gebhart/patrepeval huggingface dataset:
Analysis of a tunable coupler for superconducting phase qubits (2010)

This paper presents a theoretical analysis of the recently realized tunable coupler for superconducting phase qubits [R. C. Bialczak et al., arXiv:1007.2219 (unpublished)]. The coupling can be turned off by compensating a negative mutual inductance with a tunable Josephson inductance. The main coupling in this system is of the $XX$ type and can be zeroed exactly, while there is also a small undesired contribution of the $ZZ$ type. We calculate both couplings as functions of the tuning parameter (bias current) and focus on the residual coupling in the OFF regime. In particular, we show that for typical experimental parameters the coupling OFF/ON ratio is few times ${10}^{\ensuremath{-}3}$, and it may be zeroed by proper choice of parameters. The remaining errors due to physical presence of the coupler are on the order of ${10}^{\ensuremath{-}6}$.
Progress and Prospects for Stem Cell Engineering (2011)

Stem cells offer tremendous biomedical potential owing to their abilities to self-renew and differentiate into cell types of multiple adult tissues. Researchers and engineers have increasingly developed novel discovery technologies, theoretical approaches, and cell culture systems to investigate microenvironmental cues and cellular signaling events that control stem cell fate. Many of these technologies facilitate high-throughput investigation of microenvironmental signals and the intracellular signaling networks and machinery processing those signals into cell fate decisions. As our aggregate empirical knowledge of stem cell regulation grows, theoretical modeling with systems and computational biology methods has and will continue to be important for developing our ability to analyze and extract important conceptual features of stem cell regulation from complex data. Based on this body of knowledge, stem cell engineers will continue to develop technologies that predictably control stem cell fate with the ultimate goal of being able to accurately and economically scale up these systems for clinical-grade production of stem cell therapeutics.
TCAD-Based Statistical Analysis and Modeling of Gate Line-Edge Roughness Effect on Nanoscale MOS Transistor Performance and Scaling (2004)

The effects of line edge roughness (LER) of nanometer scale gate pattern on the MOS transistor parameter fluctuations and their technology scaling are investigated using the simplified modeling and statistical analysis based on two-dimensional technology CAD (TCAD) tools. From the simple statistical analysis, it is shown that the gate patterns without appropriate LER may cause severe device parameter and performance fluctuations in highly scaled nanometer technologies, resulting in a negative average threshold voltages shift, a subthreshold slope degradation, an unrealistic effective channel length extraction and an exponential increase in off-state leakage current due to LER-induced inhomogeneous channel potential. The characteristics of the average off-state leakage current and the threshold voltage uncertainty as a function of technology scaling provide a useful guideline for advanced gate patterning process and demand much tighter control of LER less than 3-5 nm for a successful CMOS scaling into deep nanometer scale physical gate length regime below 50 nm.
Interaction of origin binding protein with an origin of replication of herpes simplex virus 1. (1988)

Herpes simplex virus 1 encodes a protein that binds specifically to a viral DNA replication origin (oriS). This origin-binding protein has been purified to homogeneity by means of sequence-specific DNA affinity chromatography. The purified origin-binding protein, which has a molecular weight of 83,000, interacts with both parts of the oriS dyad; however, the affinity for the two sites differs by an order of magnitude. The sequence TTCGCA occurs as a nearly perfect direct repeat within the two sites and may constitute the recognition sequence for the origin-binding protein.
ATP‐dependent transport of amphiphilic cations across the hepatocyte canalicular membrane mediated by mdr1 P‐glycoprotein (1994)

The ATP-dependent transport of the three 3H-labeled, amphiphilic cations quinidine, N-(n-pentyl)-quinidinium, and N-(4',4'-azo-n-pentyl)-21-deoxyajmalinium was studied in rat canalicular plasma membrane vesicles. N-Alkylation of quinidine with an n-pentyl residue resulted in a permanently charged cationic substrate for ATP-dependent transport which exhibited a 10-fold higher transport rate relative to quinidine. The Km value was 0.4 microM for N-(n-pentyl)-quinidinium and 5 microM for quinidine. The permanently cationic and photolabile derivative of ajmaline, N-(4',4'-azo-n-pentyl)-21-deoxyajmalinium, was also an efficient substrate and served to label canalicular membrane proteins with molecular masses of 143 kDa and 108 kDa. ATP-dependent transport of the permanently charged amphiphilic cations was inhibited by the P-glycoprotein inhibitors and substrates quinidine, verapamil, and daunorubicin. The data demonstrate that N-alkylation of quinidine and ajmaline results in most efficient substrates for mdr1 P-glycoprotein-mediated ATP-dependent transport.
Granulosa Cell Ligand NPPC and Its Receptor NPR2 Maintain Meiotic Arrest in Mouse Oocytes (2010)

