gebhart/patrepeval huggingface dataset:
Trekking along the Cytoskeleton (2001)

For centuries, amateur botanists with access to microscopes, and latterly plant scientists, have marveled at the dynamic nature of the cytoplasm that is apparent in many diverse cell types. Many teachers have relied, and still do, on the dramatic cytoplasmic streaming displayed by the internodal
Stereochemical Control of Hairpin Formation in β-Peptides Containing Dinipecotic Acid Reverse Turn Segments (2000)

We examine the relationship between covalent structure and conformational propensity among a series of β-amino acid tetramers. These experiments focus on the hairpin folding motif. Among conventional peptides, the minimum increment of β-sheet secondary structure is a “β-hairpin,” in which two strands are connected via a short loop. The present studies are aimed at optimizing hairpin stability among β-peptides. Previous work from our laboratory has identified optimal substitution patterns for residues that form strands in an antiparallel β-peptide sheet (Krauthäuser et al. J. Am. Chem. Soc. 1997, 119, 11719), and we have shown that a dinipecotic acid segment can promote sheet-type interactions between attached strand residues (Chung et al. J. Am. Chem. Soc. 1998, 120, 10555). Here we compare all four possible configurations of the dinipecotic acid segment, (R,S), (S,R), (R,R) and (S,S), for the ability to induce sheet formation with a constant set of enantiomerically pure strand residues. We show that both heterochiral dinipecotic acid segments promote hairpin formation, although one is distinctly superior. Neither of the homochiral dinipecotic acid supports hairpin folding. When the strand residues are β-alanine (achiral), the heterochiral dinipecotic acid segment is again superior to the homochiral segment, but we find a difference between hairpin conformations in solution and in the solid state.
Pathological TDP‐43 distinguishes sporadic amyotrophic lateral sclerosis from amyotrophic lateral sclerosis with SOD1 mutations (2007)

These findings implicate pathological TDP-43 in the pathogenesis of sporadic ALS. In contrast, the absence of pathological TDP-43 in cases with SOD1 mutations implies that motor neuron degeneration in these cases may result from a different mechanism, and that cases with SOD1 mutations may not be the familial counterpart of sporadic ALS.
Adeno-Associated Virus as a Vector for Liver-Directed Gene Therapy (1998)

Factors relevant to the successful application of adeno-associated virus (AAV) vectors for liver-directed gene therapy were evaluated. Vectors with different promoters driving expression of human alpha-1-antitrypsin (alpha-1AT) were injected into the portal circulation of immunodeficient mice. alpha-1AT expression was stable but dependent on the promoter. Southern analysis of liver DNA revealed approximately 0.1 to 2.0 provirus copies/diploid genome in presumed head-to-tail concatamers. In situ hybridization and immunohistochemical analysis revealed expression in approximately 5% of hepatocytes clustered in the pericentral region. These results support the use of AAV as a vector for diseases treatable by targeting of hepatocytes.
High-temperature stability and selective thermal emission of polycrystalline tantalum photonic crystals (2013)

We present the results of extensive characterization of selective emitters at high temperatures, including thermal emission measurements and thermal stability testing at 1000 °C for 1h and 900 °C for up to 144 h. The selective emitters were fabricated as 2D photonic crystals (PhCs) on polycrystalline tantalum (Ta), targeting large-area applications in solid-state heat-to-electricity conversion. We characterized spectral emission as a function of temperature, observing very good selectivity of the emission as compared to flat Ta, with the emission of the PhC approaching the blackbody limit below the target cut-off wavelength of 2 μm, and a steep cut-off to low emission at longer wavelengths. In addition, we study the use of a thin, conformal layer (20 nm) of HfO(2) deposited by atomic layer deposition (ALD) as a surface protective coating, and confirm experimentally that it acts as a diffusion inhibitor and thermal barrier coating, and prevents the formation of Ta carbide on the surface. Furthermore, we tested the thermal stability of the nanostructured emitters and their optical properties before and after annealing, observing no degradation even after 144 h (6 days) at 900 °C, which demonstrates the suitability of these selective emitters for high-temperature applications.
A resistive TCAM accelerator for data-intensive computing (2011)

