gebhart/patrepeval huggingface dataset:
Disentangling by Factorising (2018)

We define and address the problem of unsupervised learning of disentangled representations on data generated from independent factors of variation. We propose FactorVAE, a method that disentangles by encouraging the distribution of representations to be factorial and hence independent across the dimensions. We show that it improves upon $β$-VAE by providing a better trade-off between disentanglement and reconstruction quality. Moreover, we highlight the problems of a commonly used disentanglement metric and introduce a new metric that does not suffer from them.
Kinetic assay of fluorescein mono-.beta.-D-galactoside hydrolysis by .beta.-galactosidase: a front-face measurement for strongly absorbing fluorogenic substrates (1991)

A novel enzymatic assay method was developed for fluorogenic substrates that have significant intrinsic absorbance and fluorescence under the assay conditions. Fluorescein mono-beta-D-galactoside (FMG) was chosen as the substrate for the fluorescence enzymatic assay because of the high fluorescence of its hydrolytic product (fluorescein) and suitability of being hydrolyzed by beta-galactosidase. The fluorescence-concentration relationships for fluorescein and for FMG in both the right-angle detection mode of a fluorometer and the front-face detection mode of a fluorescence plate reader were exactly established and used to determine the kinetics of the enzyme assay. The results show that only front-face detection in the fluorescence plate reader can overcome the fluorescence concentration quenching that inevitably results from high absorbance by the intrinsically absorbing substrate in the conventional fluorometer, which utilizes right-angle detection. Only with front-face detection was the fluorescent assay of FMG hydrolysis under conditions of high optical density possible. The enzymatic measurements on the fluorescence plate reader were particularly efficient for determination of the enzyme kinetics because of the high rate of data collection. In this assay system, Michaelis-Menten constant Km and enzymatic catalysis rate k2 of FMG were determined as 117.6 microM and 22.7 mumol-(min.mg)-1, respectively. The results and methods described in this paper can be generalized for any assay using a fluorogenic substrate whether or not it has a high background absorbance.
Sourcefinder: a construct-driven approach for locating appropriately targeted reading comprehension source texts (2007)

A fully-automated approach for locating source material for use in developing reading comprehension/verbal reasoning passages is described. The system employs a combination of classification and regression techniques to predict the acceptability status of candidate source texts downloaded from targeted on-line journals and magazines. The approach is applied to the problem of selecting source texts pitched at a particularly advanced reading level, i.e., the level expected for students seeking admission to graduate school. Results confirm that, even at this advanced level, SourceFinder behaves much like a human rater. In particular, while the human raters agreed with each other 63% of the time, the agreement between SourceFinder and a human rater ranged from 61% to 62%. This suggests that the estimated models have succeeded in capturing useful information about the characteristics of texts that affect test developers' ratings of source acceptability and that continued use of the system may help test developers find more high quality sources in less time.
Methods for evaluating, selecting and improving software clustering algorithms (2010)

SITY LIBRARIES to lend or sell copies of this disserta-tion in paper, microform or electronic formats, and b) LIBRARY AND ARCHIVES CANADA to reproduce, lend, distribute, or sell copies of this dissertation any-where in the world in microform, paper or electronic formats and to authorise or procure the reproduction, loan, distribution or sale of copies of this dissertation anywhere in the world in microform, paper or elec-tronic formats. The author reserves other publication rights, and nei-ther the dissertation nor extensive extracts for it may be printed or otherwise reproduced without the author’s written permission.
Generation of a Polyclonal Fab Phage Display Library to the Human Breast Carcinoma Cell Line BT-20 (2000)

We have previously described a vector system for generating recombinant polyclonal antibody libraries. This system uses bidirectional phagemid and mammalian expression vectors to facilitate mass transfer of selected variable light and variable heavy (VL-VH) region gene pairs from the phagemid to the mammalian vector, to express polyclonal libraries of whole IgG antibodies. We report here the first stage of generating a polyclonal antibody library to the human breast carcinoma cell line BT-20, using this vector system. VL and VH region gene pairs were obtained from a mouse immunized with BT-20 cells, and cloned, in opposite transcriptional orientations, in the bidirectional phagemid vector, to produce an Fab phage display library. This library was selected by panning on BT-20 cells and shown to bind specifically to BT-20 cells. Such libraries, after suitable negative selection to eliminate major reactivities against normal tissue, could be transferred in mass to our bidirectional mammalian expression vector for production of libraries of chimeric antibodies with mouse V regions and human constant (C) regions. These polyclonal antibody libraries will mediate effector functions and are expected to be useful for breast cancer therapy, as well as diagnosis.
Expression of HERV-Fc1, a Human Endogenous Retrovirus, Is Increased in Patients with Active Multiple Sclerosis (2012)

