gebhart/patrepeval huggingface dataset:
Refractive index of some mammalian tissues using a fiber optic cladding method (1989)

The index of refraction n of the many mammalian tissues is an important but somewhat neglected optical constant. Archival and oral papers have quoted the use of values of n for tissue generally ranging from 1.35 to 1.55. However, these values are frequently without experimental basis. They have arbitrarily used values near that of water, which is a major component of mammalian tissue, or have calculated a theoretical n from the weighted elemental composition of tissue. Since these values have not been precise and little information is available on specific indices for each tissue, a study was undertaken to develop a simple, rapid, and reliable method for the experimental determination of n. This was done using the ubiquitous quartz optical fiber. By substituting the usual cladding found on commercial quartz optics by the tissue in question and utilizing the principle of internal reflection, the value of n for the specific tissue can be calculated. This is done by utilizing the known indices for air and quartz and measuring the angle of the emergent cone of light from the output of the optical fiber. A number of indices for mammalian tissue (bovine, porcine, canine, and human) have been determined at 632.8 nm. With few exceptions, for tissues at this wavelength, n was in the 1.38-1.41 range. The species type did not appear to be a factor. Bovine muscle showed normal dispersion characteristics through the visible wavelengths. The denaturation of tissue was shown to alter significantly the refractive index.
Synthetic lethality of PARP inhibition in cancers lacking<i>BRCA1</i>and<i>BRCA2</i>mutations (2011)

Utilizing the concept of synthetic lethality has provided new opportunities for the development of targeted therapies, by allowing the targeting of loss of function genetic aberrations. In cancer cells with BRCA1 or BRCA2 loss of function, which harbor deficiency of DNA repair by homologous recombination, inhibition of PARP1 enzymatic activity leads to an accumulation of single strand breaks that are converted to double strand breaks but cannot be repaired by homologous recombination. Inhibition of PARP has therefore been advanced as a novel targeted therapy for cancers harboring BRCA1/2 mutations. Preclinical and preliminary clinical evidence, however, suggests a potentially broader scope for PARP inhibitors. Loss of function of various proteins involved in double strand break repair other than BRCA1/2 has been suggested to be synthetically lethal with PARP inhibition. Inactivation of these genes has been reported in a subset of human cancers and might therefore constitute predictive biomarkers for PARP inhibition. Here we discuss the evidence that the clinical use of PARP inhibition may be broader than targeting of cancers in BRCA1/2 germ-line mutation carriers.
Outgoing Packet Routing with MP-TCP (2009)

Multipath TCP extends the TCP protocol to allow multiple paths to be\nused simultaneously for the same TCP connection. The different paths\nare typically provided using multiple IP addresses for the same end\nsystem, each address taken from a subnet that is routed differently.\nIn this document we describe a set of conventions for how to ensure\nthat outgoing packets are routed in a manner consistent with the\nnetwork topology and constraints on use of that topology such as those\nimposed by ingress filtering on IP address prefixes.
The Tools of Biochemistry (1977)

Deals with ten basic techniques in contemporary biochemical and molecular biological studies. Examines the theoretical aspect of each technique and provides a section for its use in a carefully controlled experiment. Experiments, written in computer program format, conclude with the data that should be obtained if experiments are performed properly.
Towards a digital library of popular music (1999)

Digital libraries of music have the potential to capture popular imagination in ways that more scholarly libraries cannot. We are working towards a comprehensive digital library of musical material, including popular music. We have developed new ways of collecting musical material, accessing it through searching and browsing, and presenting the results to the user. We work with different representations of music: facsimile images of scores, the internal representation of a music editing program, page images typeset by a music editor, MIDI files, audio files representing sung user input, and textual metadata such as title, composer and arranger, and lyrics.&#13;\nThis paper describes a comprehensive suite of tools that we have built for this project. These tools gather musical material, convert between many of these representations, allow searching based on combined musical and textual criteria, and help present the results of searching and browsing. Although we do not yet have a single fully-blown digital music library, we have built several exploratory prototype collections of music, some of them very large (100,000 tunes), and critical components of the system have been evaluated.
Hypercholesterolemia of total starvation: its mechanism via tissue mobilization of cholesterol (1975)

