gebhart/patrepeval huggingface dataset:
Altering Effort Costs in Parkinson's Disease with Noninvasive Cortical Stimulation (2015)

In Parkinson's disease, patients are less willing to assign force to their affected arm. Here, we find that this pattern is direction dependent: directions for which the arm is noisier coincide with directions for which the brain is less willing to assign force. We hypothesized that if we could reduce the noise on the affected arm, then we may increase the willingness for the brain to assign force to that arm. We found a way to do this via noninvasive cortical stimulation. In addition to reducing effort costs associated with the affected arm, the cortical stimulation also improved clinical motor symptoms of the disease.
Cryptococcus neoformans Cda1 and Its Chitin Deacetylase Activity Are Required for Fungal Pathogenesis (2018)

Chitin is an essential component of the cell wall of <i>Cryptococcus neoformans</i> conferring structural rigidity and integrity under diverse environmental conditions. Chitin deacetylase genes encode the enyzmes (chitin deacetylases [Cdas]) that deacetylate chitin, converting it to chitosan. The functional role of chitosan in the fungal cell wall is not well defined, but it is an important virulence determinant of <i>C. neoformans</i> Mutant strains deficient in chitosan are completely avirulent in a mouse pulmonary infection model. <i>C. neoformans</i> carries genes that encode three Cdas (Cda1, Cda2, and Cda3) that appear to be functionally redundant in cells grown under vegetative conditions. Here we report that <i>C. neoformans</i> Cda1 is the principal Cda responsible for fungal pathogenesis. Point mutations were introduced in the active site of Cda1 to generate strains in which the enzyme activity of Cda1 was abolished without perturbing either its stability or localization. When used to infect CBA/J mice, Cda1 mutant strains produced less chitosan and were attenuated for virulence. We further demonstrate that <i>C. neoformans</i> Cda genes are transcribed differently during a murine infection from what has been measured <i>in vitro</i><b>IMPORTANCE</b><i>Cryptococcus neoformans</i> is unique among fungal pathogens that cause disease in a mammalian host, as it secretes a polysaccharide capsule that hinders recognition by the host to facilitate its survival and proliferation. Even though it causes serious infections in immunocompromised hosts, reports of infection in hosts that are immunocompetent are on the rise. The cell wall of a fungal pathogen, its synthesis, composition, and pathways of remodelling are attractive therapeutic targets for the development of fungicides. Chitosan, a polysaccharide in the cell wall of <i>C. neoformans</i> is one such target, as it is critical for pathogenesis and absent in the host. The results we present shed light on the importance of one of the chitin deacetylases that synthesize chitosan during infection and further implicates chitosan as being a critical factor for the pathogenesis of <i>C. neoformans</i>.
Translocation of molecules into cells by pH-dependent insertion of a transmembrane helix (2006)

We have previously observed the spontaneous, pH-dependent insertion of a water-soluble peptide to form a helix across lipid bilayers [Hunt, J. F., Rath, P., Rothschild, K. J. & Engelman, D. M. (1997) Biochemistry 36, 15177-15192]. We now use a related peptide, pH (low) insertion peptide, to translocate cargo molecules attached to its C terminus across the plasma membranes of living cells. Translocation is selective for low pH, and various types of cargo molecules attached by disulfides can be released by reduction in the cytoplasm, including peptide nucleic acids, a cyclic peptide (phalloidin), and organic compounds. Because a high extracellular acidity is characteristic of a variety of pathological conditions (such as tumors, infarcts, stroke-afflicted tissue, atherosclerotic lesions, sites of inflammation or infection, or damaged tissue resulting from trauma) or might be created artificially, pH (low) insertion peptide may prove a useful tool for selective delivery of agents for drug therapy, diagnostic imaging, genetic control, or cell regulation.
Low-dose CT reconstruction with MRF prior predicted from patch samples of normal-dose CT database (2018)

