gebhart/patrepeval huggingface dataset:
Initial HIV-1 Antigen-Specific CD8 + T Cells in Acute HIV-1 Infection Inhibit Transmitted/Founder Virus Replication (2012)

CD8-mediated virus inhibition can be detected in HIV-1-positive subjects who naturally control virus replication. Characterizing the inhibitory function of CD8(+) T cells during acute HIV-1 infection (AHI) can elucidate the nature of the CD8(+) responses that can be rapidly elicited and that contribute to virus control. We examined the timing and HIV-1 antigen specificity of antiviral CD8(+) T cells during AHI. Autologous and heterologous CD8(+) T cell antiviral functions were assessed longitudinally during AHI in five donors from the CHAVI 001 cohort using a CD8(+) T cell-mediated virus inhibition assay (CD8 VIA) and transmitted/founder (T/F) viruses. Potent CD8(+) antiviral responses against heterologous T/F viruses appeared during AHI at the first time point sampled in each of the 5 donors (Fiebig stages 1/2 to 5). Inhibition of an autologous T/F virus was durable to 48 weeks; however, inhibition of heterologous responses declined concurrent with the resolution of viremia. HIV-1 viruses from 6 months postinfection were more resistant to CD8(+)-mediated virus inhibition than cognate T/F viruses, demonstrating that the virus escapes early from CD8(+) T cell-mediated inhibition of virus replication. CD8(+) T cell antigen-specific subsets mediated inhibition of T/F virus replication via soluble components, and these soluble responses were stimulated by peptide pools that include epitopes that were shown to drive HIV-1 escape during AHI. These data provide insights into the mechanisms of CD8-mediated virus inhibition and suggest that functional analyses will be important for determining whether similar antigen-specific virus inhibition can be induced by T cell-directed vaccine strategies.
P1‐125: PRECLINICAL AND CLINICAL CHARACTERIZATION OF 18F‐PM‐PBB3, A PET LIGAND FOR DIVERSE TAU PATHOLOGIES (2018)

11C-pyridinylbutadienyl-benzothiazole 3 (11C-PBB3), a tau PET ligand, can visualize tau pathologies in Alzheimer's disease (AD), non-AD tauopathies and tau transgenic mice. We have developed a 18F-labeled PBB3 derivative, 18F-PM-PBB3, to improve imaging characteristics of 11C-PBB3 and wider availability. The aims of the present study are to evaluate the potential utility of this ligand in AD and non-AD tauopathies, and to establish a simplified method for quantifying tau deposits by PET with 18F-PM-PBB3. To characterize the binding property of 18F-PM-PBB3 to diverse tau inclusions, we performed preclinical evaluations of 18F-PM-PBB3 using brain samples of humans and model mice. Furthermore, to perform a head-to-head comparison between 18F-PM-PBB3 and 11C-PBB3, patients with AD and non-AD tauopathies including progressive supranuclear palsy (PSP) and cognitively healthy subjects underwent PET scans with 18F-PM-PBB3 and 11C-PBB3. To evaluate the validity of the PET quantification of 18F-PM-PBB3 binding to tau pathology, arterial blood sampling was performed to determine the binding potential (BPND) of the radioligand based on a compartmental model. BPND by a reference tissue model and standardized uptake value ratio (SUVR) using cerebellum gray matter as a reference were also calculated. These estimates were compared to the SUVR value of 11C-PBB3 in each subject. Preclinical characterization revealed that 18F-PM-PBB3 can bind diverse tau pathologies, including AD, PSP, corticobasal degeneration, and Pick's disease, with high sensitivity and specificity. It was also demonstrated that 18F-PM-PBB3 cross-reacts with neither monoamine oxidase (MAO)-A nor MAO-B. In the clinical PET study, BPND value of 18F-PM-PBB3 calculated by a compartmental model was in good agreement with BPND determined by a reference tissue model as well as SUVR minus 1. 18F-PM-PBB3 yielded approximately 2-fold higher dynamic ranges of tau- specific signals than 11C-PBB3, while the distributions of specifically bound 18F-PM-PBB3 and 11C-PBB3 were in general agreement. 18F-PM-PBB3 did not produce prominent off-target signals in the basal ganglia. 18F-PM-PBB3 is a promising PET ligand for quantifying tau pathologies in AD and non-AD tauopathy patients with suitable pharmacokinetics, high contrast and minimal parenchymal off-target binding. SUVR can be used as a robust and simplified estimate of the specific radioligand binding.
Non-Boltzmann energy distributions in spin-torque devices (2006)