Power dissipation and off-chip bandwidth restrictions are critical challenges that limit microprocessor performance. Ternary content addressable memories (TCAM) hold the potential to address both problems in the context of a wide range of data-intensive workloads that benefit from associative search capability. Power dissipation is reduced by eliminating instruction processing and data movement overheads present in a purely RAM based system. Bandwidth demand is lowered by processing data directly on the TCAM chip, thereby decreasing off-chip traffic. Unfortunately, CMOS-based TCAM implementations are severely power- and area-limited, which restricts the capacity of commercial products to a few megabytes, and confines their use to niche networking applications.
Anatomic Analysis of Pedicle Cortical and Cancellous Diameter as Related to Screw Size (1989)

The effective thoracic and lumbar pedicle diameter as related to screw size for that pedicle was studied in six fresh-frozen human cadaver spines. Measurements of the pedicle were obtained before screw insertion using axial and coronal reformatted computed tomographic (CT) images, as well as graduated sounding of the pedicle. After sequentially loading each pedicle with increasingly larger screws, measurements were taken of the outer cortical diameters. Plastic deformation of the pedicle preceded pedicle fracture or cutout when the screw thread diameter became larger than the endosteal diameter or within 80% of the outer cortical diameter as measured from the CT scan. Pedicle screws did not obtain cortical purchase within the pedicle.
High-Resolution X-ray Photoelectron Spectra of Organosulfur Monolayers on Au(111):  S(2p) Spectral Dependence on Molecular Species (1999)

We have used high-resolution X-ray photoelectron spectroscopy (XPS) to investigate the molecular dependence on sulfur chemical states of organosulfur monolayers of alkanethiol, dialkyl disulfide, monosulfide, thiophene, and aromatic thiols on a Au(111) surface. When monosulfides or thiophenes adsorbed on the Au surface, the S(2p) peaks appeared between 161 and 164 eV, and peak fitting revealed that these organosulfurs exhibited almost the same peaks as those of alkanethiol and dialklyl disulfide monolayers. The monolayer made from monosulfide with shorter alkyl chains exhibited almost the same S(2p) XPS spectrum as the typical alkanethiol or dialkyl disulfide monolayers. Another S(2p3/2) peak appeared for aromatic derivatized thiol SAMs at around 161 eV, in addition to strong doublet S(2p) peak observed at 162.0 and 163.3 eV in the S(2p) spectra. The 161 eV peak was observed even in the S(2p) XPS spectra of alkanethiol or dialkyl disulfide monolayers, at the initial stage of monolayer growth or after low-temperature (∼ 100 °C) annealing of low molecular density alkanethiol SAMs. We consider that this 161 eV peak can be formed without molecular decomposition as well as due to the atomic sulfur produced by C−S cleavage.
Connecting Binuclear Pd(III) and Mononuclear Pd(IV) Chemistry by Pd–Pd Bond Cleavage (2012)

Oxidation of binuclear Pd(II) complexes with PhICl(2) or PhI(OAc)(2) has previously been shown to afford binuclear Pd(III) complexes featuring a Pd-Pd bond. In contrast, oxidation of binuclear Pd(II) complexes with electrophilic trifluoromethylating ("CF(3)(+)") reagents has been reported to afford mononuclear Pd(IV) complexes. Herein, we report experimental and computational studies of the oxidation of a binuclear Pd(II) complex with "CF(3)(+)" reagents. These studies suggest that a mononuclear Pd(IV) complex is generated by an oxidation-fragmentation sequence proceeding via fragmentation of an initially formed, formally binuclear Pd(III), intermediate. The observation that binuclear Pd(III) and mononuclear Pd(IV) complexes are accessible in the same reactions offers an opportunity for understanding the role of nuclearity in both oxidation and subsequent C-X bond-forming reactions.
Nontransgenic models of breast cancer (2000)

Numerous models have been developed to address key elements in the biology of breast cancer development and progression. No model is ideal, but the most useful are those that reflect the natural history and histopathology of human disease, and allow for basic investigations into underlying cellular and molecular mechanisms. We describe two types of models: those that are directed toward early events in breast cancer development (hyperplastic alveolar nodules [HAN] murine model, MCF10AT human xenograft model); and those that seek to reflect the spectrum of metastatic disease (murine sister cell lines 67, 168, 4T07, 4T1). Collectively, these models provide cell lines that represent all of the sequential stages of progression in breast disease, which can be modified to test the effect of genetic changes.
Predictive Molecular Pathology (2002)