Markov random field (MRF) model-based penalty is widely used in statistical iterative reconstruction (SIR) of low dose CT (LDCT) reconstruction for noise suppression and edge-preserving. In this strategy, normal dose CT scans are usually used as a priori information to further improve the LDCT quality. However, repeated CT scans are needed and registration or segmentation is usually applied first when misalignment between the low-dose and normal-dose scans exists. The study aims to propose a new MRF prior model of SIR based on the NDCT database without registration. In the proposed model, MRF weights are predicted using optimal similar patch samples from the NDCT database. The patch samples are determined by evaluating the similarity with Euclidean distance between patches from NDCT and the target patch of LDCT. The proposed prior term is incorporated into the SIR cost function, which is to be minimized for LDCT reconstruction. The proposed method is tested on an artificial LDCT data based on a high-dose patient data. Preliminary result has proved its potential performance in edge and structure detail preservation.
P2–166: Proteomic analysis of antemortem cerebrospinal fluid for Alzheimer's disease biomarkers and in the assessment of IVIg immunotherapy (2006)

We apply a gel–based proteomics strategy to the analysis of antemortem cerebrospinal fluid from Alzheimer patients including subjects that have participated in a Phase I clinical trial for IVIg at one of four doses. Our goal is to establish antemortem biomarkers for AD diagnosis and to determine if these biomarkers correlate with clinical outcomes. We also wish to identify any changes in protein expression that correlate with IVIg treatment. Retrospective samples from definite Alzheimer patients as well as age–matched normal and neurological controls were collected from a number of CSF banks in the United States. Prospective samples were collected from a well–characterized clinical population in New York. IVIg–treated subjects from a Phase I clinical trial underwent lumbar puncture before treatment, at two times during a six month treatment course and after a three month washout. Using a traditional proteomics approach that included electrophoresis and tandem time of flight mass spectrometry, we studied approximately 2000 protein spots. Data were analyzed using the Random Forest technique for underspecified systems. We identified 23 markers that, when taken together, can distinguish AD from nonAD patients including normal, demented, and neurological controls. These proteins have functions related to AD pathology. These data were subsequently used to study IVIg subjects. We observed that the changes in the markers were highly correlated with clinical outcomes. Separately, we observed that 31 spots showed a correlation with IVIg dosing. These included several amyloid binding proteins, complement, contact/kinins and immunoglobins. One protein associated with tau pathology (Pro SAAS) and one inflammatory intermediate (vitronectin) also correlated at 0.6. Proteomics may identify antemortem CSF biomarkers when used with definite CSF cases. These biomarkers correlate with clinical outcomes observed as part of an IVIg treatment. IVIg treatment alters the expression of several CSF proteins of potential relevance to the pathophysiology of AD.
A Differentially Pumped Dual Linear Quadrupole Ion Trap (DLQIT) Mass Spectrometer: A Mass Spectrometer Capable of MS<sup>n</sup> Experiments Free From Interfering Reactions (2013)

A novel differentially pumped dual linear quadrupole ion trap (DLQIT) mass spectrometer was designed and built to facilitate tandem MS experiments free from interfering reactions. The instrument consists of two differentially pumped Thermo Scientific linear quadrupole ion trap (LQIT) systems that have been connected via an ion transfer octupole encased in a machined manifold. Tandem MS experiments can be performed in the front trap and then the resulting product ions can be transferred via axial ejection into the back trap for further, independent tandem MS experiments in a differentially pumped area. This approach allows the examination of consecutive collision-activated dissociation (CAD) and ion-molecule reactions without unwanted side reactions that often occur when CAD and ion-molecule reactions are examined in the same space. Hence, it greatly facilitates investigations of ion structures. In addition, the overall lower pressure of the DLQIT, as compared to commercial LQIT instruments, results in a reduction of unwanted side reactions with atmospheric contaminants, such as water and oxygen, in CAD and ion-molecule experiments.
Distinguishing two-qubit states using local measurements and restricted classical communication (2003)

The problem of unambiguous state discrimination consists of determining in which of a set of known quantum states a particular system is. One is allowed to fail but not to make a mistake. The optimal procedure is the one with the lowest failure probability. This procedure has been extended to bipartite states where the two parties Alice and Bob are allowed to manipulate their particles locally and communicate classically in order to determine which of two possible two-particle states they have been given. The failure probability of this local procedure is the same as if the two particles were together in the same location. Here we examine the effect of restricting the classical communication between the parties, either allowing none or eliminating the possibility that one party's measurement depends on the result of the other party's. These issues are studied for two-qubit states, and optimal procedures are found. In some cases the restrictions cause increases in the failure probability, but in other cases they do not. Applications of this procedure, in particular to secret sharing, are discussed.
Fixed Frequency and Tunable Metamaterial-Based Ring Resonators with Narrowly Spaced Resonances (2007)

