gebhart/patrepeval huggingface dataset:
Raman Signal Enhancement in Deep Spectroscopy of Turbid Media (2007)

A new, passive method for enhancing spontaneous Raman signals for the spectroscopic investigation of turbid media is presented. The main areas to benefit are transmission Raman and spatially offset Raman spectroscopy approaches for deep probing of turbid media. The enhancement, which is typically several fold, is achieved using a multilayer dielectric optical element, such as a bandpass filter, placed within the laser beam over the sample. This element prevents loss of the photons that re-emerge from the medium at the critical point where the laser beam enters the sample, the point where major photon loss occurs. This leads to a substantial increase of the coupling of laser radiation into the sample and consequently an enhanced laser photon-medium interaction process. The method utilizes the angular dependence of dielectric optical elements on impacting photon direction with its transmission spectral profile shifting to the blue with increase in the deviation of photons away from normal incidence. This feature enables it to act as a unidirectional mirror passing a semi-collimated laser beam through unhindered from one side, and at the other side, reflecting photons emerging from the sample at random directions back into it with no restrictions to the detected Raman signal. With substantial restrictions to the spectral range, the concept can also be applied to conventional backscattering Raman spectroscopy. The use of additional reflective elements around the sample to enhance the Raman signal further is also discussed. The increased signal strength yields higher signal quality, a feature important in many applications. Potential uses include sensitive noninvasive disease diagnosis in vivo, security screening, and quality control of pharmaceutical products. The concept is also applicable in an analogous manner to other types of analytical methods such as fluorescence or near-infrared (NIR) absorption spectroscopy of turbid media or it can be used to enhance the effectiveness of the coupling of laser radiation into tissue in applications such as photodynamic therapy for cancer treatment.
The protein substrate binding site of the ubiquitin-protein ligase system. (1986)

In order to gain insight into the mechanisms that determine the selectivity of the ubiquitin proteolytic pathway, the protein substrate binding site of the ubiquitin-protein ligase system was identified and examined. Previous studies had shown that the ligase system consists of three components: a ubiquitin-activating enzyme (E1), ubiquitin-carrier protein (E2), and a third enzyme, E3, the mode of action of which has not been defined. E3 from rabbit reticulocytes was further purified by a combination of affinity chromatography, hydrophobic chromatography, and gel filtration procedures. A 180-kDa protein was identified as the subunit of E3. Two independent methods indicate that E3 has the protein binding site of the ubiquitin ligase system. These are the chemical cross-linking of 125I-labeled proteins to the E3 subunit and the functional conversion of enzyme-bound labeled proteins to ubiquitin conjugates in pulse-chase experiments. The trapping of E3-bound protein for labeled product formation was allowed by the slow dissociation of E3 X protein complex. The specificity of binding of different proteins to E3, examined by both methods, showed a direct correlation with their susceptibility to degradation by the ubiquitin system. Proteins with free alpha-NH2 groups, which are good substrates, bind better to E3 than corresponding proteins with blocked NH2 termini, which are not substrates. Oxidation of methionine residues to sulfoxide derivatives greatly increases the susceptibility of some proteins to ligation with ubiquitin, with a corresponding increase in their binding to E3. However, a protein derivative which was subjected to both amino group modification and oxidation binds strongly to the enzyme, even though it cannot be ligated to ubiquitin. It thus seems that the substrate binding site of E3 participates in determining the specificity of proteins that enter the ubiquitin pathway of protein degradation.
Nutritional Issues in Nursing Home Care (1995)

