gebhart/patrepeval huggingface dataset:
Continuous bioluminescent monitoring of cytoplasmic ATP in single isolated rat hepatocytes during metabolic poisoning (1993)

We have devised a technique for monitoring cytoplasmic ATP continuously in single hepatocytes. Single isolated rat hepatocytes were injected with the ATP-dependent luminescent protein firefly luciferase, and then superfused with 45 microM luciferin in air-equilibrated medium. Signals of approx. 10-200 photoelectron counts per second could be recorded from individual healthy cells for up to 3 h. The response of the luminescent signal to chemical hypoxia (2-5 mM CN- and 5-10 mM 2-deoxyglucose) was monitored. We found a great cell-to-cell variability in the time course of the ATP decline in response to CN-, 2-deoxyglucose or to their combination; the time for the signal to fall to 10% of the original (corresponding to approx. 100 microM ATP) ranged from approx. 20 to 75 min. This resistance of the cytoplasmic ATP concentration to depletion after blockade of oxidative phosphorylation and glycolysis could be abolished by pretreatment of the cells with etomoxir, which blocks mitochondrial beta-oxidation. Etomoxir alone had no effect on the luciferase signal, but etomoxir-pre-treated cells showed a prompt fall in the luciferase signal starting within 1-2 min of application of cyanide and 2-deoxyglucose and falling to 10% of the original signal in approx. 6-10 min. The technique allows cytoplasmic ATP changes to be monitored in single hepatocytes at concentrations of 1 mM or lower, but more precise calibration of the signal will require correction for the effects of cytoplasmic pH changes.
Ink-jet printing: the present state of the art (2003)

The author presents an overview of the state of the art in drop-on-demand ink-jet printing. He discusses the different actually manufactured ink-jet print heads with piezoelectric and thermoelectric transducers. The respective advantages and disadvantages and the fundamental limitations are illustrated. Finally, he considers subjects like ink, paper, cleaning, and sealing mechanisms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A new congestion control scheme (1991)

Recently there have been many measures proposed to tackle the problem of congestion in computer networks. In this paper, we first analyze some of the measures and then present a new scheme in which the optimal operating point is obtained by evaluation of throughput gradient and resource sharing is adjusted only at the beginning and the end of a connection. Simulation results show that the scheme converges to an optimal operating point quickly and fairly.
Extending Oblivious Transfer Efficiently, or - How to get active security with constant cryptographic overhead. (2014)

Abstract. On top of the passively secure extension protocol of [IKNP03] we build a new construction secure against active adversaries. We can replace the invocation of the hash function that is used to check the receiver is well-behaved with the XOR of bit strings. This is pos-sible by applying a cut-and-choose technique on the length of the bit strings that the receiver sends in the reversed OT. We also improve on the number of seeds required for the extension, both asymptotically and practically. Moreover, the protocol used to test receiver’s behaviour en-joys unconditional security. 1
An algorithm for survivable network design employing multiple self-healing rings (2002)

The authors have developed an algorithmic approach to synthesis of restorable networks that employ several self-healing rings (SHRs). The method is near-optimal from a capacity efficiency perspective. The multi-ring design configurations that result may be used directly, or the algorithm may be used as an automated "design proposer" to complement existing ring planning analysis tools. A systematic search for an optimum multi-SHR design is structured as a greedy search for ring candidates amongst the set of cycles of the network. Novel aspects of the approach are: (i) determination and use of the cycle set of the network graph to structure a systematic search for collectively efficient ring sets that cover the network, (ii) use of several different metric functions to explore alternative search paths in the design space. Each identifies a different locally optimal network construction from which the best global candidate is easily selected. On small and medium test cases, results show that the algorithm produces good designs, strictly optimal in some cases, if assessed from the point of view of capacity efficiency. For larger networks, where the strictly optimal result is not known, the authors still show improvements over previously published results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tumor cell surface alpha 4 beta 1 integrin mediates adhesion to vascular endothelium: demonstration of an interaction with the N-terminal domains of INCAM-110/VCAM-1. (1991)

