gebhart/patrepeval huggingface dataset:
Standardization of chemical shifts of TMS and solvent signals in NMR solvents (2006)

The standard for chemical shift is dilute tetramethylsilane (TMS) in CDCl3, but many measurements are made relative to TMS in other solvents, the proton resonance of the solvent peak or relative to the lock frequency. Here, the chemical shifts of TMS and the proton and deuterium chemical shifts of the solvent signals of several solvents are measured over a wide temperature range. This allows for the use of TMS or the solvent and lock signal as a secondary reference for other NMR signals, as compared with dilute TMS in CDCl3 at a chosen temperature; 25 degrees C is chosen here. An accuracy of 0.02 ppm is achievable for dilute solutions, provided that the interaction with the solvent is not very strong. The proton chemical shift of residual water is also reported where appropriate.
The Theory Underlying the Partitioning of Permutation Networks (1980)

The age of the microcomputer has made feasible large-scale multiprocessor systems. In order to use this parallel processing power in the form of a flexible multiple-SIMD (MSIMD) system, the interconnection network must be partitionable and dynamically reconfigurable. The theory underlying the partitioning of MSIMD system permutation networks into independent subnetworks is explored. Conditions for determining if a network can be partitioned into independent subnetworks and the ways in which it can be partitioned are presented. The use of the theory is demonstrated by applying it to the Cube, Illiac, PM2I, and Shuffle-Exchange SIMD machine interconnection networks. Both recirculating (single stage) and multistage network implementations are considered.
Rehabilitation treatment of gait in patients with Parkinson's disease with freezing: A comparison between two physical therapy protocols using visual and auditory cues with or without treadmill training (2009)

Freezing is a disabling symptom in patients with Parkinson's disease. We investigated the effectiveness of a new rehabilitation strategy based on treadmill training associated with auditory and visual cues. Forty Parkinsonian patients with freezing were randomly assigned to two groups: Group 1 underwent a rehabilitation program based on treadmill training associated with auditory and visual cues, while Group 2 followed a rehabilitation protocol using cues and not associated with treadmill. Functional evaluation was based on the Unified Parkinson's Disease Rating Scale Motor Section (UPDRS III), Freezing of Gait Questionnaire (FOGQ), 6-minute walking test (6MWT), gait speed, and stride cycle. Patients in both the groups had significant improvements in all variables considered by the end of the rehabilitation program (all P = 0.0001). Patients treated with the protocol including treadmill, had more improvement than patients in Group 2 in most functional indicators (P = 0.007, P = 0.0004, P = 0.0126, and P = 0.0263 for FOGQ, 6MWT, gait speed, stride cycle, respectively). The most striking result was obtained for 6MWT, with a mean increase of 130 m in Group 1 compared with 57 m in Group 2. Our results suggest that treadmill training associated with auditory and visual cues might give better results than more conventional treatments. Treadmill training probably acts as a supplementary external cue.
The Absence of the ACE N-Domain Decreases Renal Inflammation and Facilitates Sodium Excretion during Diabetic Kidney Disease (2018)

These data indicate that increasing AcSDKP by blocking the ACE N-domain facilitates sodium excretion and ameliorates diabetic kidney disease independent of intrarenal angiotensin II regulation.
DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits. (1988)

