gebhart/patrepeval huggingface dataset:
Advanced scan chain failure analysis using laser modulation mapping and continuous wave probing (2012)

Scan chain failures are a significant fraction of yield loss. The complexity of modern design-for-test (DFT) implementation techniques and more subtle failure mechanisms of sub-40nm technologies make defect identification more challenging. Software chain diagnosis and a variety of EFA techniques have been deployed to improve scan chain failure isolation. However, we have found in practice that each of these techniques has significant limitations. In earlier papers we presented a new image-based laser technique (Modulation Mapping) to identify the first failing flop in the broken scan chain of stuck-at failures. Here we present three case studies of scan chains with more subtle resistive failure mechanisms, including transition, bridge, and slow-to-rise/fall failures, using a combination of modulation mapping (MM) and continuous-wave (CW) laser probing.
Effects of Amide-Protected and Lipid-Encapsulated Conjugated Linoleic Acid (CLA) Supplements on Milk Fat Synthesis (2004)

The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) is a potent inhibitor of milk fat synthesis; its ability to reduce milk fat output in a controlled manner as a feed supplement, has potential management applications in the dairy industry. The effectiveness of dietary supplements of trans-10, cis-12 CLA is related to the extent to which their metabolism by rumen bacteria is minimized. A number of processes have been used to manufacture "rumen-protected" feed supplements, and their efficacy can be described by the extent of protection from rumen bacteria as well as postruminal bioavailability. The objective of this study was to investigate the effects of 2 rumen-protected CLA supplements on milk fat synthesis. Using the same initial batch of CLA, supplements were manufactured by the formation of fatty acyl amide bonds or by lipid encapsulation. Three rumen fistulated Holstein cows were randomly assigned in a 3 x 3 Latin square experiment. Treatments were 1) no supplement (control), 2) amide-protected CLA supplement, and 3) lipid-encapsulated CLA supplement. Supplements were fed to provide 10 g/d of the trans-10, cis-12 CLA isomer. Over the 7-d treatment period, 21 and 22% reductions in milk fat yield were observed for the amide-protected and lipid-encapsulated supplements, respectively. Transfer of trans-10, cis-12 CLA into milk fat was also similar for the amide-protected (7.1%) and lipid-encapsulated (7.9%) supplements. Overall, the amide-protected and lipid-encapsulated CLA supplements were equally effective at reducing milk fat synthesis and had no effect on milk yield or dry matter intake.
DNA Sequences for the Specific Detection of Cryptosporidium Parvum by the Polymerase Chain Reaction (1991)

The objective of this project was to construct specific and sensitive molecular probes and amplification primers for Cryptosporidium parvum that could be used in diagnosis, retrospective tissue studies, and in epidemiologic surveys. Whole genomic DNA was extracted from oocysts of C. parvum purified from human and bovine feces. A genomic library was constructed in plasmid pUC18 and propagated in Escherichia coli DH5 alpha. Transformants were screened by colony hybridization and autoradiography. The 2.3-kilobase segment in plasmid pHC1, a clone specific for C. parvum, was sequenced by the Sanger method. Computer analysis gave a G+C content of 35%. A 400-base region (bases 470-870) was selected as an amplification target because it contained a unique restriction endonuclease site that could serve as a useful marker. Primers of 26 nucleotides each were synthesized. Sensitive and specific amplification of the target sequence was demonstrated both by ethidium bromide staining of agarose and acrylamide gels, and by hybridization with chemiluminescence-labeled synthetic oligonucleotide probes.
Large Area Vapor Phase Growth and Characterization of MoS2 Atomic Layers on SiO2 Substrate (2011)

Monolayer Molybdenum disulfide (MoS2), a two-dimensional crystal with a direct bandgap, is a promising candidate for 2D nanoelectronic devices complementing graphene. There have been recent attempts to produce MoS2 layers via chemical and mechanical exfoliation of bulk material. Here we demonstrate the large area growth of MoS2 atomic layers on SiO2 substrates by a scalable chemical vapor deposition (CVD) method. The as-prepared samples can either be readily utilized for further device fabrication or be easily released from SiO2 and transferred to arbitrary substrates. High resolution transmission electron microscopy and Raman spectroscopy on the as grown films of MoS2 indicate that the number of layers range from single layer to a few layers. Our results on the direct growth of MoS2 layers on dielectric leading to facile device fabrication possibilities show the expanding set of useful 2D atomic layers, on the heels of graphene, which can be controllably synthesized and manipulated for many applications.
A monolithic capacitive pressure sensor with pulse-period output (1980)

A new microminiature monolithic capacitive pressure transducer (CPT I) is 20 times more sensitive than piezoresistive strain-gauge pressure transducers, requires one percent of the power, and can be batch fabricated through current integrated circuit technology. A second device (CPT II) incorporates bipolar signal-processing electronics on the same silicon chip to produce a low-duty-cycle pulse-mode output with period related to pressure. This output format helps to re-solve the problem of shunting between leads, which is one of the principal causes of long-term drift in piezoresistive transducers designed for implantable medical applications. Because this device uses capacitance change as a transductional mechanism rather than piezo-resistivity, it is not susceptible to drift caused by temperature variations in the piezoresistive coefficient. Optimization for totally implantable biomedical applications places special emphasis on small size, high sensitivity, improved long-term baseline stability, and greatly reduced power consumption. These properties are also important for a wide range of pressure-sensing applications-from automotive to general industrial use.
TDP-43 proteinopathies: a new class of proteinopathies (2007)

The recent identification of TAR-DNA-binding protein-43 (TDP-43) as the major component of the pathologic inclusions characteristic to sporadic and familial frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), as well as most forms of amyotrophic lateral sclerosis (ALS), resolved a long-standing enigma concerning the nature of the ubiquitinated disease protein in these conditions and provides further evidence that ALS and FTLD-U represent a clinicopathological spectrum of neurodegenerative disorders that share similar pathomechanisms. Although the physiological function of TDP-43 in the brain and its specific role in FTLD-U and ALS pathogenesis is currently unknown, the presence of ubiquitinated, hyperphosphorylated and truncated species of TDP-43, in addition to redistribution of physiological TDP-43 from the nucleus to cytoplasmic inclusions, implicates TDP-43 in a novel and unifying mechanism of neurodegeneration in TDP-43 proteinopathies. In this review, we summarize the identification of TDP-43 and the advances in understanding TDP-43 proteinopathies, and finally we discuss the implications of these discoveries for future strategies in developing diagnostics and therapeutics for FTLD-U and ALS.
Computational Characterization of the Role of the Base in the Suzuki−Miyaura Cross-Coupling Reaction (2005)

The role of the base in the transmetalation step of the Suzuki-Miyaura cross-coupling reaction is analyzed computationally by means of DFT calculations with the Becke3LYP functional. The model system studied consists of Pd(CH=CH2)(PH3)2Br as the starting catalyst complex, CH2=CHB(OH)2 as the organoboronic acid, and OH- as the base. The two main mechanistic proposals, consisting of the base attacking first either the palladium complex or the organoboronic acid, are evaluated through geometry optimization of the corresponding intermediates and transition states. Supplementary calculations are carried out on the uncatalyzed reaction and on a process where the starting complex is Pd(CH=CH2)(PH3)2(OH). These calculations, considered together with available experimental data, strongly suggest that the main mechanism of transmetalation in the catalytic cycle starts with the reaction of the base and the organoboronic acid.
Delay discounting in current and never-before cigarette smokers: Similarities and differences across commodity, sign, and magnitude. (2003)

Research has found that nicotine-dependent individuals delay discount monetary gains at a higher rate than matched controls. Delay discount rates, however, have also been found to vary across within-subject variables such as the magnitude of the outcome (e.g., 10 dollars or 1,000 dollars), whether the outcome constitutes a gain or a loss, and the commodity being evaluated (e.g., money or health). The present study comprehensively investigated the differences in delay discounting between current and never-before cigarette smokers and across these within-subject variables. Both groups exhibited a magnitude, sign, and commodity effect. Current smokers' delay discount rates for monetary outcomes, however, were higher than never-before smokers across all magnitudes and both signs. This trend was also found for delayed health outcomes, but failed to reach significance.
Modeling α‐helical transmembrane domains: The calculation and use of substitution tables for lipid‐facing residues (1993)

Amino acid substitution tables are calculated for residues in membrane proteins where the side chain is accessible to the lipid. The analysis is based upon the knowledge of the three-dimensional structures of two homologous bacterial photosynthetic reaction centers and alignments of their sequences with the sequences of related proteins. The patterns of residue substitutions show that the lipid-accessible residues are less conserved and have distinctly different substitution patterns from the inaccessible residues in water-soluble proteins. The observed substitutions obtained from sequence alignments of transmembrane regions (identified from, e.g., hydrophobicity analysis) can be compared with the patterns derived from the substitution tables to predict the accessibility of residues to the lipid. A Fourier transform method, similar to that used for the calculation of a hydrophobic moment, is used to detect periodicity in the predicted accessibility that is compatible with the presence of an alpha-helix. If the putative transmembrane region is identified as helical, then the buried and exposed faces can be discriminated. The presence of charged residues on the lipid-exposed face can help to identify the regions that are in contact with the polar environment on the borders of the bilayer, and the construction of a meaningful three-dimensional model is then possible. This method is tested on an alignment of bacteriorhodopsin and two related sequences for which there are structural data at near atomic resolution.
THE USE OF A PIG LIVER XENOGRAFT FOR TEMPORARY SUPPORT OF A PATIENT WITH FULMINANT HEPATIC FAILURE (1995)

A 26-year-old female patient with fulminant hepatic failure and a history of autoimmune hepatitis was heterotopically transplanted with a pig hepatic xenograft to provide temporary metabolic support prior to transplantation with a human donor organ. Circulating natural antipig antibodies were removed prior to transplantation by plasmapheresis and ex vivo en bloc perfusion of the donor pig kidneys. The liver xenograft functioned after transplantation as measured by active bile production, stabilization of prothrombin levels, and reduction in the circulating levels of lactic acid and the enzymes AST and ALT. Despite the removal of greater than 90% of the recipient's natural xenoantibodies prior to transplantation, the levels of antibody rapidly returned and were associated with antibody and complement-mediated rejection of the donor graft. Immunohistochemical evidence of graft rejection could be detected by the deposition of antibody, complement components including properdin, and endothelial swelling as early as 3 hr posttransplantation. These lesions progressed in severity and were accompanied by evidence of thrombosis and ischemic necrosis of the liver xenograft by 34 hrs posttransplantation. The main portal vein, hepatic artery, and vena cava were patent. The placement of the liver graft did not result in any improvement in the neurological status of the patient and she died 34 hr after xenografting due to irreversible brain damage. The information derived from this case has renewed interest in the clinical use of bioartificial devices and whole organ perfusion using xenogeneic tissue for temporary bridging of patients prior to allografting.
Electromagnetically Induced Transparency in a Diamond Spin Ensemble Enables All-Optical Electromagnetic Field Sensing (2013)

We use electromagnetically induced transparency (EIT) to probe the narrow electron-spin resonance of nitrogen-vacancy centers in diamond. Working with a multipass diamond chip at temperatures 6-30 K, the zero-phonon absorption line (637 nm) exhibits an optical depth of 6 and inhomogeneous linewidth of ~30 GHz FWHM. Simultaneous optical excitation at two frequencies separated by the ground-state zero-field splitting (2.88 GHz) reveals EIT resonances with a contrast exceeding 6% and FWHM down to 0.4 MHz. The resonances provide an all-optical probe of external electric and magnetic fields with a projected photon-shot-noise-limited sensitivity of 0.2 V/cm/√[Hz] and 0.1 nT/√[Hz], respectively. Operation of a prototype diamond-EIT magnetometer measures a noise floor of ~/<1 nT/√[Hz] for frequencies above 10 Hz and Allan deviation of 1.3±1.1 nT for 100 s intervals. The results demonstrate the potential of diamond-EIT devices for applications ranging from quantum-optical memory to precision measurement and tests of fundamental physics.
A link between ferritin gene expression and ribonucleotide reductase R2 protein, as demonstrated by retroviral vector mediated stable expression (1996)

We have constructed a retroviral expression vector for the mammalian ribonucleotide reductase R2 component. Stable infectants, which express a myc epitope tagged R2 protein from the vector cDNA were obtained and described for the first time. Cells containing the recombinant protein exhibited increased ribonucleotide reductase activity, and were resistant to the antitumour agent hydroxyurea, which targets the R2 component of ribonucleotide reductase. Furthermore, a direct link between ferritin gene expression and R2 protein was observed, since cells containing vector expressed recombinant R2 protein exhibited increased H-chain and L-chain ferritin gene expression.
Oral Resveratrol Therapy Inhibits Cancer-Induced Skeletal Muscle and Cardiac Atrophy In Vivo (2011)

The mechanism by which cancer mediates muscle atrophy has been delineated in the past 3 decades and includes a prominent role of tumor-derived cytokines, such as IL-6, TNFα, and IL-1. These cytokines interact with their cognate receptors on muscle to activate the downstream transcription factor NF-κB and induce sarcomere proteolysis. Experimentally, inhibiting NF-κB signaling largely prevents cancer-induced muscle wasting, indicating its prominent role in muscle atrophy. Resveratrol, a natural phytoalexin found in the skin of grapes, has recently been shown to inhibit NF-κB in cancer cells, which led us to hypothesize that it might have a protective role in cancer cachexia. Therefore, we investigated whether daily oral resveratrol could protect against skeletal muscle loss and cardiac atrophy in an established mouse model. We demonstrate resveratrol inhibits skeletal muscle and cardiac atrophy induced by C26 adenocarcinoma tumors through its inhibition of NF-κB (p65) activity in skeletal muscle and heart. These studies demonstrate for the first time the utility of oral resveratrol therapy to provide clinical benefit in cancer-induced atrophy through the inhibition of NF-κB in muscle. These findings may have application in the treatment of diseases with parallel pathophysiologies such as muscular dystrophy and heart failure.
Substituted Aluminum and Zinc Quinolates with Blue-Shifted Absorbance/Luminescence Bands:  Synthesis and Spectroscopic, Photoluminescence, and Electroluminescence Characterization (1996)

Two novel lumophores based on aluminum and zinc metallo-8-hydroxyquinolates have been prepared as electroluminescent materials, and their absorbance, photoluminescence, and electroluminescence properties compared with unsubstituted versions of these same complexes. 8-Hydroxy-5-piperidinylquinolinesulfonamide (1) was synthesized in order to add an electron-withdrawing substituent at the 5-position in 8-hydroxyquinoline, increasing the solubility of the corresponding metal quinolate complexes in nonpolar solvents, and producing a blue-shift in the emission wavelength maximum, relative to complexes formed from the unsubstituted compound. The aluminum complex (Al(QS)3) and the zinc complex (Zn(QS)2) of 1 were compared with the aluminum and zinc complexes of unsubstituted 8-hydroxyquinoline (AlQ3 and ZnQ2), both as solutions and as pure thin films, or as poly(N-vinylcarbazole) (PVK) thin films doped with the metal quinolates. Ultraviolet photoelectron spectroscopy data are presented to assist in estimating the energies of the highest occupied molecular orbitals (HOMO) of AlQ3, ZnQ2, Al(QS)3, and Zn(QS)2. Electroluminescence data shows that ITO/Al(QS)3−PVK/aluminum and ITO/Zn(QS)2−PVK/aluminum devices exhibit good diode-like electrical behavior. Electroluminescence spectra mimic the photoluminescence spectra for all complexes.
Combining stem cells and biomaterial scaffolds for constructing tissues and cell delivery (2008)

Combining stem cells with biomaterial scaffolds provides a promising strategy for engineering tissues and cellular delivery. This review seeks to describe the current types of scaffolds and evaluate their use in combination with stem cells for tissue engineering applications. Potential scaffold materials are classified as natural or synthetic and the advantages and drawbacks of each material are detailed. The materials are further divided into subcategories, which describe specific examples from the literature. Finally, conclusions about the current state of biomaterial scaffolds containing stem cells for tissue engineering applications are drawn and suggestions for the future direction of the field are given. Overall, this chapter seeks to give an overview of the available biomaterials for use in combination with directed stem cell differentiation as means of replacing diseased or damaged tissues.
The A- and B-type cyclin associated cdc2 kinases in Xenopus turn on and off at different times in the cell cycle. (1990)

Cyclins play a key role in the induction of mitosis. In this paper we report the isolation of a cyclin A cDNA clone from Xenopus eggs. Its cognate mRNA encodes a protein that shows characteristic accumulation and destruction during mitotic cell cycles. The cyclin A polypeptide is associated with a protein that cross-reacts with an antibody against the conserved 'PSTAIR' epitope of p34cdc2, and the cyclin A-cdc2 complex exhibits protein kinase activity that oscillates with the cell cycle. This kinase activity rises more smoothly than that of the cyclin B-cdc2 complexes and reaches a peak earlier in the cell cycle; indeed, cyclin A is destroyed before nuclear envelope breakdown. None of the cyclin-cdc2 complexes show simple relationships between the concentration of the cyclin moiety and the kinase activity. All three cyclin associated kinases (A, B1 and B2) phosphorylate identical sites on histones with the consensus XSPXK/R, although they show significant differences in their substrate preferences. We discuss possible models for the different roles of the A- and B-type cyclins in the control of cell division.
The implications of non-invasive prenatal testing failures: a review of an under-discussed phenomenon (2016)

Recent publications suggest that patients who receive a 'no call' result are at increased risk of aneuploidy. Some professional societies have therefore recommended that these patients undergo genetic counseling and be offered invasive diagnostic testing. NIPT technology that has a high failure rate may increase the false positive rates, decrease the positive predictive value, and increase the procedure-related pregnancy loss. © 2016 John Wiley & Sons, Ltd.
Control of Viremia in Simian Immunodeficiency Virus Infection by CD8 + Lymphocytes (1999)

Clinical evidence suggests that cellular immunity is involved in controlling human immunodeficiency virus-1 (HIV-1) replication. An animal model of acquired immune deficiency syndrome (AIDS), the simian immunodeficiency virus (SIV)-infected rhesus monkey, was used to show that virus replication is not controlled in monkeys depleted of CD8+ lymphocytes during primary SIV infection. Eliminating CD8+ lymphocytes from monkeys during chronic SIV infection resulted in a rapid and marked increase in viremia that was again suppressed coincident with the reappearance of SIV-specific CD8+ T cells. These results confirm the importance of cell-mediated immunity in controlling HIV-1 infection and support the exploration of vaccination approaches for preventing infection that will elicit these immune responses.
Heparin specifically inhibits binding of V3 loop antibodies to HIV-1 gp120, an effect potentiated by CD4 binding (1994)

The modes of action of heparin and dextran sulphate differ. Dextran sulphate both inhibits CD4-gp120 binding and binds to the V3 loop of gp120. However, heparin is more selective and appears to function only by interfering with events involving the V3 loop that occur prior to HIV fusion with the plasma membrane.
Design of an artificial skin. I. Basic design principles (1980)

Individuals who suffer extensive loss of skin, commonly in fires, are acutely ill, in danger of succumbing either to massive infection of to severe fluid loss. Patients who survive these early threats must often cope with problems of rehabilitation arising from deep, disfiguring scars and crippling contractures. In this report we describe the physiocochemical, biochemical, and mechanical considerations that form the basis for two-stage design of a membrane useful as an experimental wound closure. Stage I of the design, applicable to short-term acute use, calls for a membrane which displaces efficiently air pockets from a carefully prepared woundbed, free of weak boundary layers, and maintains the moisture flux through the wound at an optimal level. Optimization of the surface energy, modulus of elasticity, energy to fracture and moisture permeability of the membrane are among the essential attributes of Stage I design. Stage 2 of the design, applicable to long-term, chronic use, focuses on a nonantigenic membrane which performs as a biodegradable template for synthesis of neodermal tissue. A survey of candidate materials suggests reasons for selection of a porous, crosslinked collagen-glycosaminoglycan coprecipitate as the chemical basis of an evolving design which was initiated 10 years ago. Over the past several years a set of membranes has been iteratively designed on this basis and has been used to cover satisfactorily large experimental full-thickness skin wounds in guinea pigs. Such membranes have effectively protected these wounds from infection and fluid loss for over 25 days without rejection and without requiring change or other invasive manipulation. When appropriately designed for the purpose, the membranes have also strongly retarded wound contraction and have become replaced by newly synthesized, stable connective tissue. Several rules relating the molecular structure and morphology of these membranes to cellular response of adjacent tissue have also been derived. This report is the first in a series which details the methodology of preparation and the record of performance.