Most previous work on energy distributions in spin-torque devices has assumed a Boltzmann form exp(−E∕kBTeff), with an effective temperature that is modified by the spin torque. We consider in this article a regime in which this is not even qualitatively true (for example, the distribution is not even monotonic in E), and give a method for quantitatively calculating the distribution. This is a necessary ingredient of any calculation of the noise spectrum or the switching current.
Supplementary Figure from CD74-NRG1 Fusions Are Oncogenic <i>In Vivo</i> and Induce Therapeutically Tractable ERBB2:ERBB3 Heterodimerization (2023)

Supplementary Figure from CD74-NRG1 Fusions Are Oncogenic &lt;i&gt;In Vivo&lt;/i&gt; and Induce Therapeutically Tractable ERBB2:ERBB3 Heterodimerization
Preparation of125I-Labeled Human Growth Hormone of High Quality Binding Properties Endowed with Long-Term Stability (1989)

125I-labeled human growth hormone (125I-labeled.hGH) was prepared by using two variants of the chloramine T labelling procedure and purified by polyacrylamide gel electrophoresis (PAGE) of the reaction mixture. Variant A produced a tracer with high specific activity (100 +/- 10 microCi/microgram), high maximal binding capacity to antibodies (93%) and long-term stability (at least 150 days at -20 degrees C). No diiodinated tyrosil residues could be detected in this tracer. Variant B was devised to obtain higher yields of labeled hormone. The electrophoresis of the iodination mixture revealed two radioactive components with Rm values of 0.49 and 0.55 which result from the iodination of hGH variants preexisting in the starting material. Both tracers had similar specific activities (70 +/- 10 microCi/microgram), high maximal binding capacity to antibodies or receptors (80-100%, after 80 days of their obtention) and high stability (at least 100 days at -20 degrees C). It is concluded that the iododerivatives of hGH obtained by either method are adequate to perform radioimmunoassay and receptor studies and have long-term stability.
Liposome-encapsulated Muramyl Tripeptide Phosphatidylethanolamine for the Treatment of Feline Mammary Adenocarcinoma-A Multicenter Randomized Double-blind Study (1995)

Forty cats with previously untreated, histologically confirmed mammary gland adenocarcinoma received a radical mastectomy of the affected mammary chain(s). All cats were stratified according to clinical stage and randomized to receive either weekly intravenous liposome-encapsulated muramyl tripeptide phosphatidylethanolamine or placebo (lipid-equivalent) for eight consecutive weeks in this double-blind study. Thirty-six of the 40 cats were available for follow-up. No significant differences in either disease-free interval or survival were found as a result of treatment. Cats with clinical stage II disease had a statistically significantly longer disease-free interval (p < 0.02), and overall survival (p < 0.005) when compared with clinical stage III cats.
Partially Adaptive STAP using the FRACTA Algorithm (2009)

A partially adaptive space-time adaptive processor (STAP) utilizing the recently developed FRACTA algorithm is presented which significantly reduces the high computational complexity and large sample support requirements of fully adaptive STAP. Multi-window post-Doppler dimensionality reduction techniques are employed to transform the data prior to application of the FRACTA algorithm. The FRACTA algorithm is a reiterative censoring (RC) and detection algorithm which has been shown to provide excellent detection performance in nonhomogeneous interference environments. Two multi-window post-Doppler dimensionality reduction techniques are considered: PRI-staggered and adjacent-bin. The partially adaptive FRACTA algorithm is applied to the KASSPER I (knowledge-aided sensor signal processing & expert reasoning) challenge datacube. The pulse repetition interval (PRI)-staggered approach with D=6 filters per Doppler bin is found to provide the best detection performance, outperforming the fully adaptive case while simultaneously reducing the runtime by a factor of ten. Using this implementation, partially adaptive FRACTA detects 197 out of 268 targets with one false alarm. The clairvoyant processor (the covariance matrix for each range cell is known) detects 198 targets with one false alarm. In addition, the partially adaptive FRACTA algorithm is shown to be resilient to jamming, and performs well for reduced sample support situations. When compared with partially adaptive STAP using traditional sliding window processing (SWP), the runtime of partially adaptive FRACTA is 14 times faster, and the detection performance is significantly increased (SWP detects 46 out of 268 targets with one false alarm).
Interferons Accelerate Decay of Replication-Competent Nucleocapsids of Hepatitis B Virus (2010)