Multiple sclerosis (MS) is considered to be an autoimmune disease with an unknown cause and with immune system dysregulation. Among environmental factors, viruses are most often connected with the etiology of MS. Human endogenous retroviruses (HERVs) constitute 5 to 8% of human genomic DNA and have been detected as transcripts and proteins in the central nervous system (CNS) and peripheral blood, frequently in the context of neuroinflammation. HERV-Fc1, which belongs to the HERV-H/F family, has received our attention largely because of the genetic association with MS. We studied the expression of a capsid (Gag) protein of HERV-H/F origin by flow cytometry in peripheral blood mononuclear cells (PBMCs) from healthy controls and from MS patients with nonactive or active disease. There was a significant increase in HERV-H/F Gag expression in CD4(+) (P < 0.001) and CD8(+) (P < 0.001) T lymphocytes and in monocytes (P = 0.0356) in PBMCs from MS patients with active disease. Furthermore, we have undertaken the first rigorous SYBR green-based absolute quantitative PCR (Q-PCR) evaluation approach to quantify extracellular HERV-Fc1 RNA viral loads in plasma from MS patients and healthy controls. We found a 4-fold increase in extracellular HERV-Fc1 RNA titers in patients with active MS compared with healthy controls (P < 0.001). These findings strengthen the link between HERV-Fc1 and the pathology of MS. The cause and biological consequences of these differential expression levels will be the subject of further investigation. HERV-Fc1 biology could be a compelling area for understanding the pathology of MS and possibly other autoimmune disorders.
Clinical evaluation of recombinant factor IX. (1998)

The pharmacokinetics, safety, and efficacy of recombinant factor IX (rFIX) have been evaluated in previously treated and untreated patients with hemophilia B. In a study of 56 previously treated patients, there was a total of 1,070 hemorrhages, which required 1,514 infusions of rFIX. Of the 1,070 episodes, 80% resolved after a single rFIX infusion. The majority of the remaining episodes requiring more than 1 infusion were either major or complicated hemorrhages. Eighty-seven percent of the 1,514 infusions were rated by the physicians or patients as providing an excellent or good response. These results are consistent with the efficacy data from other hemophilia product clinical trials. rFIX has also been administered as bolus doses or by continuous infusion in conjunction with 13 surgical procedures. Estimated blood loss during and after surgery was as expected when compared with blood loss for similar procedures in patients without hemophilia, and 97% of the clinical responses during and after surgery were rated by physicians or patients as excellent or good. Pharmacokinetic comparison of rFIX with one plasma-derived product showed a statistically significant lower recovery (28% less) of rFIX. The half-lives between the two products were comparable. Common adverse events associated with rFIX treatment have been comparable to other factor IX products. As expected, there has been no evidence of viral transmission by rFIX.
A Single 5 V, 65 ns, 16 pin, 16-kbit Dynamic N-MOS RAM (1978)

A single 5 V, 65 ns, 16 pin, 16-kbit dynamic N-MOS RAM is presented. A chip size of 3.18 × 4.96 mm2 and a power consumption of 215 mW for a 200 ns cycle time are realized with 3 ?m photolithography, unique sense circuitry and on-chip biasing technique.
<title>Genetically designed biosensing systems for high-throughput screening of pharmaceuticals, clinical diagnostics, and environmental monitoring</title> (2001)

The genetically-modified binding proteins calmodulin, the phosphate binding protein, the sulfate binding protein, and the galactose/glucose binding protein have been successfully employed as biosensing elements for the detection of phenothiazines, phosphate, sulfate, and glucose, respectively. Mutant proteins containing unique cysteine residues were utilized in the site-specific labeling of environment-sensitive fluorescent probes. Changes in the environment of the probes upon ligand-induced conformational changes of the proteins result in changes in fluorescence intensity.
Elevated Intracranial IL-18 in Humans and Mice after Traumatic Brain Injury and Evidence of Neuroprotective Effects of IL-18—Binding Protein after Experimental Closed Head Injury (2002)