Metamaterial-based composite right/left-handed transmission lines are used in the design of fixed frequency and tunable ring resonators. Under specific design conditions, the first two resonant modes can be narrowly spaced. A simple passive band-pass filter is demonstrated at 2.92 GHz with a bandwidth of about 9% using this concept. This type of design is also used as a tunable resonator and a tuning range of 30% is demonstrated.
Derivation of thyroid progenitors from human induced pluripotent stem cells (2022)

Abstract Objective Despite the availability of synthetic thyroid hormone for therapeutic use, a significant number of patients with hypothyroidism do not feel well on replacement doses of thyroid hormones suggesting that better-individualized therapy is needed. For this reason, hypothyroidism resulting from congenital lack of functional thyrocytes, surgical tissue removal, or gland ablation, represents a particularly attractive endocrine disease target that may be conceivably cured by transplantation of long-lived functional thyroid progenitors or mature follicular epithelial cells. Methods To generate thyroid follicular progenitors from human induced pluripotent stem cells (hiPSCs), we sought to develop a directed differentiation approach by activating or inhibiting endogenous developmental signaling pathways previously identified in the mouse. To facilitate tracking and purification of candidate human thyroid progenitors, we engineered a hiPSC-line carrying a tdTomato reporter targeted to the PAX8 locus and a GFP reporter targeted to the NKX2-1 locus. Results We adapted our published in vitro differentiation protocol previously used to differentiate mouse PSCs into thyroid progenitors and observed tdTomato/GFP co-expressing cells first emerging from our hiPSC line by day 12 of culture and persisting for at least 2 months of further culture in thyroid maturation media, supplemented with TSH. Thus, we profiled all cells deriving from hiPSCs by single-cell RNA sequencing &gt;6,000 cells captured on days 12 and 29 of in vitro differentiation. At day 12, tdTomato/GFP co-expression was observed in 12% of all cells and these cells appeared to be early thyroid follicular progenitors as they uniquely co-expressed the tetrad of thyroid lineage selective transcription factors, NKX2-1, PAX8, FOXE1, and HHEX. By day 29 tdTomato+/GFP+ cells represented 69% of all cells and had upregulated TG, TSHR, NIS and TPO expression in addition to the previously described four thyroid lineage markers, suggesting time-dependent differentiation and maturation of thyroid follicular epithelial cells. Conclusion Thus, we have employed a novel hiPSC line to optimize a protocol able to generate human thyroid progenitors and mature follicular epithelial cells, representing a purifiable source of human thyroid lineage cells whose functional and thyroid reconstituting potential can be tested in vivo in animal models of hypothyroidism.
A General Design Method for Phasor Estimation in Different Applications (2020)

Driven by the increasing development and complexity of bulk power systems, the requirements of phasor estimation methods differ for different scenarios and applications. In this study, a general design method for phasor estimation algorithms in different applications is proposed based on a complex finite impulse response (FIR) bandpass filter. A design framework based on mathematical error models is proposed to facilitate the design of a complex bandpass filter for different requirements and to reduce the trial and error process. The general error models between the filter gain and the error limitations of all variables measured by the phasor measurement units (PMUs) are established separately, according to the absolute value inequality. The filter design criteria obtained from the error models can determine the passband and stopband gain range of the complex bandpass filters. Three phasor algorithms for different classes of PMUs are designed, and their performances are validated and compared using experimental tests. The results demonstrate that the proposed method can design phasor algorithms to provide accurate measurements under different scenarios.
Superconducting properties of<i>in situ</i>powder-in-tube-processed MgB<sub>2</sub>tapes fabricated with sub-micrometre Mg powder prepared by an arc-plasma method (2006)