Alpha interferon (IFN-alpha) is an approved medication for chronic hepatitis B. Gamma interferon (IFN-gamma) is a key mediator of host antiviral immunity against hepatitis B virus (HBV) infection in vivo. However, the molecular mechanism by which these antiviral cytokines suppress HBV replication remains elusive. Using an immortalized murine hepatocyte (AML12)-derived cell line supporting tetracycline-inducible HBV replication, we show in this report that both IFN-alpha and IFN-gamma efficiently reduce the amount of intracellular HBV nucleocapsids. Furthermore, we provide evidence suggesting that the IFN-induced cellular antiviral response is able to distinguish and selectively accelerate the decay of HBV replication-competent nucleocapsids but not empty capsids in a proteasome-dependent manner. Our findings thus reveal a novel antiviral mechanism of IFNs and provide a basis for a better understanding of HBV pathobiology.
Sound production and modeling (2002)

Sound in multimedia, movies, games, virtual reality, and human-computer interfaces is a growing field that encompasses the disciplines of analog and digital signal processing, physics, speech, music, perception, and computer systems architecture. This overview of sound production and modeling techniques surveys the state of the art in sound technology. Sound has become a critical component in modern multimedia systems, especially multispeaker surround-sound entertainment systems. Many of the components and techniques in these systems are also applicable in virtual and augmented reality systems. With basic sound hardware now available for most (but not all, as in some palmtops) computer systems, and increasing processor speeds allowing direct real-time sound manipulation, enhancing multimodal computer-human interfaces by using the sonic channel is becoming commonplace. Sound in games and other graphics-intensive real-time applications is achieving higher levels of sophistication and promises to undergo even further advancements in realism and responsiveness.
Automatic Method for Imputing and Balancing Link Traffic Counts (2008)

Accurate measurement of traffic volumes throughout a transportation network is critical for traffic management as well as an input to simulation models. Obtaining an accurate and consistent set of traffic counts is a challenging task since not all link counts are available and even available measurements are noisy from various causes including sensor malfunctions. We present a method for imputing missing values and adjusting noisy measurements so that the final link volumes satisfy the flow conservation law. The method is based on weighted least squares regression (WLSR) approach and has a few desirable properties including: i) varying noise level of different measurements are taken into account; and ii) the method can be applied quickly in (semi-)automatic manner to a linear road section from basic configuration information on sensor geometry. The algorithm is applied to data from 50-km long freeway section of Attica Tollway in Athens, Greece.
HLA-B27 Subtypes Differentially Associated with Disease Exhibit Subtle Structural Alterations (2002)

The reasons for the association of the human major histocompatibility complex protein HLA-B27 with spondyloarthropathies are unknown. To uncover the underlying molecular causes, we determined the crystal structures of the disease-associated B*2705 and the nonassociated B*2709 subtypes complexed with the same nonapeptide (GRFAAAIAK). Both differ in only one residue (Asp(116) and His(116), respectively) in the F-pocket that accommodates the peptide C terminus. Several different effects of the Asp(116) --> His replacement are observed. The bulkier His(116) induces a movement of peptide C-terminal pLys(9), allowing the formation of a novel salt bridge to Asp(77), whereas the salt bridge between pLys(9) and Asp(116) is converted into a hydrogen bond with His(116). His(116) but not Asp(116) adopts two alternative conformations, one of which leads to breakage of hydrogen bonds. Water molecules near residue 116 differ with regard to number, position, and contacts made. Furthermore, F-pocket atoms exhibit higher B-factors in B*2709 than in B*2705, indicating an increased flexibility of the entire region in the former subtype. These changes induce subtle peptide conformational alterations that may be responsible for the immunobiological differences between these HLA-B27 subtypes.
PROGRESSIVE DILATION FOR BLADDER TISSUE EXPANSION (1999)

