gebhart/patrepeval huggingface dataset:
Synthesis of POSS‐Functionalized Polyisobutylene via Direct Initiation (2009)

POSS-functionalized polyisobutylenes (PIBs) were synthesized by carbocationic polymerization using an epoxy-POSS/TiCl(4) initiating system in hexane/methyl chloride (60:40 v/v) solvent mixture at -80 °C. (1) H NMR spectroscopy verified the incorporation of one epoxy-POSS per polymer chain. Light scattering and TEM analysis demonstrated the formation of 50-100 nm sized aggregates and micron-sized clusters.
Expression Profile of FcγRIIb on Leukocytes and Its Dysregulation in Systemic Lupus Erythematosus (2007)

FcgammaRIIb (CD32B, Online Mendelian Inheritance in Man 604590), an IgG FcR with a tyrosine-based inhibitory motif, plays a critical role in the balance of tolerance and autoimmunity in murine models. However, the high degree of homology between FcgammaRIIb and FcgammaRIIa in humans and the lack of specific Abs to differentiate them have hampered study of the normal expression profile of FcgammaRIIb and its potential dysregulation in autoimmune diseases such as systemic lupus erythematosus (SLE). Using our newly developed anti-FcgammaRIIb mAb 4F5 which does not react with FcgammaRIIa, we found that FcgammaRIIb is expressed on the cell surface of circulating B lymphocytes, monocytes, neutrophils, myeloid dendritic cells (DCs), and at very low levels on plasmacytoid DCs from some donors. Normal donors with the less frequent 2B.4 promoter haplotype have higher FcgammaRIIb expression on monocytes, neutrophils, and myeloid DCs similar to that reported for B lymphocytes, indicating that FcgammaRIIb expression on both myeloid and lymphoid cells is regulated by the naturally occurring regulatory single nucleotide polymorphisms in the FCGR2B promoter. FcgammaRIIb expression in normal controls is up-regulated on memory B lymphocytes compared with naive B lymphocytes. In contrast, in active SLE, FcgammaRIIb is significantly down-regulated on both memory and plasma B lymphocytes compared with naive and memory/plasma B lymphocytes from normals. Similar down-regulation of FcgammaRIIb on myeloid-lineage cells in SLE was not seen. Our studies demonstrate the constitutive regulation of FcgammaRIIb by natural gene polymorphisms and the acquired dysregulation in SLE autoimmunity, which may identify opportunities for using this receptor as a therapeutic target.
Indexing and entropy coding of lattice codevectors (2002)

We present two methods of entropy coding for the lattice codevectors. We compare our entropy coding methods with one method previously presented in the literature from the point of view of rate-distortion as well as of the computation complexity and memory requirements. The results are presented for artificial Laplacian and Gaussian data, as well as for LSF parameters of speech signals. In the latter case, the multiple scale lattice VQ (MSLVQ) is used for quantization, which reduces the rate gain of the entropy coding method when compared with the fixed rate case, but allows a dynamic allocation of the bits in the whole speech coding scheme.
Radiological progression in established rheumatoid arthritis. (2004)

Radiographic progression in established rheumatoid arthritis (RA) gives an objective measure of anatomical damage that defines the course of the disease and the longterm effects of treatment. This review defines the rate of joint damage, progression in individual joints, and predictive factors. Six longitudinal prospective studies of 103-378 RA patients followed for up to 20 years show that initially patients had less than 3% maximum possible damage, this rose to 11% maximal damage by 5 years and over 40% by 20 years. The rate of progression changed from an initial rate of 1.6% maximal progression annually to a later rate of 2.0% annually. Between 1977 and 1998 5 prospective studies of 40-147 hospital-based RA cases seen within 12 months of developing RA showed 60-73% of cases developed one or more erosions in the hands and wrists. However a community-based cohort of early RA patients reported, more recently showed 41% of 335 cases developed erosions. There are marked differences between joints. The wrists show most damage and in one series of 103 cases, by 20 years 18% of wrists were completely destroyed and only 25% were nonerosive. The same series showed ankle joints are rarely involved; at 20 years only 7 patients had major abnormalities with minor changes in 17 cases. Rheumatoid factor (RF) positivity is the dominant predictor of erosive damage. In one survey of 439 cases who presented with inflammatory polyarthritis, patients with an initial high RF had over twice the radiographic progression of seronegative cases. A further 8 studies, which enrolled 1395 patients, all show a strong link between radiolographic damage and RF status. The other key clinical predictor is disease activity indicated by surrogate measures such as the C-reactive protein (CRP) level. Suppressing disease activity judged by CRP levels not only decreases the progression of joint damage, but also may reduce new joint involvement to a greater extent than progression in already damaged joints. New potential markers of damage such as anticyclic citrullinated peptide ELISA tests may further improve the identification of those RA patients most at risk of erosive damage and, by implication, most in need of suppressive therapy.
Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos (2019)