We fabricated in situ powder-in-tube-processed MgB2/Fe tapes using sub-micrometre Mg powder prepared by applying an arc-plasma method. We found that the use of this sub-micrometre Mg powder was very effective in increasing the Jc values. The transport Jc value of 10 mol% SiC-added tapes fabricated with this sub-micrometre Mg powder reached 275 A mm−2 at 4.2 K and 10 T. This value was about six times that of 5 mol% SiC-added tapes fabricated with commercial Mg powder. Microstructure analyses suggest that this Jc enhancement is primarily due to the smaller MgB2 grain size.
Silicon nanoparticles with chemically tailored surfaces (2009)

Abstract Silicon nanoparticles are useful materials for optoelectronic devices, solar cells and biological markers. The synthesis of air‐stable nanoparticles with tunable optoelectronic properties is highly desirable. The mechanochemical synthesis of silicon nanoparticles via high‐energy ball milling produces a variety of covalently bonded surfaces depending on the nature of the organic liquid used in the milling process. The use of the C 8 reactants including octanoic acid, 1‐octanol, 1‐octaldehyde and 1‐octene results in passivated surfaces characterized by strong SiC bonds or strong SiO bonds. The surfaces of the nanoparticles were characterized by infrared spectroscopy and nuclear magnetic resonance spectroscopy. The nanoparticles were soluble in common organic solvents and remarkably stable against agglomeration and air oxidation. The luminescence and optical properties of the nanoparticles were very sensitive to the nature of their passivating surface. Copyright © 2009 John Wiley & Sons, Ltd.
Security-Aware Virtual Machine Allocation in the Cloud: A Game Theoretic Approach (2015)

With the growth of cloud computing, many businesses, both small and large, are opting to use cloud services compelled by a great cost savings potential. This is especially true of public cloud computing which allows for quick, dynamic scalability without many overhead or long-term commitments. However, one of the largest dissuasions from using cloud services comes from the inherent and unknown danger of a shared platform such as the hyper visor. An attacker can attack a virtual machine (VM) and then go on to compromise the hyper visor. If successful, then all virtual machines on that hyper visor can become compromised. This is the problem of negative externalities, where the security of one player affects the security of another. This work shows that there are multiple Nash equilibria for the public cloud security game. It also demonstrates that we can allow the players' Nash equilibrium profile to not be dependent on the probability that the hyper visor is compromised, reducing the factor externality plays in calculating the equilibrium. Finally, by using our allocation method, the negative externality imposed onto other players can be brought to a minimum compared to other common VM allocation methods.
Identification of a Pyridopyrimidinone Inhibitor of Orthopoxviruses from a Diversity-Oriented Synthesis Library (2011)

Orthopoxviruses include the prototypical vaccinia virus, the emerging infectious agent monkeypox virus, and the potential biothreat variola virus (the causative agent of smallpox). There is currently no FDA-approved drug for humans infected with orthopoxviruses. We screened a diversity-oriented synthesis library for new scaffolds with activity against vaccinia virus. This screen identified a nonnucleoside analog that blocked postreplicative intermediate and late gene expression. Viral genome replication was unaffected, and inhibition could be elicited late in infection and persisted upon drug removal. Sequencing of drug-resistant viruses revealed mutations predicted to be on the periphery of the highly conserved viral RNA polymerase large subunit. Consistent with this, the compound had broad-spectrum activity against orthopoxviruses in vitro. These findings indicate that novel chemical synthesis approaches are a potential source for new infectious disease therapeutics and identify a potentially promising candidate for development to treat orthopoxvirus-infected individuals.
AV1 In-loop Super-resolution Framework (2019)

The AV1 codec added a new in-loop super-resolution mode that allows a frame to be encoded at a lower resolution, and then super-resolved normatively to the full resolution, before updating the reference buffers. While encoding at lower resolution and super-resolving to a higher resolution is not a new concept, this is the first time such a mode has been normatively incorporated in a standardized video codec. To this end, AV1 has not only added support for across-scale motion prediction to allow predicting a lower resolution version of a frame from higher resolution reference buffers, but also made various simplifications to the super-resolving process itself after reconstruction to make it both software and hardware-friendly in implementation. Specifically, the super-resolving process in AV1 comprises of normative linear upscaling, followed by a restoration operation to recover the high frequencies using another AV1 tool called loop-restoration that includes a Wiener or Self-guided filter selected in a block switchable manner. Further, in order to enable a cost-effective hardware solution with limited line-buffers, this mode only allows the upscaling/downscaling operation to be horizontal. In this paper, we provide the details of the super-resolution mode in AV1 and some results showcasing the benefits of the same.
Identification of<i>Mycoplasma suis</i>antigens and development of a multiplex microbead immunoassay (2014)

The aims of the current study were to identify Mycoplasma suis antigens and develop a multiplex microbead immunoassay (MIA). A M. suis-expression library was screened for immunogens using sera from infected pigs. Based on bioinformatics, putative antigens were identified within positive inserts; gene fragments were expressed and purified as polyhistidine fusion proteins, and immunoreactivity was confirmed by Western blot. Selected antigens were used to develop a MIA. Sera from noninfected and infected pigs were used to set the median fluorescent intensity (MFI) cutoffs and as positive controls, respectively. Assay specificity was tested using sera from pigs seropositive for other pathogens (2 different pigs seropositive for each pathogen). Samples from 51 field pigs and 2 pigs during the course of acute (pig 1) and chronic (pig 2) infections were tested using MIA, indirect hemagglutination assay (IHA), and quantitative polymerase chain reaction (qPCR). Sixteen reactive plaques (52 genes) were detected. A heat-shock protein (GrpE), a nicotinamide adenine dinucleotide-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPN), and 4 proteins from paralogous gene families (PGFs) were identified as antigens by Western blot. While GrpE, GAPN, and 1 PGF protein were strong antigens, the others were not suitable as MIA targets. A MIA using GrpE, GAPN, and the strongly reactive PGF protein was developed. Cross-reactivity with sera from pigs infected with Mycoplasma hyopneumoniae, Porcine circovirus-2, Porcine parvovirus, Porcine reproductive and respiratory syndrome virus, and Porcine respiratory coronavirus with this MIA was not observed. Pig 2 was consistently positive by MIA and qPCR, whereas pig 1, initially negative, seroconverted before becoming qPCR positive. Only 2 samples (from pig 1) were IHA positive. Five (9.8%) field samples were qPCR positive and 40 (78.43%) were positive for all 3 MIA antigens; however, all were IHA negative. In summary, the MIA is specific and more sensitive than qPCR and IHA, providing simultaneous evaluation of antibody response to M. suis antigens.
IEEE 1988 Bipolar Circuits E Technology Meting A Novel Quasi-Dielectrically Isolated Bipolar Transistor Using Epitaxial Lateral Overgrowth (1988)

A new, quasi-dielectrically isolated (QDI) bipolar structure using epitaxial lateral overgrowth (ELO) is presented. A main application for QDI is in power integrated circuits (PICs) where isolation of high power devices and low power logic is necessary. The ELO-QDI structure uses a combination of dielectric isolation (DI) and junction isolation (JI), providing better isolation properties than JI, while providing better heat dissipation than DI. The EL0 silicon was grown at a low temperature, 950 C, low pressure, 150 Torr, in a RF heated pancake-type reactor. Fabricated transistors have gains, ideality factors, and leakage currents comparable to bulk devices.
A method to generate human mesenchymal stem cell-derived neurons which express and are excited by multiple neurotransmitters. (2008)

The present study describes a protocol to generate heterogenous populations of neurotransmitter-producing neurons from human mesenchymal stem cells (MSCs). MSCs are bone marrow (BM)-derived cells which undergo lineage- specific differentiation to generate bone, fat, cartilage and muscle, but are also capable of transdifferentiating into defined ectodermal and endodermal tissues. The purpose of this study is to evaluate the potential of MSCs as an alternative source of customized neurons for experimental neurobiology or other regenerative approaches. Our neuronal protocol utilizes freshly harvested human MSCs cultured on specific surfaces and exposed to an induction cocktail consisting of low serum concentration, retinoic acid (RA), growth factors and supplements. Here we report on the types of neurotransmitters produced by the neurons, and demonstrate that the cells are electrically responsive to exogenous neurotransmitter administration.