The search for markers that can predict the outcome in an individual patient with cancer or the response of an individual tumor to specific therapies is a major focus of cancer research. Despite these efforts, estrogen and progesterone receptors and the HER2/neu gene are the only molecular targets that are analyzed routinely in newly diagnosed breast cancers. Thousands of studies of putative prognostic or predictive markers have failed to identify useful molecular markers in tumors, either because the selected genes were noninformative or because initially promising data could not be reproduced in other laboratories.The search for prognostic and predictive . . .
Synthesis and Characterization of Poly(isobutylene-b-pivalolactone) Diblock and Poly(pivalolactone-b-isobutylene-b-pivalolactone) Triblock Copolymers (2002)

The synthesis of poly(isobutylene-b-pivalolactone) block copolymers comprised of amorphous rubbery/crystalline block segments was accomplished by site transformation from living cationic polymerization of isobutylene (IB) to anionic ring-opening polymerization (AROP) of pivalolactone (PVL). First, polyisobutylene (PIB) with ω-carboxylate potassium salt was prepared by capping living PIB with 1,1-diphenylethylene followed by quenching with 1-methoxy-1-trimethylsiloxypropene and hydrolysis of ω-methoxycarbonyl end groups. The resulting PIB ω-carboxylate potassium salt was successfully used as a macroinitiator for the AROP of PVL in conjunction with 18-crown-6 in tetrahydrofuran, giving poly(IB-b-PVL) copolymers. Furthermore, the same methodology was applied toward poly(PVL-b-IB-b-PVL) copolymers using PIB α,ω-carboxylate potassium salt as a difunctional macroinitiator. Characterization of the block copolymers by high-temperature GPC, 1H and 13C NMR spectroscopies, DSC, AFM, and polarized optical microscopy confirmed that the block copolymers were comprised of microphase-separated low glass transition amorphous rubbery PIB and high melting crystalline PPVL block segments with predetermined composition and high structural integrity. Comparison of DSC results with morphological studies using AFM and POM indicated that crystallization of PPVL was constrained to the cylindrical and spherical microdomains preexisting in the melt for certain di- and triblock samples.
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics (2018)

Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and "super-load" commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.
Fast fabrication of integrated surface-relief and particle-diffusing plastic diffuser by use of a hybrid extrusion roller embossing process (2008)

Most plastic diffusers are either of surface-relief or particle-diffusing types, based on different principles and fabrication methods. This paper reports an innovative extrusion roller embossing process, which enables the fabrication of diffusers with both surface-relief and particle-diffusing functions. An extruder with die is employed to fabricate the thin film of PC/bead composite; the roller micro-embossing process is used to replicate the microstructure onto the surface of PC composite film. A metallic roller mold with microstructures is fabricated using turning process. During the extrusion rolling embossing process, the extruded film of PC with diffusion beads is immediately pressed against the surface of the roller mold. Under the proper processing parameters, the plastic diffusers integrating surface-relief and particle-diffusing functions have been successfully fabricated. The shape, uniformity, and optical properties of fabricated diffuser have been verified. This method shows the great potential for continuous fabrication of high-performance plastic diffusers integrating surface-relief and particle-diffusing functions with high throughput.
The effect of knee brace on coordination and neuronal leg muscle control: an early postoperative functional study in anterior cruciate ligament reconstructed patients (2001)