Genome editing holds promise for correcting pathogenic mutations. However, it is difficult to determine off-target effects of editing due to single-nucleotide polymorphism in individuals. Here we developed a method named GOTI (genome-wide off-target analysis by two-cell embryo injection) to detect off-target mutations by editing one blastomere of two-cell mouse embryos using either CRISPR-Cas9 or base editors. Comparison of the whole-genome sequences of progeny cells of edited and nonedited blastomeres at embryonic day 14.5 showed that off-target single-nucleotide variants (SNVs) were rare in embryos edited by CRISPR-Cas9 or adenine base editor, with a frequency close to the spontaneous mutation rate. By contrast, cytosine base editing induced SNVs at more than 20-fold higher frequencies, requiring a solution to address its fidelity.
A prognostic model of survival in surgically resected squamous cell carcinoma of the lung using clinical, pathologic, and biologic markers. (1997)

The biologic behavior of tumoral cells plays a significant role in the progression of the neoplasia, because 30 to 35% of patients with Stage I squamous cell carcinoma relapse. The present study was designed to determine whether age, pathologic parameters, DNA ploidy, and a cell proliferation index (the area of nucleolar organizer regions, AgNOR), could be used to predict survival in patients who undergo resection for limited squamous cell carcinoma of the lung. For histopathologic analysis, the parameters of histologic grading, pleural involvement, vascular invasion, and residual disease were considered. The cell proliferation index was evaluated by mitotic index, AgNOR quantification, and DNA ploidy by means of digital image analysis. Fifty-two patients (median age, 60 yr +/- 8.6 yr) were staged according to the TNM staging system. Cox univariate analysis showed that stage, residual disease, vascular invasion, histologic grading, DNA ploidy, and AgNOR were significant predictors of survival. Many of the univariate predictors of cancer death, however were eliminated when Cox multivariate models were computed. The variable that exhibited the most robust predictive value for overall survival was AgNOR. We conclude that measurement of cell proliferation might serve as a prognostic marker in squamous cell carcinoma of the lung.
Quantum-state engineering with Josephson-junction devices (2001)

Quantum-state engineering, i.e., active control over the coherent dynamics of suitable quantum-mechanical systems, has become a fascinating prospect of modern physics. With concepts developed in atomic and molecular physics and in the context of NMR, the field has been stimulated further by the perspectives of quantum computation and communication. Low-capacitance Josephson tunneling junctions offer a promising way to realize quantum bits (qubits) for quantum information processing. The article reviews the properties of these devices and the practical and fundamental obstacles to their use. Two kinds of device have been proposed, based on either charge or phase (flux) degrees of freedom. Single- and two-qubit quantum manipulations can be controlled by gate voltages in one case and by magnetic fields in the other case. Both kinds of device can be fabricated with present technology. In flux qubit devices, an important milestone, the observation of superpositions of different flux states in the system eigenstates, has been achieved. The Josephson charge qubit has even demonstrated coherent superpositions of states readable in the time domain. There are two major problems that must be solved before these devices can be used for quantum information processing. One must have a long phase coherence time, which requires that external sources of dephasing be minimized. The review discusses relevant parameters and provides estimates of the decoherence time. Another problem is in the readout of the final state of the system. This issue is illustrated with a possible realization by a single-electron transistor capacitively coupled to the Josephson device, but general properties of measuring devices are also discussed. Finally, the review describes how the basic physical manipulations on an ideal device can be combined to perform useful operations.
Priming with DNA encoding E2 and boosting with E2 protein formulated with CpG oligodeoxynucleotides induces strong immune responses and protection from Bovine viral diarrhea virus in cattle (2006)