After the establishment of a relatively linear decay curve for plasma [4-14C]cholesterol, rabbits were starved for 26-32 days. The plasma cholesterol concentration increased 400% during starvation. Concurrently, the plasma triglyceride level declined by 50%. While the plasma cholesterol was rising, the cholesterol specific radioactivity of the plasma remained unchanged in starved animals, but in control animals the plasma cholesterol specific radioactivity declined substantially. The cholesterol content of the liver and adipose tissue increased with starvation. The cholesterol specific radioactivities relative to plasma for adipose tissue were lower in the starved animals versus controls. These results support the hypothesis that cholesterol stored in the lipid droplet of the adipose tissue cell is released into plasma and is the chief source of the hypercholesterolemia observed during complete caloric starvation. Cholesterol metabolism in the starved animal can be depicted as a virtually closed system in both the input from biosynthesis and diet being low or zero and the output likewise being close to zero.
Global analytics in the face of bandwidth and regulatory constraints (2015)

Global-scale organizations produce large volumes of data across geographically distributed data centers. Querying and analyzing such data as a whole introduces new research issues at the intersection of networks and databases. Today systems that compute SQL analytics over geographically distributed data operate by pulling all data to a central location. This is problematic at large data scales due to expensive transoceanic links, and may be rendered impossible by emerging regulatory constraints. The new problem of Wide-Area Big Data (WABD) consists in orchestrating query execution across data centers to minimize bandwidth while respecting regulatory constaints. WABD combines classical query planning with novel network-centric mechanisms designed for a wide-area setting such as pseudodistributed execution, joint query optimization, and deltas on cached subquery results. Our prototype, Geode, builds upon Hive and uses 250× less bandwidth than centralized analytics in a Microsoft production workload and up to 360× less on popular analytics benchmarks including TPC-CH and Berkeley Big Data. Geode supports all SQL operators, including Joins, across global data.
A Phase I Trial of Dasatinib, an Src-Family Kinase Inhibitor, in Combination with Paclitaxel and Carboplatin in Patients with Advanced or Recurrent Ovarian Cancer (2012)

Due to the high incidence of myelosuppression with subsequent cycles, the recommended phase II dose of dasatinib is 150 mg daily in combination with paclitaxel and carboplatin. The combination was safe with evidence of clinical activity.
Single-feed dual-frequency equilateral-triangularmicrostrip antenna with pair of spur lines (1998)

Novel dual-frequency operation of a single-feed equilateral-triangular microstrip antenna with a pair of spur lines is demonstrated. The two operating frequencies are of the same polarisation planes and, by varying the spur-line length, the frequency ratio of the two operating frequencies is tunable in the range of ~ 1.2 - 2.1. Details of the antenna design are described, and experimental results are presented and discussed.
&lt;title&gt;Zooming Web browser&lt;/title&gt; (1996)

The World Wide Web (WWW) is becoming increasingly important for business, education, and entertainment. Popular web browsers make access to Internet information resources relatively easy for novice users. Simply by clicking on a link, a new page of information replaces the current one on the screen. Unfortunately however, after following a number of links, people can have difficulty remembering where they've been and navigating links they have followed. As one's collection of web pages grows and as more information of interest populates the web, effective navigation becomes an issue of fundamental importance. We are developing a prototype zooming browser to explore alternative mechanisms for navigating the WWW. Instead of having a single page visible at a time, multiple pages and the links between them are depicted on a large zoomable information surface. Pages are scaled so that the page in focus is clearly readable with connected pages shown at smaller scales to provide context. As a link is followed the new page becomes the focus and existing pages are dynamically repositioned and scaled. Layout changes are animated so that the focus page moves smoothly to the center of the display surface while contextual information provided by linked pages scales down. While our browser supports multiscale representations of existing HTML pages, we have also extended HTML to support multiscale layout within a page. This extension, Multi-Scale Markup Language, is at an early stage of development. It currently supports inclusion within a page of variable-sized dynamic objects, graphics, and other interface mechanisms from our underlying Pad++ substrate. This provides sophisticated client- side interactions, permits annotations to be added to pages, and allows page constituents to be used as independent graphical objects. In this paper, we describe our prototype web browser and authoring facilities. We show how simple extensions to HTML can support sophisticated client-side interactions. Finally, we discuss the results of preliminary user-interface testing and evaluation.
Sequence of the gene for murine complement component C4 (1989)