Granulosa cells of mammalian Graafian follicles maintain oocytes in meiotic arrest, which prevents their precocious maturation. We show that mouse mural granulosa cells, which line the follicle wall, express natriuretic peptide precursor type C (Nppc) messenger RNA (mRNA), whereas cumulus cells surrounding oocytes express mRNA of the NPPC receptor NPR2, a guanylyl cyclase. NPPC increased cGMP levels in cumulus cells and oocytes and inhibited meiotic resumption in vitro. Meiotic arrest was not sustained in most Graafian follicles of Nppc or Npr2 mutant mice, and meiosis resumed precociously. Oocyte-derived paracrine factors promoted cumulus cell expression of Npr2 mRNA. Therefore, the granulosa cell ligand NPPC and its receptor NPR2 in cumulus cells prevent precocious meiotic maturation, which is critical for maturation and ovulation synchrony and for normal female fertility.
Fast Diffusion of Very Long Chain Saturated Fatty Acids across a Bilayer Membrane and Their Rapid Extraction by Cyclodextrins (2009)

Abnormalities in the transport of saturated very long chain fatty acids (VLCFA; >C18:0) contribute to their toxic levels in peroxisomal disorders of fatty acid metabolism, such as adrenoleukodystrophy and adrenomyeloneuropathy. We previously showed that VLCFA desorb much slower than normal dietary fatty acids from both albumin and protein-free lipid bilayers. The important step of transbilayer movement (flip-flop) was not measured directly as a consequence of this very slow desorption from donors, and the extremely low aqueous solubility of VLCFA precludes addition of unbound VLCFA to lipid membranes. We have overcome these limitations using methyl-beta-cyclodextrin to solubilize VLCFA for rapid delivery to "acceptor" phosphatidylcholine vesicles (small and large unilamellar) and to cells. VLCFA binding was monitored in real time with the fluorescent probe fluorescein-labeled phosphatidylethanolamine in the outer membrane leaflet, and entrapped pyranine was used to detect flip-flop across the membrane. The upper limit of the rate of flip-flop across the membrane was independent of temperature and media viscosity and was similar for model raft and non-raft membranes as well as living cells. We further showed that cyclodextrins can extract VLCFA rapidly (within seconds) from vesicles and cells, which have implications for the mechanism and potential alternative approaches to treat adrenoleukodystrophy. Because VLCFA diffuse through the lipid bilayer, proteins may not be required for their transport across the peroxisomal membrane.
Immune Response to Poxvirus Infections in Various Animals (2002)

The study of infections of vertebrate animals by poxviruses has remained a dynamic area of research for the last century. The host range of poxviruses vary from extremely narrow to exceedingly broad, and they have been shown to enter their host by either the respiratory route or through the skin. The severity of infection varies dramatically from one species to another, causing anywhere from a local, self-limiting infection, to a devastating systemic disease, such as smallpox. Although the immune response to poxvirus infections are very similar to that seen in other viral infections, the poxviruses, unlike most other viruses (with the exception of Herpes viruses), are able to defend themselves. They have been shown to carry a repertoire of proteins involved in immune evasion and immune modulation. Poxviruses encode proteins involved in blocking many of the strategies employed by the host to combat viral infections; they encode for proteins that block activity of many chemokines, cytokines, serine proteases, and even complement. Traditionally, different animal models have been used to study the pathogenesis of poxvirus infections, and the characterization of virulence genes using mutant poxviruses. Additionally, new animal models are being developed to study the possible therapeutic uses many of these poxvirus immune modulating proteins might have. This review discusses the host immune response against poxvirus infections in various animals, the viral counter response to the host, and the animal models used to study poxvirus infection and immune modulating proteins.
V-Cache: Towards Flexible Resource Provisioning for Multi-tier Applications in IaaS Clouds (2013)