The 10 distinctive polypeptides of DNA polymerase III holoenzyme, purified as individual subunits or complexes, could be reconstituted to generate a polymerase with the high catalytic rate of the isolated intact holoenzyme. Functions and interactions of the subunits can be inferred from partial assemblies of the pol III core (alpha, epsilon, and theta subunits) with auxiliary subunits. The core possesses the polymerase and proofreading activities; the auxiliary subunits provide the core with processivity, the capacity to replicate long stretches of DNA without dissociating from the template. In a sequence of reconstruction steps, the beta subunit binds the primed template in an ATP-dependent manner through the catalytic action of a complex made up of the gamma, delta, delta', chi, and psi polypeptides. With the beta subunit in place, a processive polymerase is produced upon addition of the core. When the tau subunit is lacking, binding of polymerase to the primed template is less efficient and stable. The tau-less reconstituted polymerase is more prone to dissociation upon encountering secondary structures in the template in its path, such as a hairpin region in the single strand or a duplex region formed by a strand annealed to the template. With the tau subunit present, the interaction of the core.beta complex (the basic unit of a processive polymerase) with the primed template is strengthened. The tau-containing reconstituted polymerase can replicate DNA continuously through secondary structures in the template. The two distinctive kinds of processivity demonstrated by the tau-less and tau-containing reconstituted polymerases fit nicely into a scheme in which, organized as an asymmetric dimeric holoenzyme, the tau half is responsible for continuous synthesis of one strand, and the less stable half for discontinuous synthesis of the other.
An Outbreak of Respiratory Syncytial Virus in a Bone Marrow Transplant Center (1992)

An outbreak of respiratory syncytial virus (RSV) infection occurred among 31 patients in a marrow transplant center over a 13-week period beginning in January 1990. RSV infection was also documented in 35 family members and employees. Of 18 patients with pneumonia, 14 (78%) died. None of 13 with upper respiratory infection died. Preengraftment patients tended to develop pneumonia more frequently than did engrafted patients. Early administration of ribavirin may have had a beneficial effect in patients with pneumonia. Antigenic and genomic analysis of 14 available isolates suggested that at least four different viral strains were responsible for the outbreak. One group of patients and 1 employee in spatial proximity were infected with the same strain and likely acquired their infections nosocomially. RSV infection in marrow transplant patients is a serious and life-threatening infection with a high mortality rate once pneumonia develops.
Accelerated Bonelike Apatite Growth on Porous Polymer/Ceramic Composite Scaffolds in Vitro (2006)

Although biodegradable polymer/ceramic composite scaffolds can overcome the limitations of conventional ceramic bone substitutes, the osteogenic potential of these scaffolds needs to be further enhanced for efficient bone tissue engineering. In this study, bonelike apatite was efficiently coated onto the scaffold surface by using polymer/ceramic composite scaffolds instead of polymer scaffolds and by using an accelerated biomimetic process to enhance the osteogenic potential of the scaffold. The creation of bonelike, apatite-coated polymer scaffold was achieved by incubating the scaffolds in simulated body fluid (SBF). The apatite growth on porous poly(D,L-lactic-co-glycolic acid)/nanohydroxyapatite (PLGA/ HA) composite scaffolds was significantly faster than on porous PLGA scaffolds. In addition, the distribution of coated apatite was more uniform on PLGA/HA scaffolds than on PLGA scaffolds. After a 5-day incubation period, the mass of apatite coated onto PLGA/HA scaffolds incubated in 5 x SBF was 2.3-fold higher than PLGA/HA scaffolds incubated in 1 x SBF. Furthermore, when the scaffolds were incubated in 5 x SBF for 5 days, the mass of apatite coated onto PLGA/HA scaffolds was 4.5-fold higher than PLGA scaffolds. These results indicate that the biomimetic apatite coating can be accelerated by using a polymer/ceramic composite scaffold and concentrated SBF. When seeded with osteoblasts, the apatite-coated PLGA/HA scaffolds exhibited significantly higher cell growth, alkaline phosphatase activity, and mineralization in vitro compared to the apatite-coated PLGA scaffolds. Therefore, the apatite-coated PLGA/HA scaffolds may provide enhanced osteogenic potential when used as scaffold for bone tissue engineering.
Thrombospondin 1 Promotes Tumor Macrophage Recruitment and Enhances Tumor Cell Cytotoxicity of Differentiated U937 Cells (2008)

