, including 11 human leukemic, cell lines. Compounds inhibited colony formation of all cell lines in a dose-dependent fashion. Inhibitory concentrations for 50% of the colony formation/survival (IC50) for BIBF1000 were <100 nmol/L for 3 of 11, <or=500 nmol/L for 6 of 11, and <1,000 nmol/L for 10 of 11 leukemic cell lines, with one cell line being resistant in the dose range <1,000 nmol/L. BIBF1120 was less effective with 4 of 11 leukemic cell lines being resistant within the dose range <1,000 nmol/L. Testing of myeloid 32D cells transfected with empty vector, wild-type Flt3, or Flt3 carrying an internal tandem duplication mutation revealed higher resistance for the internal tandem duplication mutant. These effects of the compounds were associated with inhibition of tyrosine phosphorylation and the mitogen-activated protein kinase pathway. Furthermore, both compounds induced apoptosis in the sensitive cell lines. In Mono-Mac1 cells, the compounds had a direct proapoptotic effect that was increasing the proapoptotic effect of 1-beta-D-arabinofuranosylcytosine. The data provide a rationale for clinical evaluation of these tyrosine kinase inhibitors in AML.
Novel black silicon PIN photodiodes (2006)

The many advantages of silicon such as low cost, abundancy and a level of maturity that allows for very large scale integration, means that silicon is the most commonly used semiconductor in microelectronics and optoelectronic devices. Silicon, however, has one disadvantage, this being that it is unable to absorb light greater than 1100 nm. The two primary telecommunications wavelengths, 1300 nm and 1550 nm, can therefore not be detected. An interesting method used to extend silicon's wavelength range is the formation of black silicon on the silicon surface. Black silicon is formed when gases that are passed over the silicon react and etch the silicon surface, forming a dark spiky pattern. When light is shone on such a pattern, it repeatedly bounces back and forth between the spikes thus reducing surface reflection and trapping the light. This reduced reflectance and light trapping increases the sensitivity of the silicon to long wavelengths and makes it viable for use in a wide range of commercial devices such as infrared detectors and solar cells. This paper presents novel black silicon PIN photodiodes of various sizes (25 mm<sup>2</sup>, 4 mm<sup>2</sup> and 1 mm<sup>2</sup>). The diodes have been extensively characterized at wafer level, with breakdown voltage, dark current, shunt resistance, threshold voltage and junction capacitance measurements being made. Extensive responsivity measurements were also performed and it was established that the black silicon surface resulted in responsivity increases of greater than 50 % at long wavelengths (&#8776; 1100 nm).
<title>Priority-based technique for the best-effort delivery of stored video</title> (1998)

In this paper, we introduce a priority-based technique for the delivery of compressed prerecorded video streams across best-effort networks. This technique uses a multi-level priority queue in conjunction with a delivery window to help smooth the video frame rate delivered to the end user while allowing it to easily adapt to changing network conditions. Compared with current approaches, our priority-based approach has several advantages. First, it acts more globally by ensuring that a minimum frame rate for the window interval has been delivered before sending enhancement layers. Second, this approach is much simpler to implement than other frame smoothing algorithms that have been presented for the delivery of stored video across best- effort networks. Finally, this approach is directly applicable for the shaping of MPEG-based video encodings with frame dependencies.
Restoration of wild-type virulence to Tri5 disruption mutants of Gibberella zeae via gene reversion and mutant complementation (1997)

Gibberella zeae is a pathogen of small grain crops and produces trichothecene mycotoxins in infected host tissue. The role of trichothecenes in the virulence of G. zeae was previously investigated using trichothecene-non-producing mutants that were generated via transformation-mediated disruption of a gene (Tri5) that encodes the first enzyme in the trichothecene biosynthetic pathway. The mutants were less virulent on some hosts than the wild-type strain from which they were derived. Here, we used two approaches to determine whether the reduced virulence of mutants was due specifically to Tri5 disruption or to non-target effects caused by the transformation process. First, we generated a revertant from a Tri5 disruption mutant by allowing the mutant to pass through the sexual phase of its life cycle. In approximately 2% of the resulting progeny the disrupted Tri5 had reverted to wild-type; however, only one of three revertant progeny also regained the ability to produce trichothecenes. In the second approach, we complemented the Tri5 mutation in a disruption mutant by transforming the mutant with a plasmid carrying a functional copy of Tri5. In all transformants examined, the ability to produce trichothecenes was restored. The restoration of trichothecene production in the revertant progeny and in the complemented mutant was accompanied by restoration of wild-type or near wild-type levels of virulence on wheat seedlings (cultivar Wheaton). The results indicate that the reduced virulence of the mutants was caused by disruption of Tri5 rather than non-target effects resulting from the transformation process. The results also provide further evidence that trichothecenes contribute to the virulence of plant-pathogenic fungi.