Although the resource elasticity offered by Infrastructure-as-a-Service (IaaS) clouds opens up opportunities for elastic application performance, it also poses challenges to application management. Cluster applications, such as multi-tier websites, further complicates the management requiring not only accurate capacity planning but also proper partitioning of the resources into a number of virtual machines. Instead of burdening cloud users with complex management, we move the task of determining the optimal resource configuration for cluster applications to cloud providers. We find that a structural reorganization of multi-tier websites, by adding a caching tier which runs on resources debited from the original resource budget, significantly boosts application performance and reduces resource usage. We propose V-Cache, a machine learning based approach to flexible provisioning of resources for multi-tier applications in clouds. V-Cache transparently places a caching proxy in front of the application. It uses a genetic algorithm to identify the incoming requests that benefit most from caching and dynamically resizes the cache space to accommodate these requests. We develop a reinforcement learning algorithm to optimally allocate the remaining capacity to other tiers. We have implemented V-Cache on a VMware-based cloud testbed. Experiment results with the RUBiS and WikiBench benchmarks show that V-Cache outperforms a representative capacity management scheme and a cloud-cache based resource provisioning approach by at least 15% in performance, and achieves at least 11% and 21% savings on CPU and memory resources, respectively.
Efficient comparison of path-lengths using Fourier multiport devices (2006)

We present a scheme for comparing effective path-lengths through a spatial region by using multipath generalizations of a Mach–Zehnder interferometer. This enables us to identify paths that have different lengths from the others with exponentially fewer measurements than would be required by repeated measurements with a standard two-path interferometer. We show that this scheme is extremely sensitive to small variations in the paths, which means it could be used to measure the variance of the path-lengths accurately and efficiently. Possible applications include accurately measuring spatial variations of potential fields and efficiently identifying which of many cavities contains an atom.
Neuronal Control of Skin Function: The Skin as a Neuroimmunoendocrine Organ (2006)

This review focuses on the role of the peripheral nervous system in cutaneous biology and disease. During the last few years, a modern concept of an interactive network between cutaneous nerves, the neuroendocrine axis, and the immune system has been established. We learned that neurocutaneous interactions influence a variety of physiological and pathophysiological functions, including cell growth, immunity, inflammation, pruritus, and wound healing. This interaction is mediated by primary afferent as well as autonomic nerves, which release neuromediators and activate specific receptors on many target cells in the skin. A dense network of sensory nerves releases neuropeptides, thereby modulating inflammation, cell growth, and the immune responses in the skin. Neurotrophic factors, in addition to regulating nerve growth, participate in many properties of skin function. The skin expresses a variety of neurohormone receptors coupled to heterotrimeric G proteins that are tightly involved in skin homeostasis and inflammation. This neurohormone-receptor interaction is modulated by endopeptidases, which are able to terminate neuropeptide-induced inflammatory or immune responses. Neuronal proteinase-activated receptors or transient receptor potential ion channels are recently described receptors that may have been important in regulating neurogenic inflammation, pain, and pruritus. Together, a close multidirectional interaction between neuromediators, high-affinity receptors, and regulatory proteases is critically involved to maintain tissue integrity and regulate inflammatory responses in the skin. A deeper understanding of cutaneous neuroimmunoendocrinology may help to develop new strategies for the treatment of several skin diseases.
Role and Regulation of Bacillus subtilis Glutamate Dehydrogenase Genes (1998)

The complete Bacillus subtilis genome contains two genes with the potential to encode glutamate dehydrogenase (GlutDH) enzymes. Mutations in these genes were constructed and characterized. The rocG gene proved to encode a major GlutDH whose synthesis was induced in media containing arginine or ornithine or, to a lesser degree, proline and was repressed by glucose. A rocG null mutant was impaired in utilization of arginine, ornithine, and proline as nitrogen or carbon sources. The gudB gene was expressed under all growth conditions tested but codes for a GlutDH that seemed to be intrinsically inactive. Spontaneous mutations in gudB that removed a 9-bp direct repeat within the wild-type gudB sequence activated the GudB protein and allowed more-efficient utilization of amino acids of the glutamate family.
Epidemiology of binge eating disorder (2018)