Proinflammatory cytokines are important mediators of neuroinflammation after traumatic brain injury. The role of interleukin (IL)-18, a new member of the IL-1 family, in brain trauma has not been reported to date. The authors investigated the posttraumatic release of IL-18 in murine brains following experimental closed head injury (CHI) and in CSF of CHI patients. In the mouse model, intracerebral IL-18 was induced within 24 hours by ether anesthesia and sham operation. Significantly elevated levels of IL-18 were detected at 7 days after CHI and in human CSF up to 10 days after trauma. Published data imply that IL-18 may play a pathophysiological role in inflammatory CNS diseases; therefore its inhibition may ameliorate outcome after CHI. To evaluate the functional aspects of IL-18 in the injured brain, mice were injected systemically with IL-18-binding protein (IL-18BP), a specific inhibitor of IL-18, 1 hour after trauma. IL-18BP-treated mice showed a significantly improved neurological recovery by 7 days, accompanied by attenuated intracerebral IL-18 levels. This demonstrates that inhibition of IL-18 is associated with improved recovery. However, brain edema at 24 hours was not influenced by IL-18BP, suggesting that inflammatory mediators other than IL-18 induce the early detrimental effects of intracerebral inflammation.
Release of vasopressin from the rat hypothalamo-neurohypophysial system by angiotensin-(1-7) heptapeptide. (1988)

We have recently shown that hydrolysis of labeled angiotensin I in canine brainstem homogenate causes a rapid accumulation of the heptapeptide angiotensin-(1-7) [Ang-(1-7)]. Although this angiotensin fragment has no vasopressor activity, its consistent generation in brain homogenate led us to study its potential neurosecretory effects in the rat hypothalamo-neurohypophysial system (HNS) in vitro. Ang-(1-7) or angiotensin II (Ang II) was added to HNS perifusate in concentrations of 0.04, 0.4, and 4 microM, and release of arginine vasopressin (AVP) during each treatment was quantified as a percentage of the AVP release detected in the preceding collection period. Base-line release of AVP averaged 281 +/- 47 pg per 15 min (mean +/- SEM) in HNS explants (five experiments, five explants per chamber) perifused in Krebs solution at 37 degrees C, after a 1-hr equilibration period. At 0.04 microM, Ang II or Ang-(1-7) did not stimulate AVP release. Ang II increased AVP release over the control value by 172% +/- 44% and 268% +/- 66% at 0.4 and 4 microM, respectively; the same concentrations of Ang-(1-7) increased AVP release by 134% +/- 12% and 216% +/- 45%. The responses to Ang II and Ang-(1-7) at the highest concentration were both significant (P less than 0.05), and comparison by two-way analysis of variance indicated that Ang II and Ang-(1-7) were equipotent in stimulating AVP release over the range of concentrations studied. In the presence of the competitive Ang II antagonist [Sar1,Thr8]Ang II (20 microM), the release of AVP increased approximately equal to 2-fold. Neither Ang II nor Ang-(1-7) (4 microM) caused a further enhancement of AVP release in the presence of [Sar1,Thr8]Ang II. These data suggest that a hydrophobic residue in position 8 of the angiotensin peptide is not essential for activation of angiotensin receptors in the rat HNS. Moreover, the equipotence of Ang II and Ang-(1-7) indicates that Ang-(1-7) may participate in the control of AVP release.
The visual microphone (2014)

When sound hits an object, it causes small vibrations of the object's surface. We show how, using only high-speed video of the object, we can extract those minute vibrations and partially recover the sound that produced them, allowing us to turn everyday objects---a glass of water, a potted plant, a box of tissues, or a bag of chips---into visual microphones. We recover sounds from high-speed footage of a variety of objects with different properties, and use both real and simulated data to examine some of the factors that affect our ability to visually recover sound. We evaluate the quality of recovered sounds using intelligibility and SNR metrics and provide input and recovered audio samples for direct comparison. We also explore how to leverage the rolling shutter in regular consumer cameras to recover audio from standard frame-rate videos, and use the spatial resolution of our method to visualize how sound-related vibrations vary over an object's surface, which we can use to recover the vibration modes of an object.
Source of heavy molecular ions based on Taylor cones of ionic liquids operating in the pure ion evaporation regime (2003)

