gebhart/patrepeval huggingface dataset:
Discrimination of late apoptotic/necrotic cells (type III) by flow cytometry in solid tumors (1997)

A method is described for the discrimination of Type III, late apoptotic, and necrotic cells, to improve the accuracy of proliferation and ploidy determinations of breast tumors. We selected an immunological probe, antitubulin antibody, and a DNA specific stain, propidium iodide (PI), both capable of crossing the permeable membranes of Type III, late apoptotic, and necrotic cells. This study utilized MDA-MB-175-VII breast carcinoma cells deprived of oxygen for up to 11 d to simulate intratumoral hypoxia, and 10 human breast tumors and mouse-human breast tumor xenografts disassociated by mechanical or enzymatic means. After 24 h under hypoxic conditions, the MDA cells displayed characteristics associated with both apoptosis and necrosis. Approximately 50% of day 1 cells showed membrane permeability by trypan blue and absence of DNA laddering; however, by day 3-4 characteristic apoptotic DNA laddering by gel electrophoresis was evident. Substantial DNA content loss, further evidenced by a reduction in PI staining and fluorescent microscopy, was obvious by day 5. By day 10, 98% of cells showed no propidium iodide staining by conventional PI live/dead cell gating, but were positive for antitubulin antibody staining. When the study was extended to the analysis of ten tumors, antitubulin antibody showed a range of 78%-96% staining with a median value of 87.5%, while PI staining showed a range of 8%-74% with a median value of 11.5%. This study demonstrates that a large percentage of cells in tumors and hypoxic cell populations have significantly reduced DNA content, such that conventional live/dead cell gating using PI may include many Type III cells as live cells, thus significantly altering data involving multicolor investigations.
Contribution to the knowledge of the genera Muntiacus and Arctogalidia in the Indo-Australian Archipelago (Mammalia, Cervidae & Viverridae) (1952)

As I have pointed out before, big game animals are very scarce in Museum collections. Many treatises are based on material from Zoological gardens, changed by captivity and often from unknown origin, from collections of frontlets, skulls and other trophies, bought haphazardly during expeditions which used all their time in thoroughly collecting the more interesting small animals. As a matter of fact, the rare species are better represented than the common ones, and the more a well-known species of game-animal is hunted, the fewer the specimens in the collections of the official Musea. The same is true for our knowledge of the biology of tropical big-game. Rare species, threatened by extinction, are studied with haste and often when it is too late to collect sufficient data. So, in preparing laws and regulations concerning the subject of hunting, one is always confronted with the fact that even the most necessary information is lacking. Barking-deer are game which is highly esteemed by hunters in our area, because they give good sport, the heads make nice trophies and perhaps also because the meat is excellent to eat. They are not scarce yet, no expensive hunting-parties are needed for an hour or two of shooting. In fact a man working on one of the large estates in Western Indonesia, may take his gun in spare-time and bring home a good buck before supper with a bit of luck.
<i>Hxt</i> encodes a basic helix-loop-helix transcription factor that regulates trophoblast cell development (1995)

Trophoblast cells are the first lineage to form in the mammalian conceptus and mediate the process of implantation. We report the cloning of a basic helix-loop-helix (bHLH) transcription factor gene, Hxt, that is expressed in early trophoblast and in differentiated giant cells. A separate gene, Hed, encodes a related protein that is expressed in maternal deciduum surrounding the implantation site. Overexpression of Hxt in mouse blastomeres directed their development into trophoblast cells in blastocysts. In addition, overexpression of Hxt induced the differentiation of rat trophoblast (Rcho-1) stem cells as assayed by changes in cell adhesion and by activation of the placental lactogen-I gene promoter, a trophoblast giant cell-specific gene. In contrast, the negative HLH regulator, Id-1, inhibited Rcho-1 differentiation and placental lactogen-I transcription. These data demonstrate a role for HLH factors in regulating trophoblast development and indicate a positive role for Hxt in promoting the formation of trophoblast giant cells.
THE EFFECTS OF CAFFEINE ON THE KINETICS OF O2UPTAKE, CO2PRODUCTION AND EXPIRATORY VENTILATION IN HUMANS DURING THE ON-TRANSIENT OF MODERATE AND HEAVY INTENSITY EXERCISE (1999)

