gebhart/patrepeval huggingface dataset:
The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms (2005)

Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.
Quantum noise in the parametric oscillator: From squeezed states to coherent-state superpositions (1988)

We compare the nonclassical states of light produced by a parametric oscillator for quantum noise of different strengths. Increasing noise strength brings a transition from a slightly perturbed classical state showing squeezing to a superposition of coherent states. We use the positive-P representation to illustrate the roles of quantum noise, quantum coherence, nonlinearity, and dissipation in this simple quantum dynamical system.
Unsteady flow volumes (1995)

Flow volumes [1] are extended for use in unsteady (time-dependent) flows. The resulting unsteady flow volumes are the 3 dimensional analog of streaklines. There are few examples where methods other than particle tracing have been used to visualize time varying flows. Since particle paths can become convoluted in time there are additional considerations to be made when extending any visualization technique to unsteady flows. We will present some solutions to the problems which occur in subdivision, rendering, and system design. We will apply the unsteady flow volumes to a variety of field types including moving multi-zoned curvilinear grids.
SlowFast Networks for Video Recognition (2018)

We present SlowFast networks for video recognition. Our model involves (i) a Slow pathway, operating at low frame rate, to capture spatial semantics, and (ii) a Fast pathway, operating at high frame rate, to capture motion at fine temporal resolution. The Fast pathway can be made very lightweight by reducing its channel capacity, yet can learn useful temporal information for video recognition. Our models achieve strong performance for both action classification and detection in video, and large improvements are pin-pointed as contributions by our SlowFast concept. We report state-of-the-art accuracy on major video recognition benchmarks, Kinetics, Charades and AVA. Code has been made available at: https://github.com/facebookresearch/SlowFast
Interactions of erythro-ifenprodil, threo-ifenprodil, erythro-iodoifenprodil, and eliprodil with subtypes of σ receptors (1995)

Observations of sigma (sigma) receptor heterogeneity have prompted interest in identifying ligands for sigma receptor subtypes. Selective ligands for the sigma-2 are unavailable, but [3H]ifenprodil labels sigma-2 sites. Therefore, isomers and analogues of ifenprodil were compared as potential sigma-2 ligands. Threo-ifenprodil and erythro-ifenprodil had high affinity (Ki congruent to 2 nM) for sigma-2 sites; erythro-iodoifenprodil had moderate affinity (Ki congruent to 46 nM); eliprodil had lowest affinity (Ki congruent to 630 nM). Threo-ifenprodil, which has less affinity for alpha 1-adrenoceptors than erythro-ifenprodil, was slightly more selective than erythro-ifenprodil for sigma-2 sites. These results identify threo-ifenprodil as potentially useful for studies of sigma-2 receptors.
Genetic engineering of human stem cells for enhanced angiogenesis using biodegradable polymeric nanoparticles (2009)

Stem cells hold great potential as cell-based therapies to promote vascularization and tissue regeneration. However, the use of stem cells alone to promote angiogenesis remains limited because of insufficient expression of angiogenic factors and low cell viability after transplantation. Here, we have developed vascular endothelial growth factor (VEGF) high-expressing, transiently modified stem cells for the purposes of promoting angiogenesis. Nonviral, biodegradable polymeric nanoparticles were developed to deliver hVEGF gene to human mesenchymal stem cells (hMSCs) and human embryonic stem cell-derived cells (hESdCs). Treated stem cells demonstrated markedly enhanced hVEGF production, cell viability, and engraftment into target tissues. S.c. implantation of scaffolds seeded with VEGF-expressing stem cells (hMSCs and hESdCs) led to 2- to 4-fold-higher vessel densities 2 weeks after implantation, compared with control cells or cells transfected with VEGF by using Lipofectamine 2000, a leading commercial reagent. Four weeks after intramuscular injection into mouse ischemic hindlimbs, genetically modified hMSCs substantially enhanced angiogenesis and limb salvage while reducing muscle degeneration and tissue fibrosis. These results indicate that stem cells engineered with biodegradable polymer nanoparticles may be therapeutic tools for vascularizing tissue constructs and treating ischemic disease.
Elements of morphology: Standard terminology for the ear (2009)

An international group of clinicians working in the field of dysmorphology has initiated the standardization of terms used to describe human morphology. The goals are to standardize these terms and reach consensus regarding their definitions. In this way, we will increase the utility of descriptions of the human phenotype and facilitate reliable comparisons of findings among patients. Discussions with other workers in dysmorphology and related fields, such as developmental biology and molecular genetics, will become more precise. Here we introduce the anatomy of the ear and define and illustrate the terms that describe the major characteristics of the ear.
A Simplicial CNN Visual Processor in 3D SOI-CMOS (2006)