The current article presents the findings of a recent systematic review of the epidemiology of BED and discusses the case for including BED as a new cause in future iterations of GBD.
Inhibition of GSK-3β leading to the loss of phosphorylated MAP-1B is an early event in axonal remodelling induced by WNT-7a or lithium (1998)

WNT-7a induces axonal spreading and branching in developing cerebellar granule neurons. This effect is mediated through the inhibition of GSK-3beta, a serine/threonine kinase and a component of the WNT pathway. Lithium, an inhibitor of GSK-3beta, mimics WNT-7a in granule cells. Here we examined further the effect of GSK-3beta inhibition on cytoskeletal re-organisation. Lithium induces axonal spreading and increases growth cone area and perimeter. This effect is associated with the absence or reduction of stable microtubules in spread areas. Lithium induces the loss of a phosphorylated form of MAP-1B, a microtubule associated protein involved in axonal outgrowth. Down-regulation of the phosphorylated MAP-1B, MAP-1B-P, from axonal processes occurs before axonal remodelling is evident. In vitro phosphorylation assays show that MAP-1B-P is generated by direct phosphorylation of MAP-1B by GSK-3beta. WNT-7a, like lithium, also leads to loss of MAP-1B-P from spread axons and growth cones. Our data suggest that WNT-7a and lithium induce changes in microtubule dynamics by inhibiting GSK-3beta which in turn lead to changes in the phosphorylation of MAP-1B. These findings suggest a novel role for GSK-3beta and WNTs in axonal remodelling and identify MAP-1B as a new target for GSK-3beta and WNT.
USP9X counteracts differential ubiquitination of NPHP5 by MARCH7 and BBS11 to regulate ciliogenesis (2017)

Ciliogenesis is a fundamental biological process central to human health. Precisely how this process is coordinated with the cell cycle remains an open question. We report that nephrocystin-5 (NPHP5/IQCB1), a positive regulator of ciliogenesis, is a stable and low turnover protein subjected to cycles of ubiquitination and deubiquitination. NPHP5 directly binds to a deubiquitinating enzyme USP9X/FAM and two E3 ubiquitin ligases BBS11/TRIM32 and MARCH7/axotrophin. NPHP5 undergoes K63 ubiquitination in a cell cycle dependent manner and K48/K63 ubiquitination upon USP9X depletion or inhibition. In the G0/G1/S phase, a pool of cytoplasmic USP9X recruited to the centrosome by NPHP5 protects NPHP5 from ubiquitination, thus favouring cilia assembly. In the G2/M phase, USP9X dissociation from the centrosome allows BBS11 to K63 ubiquitinate NPHP5 which triggers protein delocalization and loss of cilia. BBS11 is a resident centrosomal protein, whereas cytoplasmic USP9X sequesters the majority of MARCH7 away from the centrosome during interphase. Depletion or inhibition of USP9X leads to an accumulation of centrosomal MARCH7 which K48 ubiquitinates NPHP5, triggering protein degradation and cilia loss. At the same time, BBS11 K63 ubiquitinates NPHP5. Our data suggest that dynamic ubiquitination and deubiquitination of NPHP5 plays a crucial role in the regulation of ciliogenesis.
An analytic study of (GaAl)As gain guided lasers at threshold (1982)

An analysis of gain-guided diode lasers at threshold is presented. After describing the formulation, the effects of charge induced real refractive index antiguiding and gain-charge density relations are studied in detail. Their influence on the threshold current, modal distributions, and the lateral fax-field radiation patterns is discussed. Next a "model" laser is defined and each parameter including dimensions, compositions, stripewidth, diffusion constants, current spreading resistance, and facet reflectivities is individually varied to determine the resulting modifications in laser properties.
Carbonate-coordinated metal complexes precede the formation of liquid amorphous mineral emulsions of divalent metal carbonates (2011)