Inhibition of tumor growth by thrombospondin (TSP) 1 is generally attributed to its antiangiogenic activity, but effects on tumor immunity should also be considered. We show that overexpression of TSP1 in melanoma cells increases macrophage recruitment into xenograft tumors grown in nude or beige/nude mice. In vitro, TSP1 acutely induces expression of plasminogen activator inhibitor-1 (PAI-1) by monocytic cells, suggesting that TSP1-induced macrophage recruitment is at least partially mediated by PAI-1. Tumor-associated macrophages (TAM) can either promote or limit tumor progression. The percentage of M1-polarized macrophages expressing inducible nitric oxide synthase is increased in TSP1-expressing tumors. Furthermore, soluble TSP1 stimulates killing of breast carcinoma and melanoma cells by IFN-gamma-differentiated U937 cells in vitro via release of reactive oxygen species. TSP1 causes a significant increase in phorbol ester-mediated superoxide generation from differentiated monocytes by interaction with alpha(6)beta(1) integrin through its NH(2)-terminal region. The NH(2)-terminal domain of TSP2 also stimulates monocyte superoxide production. Extracellular calcium is required for the TSP1-induced macrophage respiratory burst. Thus, TSP1 may play an important role in antitumor immunity by enhancing recruitment and activation of M1 TAMs, which provides an additional selective pressure for loss of TSP1 and TSP2 expression during tumor progression.
Zero Phase Error Tracking Algorithm for Digital Control (1987)

A digital feedforward control algorithm for tracking desired time varying signals is presented. The feedforward controller cancels all the closed-loop poles and cancellable closed-loop zeros. For uncancellable zeros, which include zeros outside the unit circle, the feedforward controller cancels the phase shift induced by them. The phase cancellation assures that the frequency response between the desired output and actual output exhibits zero phase shift for all the frequencies. The algorithm is particularly suited to the general motion control problems including robotic arms and positioning tables. A typical motion control problem is used to show the effectiveness of the proposed feedforward controller.
Renal vein thrombosis and inferior vena cava thrombosis in systemic lupus erythematosus (1984)

Phlebography of the inferior vena cava with selective study of the renal veins was performed in 43 patients with systemic lupus erythematosus (SLE). Inferior vena cava thrombosis (IVCT) or renal vein thrombosis (RVT) was found in 3 of 11 patients (27%) with nephrotic syndrome, in 8 of 13 (61.5%) with previous thrombophlebitis, and in 3 of 4 (75%) with suggestive acute clinical picture. In contrast, none of the 20 control patients with SLE had IVCT or RVT. These results show that SLE patients with thrombophlebitis have a very high risk of developing IVCT or RVT; patients with nephrotic syndrome have a smaller risk. Neither IVCT nor RVT was found in SLE patients without antecedent thrombophlebitis or nephrotic syndrome.
Peroxisome Proliferator-activated Receptor β/δ Induces Myogenesis by Modulating Myostatin Activity (2012)

Classically, peroxisome proliferator-activated receptor β/δ (PPARβ/δ) function was thought to be restricted to enhancing adipocyte differentiation and development of adipose-like cells from other lineages. However, recent studies have revealed a critical role for PPARβ/δ during skeletal muscle growth and regeneration. Although PPARβ/δ has been implicated in regulating myogenesis, little is presently known about the role and, for that matter, the mechanism(s) of action of PPARβ/δ in regulating postnatal myogenesis. Here we report for the first time, using a PPARβ/δ-specific ligand (L165041) and the PPARβ/δ-null mouse model, that PPARβ/δ enhances postnatal myogenesis through increasing both myoblast proliferation and differentiation. In addition, we have identified Gasp-1 (growth and differentiation factor-associated serum protein-1) as a novel downstream target of PPARβ/δ in skeletal muscle. In agreement, reduced Gasp-1 expression was detected in PPARβ/δ-null mice muscle tissue. We further report that a functional PPAR-responsive element within the 1.5-kb proximal Gasp-1 promoter region is critical for PPARβ/δ regulation of Gasp-1. Gasp-1 has been reported to bind to and inhibit the activity of myostatin; consistent with this, we found that enhanced secretion of Gasp-1, increased Gasp-1 myostatin interaction and significantly reduced myostatin activity upon L165041-mediated activation of PPARβ/δ. Moreover, we analyzed the ability of hGASP-1 to regulate myogenesis independently of PPARβ/δ activation. The results revealed that hGASP-1 protein treatment enhances myoblast proliferation and differentiation, whereas silencing of hGASP-1 results in defective myogenesis. Taken together these data revealed that PPARβ/δ is a positive regulator of skeletal muscle myogenesis, which functions through negatively modulating myostatin activity via a mechanism involving Gasp-1.
Effectiveness of reverse body bias for leakage control in scaled dual Vt CMOS ICs (2001)