In order to test the hypothesis that glycogen sparing observed early during exercise following caffeine ingestion was a consequence of tighter metabolic control reflected in faster VO2 kinetics, we examined the effect of caffeine ingestion on oxygen uptake (VO2), carbon dioxide production (VCO2) and expiratory ventilation (VE) kinetics at the onset of both moderate (MOD) and heavy (HVY) intensity exercise. Male subjects (n = 10) were assigned to either a MOD (50 % VO2,max, n = 5) or HVY (80 % VO2,max, n = 5) exercise condition. Constant-load cycle ergometer exercise was performed as a step function from loadless cycling 1 h after ingestion of either dextrose (placebo, PLAC) or caffeine (CAFF; 6 mg (kg body mass)-1). Alveolar gas exchange was measured breath-by-breath. A 2- or 3-component exponential model, fitted through the entire exercise transient, was used to analyse gas exchange and ventilatory data for the determination of total lag time (TLT: the time taken to attain 63 % of the total exponential increase). Caffeine had no effect on TLT for VO2 kinetics at either exercise intensity (MOD: 36 ± 14 s (PLAC) and 41 ± 10 s (CAFF); HVY: 99 ± 30 s (PLAC) and 103 ± 26 (CAFF) (mean ± S.D.)). TLT for VE was increased with caffeine at both exercise intensities (MOD: 50 ± 20 s (PLAC) and 59 ± 21 s (CAFF); HVY: 168 ± 35 s (PLAC) and 203 ± 48 s (CAFF)) and for VCO2 during MOD only (MOD: 47 ± 14 s (PLAC) and 53 ± 17 s (CAFF); HVY: 65 ± 13 s (PLAC) and 69 ± 17 s (CAFF)). Contrary to our hypothesis, the metabolic effects of caffeine did not alter the on-transient VO2 kinetics in moderate or heavy exercise. VCO2 kinetics were slowed by a reduction in CO2 stores reflected in pre-exercise and exercise end-tidal CO2 pressure (PET,CO2) and plasma PCO2 which, we propose, contributed to slowed VE kinetics.
Optimal control of a plug flow reactor with a complex reaction mechanism (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptimal control of a plug flow reactor with a complex reaction mechanismAtipat Rojnuckarin, Christodoulos A. Floudas, Herschel Rabitz, and Richard A. YetterCite this: J. Phys. Chem. 1993, 97, 45, 11689–11695Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/j100147a023https://doi.org/10.1021/j100147a023research-articleACS PublicationsRequest reuse permissionsArticle Views520Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Optimal Management of the Hepatitis B Patient Who Desires Pregnancy or Is Pregnant (2012)

Women of childbearing age with recognized hepatitis B infection should have their liver disease assessed before pregnancy occurs since the management of hepatitis B virus (HBV) infection in this setting is complex. Initiation of treatment in a woman of child-bearing age will depend on when she intends on conceiving, as well as the severity of her liver disease. During pregnancy, all decisions about initiating, continuing or stopping HBV therapy must include an analysis of the risks and benefits for both mother and fetus. The trimester of the pregnancy and the stage of the mother's liver disease are important factors. Treatment in the third trimester may be considered to aid in prevention of perinatal transmission, which appears to be most pronounced in mothers with high viral loads. Consideration of initiation of third trimester treatment should occur after a high viral load is documented in the latter part of the second trimester, to allow adequate time for initiation of antiviral therapy with significant viral suppression before delivery. This discussion should include the topic of breastfeeding, since it is generally not recommended while on antiviral therapy. Until recently lamivudine and tenofovir appeared to be the therapeutic options with the most reasonable safety data in pregnancy. There are emerging data that telbivudine may also be considered in this setting.
Resurrecting the sigmoid in deep learning through dynamical isometry: theory and practice (2017)

It is well known that the initialization of weights in deep neural networks can have a dramatic impact on learning speed. For example, ensuring the mean squared singular value of a network's input-output Jacobian is $O(1)$ is essential for avoiding the exponential vanishing or explosion of gradients. The stronger condition that all singular values of the Jacobian concentrate near $1$ is a property known as dynamical isometry. For deep linear networks, dynamical isometry can be achieved through orthogonal weight initialization and has been shown to dramatically speed up learning; however, it has remained unclear how to extend these results to the nonlinear setting. We address this question by employing powerful tools from free probability theory to compute analytically the entire singular value distribution of a deep network's input-output Jacobian. We explore the dependence of the singular value distribution on the depth of the network, the weight initialization, and the choice of nonlinearity. Intriguingly, we find that ReLU networks are incapable of dynamical isometry. On the other hand, sigmoidal networks can achieve isometry, but only with orthogonal weight initialization. Moreover, we demonstrate empirically that deep nonlinear networks achieving dynamical isometry learn orders of magnitude faster than networks that do not. Indeed, we show that properly-initialized deep sigmoidal networks consistently outperform deep ReLU networks. Overall, our analysis reveals that controlling the entire distribution of Jacobian singular values is an important design consideration in deep learning.
A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase (2014)

Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5'-to-3' exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E-DNA-ddNTP) and binary (E-DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5'-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.
Lithosphere-atmosphere-ionosphere coupling as governing mechanism for preseismic short-term events in atmosphere and ionosphere (2004)

Abstract. We present a general concept of mechanisms of preseismic phenomena in the atmosphere and ionosphere. After short review of observational results we conclude: 1. Upward migration of fluid substrate matter (bubble) can lead to ousting of the hot water/gas near the ground surface and cause an earthquake (EQ) itself in the strength-weakened area; 2. Thus, time and place of the bubble appearance could be random values, but EQ, geochemistry anomaly and foreshocks (seismic, SA and ULF electromagnetic ones) are casually connected; 3. Atmospheric perturbation of temperature and density could follow preseismic hot water/gas release resulting in generation of atmospheric gravity waves (AGW) with periods in a range of 6–60min; 4. Seismo-induced AGW could lead to modification of the ionospheric turbulence and to the change of over-horizon radio-wave propagation in the atmosphere, perturbation of LF waves in the lower ionosphere and ULF emission depression at the ground.
Purification and characterization of methylmalonyl-CoA epimerase from <i>Propionibacterium shermanii</i> (1981)

Methylmalonyl-CoA epimerase, which specifically interconverts the (2R)- and (2S)- epimers of methylmalonyl-CoA, was purified 95-fold from Propionibacterium shermanii by a new method that affords apparently homogeneous enzyme, in 80-100mg quantities, in yields representing about 40% of the activity in cell-free extracts. The specific activity of the purified enzyme, 10.1 mukat/mg, is much greater than previously reported. Native methylmalonyl-CoA epimerase has Mr about 33000, and apparently consists of two identical subunits. The purified enzyme is stable indefinitely when stored at -20 degrees C and pH 8.5, but contrary to previous reports it is not unusually acid-stable. The activity of methylmalonyl-CoA epimerase is increased by Co2+, and to a smaller extent by Ni2+, Mn2+ and Zn2+.
Enzalutamide: targeting the androgen signalling pathway in metastatic castration‐resistant prostate cancer (2015)

Significant progress has been made in the understanding of the underlying cancer biology of castration-resistant prostate cancer (CRPC) with the androgen receptor (AR) signalling pathway remaining implicated throughout the prostate cancer disease continuum. Reactivation of the AR signalling pathway is considered to be a key driver of CRPC progression and, as such, the AR is a logical target for therapy in CRPC. The objective of this review was to understand the importance of AR signalling in the treatment of patients with metastatic CRPC (mCRPC) and to discuss the clinical benefits associated with inhibition of the AR signalling pathway. A search was conducted to identify articles relating to the role of AR signalling in CRPC and therapies that inhibit the AR signalling pathway. Current understanding of prostate cancer has identified the AR signalling pathway as a logical target for the treatment of CRPC. Available therapies that inhibit the AR signalling pathway include AR blockers, androgen biosynthesis inhibitors, and AR signalling inhibitors. Enzalutamide, the first approved AR signalling inhibitor, has a novel mode of action targeting AR signalling at three key stages. The direct mode of action of enzalutamide has been shown to translate into clinical responses in patients with mCRPC. In conclusion, the targeting of the AR signalling pathway in patients with mCRPC results in numerous clinical benefits. As the number of treatment options increase, more trials evaluating the sequencing and combination of treatments are required. This review highlights the continued importance of targeting a key driver in the progression of CRPC, AR signalling, and the clinical benefits associated with inhibition of the AR signalling pathway in the treatment of patients with CRPC.
Generation of closely-spaced, doublet, CFA cathode pulses with a line-type modulator (2002)

It is noted that the radar system pulse format requirement for the generation of closely spaced, doublet RF pulses seems to preclude the use of line-type modulators. The author describes the dual channel, line-type modulators used to generate doublet cross-field amplifier (CFA) cathode pulses in a 1.25 MW peak RF power output master oscillator power amplifier (MOPA) transmitter chain. The high-power RF amplifier chain consists of a 20 kW peak power traveling wave tube (TWT) , a 150 kW peak power intermediate CFA, and the final CFA stage which amplifies the doublet RF pulses to the 1.25 MW peak power level. A comparison of a typical hard tube modulator circuit to the dual channel line-type modulator circuit is presented. The intermediate CFA stage modulator (22 kV and 14 A pk) and the final CFA stage modulator (35 kV and 77 A pk) are described with equipment photographs, test data, and results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Amperometric Biosensors Based on Redox Polymer−Carbon Nanotube−Enzyme Composites (2005)