This paper presents the architecture for a SIMD digital visual processor unit (VPU) that is based on the simplicial CNN (S-CNN) algorithm. The system is designed for three dimensional CMOS integration in the three tier MITLL 3D SOI-CMOS 0.18 mum technology. The architecture includes input/output sub-systems, in the third tier, arithmetic logic units (ALU) and register files on the third and second tiers and instruction cache memory and a timing state machine on the first tier. The partition of the architecture exploits its physical realization in three dimensional CMOS. Parallel optical data input through an array of photodetectors and analog interface circuits in the third tier facilitate testing and characterization
Studies on the anti-tumor efficacy of systemically administered recombinant tumor necrosis factor against several murine tumors in vivo. (1987)

The anti-tumor activity of recombinant human tumor necrosis factor (rHTNF) was examined against four newly induced murine sarcomas (MCA-101, -102, -105, and -106) and a murine adenocarcinoma (MCA-38) transplanted s.c. into C57BL/6 mice. The serum half-life after a single i.v. injection of rHTNF was determined to be 30 +/- 2 min. Tumor-bearing mice were more susceptible to the toxic side effects of rHTNF than were normal mice. Forty-eight percent (41/86) of tumor bearing animals that received 10 micrograms rHTNF died within 48 hr after treatment compared with no deaths in 28 normal animals receiving this dose. Treatment of mice bearing either the MCA-101, -102, -105, or -106 sarcoma or the MCA-38 adenocarcinoma with rHTNF resulted in a marked necrosis of the central portion of each tumor within 24 hr. Animals bearing the weakly immunogenic tumors MCA-105, -106, and -38 experienced a reduction in average tumor area of 47% +/- 5, 46% +/- 6, and 37% +/- 11, respectively, by 3 to 4 days after treatment with rHTNF compared with pre-treatment values (p less than 0.001); increases of 79% +/- 11, 74% +/- 10, and 41% +/- 6 were seen in excipient-treated control animals over the same period. In contrast, animals bearing the non-immunogenic tumors MCA-101 and -102 experienced little if any decrease in tumor area at the doses of rHTNF used. rHTNF failed to mediate cures in animals bearing MCA-38, -101, or -102. In contrast, 67 and 28% of animals bearing MCA-105 and -106, respectively, which received 6 to 10 micrograms rHTNF were cured. Likewise, animals bearing MCA-105 and -106 sarcomas treated with 6 to 10 micrograms rHTNF had significantly increased survival compared with excipient-treated control animals. In contrast, no significant difference in mean survival was observed between excipient and rHTNF treated animals bearing MCA-38, -101, or -102. Histologically, the necrotic response of immunogenic MCA-106 and non-immunogenic MCA-102 tumors to systemically administered rHTNF was very similar. These two tumors differed morphologically, however, by the greater degree of chronic inflammation that was present at the periphery of the MCA-106 tumor in comparison with the MCA-102. By 72 hr after rHTNF administration, the sites of regressed MCA-106 tumors were replaced by a heterogeneous population of inflammatory cells and tumor cell "ghosts".(ABSTRACT TRUNCATED AT 400 WORDS)
Refocusing neutralizing antibody response by targeted dampening of an immunodominant epitope (1997)

Immunodominant epitopes are known to suppress a primary immune response to other antigenic determinants by a number of mechanisms. Many pathogens have used this strategy to subvert the immune response and may be a mechanism responsible for limited vaccine efficacies. HIV-1 vaccine efficacy appears to be complicated similarly by a limited, immunodominant, isolate-restricted immune response generally directed toward determinants in the third variable domain (V3) of the major envelope glycoprotein, gp120. To overcome this problem, we have investigated an approach based on masking the V3 domain through addition of N-linked carbohydrate and reduction in net positive charge. N-linked modified gp120s were expressed by recombinant vaccinia virus and used to immunize guinea pigs by infection and protein boosting. This modification resulted in variable site-specific glycosylation and antigenic dampening, without loss of gp120/CD4 binding or virus neutralization. Most importantly, V3 epitope dampening shifted the dominant type-specific neutralizing Ab response away from V3 to an epitope in the first variable domain (V1) of gp120. Interestingly, in the presence of V3 dampening V1 changes from an immunodominant non-neutralizing epitope to a primary neutralizing epitope with broader neutralizing properties. In addition, Ab responses were also observed to conserved domains in C1 and C5. These results suggest that selective epitope dampening can lead to qualitative shifts in the immune response resulting in second order neutralizing responses that may prove useful in the fine manipulation of the immune response and in the development of more broadly protective vaccines and therapeutic strategies.
Nanotube Molecular Wires as Chemical Sensors (2000)