Hematogenous metastasis involves adhesive interactions between blood-borne tumor cells and the vessel wall. By the use of in vitro assays, the adhesion of human melanoma, osteosarcoma, and kidney carcinoma (but not colon carcinoma) cell lines was shown to involve the cytokine-inducible endothelial cell surface protein inducible cell adhesion molecule 110 (INCAM-110) and the alpha 4 beta 1 integrin, molecules normally involved in endothelial-leukocyte interactions. Tumor adhesion to human endothelial cell monolayers was increased 1.9- to 8.2-fold by endothelial activation with the cytokine tumor necrosis factor (TNF) and inhibited by the anti-INCAM-110 monoclonal antibody (mAb) E1/6. Each of these tumor cells expressed members of the beta 1 integrin family of adhesion molecules, and antibodies to the alpha 4 and beta 1 integrin subunits inhibited tumor-endothelial adhesion (48-87% inhibition). A cDNA encompassing the three N-terminal Ig-like domains of vascular cell adhesion molecule 1 (VCAM-1) encoded a protein recognized by the anti-INCAM-110 mAb E1/6 and, when captured onto plastic, supported melanoma cell adhesion by an alpha 4 integrin-dependent mechanism. In contrast to mAb E1/6, a second anti-INCAM-110 mAb Hu8/4 neither inhibited adhesion to activated endothelium nor bound the first three Ig-like domains of INCAM-110/VCAM-1. These data indicate that the adherence of several human tumors to activated endothelium is mediated by an interaction of alpha 4 beta 1 integrin and the N-terminal Ig-like domains of endothelial INCAM-110/VCAM-1. Tumor acquisition of the alpha 4 integrin subunit and endothelial expression of INCAM-110 may affect the frequency and distribution of metastasis.
Specific Activation of Smad1 Signaling Pathways by the BMP7 Type I Receptor, ALK2 (1998)

BMP7 and activin are members of the transforming growth factor beta superfamily. Here we characterize endogenous activin and BMP7 signaling pathways in P19 embryonic carcinoma cells. We show that BMP7 and activin bind to the same type II receptors, ActRII and IIB, but recruit distinct type I receptors into heteromeric receptor complexes. The major BMP7 type I receptor observed was ALK2, while activin bound exclusively to ALK4 (ActRIB). BMP7 and activin elicited distinct biological responses and activated different Smad pathways. BMP7 stimulated phosphorylation of endogenous Smad1 and 5, formation of complexes with Smad4 and induced the promoter for the homeobox gene, Tlx2. In contrast, activin induced phosphorylation of Smad2, association with Smad4, and induction of the activin response element from the Xenopus Mix.2 gene. Biochemical analysis revealed that constitutively active ALK2 associated with and phosphorylated Smad1 on the COOH-terminal SSXS motif, and also regulated Smad5 and Smad8 phosphorylation. Activated ALK2 also induced the Tlx2 promoter in the absence of BMP7. Furthermore, we show that ALK1 (TSRI), an orphan receptor that is closely related to ALK2 also mediates Smad1 signaling. Thus, ALK1 and ALK2 induce Smad1-dependent pathways and ALK2 functions to mediate BMP7 but not activin signaling.
The Staphylococcus aureus lrgAB Operon Modulates Murein Hydrolase Activity and Penicillin Tolerance (2000)

Previous studies in our laboratory have shown that the Staphylococcus aureus LytSR two-component regulatory system affects murein hydrolase activity and autolysis. A LytSR-regulated dicistronic operon has also been identified and shown to encode two potential membrane-associated proteins, designated LrgA and LrgB, hypothesized to be involved in the control of murein hydrolase activity. In the present study, a lrgAB mutant strain was generated and analyzed to test this hypothesis. Zymographic and quantitative analysis of murein hydrolase activity revealed that the lrgAB mutant produced increased extracellular murein hydrolase activity compared to that of the wild-type strain. Complementation of the lrgAB defect by providing the lrgAB genes in trans restored the wild-type phenotype, indicating that these genes confer negative control on extracellular murein hydrolase activity. In addition to these effects, the influence of the lrgAB mutation on penicillin-induced lysis and killing was examined. These studies demonstrated that the lrgAB mutation enhanced penicillin-induced killing of cells approaching the stationary phase of growth, the time at which the lrgAB operon was shown to be maximally expressed. This effect of the lrgAB mutation on penicillin-induced killing was shown to be independent of cell lysis. In contrast, the lrgAB mutation did not affect penicillin-induced killing of cells growing in early-exponential phase, a time in which lrgAB expression was shown to be minimal. However, expression of the lrgAB operon in early-exponential-phase cells inhibited penicillin-induced killing, again independent of cell lysis. The data generated by this study suggest that penicillin-induced killing of S. aureus involves a novel regulator of murein hydrolase activity.
Caching strategies to improve disk system performance (1994)