The most common nutritional problems in nursing home residents are weight loss and concomitant protein energy undernutrition. Although the causes of weight loss in these patients can usually be treated, they are rarely identified in the nursing home. Depression and adverse drug effects are the most common causes of weight loss. We discuss the appropriate use of feeding tubes in the nursing home and the early use of enteral feeding to prevent the development of severe protein energy undernutrition. Vitamin deficiencies, especially folate and pyridoxine deficiencies, frequently develop in nursing home residents. Hip fractures are often associated with vitamin D deficiency. Trace mineral deficiencies (for example, zinc deficiency) can aggravate immune deficiency and slow wound healing. Inadequate fluid intake leads to dehydration, hypotension, and, in persons with diabetes mellitus, hyperosmolarity. Finally, food intake itself can cause postprandial hypotension (which in turn may precipitate falls), produce electrolyte shifts, and result in aspiration pneumonia. Physical activity programs are an important component of nursing home care that may have an effect on nutritional status, and simple, cost-effective programs may be as beneficial as high-technology programs. Careful attention to the nutritional intake of nursing home residents is both a clinical and a quality-of-life issue.
Inosine-5’-monophosphate dehydrogenase (IMPDH) inhibitors: a patent and scientific literature review (2002-2016) (2017)

Inosine-5'-monophosphate dehydrogenase (IMPDH) is an enzyme involved in the de novo biosynthesis of guanine nucleotides. To date human IMPDH inhibitors have been approved for prevention of organ transplant rejection and as anti-viral agents. More recently, the use of IMPDH inhibitors for other indications including cancer and pathogenic microorganisms has been pursued. Areas covered: IMPDH inhibitors disclosed primarily in the patent and scientific literature from 2002 to the present are discussed. Several interesting chemotypes that have not been pursued by patent protection are also highlighted. Expert opinion: Progress has been made in the development of IMPDH inhibitors, particularly compounds that are structurally distinct from mycophenolic acid and nucleoside-based inhibitors. However, clinical progression has been hampered primarily by a limited understanding of the enzyme's role in disease pathophysiology. Finally, most of the IMPDH inhibitors developed over the past fourteen years fall within a relatively narrow set of chemotypes. This provides opportunities for expanding IMPDH inhibitor chemical space to further evaluate this class of molecular targets.
TRANSCRIPTION FACTORS AND CONGENITAL HEART DEFECTS (2005)

Although there have been important advances in diagnostic modalities and therapeutic strategies for congenital heart defects (CHD), these malformations still lead to significant morbidity and mortality in the human population. Over the past 10 years, characterization of the genetic causes of CHD has begun to elucidate some of the molecular causes of these defects. Linkage analysis and candidate-gene approaches have been used to identify gene mutations that are associated with both familial and sporadic cases of CHD. Complementation of the human studies with developmental studies in mouse models provides information for the roles of these genes in normal development as well as indications for disease pathogenesis. Biochemical analysis of these gene mutations has provided further insight into the molecular effects of these genetic mutations. Here we review genetic, developmental, and biochemical studies of six cardiac transcription factors that have been identified as genetic causes for CHD in humans.
Enhanced Signals and Fast Nucleic Acid Hybridization By Microfluidic Chaotic Mixing (2006)

Order from chaos: Microfluidic chaotic mixing shows a significant improvement in the equilibration time of hybridization in DNA microarrays over conventional techniques. These results illustrate a new concept for performing kinetics studies in microfluidic devices. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503830_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Production and characterization of a monoclonal antibody to human Type IV collagen. (1982)

We have produced a monoclonal antibody to human basement membrane Type IV collagen. The antibody reacts with the pepsin-resistant, collagenase-sensitive domain of Type IV collagen isolated from placental membranes, but not with human collagens of Types I, II, III, V, 1alpha, 2alpha, and 3alpha. The antibody precipitates biosynthetically labeled human Type IV procollagen, and the precipitate contains both the alpha1 (IV) and alpha2 (IV) chains, suggesting the occurrence of both of these chains within the same triple-helical molecule. When used in indirect immunofluorescence, the antibody gives brilliant staining of basement membranes from a variety of human tissues but does not stain tissues of bovine, canine, rabbit, rat, or mouse origin. It is suggested that this antibody will be of value in research on the structure of human basement membrane collagen, on the distribution of this collagen in various basement membranes, and particularly for the study of basement membranes in normal human development and pathologic processes.
Short Intertrial Intervals Impair Water Maze Performance in Old Fischer 344 Rats (1996)