Two studies were carried out after anterior cruciate ligament (ACL) reconstruction to determine the effect of a knee brace on coordination (test 1) and electromyographic muscle activity in drop jumps (test 2). Test 1 studied 25 patients with ACL reconstruction under three test conditions (one-leg static, two-legged static, two-legged dynamic) compared with a control (n=30). The results showed highly significant improvements in all braced conditions. In test 2 ten patients with ACL reconstruction and ten healthy subjects performed a two-legged drop-jump; this was repeated 15 times and again 15 times with a knee brace worn on the reconstructed limb. Changes in electromyographically determined muscle activity (vastus medialis, vastus lateralis, biceps femoris, gastrocnemius) were observed, but they were significant in only few cases because of high variability. Drop-jumps with knee brace improved jumping height, increased the maximum knee angle in the ground contact phase, and reduced the maximum knee angle in the landing phase. Patients thus develop an increased confidence in the stability of their knees. We conclude that the benefits of the knee brace are due to the mechanical action, an enhanced coordination, and a psychological effect.
Broad cellular immunity with robust memory responses to simian immunodeficiency virus following serial vaccination with adenovirus 5- and 35-based vectors (2005)

Adenovirus serotype 35 (Ad35) is a promising vaccine platform for human immunodeficiency virus (HIV) infection and emerging infectious diseases as it is uncommon in humans worldwide and is distinct from Ad5, the major vaccine serotype for which many individuals have pre-existing immunity. The immunogenicity of a first-generation, replication-competent Ad35-based vaccine was tested in the simian immunodeficiency virus (SIV) rhesus macaque model by evaluating its capacity to boost immunity generated by Ad5-based vectors. A series of four immunizations with replication-defective Ad5 vectors expressing SIVmac239 gag induced high-frequency responses mediated by both CD8(+) and CD4(+) T cells directed against several epitopes. Ad5-specific neutralizing antibody responses that did not neutralize Ad35 were rapidly induced but waned over time. Subsequent immunization with Ad5-based vectors was minimally effective, whereas immunization with Ad35-based vectors generated a strong increase in the frequency of Gag-specific T cells with specificities that were unchanged. While this boosting response was relatively transient, challenge with the distinct pathogenic isolate SIV/DeltaB670 generated robust and selective recall responses to Gag with similar specificities as induced by vaccination that were elevated for 25 weeks relative to controls. Vaccination had measurable albeit minor effects on virus load. Unexpectedly, regional hypervariability within the Gag sequence of SIV/DeltaB670 was associated with mutation of the conserved CD8(+) T-cell epitope CM9 without concurrent flanking mutations and in the absence of immune pressure. These findings support the further development of Ad35 as a vaccine vector, and promote vaccine regimens that utilize serial administration of heterologous adenoviruses.
Fatty Acid Synthase Expression Is Induced by the Epstein-Barr Virus Immediate-Early Protein BRLF1 and Is Required for Lytic Viral Gene Expression (2004)

The Epstein-Barr virus (EBV) immediate-early (IE) protein BRLF1 (R) is a transcription factor that induces the lytic form of EBV infection. R activates certain early viral promoters through a direct binding mechanism but induces transcription of the other EBV IE gene, BZLF1 (Z), indirectly through cellular factors binding to a CRE motif in the Z promoter (Zp). Here we demonstrate that R activates expression of the fatty acid synthase (FAS) cellular gene through a p38 stress mitogen-activated protein kinase-dependent mechanism. B-cell receptor engagement of Akata cells also increases FAS expression. The FAS gene product is required for de novo synthesis of the palmitate fatty acid, and high-level FAS expression is normally limited to liver, brain, lung, and adipose tissue. We show that human epithelial tongue cells lytically infected with EBV (from oral hairy leukoplakia lesions) express much more FAS than uninfected cells. Two specific FAS inhibitors, cerulenin and C75, prevent R activation of IE (Z) and early (BMRF1) lytic EBV proteins in Jijoye cells. In addition, cerulenin and C75 dramatically attenuate IE and early lytic gene expression after B-cell receptor engagement in Akata cells and constitutive lytic viral gene expression in EBV-positive AGS cells. However, FAS inhibitors do not reduce lytic viral gene expression induced by a vector in which the Z gene product is driven by a strong heterologous promoter. In addition, FAS inhibitors do not reduce R activation of a naked DNA reporter gene construct driven by the Z promoter (Zp). These results suggest that cellular FAS activity is important for induction of Z transcription from the intact latent EBV genome, perhaps reflecting the involvement of lipid-derived signaling pathways or palmitoylated proteins. Furthermore, using FAS inhibitors may be a completely novel approach for blocking the lytic form of EBV replication.
ILLICIT DRUG USE AND THE RISK OF NEW-ONSET SEIZURES (1990)