Based on their size and unique electrical properties, carbon nanotubes offer the exciting possibility of developing ultrasensitive, electrochemical biosensors. In this study, we describe the construction of amperometric biosensors based on the incorporation of single-walled carbon nanotubes modified with enzyme into redox polymer hydrogels. The composite films were constructed by first incubating an enzyme in a single-walled carbon nanotube (SWNTs) solution and then cross-linking within a poly[(vinylpyridine)Os(bipyridyl)(2)Cl(2+/3+)] polymer film. Incorporation of SWNTs, modified with glucose oxidase, into the redox polymer films resulted in a 2-10-fold increase in the oxidation and reduction peak currents during cyclic voltammetry, while the glucose electrooxidation current was increased 3-fold to approximately 1 mA/cm(2) for glucose sensors. Similar effects were also observed when SWNTs were modified with horseradish peroxidase prior to incorporation into redox hydrogels.
Changes in Product Attributes and Costs as Drivers of New Product Diffusion and Substitution (2005)

Diffusion theory has typically focused on how communication, internal or external to a social system, leads to adoptions and diffusion of an innovation. We develop a diffusion and substitution model based on a somewhat different perspective. In some cases, progressive improvements in product attributes and/or continual cost reduction seem to be a key driver of the diffusion process. For example, after introduction of the 5.25‐inch disk drive, its capacity continually increased, and accordingly, so did customer willingness‐to‐pay. Our model is based on a linear reservation price framework, in which a product is described by its depth (defined as the difference between a product̂s maximum reservation price and its production cost), and its breadth (related to the slope of its reservation price curve), indicating how broadly it appeals across various customer segments. Because of changes in product depths and breadths over time, customers who previously preferred the old product may later prefer the new product, thus creating the diffusion process. While the Bass model describes diffusion as a function of the coefficients of innovation and imitation, in our model, it is described by the coefficients of depth and breadth (the rates of change in relative depth and breadth), along with an S‐coefficient that we associate with the technology S‐curve. We fit our model to data from the disk‐drive and the microprocessor industries.
Integrated Cu-based TM-pass polarizer using CMOS technology platform (2010)

A transverse-magnetic-pass (TM-pass) copper (Cu) polarizer is proposed and analyzed using the previously published two-dimensional Method-of-Lines beam-propagation model. The proposed polarizer exhibits a simulated high-pass filter characteristics, with TM <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> and TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> mode transmissivity of >70% and <5%, respectively, in the wavelength regime of 1.2–1.6 μm. The polarization extinction ratio (PER) given by 10 log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> (PTM <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> )/(PTE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> ) is +11.5 dB across the high-pass wavelength regime. To the best of the authors' knowledge, we report here the smallest footprint CMOS-platform compatible TM-polarizer.
Automatic Feature Selection Technique for Next Generation Self-Organizing Networks (2018)

Despite self-organizing networks (SONs) pursue the automation of management tasks in current cellular networks, the selection of the most useful performance indicators (PIs), used as inputs for SON functions, is still performed by network experts. In this letter, a novel supervised technique for the automatic selection of PIs for self-healing functions is proposed, relying on the dissimilarity of their statistical behavior under different network states. Results using data from a live network show that the proposed method outperforms an expert's selection, allowing the volume and complexity of both network databases and SON functions to be reduced without an expert's intervention.
Labeling Biomolecules with Radiorhenium - A Review of the Bifunctional Chelators (2007)

For radiotherapy, biomolecules such as intact antibodies, antibody fragments, peptides, DNAs and other oligomers have all been labeled with radiorhenium ((186)Re and (188)Re). Three different approaches have been employed that may be referred to as direct, indirect and integral labeling. Direct labeling applies to proteins and involves the initial reduction of endogenous disulfide bridges to provide chelation sites. Indirect labeling can apply to most biomolecules and involves the initial attachment of an exogenous chelator. Finally, integral labeling is a special case applying only to small molecules in which the metallic radionuclide serves to link two parts of a biomolecule together in forming the labeled complex. While the number of varieties for the direct and integral radiolabeling approaches is rather limited, a fairly large and diverse number of chelators have been reported in the case of indirect labeling. Our objective herein is to provide an overview of the various chelators that have been used in the indirect labeling of biomolecules with radiorhenium, including details on the labeling procedures, the stability of the radiolabel and, where possible, the influence of the label on biological properties.