The full spray emitted by Taylor cones of the ionic liquid 1-ethyl-3-methyl imidazolium tetrafluoroborate (EMI+BF4−) held in a vacuum is investigated at room temperature by time of flight mass spectrometry. The current is composed mainly of ions under most conditions studied, but contains a small component of nanometer drops that tends to dominate the emitted mass flow. Exceptionally, drop ejection vanishes close to the smallest flow rate at which the Taylor cone is steady. The present discovery of a stable strictly ionic regime in Taylor cones of substances other than liquid metals owes much to earlier observations with sulfuric acid, where most but not all the current was ionic. Most striking is the fact that this purely ionic regime is obtained at an electrical conductivity K of only 1.3 S/m, much smaller than that of sulfuric acid, and smaller than that at which formamide electrolytes with K&amp;gt;2 S/m do still emit substantial drop currents. The ion emission includes primarily the dimer (EMI–BF4)EMI+, accompanied by fair currents of the monomer EMI+ and the trimer ions. The modest spread of ion energies observed and considerable currents attained (0.6 μA) suggests the use of this and other ionic liquids as ion beam sources with a much wider range of mass/charge and chemical compositions than previously available. The present data provide a direct proof of the reality of the often doubted mechanism of ion evaporation from liquid surfaces.
Brush-border tyrosine phosphorylation stimulates ileal neutral NaCl absorption and brush-border Na(+)-H+ exchange (1994)

The drug genistein, a tyrosine (Tyr) kinase inhibitor, was used to define a role for Tyr phosphorylation in regulation of basal and stimulated neutral NaCl absorption in rabbit ileum. Brush-border vesicles contain Tyr-phosphorylated peptides. Genistein freeze-thawed into the vesicles caused a concentration-dependent inhibition of at least three peptides with M(r) 111,000, 83,000, and 80,000. Studied with the Ussing chamber-voltage clamp technique, genistein added to the ileal mucosal surface inhibited neutral NaCl absorption. Direct addition of genistein to brush-border vesicles made from ileal villus cells inhibited brush-border Na(+)-H+ exchange but not D-glucose-stimulated Na+ uptake. These effects were not duplicated by genistin, a drug with similar structure to genistein but lacking Tyr kinase inhibiting properties. Serosal but not mucosal epidermal growth factor (EGF) stimulated NaCl absorption. Mucosal genistein but not genistin also altered second-messenger regulation of neutral NaCl absorption, inhibiting the effect of Ca2+ ionophore A-23187 and of serosal EGF but not affecting the transport changes caused by 8-bromoadenosine 3',5'-cyclic monophosphate (8-BrcAMP). In contrast, the Cl secretory effects indicated by the increase in short-circuit current for all three agents, A-23187, EGF, and 8-BrcAMP, were inhibited by mucosal genistein. These results suggest that 1) a Tyr kinase is involved in basally stimulating ileal neutral NaCl absorption and brush-border Na(+)-H+ exchange; 2) EGF stimulates NaCl absorption by an effect exerted from the serosal surface, but the effect also involves a brush-border Tyr kinase; 3) brush-border Tyr kinase is involved in the ability of Ca2+ ionophore A-23187 to inhibit neutral NaCl absorption but is not involved in the transport effects of cAMP. This study suggests that Tyr kinase(s) acting over short time periods is involved in stimulation of neutral NaCl absorption and brush-border Na(+)-H+ exchange and also in Ca(2+)-induced inhibition of NaCl absorption. These studies represent the first example of a brush-border Tyr kinase being involved in short-term signal transduction in intestinal epithelial cells.
Tracking Fluorescence-Labeled Rabies Virus: Enhanced Green Fluorescent Protein-Tagged Phosphoprotein P Supports Virus Gene Expression and Formation of Infectious Particles (2004)