Chemical sensors based on individual single-walled carbon nanotubes (SWNTs) are demonstrated. Upon exposure to gaseous molecules such as NO(2) or NH(3), the electrical resistance of a semiconducting SWNT is found to dramatically increase or decrease. This serves as the basis for nanotube molecular sensors. The nanotube sensors exhibit a fast response and a substantially higher sensitivity than that of existing solid-state sensors at room temperature. Sensor reversibility is achieved by slow recovery under ambient conditions or by heating to high temperatures. The interactions between molecular species and SWNTs and the mechanisms of molecular sensing with nanotube molecular wires are investigated.
Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis (2000)

Eglin c from the leech Hirudo medicinalis is a potent protein inhibitor of many serine proteinases including chymotrypsin and subtilisins. Unlike most small protein inhibitors whose solvent-exposed enzyme-binding loop is stabilized primarily by disulfide bridges flanking the reactive-site peptide bond, eglin c possesses an enzyme-binding loop supported predominantly by extensive electrostatic/H-bonding interactions involving three Arg residues (Arg48, Arg51, and Arg53) projecting from the scaffold of the inhibitor. As an adjacent residue, the C-terminal Gly70 participates in these interactions via its alpha-carboxyl group interacting with the side chain of Arg51 and the main chain of Arg48. In addition, the amide NH group of Gly70 donates an H-bond to the carbonyl C=O groups of Arg48 and Arg51. To understand the structural and functional relevance of the electrostatic/H-bonding network, we chemically synthesized wild-type eglin c and three analogues in which Gly70 was either deleted or replaced by glycine amide (NH(2)CH(2)CONH(2)) or by alpha-hydroxylacetamide (HOCH(2)CONH(2)). NMR analysis indicated that the core structure of eglin c was maintained in the analogues, but that the binding loop was significantly perturbed. It was found that deletion or replacement of Gly70 destabilized eglin c by an average of 2.7 kcal/mol or 20 degrees C in melting temperature. As a result, these inhibitors become substrates for their target enzymes. Binding assays on these analogues with a catalytically incompetent subtilisin BPN' mutant indicated that loss or weakening of the interactions involving the carboxylate of Gly70 caused a decrease in binding by approximately 2 orders of magnitude. Notably, for all four synthetic inhibitors, the relative free energy changes (DeltaDeltaG) associated with protein destabilization are strongly correlated (slope = 0.94, r(2) = 0. 9996) with the DeltaDeltaG values derived from a decreased binding to the enzyme.
High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing (2011)

Despite the rapid proliferation of targeted therapeutic agents, systematic methods to profile clinically relevant tumor genomic alterations remain underdeveloped. We describe a sequencingbased approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.
Electrodeposition of electrochromic V2O5 thin films. (1985)

A uniform and adherent deposit of V2O5 thin film onto electroconductive glasses (ITO) has been obtained by electrolyzing colloidal V2O5 solution.A V2O5 sol was prepared from dilute solution of ammonium metavandate by passing the solution through an ion-exchange column (filled with Dowex 50 WX2 resin). The sol was then allowed to stand in a 40°C thermostat for 80 hrs. The viscosity of this sol increased with time, The measurement of the zeta potential of this sol indicated that the sol was negatively charged. Cathodic deposition of V2O5 is not a simple electrophoretic nature, since actually the V2O5 deposition occurred at the negative pole. We propose a following mechanism; the reduction of polyvanadic acid sol yielded a kind of vanadium bronze which coagulated onto the cathode (ITO) to form a solid film.On cathodic reduction the color of V2O5 film changes to green and on anodic oxidation it changes to light orange. The intermediate color tone has been also obtainable, therefore this system can be used as a multicolor device. The reversibility and durability for the electrochromic uses was almost comparable to a vacuum evaporated film.
Reducing the Number of Context Switches in Real Time Systems (2011)