The gene for murine complement component C4 lies in the S region of the murine major histocompatibility (H-2) complex; in this paper, we report the nucleotide sequence of this gene. The present sequence extends from a SmaI restriction enzyme cleavage site near the 5' end of the gene to a KpnI restriction enzyme cleavage site 569 nucleotides 3' of the polyadenylation site. The sequence spans 15,956 base pairs and together with previously reported data provides a complete sequence extending from the site of transcriptional initiation to the polyadenylation site. The sequence reveals that the C4 gene has 40 introns which range from 75 to 1089 base pairs in length and which include three murine B1 middle repetitive elements, a MT repeat element, and an apparently novel repeat sequence that is also found in noncoding regions of the murine beta-glucuronidase, lymphotoxin (TNF-beta), and rat alpha-crystallin genes. An intron splits the protein coding sequence precisely at the site of proteolytic activation of C4 by complement protease C1s; however, except for this one case, the intron positions show no striking relationship to the structural features of the C4 protein. The length of the murine C4 gene relative to the isotypic C4A and C4B genes in man suggests the independent loss of a 6-kilobase intron from both murine and human C4 genes.
Automated enzymic determination of ethanol in blood, serum, and urine with a miniature centrifugal analyzer. (1976)

We describe an automated spectrophotometric reaction-rate method for determination of ethanol in serum and urine with a miniature centrifugal analyzer. The theanol is selectively oxidized in the presence of alcochol dehydrogenase and NAD+ to form NADH, which is measured by the rate of change of its absorbance. Reaction rates are determined automatically, and unknown concentrations are calculated from a computer-generated working curve based on aqueous ethanol standards. Blood, serum, or urine specimens need not be deproteinized. The method permits duplicate analysis of at least 30 samples per hour. Coefficients of variation and relative errors are about 2-3% for ethanol concentrations of 0.3-3.0 mug per 2 mul of sample. Analytical recovery of ethanol added to serum is 92-103% (average, 98.5%). Comparisons with distillation-oxidation, gas-chromatographic, and conventional enzymic procedures give satisfactory agreement.
Effect of feeding diets containing an antibiotic, a probiotic, or yucca extract on growth and intestinal urease activity in broiler chicks (1997)

A 6-wk study was conducted to determine the effect of feeding diets containing an antibiotic, a probiotic, or yucca extract on daily gain, feed conversion ratio, and urease activity and ammonia production in intestinal contents of broiler chicks. Four replicates of 10 broiler chicks (average body weight, 48 g) each were assigned to a control or diets containing 0.1% chloroxytetracycline (antibiotic), 0.1% Lactobacillus casei (probiotic), or 0.2% yucca extract. Feeding a diet containing the probiotic significantly (P < 0.05) increased average daily gain during the first 3-wk period compared to the control (30.7 vs 28.7 g). This increase was partly accounted for by increased feed intake. During the first 3 wk, feeding the diet containing probiotic significantly (P < 0.05) decreased urease activity (per gram of collected contents) in small intestinal contents but not in large intestinal contents, compared with the control. Urease activity determined at 6 wk of age was not significantly affected by diet. Our studies indicate that dietary probiotic decreases urease activity in the small intestinal contents of young chicks and thus may be beneficial for improving animal health and growth, especially during early life.
Novel dissociation mechanism of a polychaetous annelid extracellular haemoglobin (2006)