The authors studied the use of heroin, marijuana, and cocaine before the onset of a first seizure in 308 patients with seizures and 294 controls at Harlem Hospital Center, New York City, between 1981 and 1984. Heroin use, both past and present, appeared to be a risk factor for all first seizures (adjusted odds ratio = 2.80, 95% confidence interval (CI) 1.53-5.74). For unprovoked seizures, the adjusted odds ratio was 2.58 (95% CI 1.36-4.90) for ever heroin use and 4.70 (95% CI 0.86-25.78) for heroin use within 24 hours of hospitalization. For provoked seizures, respective adjusted odds ratios were 3.65 (95% CI 1.54-8.65) and 27.74 (95% CI 3.57-215.52). Marijuana use appeared to be a protective factor against first seizures in men. For men with unprovoked seizures, the adjusted odds ratio was 0.42 (95% CI 0.22-0.82) for ever marijuana use and 0.36 (95% CI 0.18-0.74) for marijuana use within 90 days of hospitalization. For men with provoked seizures, respective adjusted odds ratios were 1.03 (95% CI 0.36-2.89) and 0.18 (95% CI 0.04-0.84). Cocaine use, while common among study subjects, was not shown to be a significant risk factor either for all first seizures or for subgroups of seizures, regardless of the time of last use. The authors conclude that heroin use is a risk factor and marijuana use a protective factor for new-onset seizures.
Single intraluminal delivery of antisense cdc2 kinase and proliferating-cell nuclear antigen oligonucleotides results in chronic inhibition of neointimal hyperplasia. (1993)

To develop an effective strategy to prevent neointima formation after angioplasty injury, we have identified cell-cycle regulatory proteins as targets for inhibition by using antisense oligonucleotides (ODNs). We utilized an intraluminal molecular delivery method that employs the protein coat of a Sendai virus complexed with liposomes that enhances markedly the efficiency of ODNs uptake. First, we examined the effect of antisense cdc2 kinase and proliferating-cell nuclear antigen (PCNA) ODNs in vitro. Cotransfection of antisense cdc2 kinase and PCNA ODNs inhibited serum-stimulated vascular smooth muscle cell growth, whereas antisense cdc2 kinase ODNs alone or PCNA ODNs alone failed to show any inhibitory effect. Transfection of the combination of antisense cdc2 kinase and PCNA ODNs into balloon-injured arteries in vivo provided a marked decrease in cdc2 and PCNA mRNA expression as determined by reverse transcription-PCR, compared to sense controls. Antisense ODN treatment significantly inhibited the increase in DNA synthesis induced by balloon injury. Moreover, antisense ODN administration inhibited completely neointima formation at 2 weeks after angioplasty in an apparent dose-dependent manner. Moreover, the inhibitory effect of antisense ODN on neointima formation persisted up to 8 weeks after a single transfection. The present study documents that a single intraluminal molecular delivery of combined cdc2 kinase and PCNA antisense ODNs results in a sustained inhibition of neointima formation in the rat carotid balloon-injury model.
Oxidative damage pathways in relation to normal tissue injury (2007)

Given the increasing population of long-term cancer survivors, the need to mitigate or treat late effects has emerged as a primary area of radiation biology research. Once thought to be irreversible, radiation-induced late effects are now viewed as dynamic multicellular interactions between multiple cell types within a particular program that can be modulated. The molecular, cellular and biochemical pathways responsible for radiation-induced late morbidity remain ill-defined. This review provides data in support of the hypothesis that these late effects are driven, in part, by a chronic oxidative stress. Irradiating late responding normal tissues leads to chronic increases in reactive oxygen/reactive nitrogen oxide species that serve as intracellular signaling species to alter cell function/phenotype, resulting in chronic inflammation, organ dysfunction, and ultimate fibrosis and/or necrosis. Furthermore, we hypothesize that the effectiveness of renin-angiotensin system blockers in preventing or mitigating the severity of radiation-induced late effects reflects, in part, inhibition of reactive oxygen species generation and the resultant chronic oxidative stress. These findings provide a robust rationale for anti-inflammatory-based interventional therapies in the treatment of late normal tissue injury.