The objective of this study was to develop an optimal vaccination strategy for Bovine viral diarrhea virus (BVDV). The E2 protein of BVDV plays a major protective role against BVDV infection. In order to be able to compare DNA, protein and DNA prime-protein boost regimens, a plasmid was constructed encoding a secreted form of the NADL strain E2 protein (pMASIA-tPAsDeltaE2). Furthermore, a pure secreted recombinant DeltaE2 (rDeltaE2) protein was produced. The rDeltaE2 protein was formulated with a combination of Emulsigen and CpG oligodeoxynucleotide. Groups of calves were immunized with pMASIA-tPAsDeltaE2 or with rDeltaE2, or first with pMASIA-tPAsDeltaE2 and then with rDeltaE2. To evaluate the protection against BVDV, calves were challenged with BVDV strain NY-1 after the last immunization. Although all immunized calves developed humoral and cellular immune responses, the antibody responses in the DNA prime-protein boost group were stronger than those elicited by either the DNA vaccine or the protein vaccine. In particular, E2-specific antibody titres were enhanced significantly after boosting the DeltaE2 DNA-primed calves with rDeltaE2 protein. Moreover, protection against BVDV challenge was obtained in the calves treated with the DNA prime-protein boost vaccination regimen, as shown by a significant reduction in weight loss, viral excretion and lymphopenia, compared with the unvaccinated calves and the animals immunized with the DNA or protein only. These results demonstrate the advantage of a DNA prime-protein boost vaccination approach in an outbred species.
ChemInform Abstract: DEHYDRATION OF 2‐(TRIFLUOROMETHYL)‐3,3,3‐TRIFLUOROPROPANOL WITH BASE (1984)

Abstract Ausgehend vom Ether (I) wird über (II) der Alkohol (III) synthetisiert, der unerwarteterweise mit festem KOH oder NaOH zum 2‐Trifluormethyl‐3,3,3‐trifluorpropen (IV) dehydratisiert werden kann.
Interferon-gamma (IFN-γ) down-regulates the rhinovirus-induced expression of intercellular adhesion molecule-1 (ICAM-1) on human airway epithelial cells (1997)

Human rhinoviruses (HRV) are a major cause of upper respiratory tract infections in man, and can exacerbate existing pulmonary disease. The major group of HRV attach to ICAM-1, which is expressed on nasal and bronchial epithelial cells. To study the influence of biological mediators on ICAM-1 expression, and consequently HRV attachment and infection, we compared the effects of various cytokines, alone and in combination, on ICAM-1 expression by an uninfected and HRV-infected bronchial epithelial cell line H292. Cytokines known to be released soon after viral infection, such as tumour necrosis factor-alpha (TNF-alpha), IL-1beta and the chemokine IL-8 increase ICAM-1 expression on uninfected cells. Epithelial cells infected with live HRV-14 displayed marked up-regulation of ICAM-1 compared with baseline. TNF-alpha further enhanced the HRV-induced increase in ICAM-1 expression on epithelial cells, peaking at day 4 after infection, whilst IL-8 exhibited a steady increase in ICAM-1 expression over 14 days. In contrast, IFN-gamma, a known Th1 antiviral lymphokine, whilst increasing the level of ICAM-1 on uninfected cells, induced a significant persistent down-regulation of ICAM-1 expression on HRV-infected epithelial cells. With combinations of TNF-alpha and IFN-gamma, ICAM-1 expression on HRV-infected cells was reduced to basal levels. The effects of IFN-gamma were paralleled by a reduction in viral titres. Our in vitro model has provided useful insights into the early pathogenic events of HRV infection at the level of the host cell-virus interaction. Our data confirm that biological mediators play a crucial role in the pathogenesis as well as the course of HRV infection which is modulated by the types, and time kinetics of inflammatory cytokines in the immediate microenvironment.
Hydrogen Sulfide in Physiology and Diseases of the Digestive Tract (2015)