I/O subsystem manufacturers attempt to reduce latency by increasing disk rotation speeds, incorporating more intelligent disk scheduling algorithms, increasing I/O bus speed, using solid-state disks, and implementing caches at various places in the I/O stream. In this article, we examine the use of caching as a means to increase system response time and improve the data throughput of the disk subsystem. Caching can help to alleviate I/O subsystem bottlenecks caused by mechanical latencies. This article describes a caching strategy that offers the performance of caches twice its size. After explaining some basic caching issues, we examine some popular caching strategies and cache replacement algorithms, as well as the advantages and disadvantages of caching at different levels of the computer system hierarchy. Finally, we investigate the performance of three cache replacement algorithms: random replacement (RR), least recently used (LRU), and a frequency-based variation of LRU known as segmented LRU (SLRU).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multiresolution curves (1994)

We describe a multiresolution curve representation, based on wavelets, that conveniently supports a variety of operations: smoothing a curve; editing the overall form of a curve while preserving its details; and approximating a curve within any given error tolerance for scan conversion. We present methods to support continuous levels of smoothing as well as direct manipulation of an arbitrary portion of the curve; the control points, as well as the discrete nature of the underlying hierarchical representation, can be hidden from the user. The multiresolution representation requires no extra storage beyond that of the original control points, and the algorithms using the representation are both simple and fast.
Pegylation: Engineering Improved Biopharmaceuticals for Oncology (2003)

Pegylation, the technology of polyethylene glycol (PEG) conjugation, holds significant promise in maintaining effective plasma concentrations of systemically administered drugs that might otherwise be hampered in vivo by a number of factors, such as rapid elimination by the kidneys. Mobile, nontoxic PEG chains can be conjugated to biotherapeutics, increasing their hydrodynamic volume, which can in turn prolong their plasma retention time, increase their solubility, and shield antigenic determinants on the drug from detection by the immune system. Attaching PEG molecules for optimal pharmacokinetics without obstructing the active sites that are essential for drug efficacy is a major challenge in pegylation. Current pegylation technology uses linkerless conjugation methods to produce coupling without added toxicity or immunogenicity, and may keep the innate surface charge of the pegylated molecule intact. In addition to controlling the size and complexity of PEG molecules, the attachment site can be manipulated to avoid steric hindrance of the drug's active receptor-recognition or substrate-interaction site. A few pegylated drugs have been engineered to have an improved pharmacokinetic profile with preserved bioactivity. They often have prolonged steady plasma concentrations in vivo, thereby making a reduced number of doses possible. Other interesting effects have also emerged, such as the self-regulating pharmacokinetics of pegfilgrastim, a pegylated version of the granulocyte colony-stimulating factor filgrastim that is administered for management of chemotherapy-induced neutropenia. The improved dosing schedule, with longer intervals between administrations of the pegylated agents, will improve compliance and quality of life in patients with chronic disease.
Characterization of ROS1 cDNA from a human glioblastoma cell line. (1990)

We have isolated and characterized a human ROS1 cDNA from the glioblastoma cell line SW-1088. The cDNA, 8.3 kilobases long, has the potential to encode a transmembrane tyrosine-specific protein kinase with a predicted molecular mass of 259 kDa. The putative extracellular domain of ROS1 is homologous to the extracellular domain of the sevenless gene product from Drosophila. No comparable similarities in the extracellular domains were found between ROS1 and other receptor-type tyrosine kinases. Together, ROS1 and sevenless gene products define a distinct subclass of transmembrane tyrosine kinases.
The Effects of Calcium, Phosphate, and Vitamin D (1995)