The extracellular haemoglobin of the marine polychaete, Arenicola marina, is a hexagonal bilayer haemoglobin of approximately 3600 kDa, formed by the covalent and noncovalent association of many copies of both globin subunits (monomer and trimer) and nonglobin or 'linker' subunits. In order to analyse the interactions between globin and linker subunits, dissociation and reassociation experiments were carried out under whereby Arenicola hexagonal bilayer haemoglobin was exposed to urea and alkaline pH and the effect was followed by gel filtration, SDS/PAGE, UV-visible spectrophotometry, electrospray-ionization MS, multiangle laser light scattering and transmission electron microscopy. The analysis of Arenicola haemoglobin dissociation indicates a novel and complex mechanism of dissociation compared with other annelid extracellular haemoglobins studied to date. Even though the chemically induced dissociation triggers partial degradation of some subunits, spontaneous reassociation was observed, to some extent. Parallel dissociation of Lumbricus haemoglobin under similar conditions shows striking differences that allow us to propose a hypothesis on the nature of the intersubunit contacts that are essential to form and to hold such a complex quaternary structure.
Cloning and characterization of a cDNA from Aspergillus parasiticus encoding an O-methyltransferase involved in aflatoxin biosynthesis (1993)

Aflatoxins are polyketide-derived secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. Among the catalytic steps in the aflatoxin biosynthetic pathway, the conversion of sterigmatocystin to O-methylsterigmatocystin and the conversion of dihydrosterigmatocystin to dihydro-O-methylsterigmatocystin are catalyzed by an S-adenosylmethionine-dependent O-methyltransferase. A cDNA library was constructed by using RNA isolated from a 24-h-old culture of wild-type A. parasiticus SRRC 143 and was screened by using polyclonal antiserum raised against a purified 40-kDa O-methyltransferase protein. A clone that harbored a full-length cDNA insert (1,460 bp) containing the 1,254-bp coding region of the gene omt-1 was identified by the antiserum and isolated. The complete cDNA sequence was determined, and the corresponding 418-amino-acid sequence of the native enzyme with a molecular weight of 46,000 was deduced. This 46-kDa native enzyme has a leader sequence of 41 amino acids, and the mature form of the enzyme apparently consists of 377 amino acids and has a molecular weight of 42,000. Direct sequencing of the purified mature enzyme from A. parasiticus SRRC 163 showed that 19 of 22 amino acid residues were identical to the amino acid residues in an internal region of the deduced amino acid sequence of the mature protein. The 1,460-bp omt-1 cDNA was cloned into an Escherichia coli expression system; a Western blot (immunoblot) analysis of crude extracts from this expression system revealed a 51-kDa fusion protein (fused with a 5-kDa beta-galactosidase N-terminal fragment).(ABSTRACT TRUNCATED AT 250 WORDS)
Engineering of regulated stochastic cell fate determination (2013)

Both microbes and multicellular organisms actively regulate their cell fate determination to cope with changing environments or to ensure proper development. Here, we use synthetic biology approaches to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors. We realize this experimentally by linking a synthetic GRN to a natural output of galactose metabolism regulation in yeast. Combining mathematical modeling and flow cytometry, we show that our engineered systems are bistable and that inherent gene expression stochasticity does not induce spontaneous state transitioning at steady state. Mathematical analysis predicts that stochastic cell fate determination in this case can only be realized when gene expression fluctuation occurs on or near attractor basin boundaries (the points of instability). Guided by numerical simulations, experiments are designed and performed with quantitatively diverse gene networks to test model predictions, which are verified by both flow cytometry and single-cell microscopy. By interfacing rationally designed synthetic GRNs with background gene regulation mechanisms, this work investigates intricate properties of networks that illuminate possible regulatory mechanisms for cell differentiation and development that can be initiated from points of instability.
Essential role of the cryptic epitope SLAYGLR within osteopontin in a murine model of rheumatoid arthritis (2003)