Hydrogen sulfide (H₂S) is a Janus-faced molecule. On one hand, several toxic functions have been attributed to H₂S and exposure to high levels of this gas is extremely hazardous to health. On the other hand, H₂S delivery based clinical therapies are being developed to combat inflammation, visceral pain, oxidative stress related tissue injury, thrombosis and cancer. Since its discovery, H₂S has been found to have pleiotropic effects on physiology and health. H₂S is a gasotransmitter that exerts its effect on different systems, such as gastrointestinal, neuronal, cardiovascular, respiratory, renal, and hepatic systems. In the gastrointestinal tract, in addition to H₂S production by mammalian cystathionine-β-synthase (CBS), cystathionine-γ-lyase (CSE), H₂S is also generated by the metabolic activity of resident gut microbes, mainly by colonic Sulfate-Reducing Bacteria (SRB) via a dissimilatory sulfate reduction (DSR) pathway. In the gut, H₂S regulates functions such as inflammation, ischemia/ reperfusion injury and motility. H₂S derived from gut microbes has been found to be associated with gastrointestinal disorders such as ulcerative colitis, Crohn's disease and irritable bowel syndrome. This underscores the importance of gut microbes and their production of H₂S on host physiology and pathophysiology.
Iniparib Nonselectively Modifies Cysteine-Containing Proteins in Tumor Cells and Is Not a Bona Fide PARP Inhibitor (2011)

Iniparib nonselectively modifies cysteine-containing proteins in tumor cells, and the primary mechanism of action for iniparib is likely not via inhibition of PARP activity.
The expression of cytoskeleton regulatory protein Mena in colorectal lesions. (2008)

The actin regulatory proteins Ena/VASP (Enabled/Vasodilator stimulated phosphoprotein) family is involved in the control of cell motility and adhesion. They are important in the actin-dependent processes where dynamic actin reorganization it is necessary. The deregulation of actin cycle could have an important role in the cells' malignant transformation, tumor invasion or metastasis. Recently studies revealed that the human orthologue of murine Mena is modulated during the breast carcinogenesis. In our study, we tried to observe the immunohistochemical expression of mammalian Ena (Mena) in the colorectal polyps and carcinomas. We analyzed 10 adenomatous polyps (five with dysplasia) and 36 adenocarcinomas. We used the indirect immunoperoxidase staining. BD Biosciences have provided the Mena antibody. We observed that Mena was not expressed in the normal colorectal mucosa neither in polyps without dysplasia, but its expression was very high in polyps with high dysplasia. In colorectal carcinomas, Mena marked the tumoral cells in 80% of cases. In 25% of positive cases, the intensity was 3+, in 60% 2+ and in the other 15% 1+. The Mena intensity was higher in the microsatellite stable tumors (MSS) and was correlated with vascular invasion, with intensity of angiogenesis marked with CD31 and CD105 and with c-erbB-2 and p53 expression. This is the first study in the literature about Mena expression in colorectal lesions.
Selective elimination of leukemic CD34+ progenitor cells by cytotoxic T lymphocytes specific for WT1 (2000)

Hematologic malignancies such as acute and chronic myeloid leukemia are characterized by the malignant transformation of immature CD34(+) progenitor cells. Transformation is associated with elevated expression of the Wilm's tumor gene encoded transcription factor (WT1). Here we demonstrate that WT1 can serve as a target for cytotoxic T lymphocytes (CTL) with exquisite specificity for leukemic progenitor cells. HLA-A0201- restricted CTL specific for WT1 kill leukemia cell lines and inhibit colony formation by transformed CD34(+) progenitor cells isolated from patients with chronic myeloid leukemia (CML), whereas colony formation by normal CD34(+) progenitor cells is unaffected. Thus, the tissue-specific transcription factor WT1 is an ideal target for CTL-mediated purging of leukemic progenitor cells in vitro and for antigen-specific therapy of leukemia and other WT1-expressing malignancies in vivo.
Incidence of Subsequent Vertebral Fracture after Kyphoplasty (2004)

This study demonstrated a higher rate of subsequent fracture after kyphoplasty compared with natural history data for untreated fractures. Most of these occurred at an adjacent level within 2 months of the index procedure. After this 2-month period, there were only occasional subsequent fractures, which occurred at remote levels. This confirms biomechanical studies showing that cement augmentation places additional stress on adjacent levels. Patients with an increase in back pain after kyphoplasty should be evaluated carefully for subsequent adjacent fractures, especially during the first 2 months after the index procedure.
Altered expression of vascular endothelial growth factor, fibroblast growth factor‐2 and endostatin in patients with hepatocellular carcinoma (2005)

The results suggest that VEGF, FGF-2, and endostatin concentrations are elevated prior to the emergence of HCC and that the distribution of VEGF changes dynamically during the development of HCC.
Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing (2013)