Secondary hyperparathyroidism is characterized by an increase in parathyroid (PT) cell number, and parathyroid hormone (PTH) synthesis and secretion. It is still unknown as to what stimuli regulate PT cell proliferation and how they do this. We have studied rats with dietary-induced secondary hyper- and hypoparathyroidism, rats given 1,25dihydroxyvitamin D3 (1,25(OH)2D3) and rats after 5/6 nephrectomy for the presence of PT cell proliferation and apoptosis. PT cell proliferation has been measured by staining for proliferating cell nuclear antigen (PCNA) and apoptosis by in situ detection ofnuclearDNA fragmentation and correlated with serum biochemistry and PTH mRNA levels. A low calcium diet led to increased levels of PTH mRNA and a 10-fold increase in PT cell proliferation. A low phosphate diet led to decreased levels of PTH mRNA and the complete absence of PT cell proliferation.
Vascular endothelial growth factor in cervical carcinoma (1999)

Intratumoral protein level of vascular endothelial growth factor in cervical cancer tissue correlates well with local tumor progression and tumor metastasis. Vascular endothelial growth factor might be a marker for evaluating disease severity.
Design of Oil Refineries Hydrogen Network Using Process Integration Principles (2008)

This paper describes the application of process integration principles to the design of oil refineries hydrogen network. In this regard, a design hierarchy as well as heuristics and required guidelines are proposed. The recommended rules compensate lack of procedure to the design and make the design process easier. The guiding principles of the design are based upon pinch technology and extending the heat integration concepts to mass integration. This research makes a designer able to maximise the amount of hydrogen recovered across the site during the design. Besides, it provides an opportunity for refineries to make most efficient use of hydrogen. The study is illustrated with an industrial case study. The work stages such as targeting, simulation etc. are performed in the REFOPT software environment. It is finally shown that this approach can design a network, which saves the total cost by $ 6.3459 million per year.
Minireview: Weapons of Lean Body Mass Destruction: The Role of Ectopic Lipids in the Metabolic Syndrome (2003)

The obesity crisis in the United States has been associated with an alarming increase in the prevalence of the metabolic syndrome (MSX) disease cluster. Here we review evidence that the MSX reflects a failure of a system of intracellular lipid homeostasis that prevents lipotoxicity in the organs of overnourished individuals by confining the lipid overload to cells specifically designed to store large quantities of surplus calories, the white adipocytes. Normally, early in obesity, adipocytes increase leptin and adiponectin secretion, hormones that enhance oxidation of surplus liquids in nonadipose tissues by activating AMP-activated protein kinase and reducing the activity and expression of lipogenic enzymes. These events combine to lower malonyl coenzyme A. Deficiency of and/or unresponsiveness to leptin prevents these protective events and results in ectopic accumulation of lipids. Increased de novo ceramide formation is probably the most damaging lipid and is a cause of lipoapoptosis, abetted by a decline in tissue Bcl-2. Pancreatic beta-cells and myocardiocytes are cellular victims of the process, leading to non-insulin-dependent diabetes and lipotoxic cardiomyopathy. The MSX is particularly prevalent in visceral obesity, probably because visceral adipocytes make less leptin than sc adipocytes. Cushing's syndrome, the lipodystrophy associated with protease inhibitor therapy of AIDS, polycystic ovarian disease, as well as diet-induced visceral obesity, all have a high waist/hip ratio, and all exhibit MSX. Increased lipid content in the heart and skeletal muscle organs of such patients is now under study.
Conduction in Charged PbSe Nanocrystal Films (2005)

Conduction in thin films of PbSe nanocrystals doped by electrochemical gating has been studied. Charging the film, with either electrons or holes, increases the conductance by orders of magnitude. The electrons in the 1S(e) state of nanocrystals in these films have a mobility as high as 5.0 x 10(-3) cm(2) V(-1) s(-1). Electrons in the 1P(e) state were found to have a differential mobility up to 3-5 times greater than the electrons in the 1S(e) state, and a mobility minima was found corresponding to the complete filling of the 1S(e) state. The temperature and electric field dependence of conductance in the film, measured between 4.3 and 135 K, were both well described by a variable range hopping model.
Consistent chromosome abnormalities in adenocarcinoma of the pancreas. (1995)

Little is known about the somatic genetic changes which characterize pancreatic adenocarcinoma. The identification of acquired genomic alterations would further our understanding of the biology of this neoplasm. We have studied 62 primary pancreatic adenocarcinomas obtained from surgical resections using classical cytogenetics and fluorescent in situ hybridization methods. Clonally abnormal karyotypes were observed in 44 neoplasms. Karyotypes were generally complex (greater than three abnormalities) and included both numerical and structural chromosome abnormalities. Many tumors contained at least one marker chromosome. The most frequent whole chromosomal gains were chromosomes 20 (eight tumors) and 7 (seven tumors). Losses were much more frequent: chromosome 18 was lost in 22 tumors followed in frequency by chromosomes 13 (16 tumors), 12 (13 tumors), 17 (13 tumors), and 6 (12 tumors). Structural abnormalities were frequent. Two hundred nine chromosome breakpoints were identified. Excluding Robertsonian translocations, the chromosomal arms most frequently involved were 1p (12); 6q (11); 7q and 17p (9 each); and 1q, 3p, 11p, and 19q (8 each). Portions of the long arm of chromosome 6 appeared to be lost in nine tumors. To determine whether the apparent losses of portions of 6q are real, four tumors with 6q deletions were hybridized with a biotin-labeled microdissection probe from 6q24-ter. Loss of one copy of this region was verified in three of four tumors. In addition, double minute chromosomes were identified in eight cases. To our knowledge, these represent the first primary specimens of pancreatic adenocarcinoma with cytogenetic evidence of gene amplification.
Geometric Deep Learning: Going beyond Euclidean data (2017)

Geometric deep learning is an umbrella term for emerging techniques attempting to generalize (structured) deep neural models to non-Euclidean domains, such as graphs and manifolds. The purpose of this article is to overview different examples of geometric deep-learning problems and present available solutions, key difficulties, applications, and future research directions in this nascent field.
Phase retrieval with the transport-of-intensity equation II Orthogonal series solution for nonuniform illumination (1996)

In a previous paper [ J. Opt. Soc. Am. A12, 1932 ( 1995)] we presented a method for phase recovery with the transport-of-intensity equation by use of a series expansion. Here we develop a different method for the solution of this equation, which allows recovery of the phase in the case of nonuniform illumination. Though also based on the orthogonal series expansion, the new method does not require any separate boundary conditions and can be more easily adjusted for apertures of various shapes. The discussion is primarily for the case of a circular aperture and Zernike polynomials, but we also outline the solution for a rectangular aperture and Fourier harmonics. The latter example may have some substantial advantages, given the availability of the fast Fourier transform.
Detection of a single viable Cryptosporidium parvum oocyst in environmental water concentrates by reverse transcription-PCR (1996)

Current methods for detection of Cryptosporidium parvum oocysts in water are time-consuming and difficult. We have developed a reverse transcription (RT)-PCR which can detect the presence of a single viable oocyst spiked into concentrated environmental water samples. The test is based on the detection of mRNA from a C. parvum heat shock protein (hsp). The synthesis of hsp was induced by a short 45 degrees C incubation followed by oocyst lysis by a freeze-thaw process. Hsp70 mRNA, produced only from viable oocysts, was then isolated by hybridization to oligo(dT)25-coated magnetic beads. Detection was achieved by RT-PCR amplification of a 590-bp region of hsp70 mRNA specific for C. parvum. To test the method, samples of reticulated, reservoir, bore, and river water were concentrated by chemical flocculation and Percoll-sucrose gradient centrifugation and then spiked with dilutions of oocysts. In all four of the water types examined, the detection of single oocysts was possible by RT-PCR combined with Southern hybridization. RT-PCR products were not obtained from formalin-inactivated oocysts. An RNA internal positive control fragment was synthesized that was included with each reaction to guard against RT-PCR false-negative results that may be caused by the presence of inhibitory substances. However, when the magnetic beads were used to extract and concentrate mRNA, no inhibition was observed. The technique is versatile, straightforward, and rapid (1 day) and provides a sensitive and economic means of screening concentrated water samples for the presence of C. parvum.