The system of progressive dilation is effective in expanding bladder tissue which is able to retain normal phenotypic and functional characteristics.
AC brushless drive with low-resolution Hall-effect sensors for surface-mounted PM Machines (2006)

An ac brushless drive in which Hall-effect sensors are used as rotor position sensors is presented in this paper. Three different methods to obtain a high-resolution position estimation from the low-resolution sensors are described and compared through simulation and experimental testing. The proposed control algorithm's most innovative feature is its adaptability to the entire speed range, including startup, when using any of the three estimation algorithms. The control algorithm has been implemented and tested in order to drive a slotless axial-flux permanent-magnet (PM) machine for domestic appliance applications.
Time-varying surface appearance (2006)

For computer graphics rendering, we generally assume that the appearance of surfaces remains static over time. Yet, there are a number of natural processes that cause surface appearance to vary dramatically, such as burning of wood, wetting and drying of rock and fabric, decay of fruit skins, and corrosion and rusting of steel and copper. In this paper, we take a significant step towards measuring, modeling, and rendering time-varying surface appearance. We describe the acquisition of the first time-varying database of 26 samples, encompassing a variety of natural processes including burning, drying, decay, and corrosion. Our main technical contribution is a Space-Time Appearance Factorization (STAF). This model factors space and time-varying effects. We derive an overall temporal appearance variation characteristic curve of the specific process, as well as space-dependent textures, rates, and offsets. This overall temporal curve controls different spatial locations evolve at the different rates, causing spatial patterns on the surface over time. We show that the model accurately represents a variety of phenomena. Moreover, it enables a number of novel rendering applications, such as transfer of the time-varying effect to a new static surface, control to accelerate time evolution in certain areas, extrapolation beyond the acquired sequence, and texture synthesis of time-varying appearance.
NHC–Cu-Catalyzed Silyl Conjugate Additions to Acyclic and Cyclic Dienones and Dienoates. Efficient Site-, Diastereo- and Enantioselective Synthesis of Carbonyl-Containing Allylsilanes (2012)

Efficient and highly diastereo- and enantioselective conjugate additions of phenyldimethylsilyl units to acyclic and cyclic dienones and dienoates are disclosed. The C-Si bond forming reactions are catalyzed by 2.0-2.5 mol % of a copper complex of a chiral monodentate N-heterocyclic carbene; the requisite reagent, PhMe(2)Si-B(pin), is commercially available or can be easily prepared. Transformations generate allylsilanes in up to 98% yield and >99:1 enantiomeric ratio, and proceed with complete 1,4-selectivity, unless the dienone or dienoate carries a trisubstituted alkene conjugated to the carbonyl group; in the latter cases, 1,6-addition products are obtained exclusively and in up to >98% Z selectivity.
The role of simulation in the teaching of communications (2002)

Faculty from Virginia Tech and the University of Missouri-Rolla, with support from the NSF/CRCD program, are developing a three-course sequence in wireless communications. The third course in the sequence is devoted to the simulation of communication systems. The simulation course not only provides students with the knowledge required to effectively use simulation in the design and analysis process but also, through the use of projects, gives students needed experience in proposal preparation and in research management. A number of MATLAB-based examples, demonstrations and analysis programs are being developed as a part of this effort.
Differential cross sections for H+D2→HD (v′=2, J′=0,3,5)+D at 1.55 eV (1999)

The photoloc technique with core extraction of the nascent product laboratory speed distribution in a Wiley–McLaren time-of-flight spectrometer has been used to measure differential cross sections for the reaction H+D2→HD (v′=2, J′=0,3,5)+D at collision energies ∼1.55 eV. We find that the peak of each angular distribution shifts from complete backward scattering toward side scattering as the rotational excitation of the product increases. We found the same trend in our previous study of H+D2→HD (v′=1, J′=1,5,8)+D at ∼1.70 eV. We conclude that the same type of correlation exists between impact parameter and rotational quantum number in both product vibrational manifolds. Further analysis of the HD (v′=2, J′) differential cross section data reveals, however, a clear tendency of this vibrational manifold to scatter sideways at lower J′ than HD(v′=1, J′). Within the framework of a line-of-centers model with nearly elastic specular scattering, this result implies that smaller impact parameters lead to more vibrationally excited products.
High quantum yield boron-doped carbon dots: a ratiometric fluorescent probe for highly selective and sensitive detection of Mg2+ ions (2020)

Highly fluorescent boron-doped carbon dots were synthesized from catechol and naphthalene boronic acid by a solvothermal method. They showed violet luminescence under UV illumination and were explored for highly selective detection of Mg<sup>2+</sup> ions, with an LOD of ~39 μM.
Genomic imbalance in the centromeric 11p15 imprinting center in three families: Further evidence of a role for IC2 as a cause of Russell–Silver syndrome (2016)

Russell-Silver syndrome is a heterogeneous disorder characterized by intrauterine growth retardation, postnatal growth deficiency, characteristic facial appearance, and other variable features. Genetic and epigenetic alterations are identified in about 60% of individuals with Russell-Silver syndrome. Most frequently, Russell-Silver syndrome is caused by altered gene expression on chromosome 11p15 due to loss of methylation at the telomeric imprinting center. To date there have been a handful of isolated clinical reports implicating the centromeric imprinting center 2 in the etiology of Russell-Silver syndrome. Here we report three new families with genomic imbalances, involving imprinting center 2 resulting in gain of methylation at this center and a Russell-Silver syndrome phenotype, including two families with a maternally inherited microduplication and the first pediatric patient with a paternally derived microdeletion. The findings in our families provide additional evidence of a role for imprinting center 2 in the etiology of Russell-Silver syndrome and suggest that imprinting center 2 imprinting abnormalities may be a more common cause of Russell-Silver syndrome than previously recognized. Furthermore, our findings together with previous clinical reports of genomic imbalances involving imprinting center 2 serve to underscore the complexity of the epigenetic regulation of the 11p15 region making it challenging to predict phenotype on the basis of genotype alone. © 2016 Wiley Periodicals, Inc.
RETRACTED ARTICLE: OCT4 as a target of miR-34a stimulates p63 but inhibits p53 to promote human cell transformation (2014)

Human cell transformation is a key step for oncogenic development, which involves multiple pathways; however, the mechanism remains unclear. To test our hypothesis whether cell oncogenic transformation shares some mechanisms with the process of reprogramming non-stem cells to induced pluripotent stem cells (iPSC), we studied the relationship among the key factors for promoting or inhibiting iPSC in radiation-transformed human epithelial cell lines derived from different tissues (lung, breast and colon). We unexpectedly found that p63 and OCT4 were highly expressed (accompanied by low expressed p53 and miR-34a) in all transformed cell lines examined when compared with their non-transformed counterparts. We further elucidated the relationship of these factors: the 3p strand of miR-34a directly targeted OCT4 by binding to the 3' untranslated region (3'-UTR) of OCT4 and, OCT4, in turn, stimulated p63 but inhibited p53 expression by binding to a specific region of the p63 or p53 promoter. Moreover, we revealed that the effects of OCT4 on promoting cell oncogenic transformation were by affecting p63 and p53. These results support that a positive loop exists in human cells: OCT4 upregulation as a consequence of inhibition of miR-34a, promotes p63 but suppresses p53 expression, which further stimulates OCT4 upregulation by downregulating miR-34a. This functional loop contributes significantly to cell transformation and, most likely, also to the iPSC process.
The Evaluation of Secondary Amine Protecting Groups for Nitration (2019)

Abstract Nitramines (for example RDX, HMX and CL‐20) are frequently made by nitrolyzing tertiary amides. While generally high yielding, sometimes the amides can be difficult to remove while keeping any ring systems intact. This study investigates twelve acyl hexahydro‐ s ‐triazines for their ease of conversion into nitramines using four common nitration conditions. Several new amide protecting group have been examined and one (cyclopropanecarboxamide) has been found to be better than those amides currently employed. The amide groups have been found to be nitrolyzable in the following order: Cyclopropyl&gt;Ethyl&gt;Propyl&gt;Methyl&gt; i ‐Propyl≈ t ‐Butyl≈Methoxymethyl≫Hydrogen&gt;Pentafluorophenyl.