Examines the effectiveness of opportunistic use of reverse body bias (RBB) to reduce leakage power during active operation, burn-in, and standby in 0.18 /spl mu/m single-V/sub t/ and 0.13 /spl mu/m dual-V/sub t/ logic process technologies. Investigates its dependencies on channel length, target V/sub t/, temperature and technology generation. Shows that RBB becomes less effective for leakage reduction at shorter channel lengths and lower V/sub t/ at both high and room temperatures, especially when target intrinsic leakage currents are high. RBB effectiveness also diminishes with technology scaling primarily because of worsening short-channel effects (SCE), particularly when target V/sub t/ values are low. A model is given that relates different transistor leakage components to full-chip leakage current, and is validated through test-chip measurements across a range of RBB values.
Subcellular sites for bacterial protein export (2004)

Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA-YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the secretory protein pre-AmyQ, were analysed using green fluorescent protein fusions, immunostaining and/or immunogold labelling techniques. It is shown that SecA, SecY and (pre-)AmyQ are located at specific sites near and/or in the cytoplasmic membrane of Bacillus subtilis. The localization patterns of these proteins suggest that the Sec machinery is organized in spiral-like structures along the cell, with most of the translocases organized in specific clusters along these structures. However, this localization appears to be independent of the helicoidal structures formed by the actin-like cytoskeletal proteins, MreB or Mbl. Interestingly, the specific localization of SecA is dynamic, and depends on active translation. Moreover, reducing the phosphatidylglycerol phospholipids content in the bacterial membrane results in delocalization of SecA, suggesting the involvement of membrane phospholipids in the localization process. These data show for the first time that, in contrast to the recently reported uni-ExPortal site in the coccoïd Streptococcus pyogenes, multiple sites dedicated to protein export are present in the cytoplasmic membrane of rod-shaped B. subtilis.
Molecular Engineering of Acoustic Protein Nanostructures (2016)

Ultrasound is among the most widely used biomedical imaging modalities, but has limited ability to image specific molecular targets due to the lack of suitable nanoscale contrast agents. Gas vesicles-genetically encoded protein nanostructures isolated from buoyant photosynthetic microbes-have recently been identified as nanoscale reporters for ultrasound. Their unique physical properties give gas vesicles significant advantages over conventional microbubble contrast agents, including nanoscale dimensions and inherent physical stability. Furthermore, as a genetically encoded material, gas vesicles present the possibility that the nanoscale mechanical, acoustic, and targeting properties of an imaging agent can be engineered at the level of its constituent proteins. Here, we demonstrate that genetic engineering of gas vesicles results in nanostructures with new mechanical, acoustic, surface, and functional properties to enable harmonic, multiplexed, and multimodal ultrasound imaging as well as cell-specific molecular targeting. These results establish a biomolecular platform for the engineering of acoustic nanomaterials.
Deep Convolutional Network Cascade for Facial Point Detection (2013)

We propose a new approach for estimation of the positions of facial key points with three-level carefully designed convolutional networks. At each level, the outputs of multiple networks are fused for robust and accurate estimation. Thanks to the deep structures of convolutional networks, global high-level features are extracted over the whole face region at the initialization stage, which help to locate high accuracy key points. There are two folds of advantage for this. First, the texture context information over the entire face is utilized to locate each key point. Second, since the networks are trained to predict all the key points simultaneously, the geometric constraints among key points are implicitly encoded. The method therefore can avoid local minimum caused by ambiguity and data corruption in difficult image samples due to occlusions, large pose variations, and extreme lightings. The networks at the following two levels are trained to locally refine initial predictions and their inputs are limited to small regions around the initial predictions. Several network structures critical for accurate and robust facial point detection are investigated. Extensive experiments show that our approach outperforms state-of-the-art methods in both detection accuracy and reliability.
Expression of Herpes Simplex Virus ICP0 Inhibits the Induction of Interferon-Stimulated Genes by Viral Infection (2002)