Rhabdoviruses such as rabies virus (RV) encode only five multifunctional proteins accomplishing viral gene expression and virus formation. The viral phosphoprotein, P, is a structural component of the viral ribonucleoprotein (RNP) complex and an essential cofactor for the viral RNA-dependent RNA polymerase. We show here that RV P fused to enhanced green fluorescent protein (eGFP) can substitute for P throughout the viral life cycle, allowing fluorescence labeling and tracking of RV RNPs under live cell conditions. To first assess the functions of P fusion constructs, a recombinant RV lacking the P gene, SAD DeltaP, was complemented in cell lines constitutively expressing eGFP-P or P-eGFP fusion proteins. P-eGFP supported the rapid accumulation of viral mRNAs but led to low infectious-virus titers, suggesting impairment of virus formation. In contrast, complementation with eGFP-P resulted in slower accumulation of mRNAs but similar infectious titers, suggesting interference with polymerase activity rather than with virus formation. Fluorescence microscopy allowed the detection of eGFP-P-labeled extracellular virus particles and tracking of cell binding and temperature-dependent internalization into intracellular vesicles. Recombinant RVs expressing eGFP-P or an eGFP-P mutant lacking the binding site for dynein light chain 1 (DLC1) instead of P were used to track interaction with cellular proteins. In cells expressing a DsRed-labeled DLC1, colocalization of DLC1 with eGFP-P but not with the mutant P was observed. Fluorescent labeling of RV RNPs will allow further dissection of virus entry, replication, and egress under live-cell conditions as well as cell interactions.
Photochemical Synthesis of Pentacene and its Derivatives (2005)

A novel alpha-diketone precursor of pentacene, 6,13-dihydro-6,13-ethanopentacene-15,16-dione, was prepared and converted successfully to pentacene in 74 % yield by photolysis of the precursor in toluene: Irradiation of the diketone solution in toluene with light of 460 nm under an Ar atmosphere caused the solution to change from yellow to fluorescent orange-pink within a few minutes, after which, purple precipitates appeared. After 35 min, the solution changed to colorless and the purple precipitates were filtered to give pentacene in 74 % yield. By contrast, in the presence of oxygen, the color of the solution changed from yellow to pale yellow, and only 6,13-endoperoxide of pentacene was quantitatively obtained. The rate of the reaction upon photolysis was measured by observing the decay of n-pi* absorption of the precursor at 460 nm, and was found to be similar in both the presence and absence of oxygen. Therefore, the photoreaction of the alpha-diketone precursor seemed to occur via the singlet excited state. Because the T-T absorption of pentacene was observed upon photolysis of the precursor in the nanosecond transient absorption measurement under an Ar atmosphere, the excited triplet state of the pentacene generated singlet oxygen by sensitization, and it reacted with the ground-state pentacene to give the 6,13-endoperoxide. The alpha-diketone deposited on glass was also converted successfully to pentacene film by photoirradiation. In addition, diketone precursors of a mixture of 2,8- and 2,9-dibromopentacene and 2,6-trianthrylene were also prepared and their photoconversion was performed.
A 250-Mb/s Data Rate IR-UWB Transmitter Using Current-Reused Technique (2017)

This paper describes the design, simulation, implementation and testing of an impulse-radio ultra-wideband bi-phase shift keying (IR-UWB BPSK) transmitter, working in the frequency range between 3.5 and 6.5 GHz. The transmitter has been optimized to achieve the maximum distance of transmission while working within the power limits specified by the Federal Communications Commission (FCC). In this transmitter, the IR-UWB signal is generated by differentiating a Gaussian signal and then amplifying the differentiated signal. This is accomplished using a current-reused power amplifier circuit as both the differentiator and amplifier. A theoretical analysis is performed to obtain the relationship between the output amplitude and the data rate of the transmitted signal. The simulations and experimental results of the IR-UWB BPSK transmitter, implemented in a 180-nm CMOS process, are then presented. The transmitter was found to function at data rates up to 250 Mb/s with a maximum peak amplitude of 0.5 V. The dc energy consumption of the transmitter is 86 pJ/pulse. The energy efficiency is 26.2% for the pulsewidth of 1 ns. The experimental results show that power spectral density of the transmitter agrees with the simulated results and is within the FCC limits. The total core area of the chip is 0.22 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .