gebhart/patrepeval huggingface dataset:
Isolation and Characterization of Pichia heedii Mutants Defective in Xylose Uptake (1990)

To investigate the role of xylose uptake in xylose metabolism in yeasts, we isolated a series of mutated strains of the yeast Pichia heedii which are defective in xylose utilization. Four of these demonstrated defects in xylose uptake. Overlaps between the functional or regulatory mechanisms for glucose and xylose uptake may exist in this yeast since some of the mutants defective in xylose uptake were also defective in glucose transport. None of the mutants were defective in xylose reductase or xylitol dehydrogenase activities.
Physical Unclonable Functions in Cryptographic Protocols: Security Proofs and Impossibility Results. (2012)

We investigate the power of physical unclonable functions (PUFs) as a new primitive in cryptographic protocols. Our contributions split into three parts. Firstly, we focus on the realiza bility of PUF-protocols in a special type of stand-alone setting (the “stand-alone, good PUF setting”) under minimal assumptions. We provide new PUF definitions that require only weak average security properties of the PUF, and prove that these definitions suffice to realize secure PUF-based oblivious transfer (OT), bit com mitment (BC) and key exchange (KE) in said setting. Our protocols for OT, BC and KE are partly new, and have certain practicality and security advantages compared to existing schemes. In the second part of the paper, we formally prove that there are very sharp limits on the usability of PUFs for OT and KE beyond the above stand-alone, good PUF scenario. We introduce two new and realistic attack models, the so-called posterior access model (PAM) and the bad PUF model, and prove several impossibility results in these models. First, OT and KE protocols whose security is solely based on PUFs are generally impossible in the PAM. More precisely, one-time access of an adversary to the PUF after the end of a single protocol (sub-)session makes all previous (sub-)sessions provably insecure. Second, OT whose security is solely based on PUFs is impossible in the bad PUF model, even if only a stand alone execution of the protocol is considered (i.e., even if no adversarial PUF access after the protocol is allowed). Our impossibility proofs do not only hold for the weak PUF definition of the first part of the paper, but even apply if ideal rand omness and unpredictability is assumed in the PUF, i.e., if the PUF is modeled as a random permutation oracle. In the third part, we investigate the feasibility of PUF-based bit commitment beyond the stand-alone, good PUF setting. For a number of reasons, this case is more complicated than OT and KE. We first prove that BC is impossible in the bad PUF model if players have got access to the PUF between the commit and the reveal phase. Again, this result holds even if the PUF is “ideal” and modeled as a random permutation oracle. Secondly, we sketch (without proof) two new BC-protocols, which can deal with bad PUFs or with adversarial access between the commit and reveal phase, but not with both. We hope that our results can contribute to a clarification of the usability of PUF s in cryptographic protocols. They show that new hardware properties such as offline certifiability and the erasure of PUF responses would be required in order to make PUFs a broadly applicable cryptographic tool. These features have not yet been realized in practical PUF-implementations and generally seem hard to achieve at low costs. Our findings also show that the question how PUFs can be modeled comprehensively in a UC-setting must be considered at least partly open.
Genomic DNA Amplification from a Single Bacterium (2005)

Genomic DNA was amplified about 5 billion-fold from single, flow-sorted bacterial cells by the multiple displacement amplification (MDA) reaction, using phi 29 DNA polymerase. A 662-bp segment of the 16S rRNA gene could be accurately sequenced from the amplified DNA. MDA methods enable new strategies for studying non-culturable microorganisms.
Highly Efficient Differentiation and Enrichment of Spinal Motor Neurons Derived from Human and Monkey Embryonic Stem Cells (2009)

The series of procedures we established here, namely neural induction, NSC expansion, sMN differentiation and sMN purification, can provide large quantities of naïve sMNs derived from human and monkey pluripotent stem cells. Using small molecule reagents, reduction of culture cost could be achieved.
Downregulation of Activating Transcription Factor 5 Is Required for Differentiation of Neural Progenitor Cells into Astrocytes (2005)

The mechanisms that regulate neural progenitor cell differentiation are primarily unknown. The transcription factor activating transcription factor 5 (ATF5) is expressed in neural progenitors of developing brain but is absent from mature astrocytes and neurons. Here, we demonstrate that ATF5 regulates the conversion of ventricular zone (VZ) and subventricular zone (SVZ) neural progenitors into astrocytes. Constitutive ATF5 expression maintains neural progenitor cell proliferation and blocks their in vitro and in vivo differentiation into astrocytes. Conversely, loss of ATF5 function promotes cell-cycle exit and allows astrocytic differentiation in vitro and in vivo. CNTF, a promoter of astrocytic differentiation, downregulates endogenous ATF5, whereas constitutively expressed ATF5 suppresses CNTF-promoted astrocyte genesis. Unexpectedly, constitutive ATF5 expression in neonatal SVZ cells both in vitro and in vivo causes them to acquire properties and anatomic distributions of VZ cells. These findings identify ATF5 as a key regulator of astrocyte formation and potentially of the VZ to SVZ transition.
Internal standard versus external standard calibration: an uncertainty case study of a liquid chromatography analysis (2010)

Traditionally, in the cigarettes industry, the determination of ammonium ion in the mainstream smoke is performed by ion chromatography. This work studies this determination and compares the results of this technique with the use of external and internal standard calibration. A reference cigarette sample presented measurement uncertainty of 2.0 μg/cigarette and 1.5 μg/cigarette, with external and internal standard, respectively. It is observed that the greatest source of uncertainty is the bias correction factor and that it is even more significant when using external standard, confirming thus the importance of internal standardization for this correction.
Complete Sequences of Glucagon-like Peptide-1 from Human and Pig Small Intestine (1989)

In the small intestine, proglucagon is processed into the previously characterized peptide "glicentin" (proglucagon (PG) 1-69) and two smaller peptides showing about 50% homology with glucagon: glucagon-like peptide-1 and -2. It was assumed that the sites of post-translational cleavage in the small intestine of the proglucagon precursor were determined by pairs of basic amino acid residues flanking the two peptides. Earlier studies have shown that synthetic glucagon-like peptide-1 (GLP-1) synthesized according to the proposed structure (proglucagon 71-108 or because residue 108 is Gly, 72-107 amide) had no physiological effects, whereas a truncated from of GLP-1, corresponding to proglucagon 78-107 amide, strongly stimulated insulin secretion and depressed glucagon secretion. To determine the amino acid sequence of the naturally occurring peptide we isolated GLP-1 from human small intestine by hydrophobic, gel permeation, and reverse-phase high performance liquid chromatography. By analysis of composition and sequence it was determined that the peptide corresponded to PG 78-107. By mass spectrometry the molecular mass was determined to be 3295, corresponding to PG 78-107 amide. Furthermore, mass spectrometry of the methyl-esterified peptide showed an increase in mass compatible with the presence of alpha-carboxyl amidation. Thus, the gut-derived insulinotrophic hormone GLP-1 is shown to be PG 78-107 amide.
Placenta‐Derived Multipotent Cells Exhibit Immunosuppressive Properties That Are Enhanced in the Presence of Interferon‐γ (2006)

Several types of nonhematopoietic stem cells, including bone marrow mesenchymal stem cells (BMMSCs) and embryonic stem cells, have been shown to have immunosuppressive properties. We show that human placenta-derived multipotent cells (PDMCs), which are isolated from a source without ethical concern and harbor multilineage differentiation potential, have strong immunosuppressive properties. PDMCs suppress both mitogen-induced and allogeneic lymphocyte proliferation in both CD4 and CD8 populations. The immunosuppression seen with PDMCs was significantly stronger than that with BMMSCs. Both PDMCs and BMMSCs express indoleamine 2,3-dioxygenase, but only PDMCs are positive for intracellular human leukocyte antigen-G (HLA). Mechanistically, suppression of lymphocyte reactivity by PDMCs is not due to cell death but to decreased cell proliferation and increased numbers of regulatory T cells. Addition of neutralizing antibodies to interleukin-10 and transforming growth factor (TGF)-beta partially restored lymphocyte proliferation. Unlike BMMSCs, PDMCs treated with interferon-gamma for 3 days only very minimally upregulated HLA-DR. On the contrary, PD-L1, a cell surface marker that plays an inhibitory role in T-cell activation, was upregulated and TGF-beta expression was seen. The immunosuppressive properties of PDMCs, along with their multilineage differentiation potential, ease of accessibility, and abundant cell numbers, may render these cells as good potential sources for future therapeutic applications.
Transforming Potential of Human c- sis Nucleotide Sequences Encoding Platelet-Derived Growth Factor (1984)

The nucleotide sequence of a transforming human c-sis complementary DNA shows an open reading frame 723 base pairs in length located downstream from an in-phase terminator thymine-guanine-adenine codon. Sequences within this region were identical to those previously determined for the exons of the normal human c-sis gene. Thus, the predicted transforming product, a protein of 27,281 daltons, may be the actual precursor for normal human platelet-derived growth factor chain A.
Manure Best Management practices (1999)

Recent advances have been made in feed formulation to reduce nitrogen (N) and phosphorus (P) excretion without reducing animal performance.The ideal protein concept is a feeding method in which crude protein levels are reduced and amino acids are supplemented in order to reduce N excretion.For reduction of P excretion, adding phytase to the diet has been shown to increase P availability to hogs and chickens.Most of the research on nutritional approaches to reducing manure nutrient excretion has been done on monogastrics, but research is now in progress on cattle feeding methods for this purpose.
Allogenic mouse cell vaccine inhibits lung cancer progression by inhibiting angiogenesis (2020)

<b>Aim</b>: This research investigated the therapeutic effect of an allogeneic mouse brain microvascular endothelial cell vaccine on lung cancer and further elucidated its potential anti-angiogenic mechanism. <b>Materials & methods</b>: The immune effect of the allogeneic bEnd.3 vaccine and DC vaccine loaded with bEnd.3 antigen on the subcutaneous transplantation of Lewis lung cancer (LLC) was assessed by ELISA, the CCK test and the CTL killing test. The mechanism was preliminarily revealed by immunohistochemistry and immunoblot analysis. <b>Results</b>: This study revealed that tumor volume was decreased (<i>p</i> < .01) and the survival was prolonged significantly (<i>p</i> < .05) by the bEnd.3 vaccine in subcutaneous LLC transplantation in the vaccine prevention group. In contrast, both tumor volume in the serum therapeutic group and survival of bEnd.3 vaccine were not significantly different from those of the control group (<i>p</i> > .05). Importantly, tumor volume and survival of the T lymphocyte therapeutic group were decreased and prolonged (<i>p</i> < .05). In addition, both tumor volume and survival of DC vaccine loaded with bEnd.3 in the vaccine prevention group were decreased and prolonged significantly (<i>p</i> < .01). Furthermore, bEnd.3 vaccine and DC vaccine loaded with bEnd.3 both produced the activity of killing bEnd.3 target cells in vitro.The reason may induce the immune mice to produce anti-VEGFR-II, anti-endoglin and anti-integrin αν antibodies to have an anti-angiogenesis function. <b>Conclusion</b>: The allogeneic mouse bEnd.3 cell vaccine can block angiogenesis and prevent the development of lung cancer transplantation tumors.
Ena/VASP Proteins Enhance Actin Polymerization in the Presence of Barbed End Capping Proteins (2005)

Ena/VASP proteins influence the organization of actin filament networks within lamellipodia and filopodia of migrating cells and in actin comet tails. The molecular mechanisms by which Ena/VASP proteins control actin dynamics are unknown. We investigated how Ena/VASP proteins regulate actin polymerization at actin filament barbed ends in vitro in the presence and absence of barbed end capping proteins. Recombinant His-tagged VASP increased the rate of actin polymerization in the presence of the barbed end cappers, heterodimeric capping protein (CP), CapG, and gelsolin-actin complex. Profilin enhanced the ability of VASP to protect barbed ends from capping by CP, and this required interactions of profilin with G-actin and VASP. The VASP EVH2 domain was sufficient to protect barbed ends from capping, and the F-actin and G-actin binding motifs within EVH2 were required. Phosphorylation by protein kinase A at sites within the VASP EVH2 domain regulated anti-capping and F-actin bundling by VASP. We propose that Ena/VASP proteins associate at or near actin filament barbed ends, promote actin assembly, and restrict the access of barbed end capping proteins.
Transmitter equalization for 4-Gbps signaling (1997)

Most digital systems today use full-swing, unterminated signaling methods that are unsuited for data rates over 100 MHz on 1-meter wires. We are currently developing 0.5-micron CMOS transmitter and receiver circuits that use active equalization to overcome the frequency-dependent attenuation of copper lines. The circuits will operate at 4 Gbps over up to 6 meters of 24AWG twisted pair or up to 1 meter of 5-mil 0.5-oz. PC trace. In addition to frequency-dependent attenuation, timing uncertainty (skew and jitter) and receiver bandwidth are also major obstacles to high-data rates. To address all of these issues, we've given our system the following characteristics: An active transmitter equalizer compensates for the frequency-dependent attenuation of the transmission line. The system performs closed-loop clock recovery independently for each signal line in a manner that cancels all clock and data skew and the low-frequency components of clock jitter. The delay line that generates the transmit and receive clocks (a 400-MHz clock with 10 equally spaced phases) uses several circuit techniques to achieve a total simulated jitter of less than 20 ps in the presence of supply and substrate noise. A clocked receive amplifier with a 50-ps aperture time senses the signal during the center of the eye at the receiver.
Pulmonary delivery of flecainide causes a rate‐dependent predominant effect on atrial compared with ventricular depolarization duration revealed by intracardiac recordings in an intact porcine model (2018)

Intratracheal flecainide exerts a rate-dependent, predominant effect on atrial compared with ventricular depolarization duration. Pulmonary delivery of flecainide could facilitate AF conversion to sinus rhythm with reduced ventricular proarrhythmia risk.
In Vivo Application of an RNAi Strategy for the Selective Suppression of a Mutant Allele (2010)

Gene therapy for dominantly inherited diseases with small interfering RNA (siRNA) requires mutant allele-specific suppression when genes in which mutation causes disease normally have an important role. We previously proposed a strategy for selective suppression of mutant alleles; both mutant and wild-type alleles are inhibited by most effective siRNA, and wild-type protein is restored using mRNA mutated to be resistant to the siRNA. Here, to prove the principle of this strategy in vivo, we applied it to our previously reported anti-copper/zinc superoxide dismutase (SOD1) short hairpin RNA (shRNA) transgenic (Tg) mice, in which the expression of the endogenous wild-type SOD1 gene was inhibited by more than 80%. These shRNA Tg mice showed hepatic lipid accumulation with mild liver dysfunction due to downregulation of endogenous wild-type SOD1. To rescue this side effect, we generated siRNA-resistant SOD1 Tg mice and crossed them with anti-SOD1 shRNA Tg mice, resulting in the disappearance of lipid accumulation in the liver. Furthermore, we also succeeded in mutant SOD1-specific gene suppression in the liver of SOD1(G93A) Tg mice, a model for amyotrophic lateral sclerosis, using intravenously administered viral vectors. Our method may prove useful for siRNA-based gene therapy for dominantly inherited diseases.
Residual Convolutional Neural Network for the Determination of IDH Status in Low- and High-Grade Gliomas from MR Imaging (2017)

<b>Purpose:</b> Isocitrate dehydrogenase (<i>IDH</i>) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the <i>IDH</i> status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data.<b>Experimental Design:</b> Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming.<b>Results:</b> With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively.<b>Conclusions:</b> We developed a deep learning technique to noninvasively predict <i>IDH</i> genotype in grade II-IV glioma using conventional MR imaging using a multi-institutional data set. <i>Clin Cancer Res; 24(5); 1073-81. ©2017 AACR</i>.
Role of Essential Genes in Mitochondrial Morphogenesis inSaccharomyces cerevisiae (2005)

Mitochondria are essential organelles of eukaryotic cells. Inheritance and maintenance of mitochondrial structure depend on cytoskeleton-mediated organelle transport and continuous membrane fusion and fission events. However, in Saccharomyces cerevisiae most of the known components involved in these processes are encoded by genes that are not essential for viability. Here we asked which essential genes are required for mitochondrial distribution and morphology. To address this question, we performed a systematic screen of a yeast strain collection harboring essential genes under control of a regulatable promoter. This library contains 768 yeast mutants and covers approximately two thirds of all essential yeast genes. A total of 119 essential genes were found to be required for maintenance of mitochondrial morphology. Among these, genes were highly enriched that encode proteins involved in ergosterol biosynthesis, mitochondrial protein import, actin-dependent transport processes, vesicular trafficking, and ubiquitin/26S proteasome-dependent protein degradation. We conclude that these cellular pathways play an important role in mitochondrial morphogenesis and inheritance.
Opposite signs of voltage-induced perpendicular magnetic anisotropy change in CoFeB|MgO junctions with different underlayers (2013)

We report a voltage-induced perpendicular magnetic anisotropy (PMA) change in sputter-deposited Ta|CoFeB|MgO and Ru|CoFeB|MgO junctions. The PMA change is quantitatively evaluated by the field dependence of the tunneling magnetoresistance for various bias voltages. We find that both the sign and amplitude of the voltage effect depend on the underlayer, Ta or Ru, below the CoFeB layer. The rf voltage-induced ferromagnetic resonance spectra also support the underlayer-material-dependent direction of the voltage torque. The present study shows that the underlayer is one of the key parameters for controlling the voltage effect.
Comparison Among Various&lt;tex&gt;$hbox Si_3hboxN _4$&lt;/tex&gt;Waveguide Geometries Grown Within a CMOS Fabrication Pilot Line (2004)

Low-pressure chemical-vapor deposition (LPCVD) thin-film Si/sub 3/N/sub 4/ waveguides have been fabricated on Si substrate within a complementary metal-oxide-semiconductor (CMOS) fabrication pilot line. Three kinds of geometries (channel, rib, and strip-loaded) have been simulated, fabricated, and optically characterized in order to optimize waveguide performances. The number and optical confinement factors of guided optical modes have been simulated, taking into account sidewall effects caused by the etching processes, which have been studied by scanning electron microscopy. Optical guided modes have been observed with a mode analyzer and compared with simulation expectations to confirm the process parameters. Propagation loss measurements at 780 and 632.8 nm have been performed by both using the cutback technique and measuring the drop of intensity of the top scattered light along the length of the waveguide. Loss coefficients of approximately 0.1 dB/cm have been obtained for channel waveguides. These data are very promising in view of the development of Si-integrated photonics.
Cytokine-induced neutrophil-derived interleukin-8. (1992)

During acute inflammation, the first line of cellular response for host defense is the neutrophil. In addition to the historic role of the neutrophil as a phagocyte, recent studies have identified this cell as an important source of a number of cytokines. In this study, we provide evidence that the neutrophil is a significant source of interleukin-8 (IL-8). Neutrophils freshly isolated from whole blood were not found to constitutively express IL-8 mRNA. In contrast, when these leukocytes were cultured on plastic they were activated, leading to the significant expression of de novo steady-state levels of IL-8 mRNA. In addition, when neutrophils were treated with cycloheximide, there was evidence for "superinduction" of steady-state levels of IL-8 mRNA and inhibition of antigenic IL-8 production. Neutrophils were subsequently stimulated with lipopolysaccharide (LPS), tumor necrosis factor-alpha, or interleukin-1-beta and were found to express IL-8 mRNA and antigen in both a time- and dose-dependent manner. Furthermore, neutrophils stimulated with traditional chemotactic/activating factors, such as the split product of the fifth component of complement (C5a), formylmethionyleucylphenylalanine (fMLP), and leukotriene B4 (LTB4) in a dose-dependent manner did not produce significant antigenic IL-8, as compared with unstimulated controls. In contrast, when neutrophils were exposed to either of these neutrophil agonists in the presence of LPS, the production of antigenic IL-8 was significantly elevated, as compared with either of the stimuli alone, suggesting a synergistic response. These data would suggest that the neutrophil can no longer be viewed as only a phagocyte or warehouse for proteolytic enzymes, but is a pivotal effector cell that is able to respond to mediators in its environment and generate cytokines. This latter neutrophil response may be important for either the elicitation of additional neutrophils or to orchestrate the conventional immune response at sites of inflammation.