In real time scheduling, preemption is one of the causes of run time overhead and large memory requirements. This paper focuses on reducing the number of preemptions in Earliest Deadline First (EDF) scheduling using a technique called Dynamic Preemption Threshold Scheduling (DPTS) in uniprocessor platform. This method is an improvement over existing threshold algorithms, but the complexity is slightly higher. The simulation results show that context switches are reduced by about 91% on an average. This technique is also applied for scheduling of sporadic requests along with periodic tasks. Preemptions that occur when tasks share resources and are required to synchronize are also reduced in this work. Our work also focuses on task set generation with limited hyperperiod (L.C.M. of periods of the tasks).
Mitochondrial proteome: Altered cytochrome c oxidase subunit levels in prostate cancer (2003)

Laser capture microdissection was combined with reverse phase protein lysate arrays to quantitatively analyze the ratios of mitochondrial encoded cytochrome c oxidase subunits to nuclear encoded cytochrome c oxidase subunits, and to correlate the ratios with malignant progression in human prostate tissue specimens. Cytochrome c oxidase subunits I-III comprise the catalytic core of the enzyme and are all synthesized from mitochondrial DNA. The remaining subunits (IV-VIII) are synthesized from cellular nuclear DNA. A significant (P < 0.001, 30/30 prostate cases) shift in the relative concentrations of nuclear encoded cytochrome c oxidase subunits IV, Vb, and VIc compared to mitochondrial encoded cytochrome c oxidase subunits I and II was noted during the progression of prostate cancer from normal epithelium through premalignant lesions to invasive carcinoma. Significantly, this shift was discovered to begin even in the premalignant stage. Reverse phase protein lysate array-based observations were corroborated with immunohistochemistry, and extended to a few human carcinomas in addition to prostate. This analysis points to a role for nuclear DNA encoded mitochondrial proteins in carcinogenesis; underscoring their potential as targets for therapy while highlighting the need for full characterization of the mitochondrial proteome.
Antiangiogenic Agents: an Update on Small Molecule VEGFR Inhibitors (2007)

Angiogenesis is a tightly regulated process that leads to the formation of new blood vessels sprouting from pre-existing microvasculature and occurs in limited physiological conditions or under pathological situations such as retinopathies, arthritis, endometriosis and cancer. Blockade of angiogenesis is an attractive approach for the treatment of such diseases. Particularly in malignancies, antiangiogenic therapy should be less toxic in comparison with conventional treatments such as chemotherapy, as angiogenesis is a process relatively restricted to the growing tumor. Vascular endothelial growth factor (VEGF) is one of the most important inducers of angiogenesis and exerts its cellular effects mainly by interacting with two high-affinity transmembrane tyrosine kinase receptors: VEGFR-1 (Flt-1) and VEGFR-2 (KDR/Flk-1). It has been proven that inhibition of VEGF receptor activity reduces angiogenesis. For these reasons, the inhibition of VEGF or its receptor signalling system is an attractive target for therapeutic intervention. The most studied and developed inhibitors are monoclonal antibodies that neutralize VEGF, ribozymes, and small molecule VEGFR kinase inhibitors. Many important reviews dealing with VEGF-induced angiogenesis and its inhibition through the block of VEGF receptors have been reported, especially from a biological point of view. Here, we will review small synthetic VEGFR inhibitors that have appeared in literature in the last few years, focusing our attention on their medicinal chemistry in terms of chemical structure, mechanisms of action and structure-activity relationships. In fact, there have been an increased number of tyrosine kinase inhibitors in the most recent literature reports; their biological profile is extremely interesting and could be of great importance to medicinal chemists working in this area in improving their efficacy.
Three-dimensional multimodal brain warping using the Demons algorithm and adaptive intensity corrections (2001)

This paper presents an original method for three-dimensional elastic registration of multimodal images. The authors propose to make use of a scheme that iterates between correcting for intensity differences between images and performing standard monomodal registration. The core of the authors' contribution resides in providing a method that finds the transformation that maps the intensities of one image to those of another. It makes the assumption that there are at most two functional dependencies between the intensities of structures present in the images to register, and relies on robust estimation techniques to evaluate these functions. The authors provide results showing successful registration between several imaging modalities involving segmentations, T1 magnetic resonance (MR), T2 MR, proton density (PD) MR and computed tomography (CT). The authors also argue that their intensity modeling may be more appropriate than mutual information (MI) in the context of evaluating high-dimensional deformations, as it puts more constraints on the parameters to be estimated and, thus, permits a better search of the parameter space.