It has been shown that osteopontin (OPN) plays a pivotal role in the pathogenesis of rheumatoid arthritis (RA). However, the molecular mechanism of OPN action is yet to be elucidated. Splenic monocytes obtained from arthritic mice exhibited a significant capacity for cell migration toward thrombin-cleaved OPN but not toward full-length OPN. Migratory monocytes expressed alpha9 and alpha4 integrins. Since cleavage of OPN by thrombin exposes the cryptic epitope recognized by alpha9 and alpha4 integrins, we investigated the role of the cryptic epitope SLAYGLR in a murine RA model by using a specific antibody (M5) reacting to SLAYGLR sequence. The M5 antibody could abrogate monocyte migration toward the thrombin-cleaved form of OPN. Importantly, M5 antibody could inhibit the proliferation of synovium, bone erosion, and inflammatory cell infiltration in arthritic joints. Thus, we demonstrated that a cryptic epitope, the SLAYGLR sequence of murine OPN, is critically involved in the pathogenesis of a murine model of RA.
Cross-layer optimization for OFDM wireless networks-part I: theoretical framework (2005)

In this paper, we provide a theoretical framework for cross-layer optimization for orthogonal frequency division multiplexing (OFDM) wireless networks. The utility is used in our study to build a bridge between the physical layer and the media access control (MAC) layer and to balance the efficiency and fairness of wireless resource allocation. We formulate the cross-layer optimization problem as one that maximizes the average utility of all active users subject to certain conditions, which are determined by adaptive resource allocation schemes. We present necessary and sufficient conditions for utility-based optimal subcarrier assignment and power allocation and discuss the convergence properties of optimization. Numerical results demonstrate a significant performance gain for the cross-layer optimization and the gain increases with the number of active users in the networks.
Identifying Chemical Carcinogens and Assessing Potential Risk in Short-Term Bioassays Using Transgenic Mouse Models (1995)

Cancer is a worldwide public health concern. Identifying carcinogens and limiting their exposure is one approach to the problem of reducing risk. Currently, epidemiology and rodent bioassays are the means by which putative human carcinogens are identified. Both methods have intrinsic limitations: they are slow and expensive processes with many uncertainties. The development of methods to modify specific genes in the mammalian genome has provided promising new tools for identifying carcinogens and characterizing risk. Transgenic mice may provide advantages in shortening the time required for bioassays and improving the accuracy of carcinogen identification; transgenic mice might now be included in the testing armamentarium without abandoning the two-year bioassay, the current standard. We show that mutagenic carcinogens can be identified with increased sensitivity and specificity using hemizygous p53 mice in which one allele of the p53 gene has been inactivated. Furthermore, the TG.AC transgenic model, carrying a v-Ha-ras construct, has developed papillomas and malignant tumors in response to a number of mutagenic and nonmutagenic carcinogens and tumor promoters, but not to noncarcinogens. We present a decision-tree approach that permits, at modest extra cost, the testing of more chemicals with improved ability to extrapolate from rodents to humans.
Ultraviolet laser emission properties of Ce^3+-doped LiSrAlF_6 and LiCaAlF_6 (1994)

The UV laser properties of trivalent cerium-doped LiSrAlF6 (Ce:LiSAF) and LiCaAlF6 (Ce:LiCAF) are reported. The polarized absorption, emission, and excited-state absorption cross sections for both Ce:LiSAF and Ce:LiCAF were determined for the 266-nm pump and 290-nm laser emission wavelengths. The single-exponential emission lifetime was measured to be 28 ± 2 and 25 ± 2 ns for Ce:LiSAF and Ce:LiCAF, respectively. The gain was found to be highest when the probe was polarized parallel to the optical axis of the crystal, owing to the anisotropic nature of the excited-state absorption. The excited-state absorption was ascribed to a transition from the 5d orbital of Ce3+ to the conduction band of the host. Laser slope efficiencies as high as 29% and 21%, respectively, were measured for Ce:LiSAF and Ce:LiCAF when the 266-nm pulsed pump beam was polarized parallel to the optical or the c axis. These are the highest laser slope efficiencies yet observed to our knowledge for any known solid-state UV laser material. When the pump beam was polarized perpendicular to the optical axis of the crystals, the gain and the laser efficiencies dropped by as much as an order of magnitude. The magnitude of pump-induced solarization was found to be highly variable for different crystals and to have an insignificant effect on the laser performance when favorable crystals were used.