Using a novel approach combining DNA arrays, exome sequencing, and immunohistochemistry, we were able to identify 10 target genes in GIST, of which three showed hithero unknown clinical relevance. Because the identified target genes SYNE2, MAPK8IP2, and DIAPH1 have been shown to be involved in MAP kinase signaling, our data further indicate the important role of this pathway in GIST.
Insertion of Two Independent Enhancers in the Long Terminal Repeat of a Self-Inactivating Vector Results in High-Titer Retroviral Vectors with Tissue-Specific Expression (1998)

The use of retroviral vectors (RVs) derived from the murine oncoretroviruses for gene therapy is associated with the risk of malignant transformation of infected cells and ectopic expression of the proteins of interest. Targeting retroviral vectors to specific tissues would increase their safety and clinical applicability. To explore the potential of targeting vector expression to skeletal muscle, the murine leukemia virus broad transcriptional tropism was modified by substituting the viral promoter and/or enhancer with a transcriptional cassette containing the human T cell leukemia virus type I Tax-responsive element and the minimal muscle creatine kinase enhancer and promoter. The resulting retroviral vectors could be transcriptionally trans-activated by tax. In the absence of Tax, however, the viruses showed muscle-specific expression. Trans-complementing packaging and indicator cells stably expressing Tax were used to isolate high-titer producer cell clones (10 6 CFU/ml). In vitro, the levels of expression of these RVs in Tax-expressing fibroblasts were 10,000-fold higher than in normal fibroblasts and 1000-fold higher in C2C12 myotubes than in C2C12 myoblasts. Expression of the vectors and the endogenous muscle creatine kinase gene was similarly dependent on the maturity of the muscle cultures. One vector with modified LTRs was also tested in vivo in regenerating muscle and showed a delayed pattern of expression in myofibers compared with the vector containing the wild-type LTRs. These vectors can be easily modified to contain different tissue-specific enhancer and promoter elements and the availability of complementing packaging and indicator cells expressing Tax should allow their application in a variety of gene therapy settings.
Regulation of Squalene Synthase, a Key Enzyme of Sterol Biosynthesis, in Tobacco (2002)

Squalene synthase (SS) represents a putative branch point in the isoprenoid biosynthetic pathway capable of diverting carbon flow specifically to the biosynthesis of sterols and, hence, is considered a potential regulatory point for sterol metabolism. For example, when plant cells grown in suspension culture are challenged with fungal elicitors, suppression of sterol biosynthesis has been correlated with a reduction in SS enzyme activity. The current study sought to correlate changes in SS enzyme activity with changes in the level of the corresponding protein and mRNA. Using an SS-specific antibody, the initial suppression of SS enzyme activity in elicitor-challenged cells was not reflected by changes in the absolute level of the corresponding polypeptide, implicating a post-translational control mechanism for this enzyme activity. In comparison, the absolute level of the SS mRNA did decrease approximately 5-fold in the elicitor-treated cells, which is suggestive of decreased transcription of the SS gene. Study of SS in intact plants was also initiated by measuring the level of SS enzyme activity, the level of the corresponding protein, and the expression of SS gene promoter-reporter gene constructs in transgenic plants. SS enzyme activity, polypeptide level, and gene expression were all localized predominately to the shoot apical meristem, with much lower levels observed in leaves and roots. These later results suggest that sterol biosynthesis is localized to the apical meristems and that apical meristems may be a source of sterols for other plant tissues.
Imprint Lithography with Degradable Elastomeric Polyanhydrides (2012)

A photocurable, degradable polyanhydride cross-linked elastomer that can be used as a stamp in imprint lithography applications has been developed. The degradable stamp materials are based on polyanhydrides synthesized using thiol-ene polymerization. In this study, curing the monomers 4-pentenoic anhydride and pentaerythritol tetrakis(3-mercaptopropionate) on a master mold yields low modulus, elastomeric, degradable polyanhydride polymer stamps that are a negative of the master. These stamps can be then used as a sacrificial template during the fabrication of a replica of the master, and can be readily degraded away from the replica using water. The resultant imprinted materials exhibited excellent uniformity over a large area. Compared with other conventional imprint lithography stamp materials, the thiol-ene polymerized polyanhydrides are degradable, master mold safe, show great release properties, have fast cure rates, are relatively low cost, and can be fabricated onto variety of substrates and materials.