During the mineralisation of metal carbonates MCO3 (M=Ca, Sr, Ba, Mn, Cd, Pb) liquid-like amorphous intermediates emerge. These intermediates that form via a liquid/liquid phase separation behave like a classical emulsion and are stabilized electrostatically. The occurrence of these intermediates is attributed to the formation of highly hydrated networks whose stability is mainly based on weak interactions and the variability of the metal-containing pre-critical clusters. Their existence and compositional freedom are evidenced by electrospray ionization mass spectrometry (ESI-MS). Liquid intermediates in non-classical crystallisation pathways seem to be more common than assumed.
Characterization of Dengue Virus Complex-Specific Neutralizing Epitopes on Envelope Protein Domain III of Dengue 2 Virus (2008)

The surface of the mature dengue virus (DENV) particle is covered with 180 envelope (E) proteins arranged as homodimers that lie relatively flat on the virion surface. Each monomer consists of three domains (ED1, ED2, and ED3), of which ED3 contains the critical neutralization determinant(s). In this study, a large panel of DENV-2 recombinant ED3 mutant proteins was used to physically and biologically map the epitopes of five DENV complex-specific monoclonal antibodies (MAbs). All five MAbs recognized a single antigenic site that includes residues K310, I312, P332, L389, and W391. The DENV complex antigenic site was located on an upper lateral surface of ED3 that was distinct but overlapped with a previously described DENV-2 type-specific antigenic site on ED3. The DENV complex-specific MAbs required significantly higher occupancy levels of available ED3 binding sites on the virion, compared to DENV-2 type-specific MAbs, in order to neutralize virus infectivity. Additionally, there was a great deal of variability in the neutralization efficacy of the DENV complex-specific MAbs with representative strains of the four DENVs. Overall, the differences in physical binding and potency of neutralization observed between DENV complex- and type-specific MAbs in this study demonstrate the critical role of the DENV type-specific antibodies in the neutralization of virus infectivity.
β1 Integrin Is Essential for Teratoma Growth and Angiogenesis (1997)

Teratomas are benign tumors that form after ectopic injection of embryonic stem (ES) cells into mice and contain derivatives of all primitive germ layers. To study the role of beta 1 integrin during teratoma formation, we compared teratomas induced by normal and beta1-null ES cells. Injection of normal ES cells gave rise to large teratomas. In contrast, beta 1-null ES cells either did not grow or formed small teratomas with an average weight of <5% of that of normal teratomas. Histological analysis of beta 1-null teratomas revealed the presence of various differentiated cells, however, a much lower number of host-derived stromal cells than in normal teratomas. Fibronectin, collagen I, and nidogen were expressed but, in contrast to normal teratomas, diffusely deposited in beta1-null teratomas. Basement membranes were present but with irregular shape and detached from the cell surface. Normal teratomas had large blood vessels with a smooth inner surface, containing both host- and ES cell-derived endothelial cells. In contrast, beta 1-null teratomas had small vessels that were loosely embedded into the connective tissue. Furthermore, endothelial cells were always of host-derived origin and formed blood vessels with an irregular inner surface. Although beta 1- deficient endothelial cells were absent in teratomas, beta 1-null ES cells could differentiate in vitro into endothelial cells. The formation of a complex vasculature, however, was significantly delayed and of poor quality in beta1-null embryoid bodies. Moreover, while vascular endothelial growth factor induced proliferation of endothelial cells as well as an extensive branching of blood vessels in normal embryoid bodies, it had no effect in beta 1-null embryoid bodies.
Concentration-Time Relationship for Fumigant Efficacy of Sulfuryl Fluoride Against the Formosan Subterranean Termite (Isoptera: Rhinotermitidae) (1989)

The Formosan subterranean termite, Coptotermes formosanus, was exposed to sulfuryl fluoride over a range of six accumulated concentrations (10-60 mg h/liter) and 12 exposure times (1-96 h), to determine the concentration-time relationship on termite mortality. Time threshold in sulfuryl fluoride fumigation was<1h. The results demonstrated that C0.93t = k was a satisfactory model to describe the response relationship in fumigant efficacy of sulfuryl fluoride against this termite. Because the toxicity index (n = 0.93) approximates to 1, the assumption that the exposure time is equally important to concentration is functionally valid.