The herpes simplex virus type 1 (HSV-1) mutant d109 does not express any of the immediate-early (IE) proteins and persists in cells for a prolonged length of time. As has been shown by Nicholl et al. (J. Gen. Virol. 81:2215-2218, 2000) and Mossman et al. (J. Virol. 75:750-758, 2001) using other mutants defective for IE gene expression, infection with d109 induced the expression of a number of interferon-stimulated genes. Induction of these genes was significantly greater at multiplicities of infection (MOI) of 10 PFU/cell or greater, and the resulting antiviral effect was only seen at MOIs greater than 10 PFU/cell. Using mutants defective for sets of IE genes established that the lack of ICP0 expression was necessary for high levels of interferon-stimulated gene expression in HEL cells. The induction of interferon-stimulated genes by d109 could also be inhibited by infection with an E1-:E3-:E4- adenovirus expressing levels of ICP0 that are comparable to those expressed within the first hour of wild-type virus infection. Lastly, the addition of the proteasome inhibitor MG132 to cells infected with a mutant that expresses ICP0, d106, also resulted in the induction of interferon-stimulated genes. Thus, ICP0 may function through the proteasome very early in HSV infection to inhibit a cellular antiviral response induced by the virion.
Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4 (1992)

The DNA polymerase from the bacteriophage T4 is part of a multienzyme complex required for the synthesis of DNA. As a first step in understanding the contributions of individual proteins to the dynamic properties of the complex, e.g., turnover, processivity, and fidelity of replication, the minimal kinetic schemes for the polymerase and exonuclease activities of the gene 43 protein have been determined by pre-steady-state kinetic methods and fit by computer simulation. A DNA primer/template (13/20-mer) was used as substrate; duplexes that contained more single-strand DNA resulted in nonproductive binding of the polymerase. The reaction sequence features an ordered addition of 13/20-mer followed by dATP to the T4 enzyme (dissociation constants of 70 nM and 20 microM) followed by rapid conversion (400 s-1) of the T4.13/20-mer.dATP complex to the T4.14/20-mer.PPi product species. A slow step (2 s-1) following PPi release limits a single turnover, although this step is bypassed in multiple incorporations (13/20-mer-->17/20-mer) which occur at rates > 400 s-1. Competition between correct versus incorrect nucleotides relative to the template strand indicates that the dissociation constants for the incorrect nucleotides are at millimolar values, thus providing evidence that the T4 polymerase, like the T7 but unlike the Klenow fragment polymerases, discriminates by factors > 10(3) against misincorporation in the nucleotide binding step. The exonuclease activity of the T4 enzyme requires an activation step, i.e., T4.DNA-->T4.(DNA)*, whose rate constants reflect whether the 3'-terminus of the primer is matched or mismatched; for matched 13/20-mer the constant is 1 s-1, and for mismatched 13T/20-mer, 5 s-1. Evidence is presented from crossover experiments that this step may represent a melting of the terminus of the duplex, which is followed by rapid exonucleolytic cleavage (100s-1). In the presence of the correct dNTP, primer extension is the rate-limiting step rather than a step involving travel of the duplex between separated exonuclease and polymerase sites. Since the rate constant for 13/20-mer or 13T/20-mer dissociation from the enzyme is 6 or 8 s-1 and competes with that for activation, the exonucleolytic editing by the enzyme alone in a single pass is somewhat inefficient (5 s-1/(8 s-1+5 s-1)), ca. 40%. Consequently, a major role for the accessory proteins may be to slow the rate of enzyme.substrate dissociation, thereby increasing overall fidelity and processivity.