Male and female Fischer 344 rats (N = 55) aged approximately 18, 21, and 24 months were tested for spatial learning in the water maze with intertrial intervals of 1-4 min (Massed) or 23-33 min (Spaced). Animals tested in the Massed condition showed an age-related impairment on trials to criterion; rats aged 24 months performed more poorly than younger subjects. Spaced animals did not differ at any age nor did they differ from 18- or 21-month-old Massed subjects. The youngest rats in both groups were comparable to animals aged 7-8 months tested under Massed conditions. Tests on swim distance, swim speed, and escape latency produced similar results. Our data suggest that acquisition deficits in 24-month-old rats tested with long intertrial intervals are due at least in part to increased susceptibility to fatigue and/or thermal stress. Caution should be used, therefore, when interpreting age-related impairments in water maze performance.
Prospective origins of prostate carcinoma: Prostatic intraepithelial neoplasia and atypical adenomatous hyperplasia (1996)

The significance of recognizing PIN is based on its strong association with prostatic carcinoma. PIN coexists with carcinoma in most cases, but retains an intact or fragmented basal cell layer, unlike carcinoma, which lacks a basal cell layer. High grade PIN in biopsies predicts the presence of carcinoma in subsequent biopsies, and PIN provides the highest risk ratio of all known predictive factors. This finding indicates the need for repeat biopsy and follow-up when PIN is identified in a biopsy, especially in patients with an elevated serum prostate specific antigen concentration. PIN also offers promise as an intermediate endpoint in studies of chemoprevention of prostatic carcinoma. Unlike PIN, AAH is weakly linked to carcinoma, and current data indicate that no follow-up is necessary for patients with this finding.
Bevacizumab for glioblastoma (2015)

Individuals with glioblastoma are often characterized by older age, advanced neurologic manifestations at the primary stage, and unresectable tumors, and these factors are associated with poor treatment outcomes. Administration of bevacizumab (BV, Avastin(®)) promotes tumor regression and improves cerebral edema, and is expected to improve neurologic findings in many patients with malignant gliomas, including glioblastoma. Although the addition of BV to the conventional standard therapy (chemoradiotherapy with temozolomide) for newly diagnosed glioblastoma prolonged the progression-free survival time and the performance status of patients, it failed to extend overall survival time. However, more than 50% of glioblastoma patients show Karnofsky performance status ≤70 at initial presentation; therefore, BV should be used to improve or maintain their performance status as an initial treatment. Most of the adverse events of BV, except hypertension and proteinuria, occur as complications of glioblastoma, and explanation of the advantages and disadvantages of BV administration to patients is important. Herein, the efficacy, safety, and challenges of using BV for treating glioblastoma were reviewed.
Analysis of Heparins Derived From Bovine Tissues and Comparison to Porcine Intestinal Heparins (2016)

Heparin is a widely used clinical anticoagulant. It is also a linear glycosaminoglycan with an average mass between 10 and 20 kDa and is primarily made up of trisulfated disaccharides comprised of 1,4-linked iduronic acid and glucosamine residues containing some glucuronic acid residues. Heparin is biosynthesized in the Golgi of mast cells commonly found in the liver, intestines, and lungs. Pharmaceutical heparin currently used in the United States is primarily extracted from porcine intestines. Other sources of heparin including bovine intestine and bovine lung are being examined as potential substitutes for porcine intestinal heparin. These additional sources are intended to serve to diversify the heparin supply, making this lifesaving drug more secure. The current study examines bovine heparins prepared from both intestines and lung and compares these to porcine intestinal heparin. The structural properties of these heparins are examined using nuclear magnetic resonance, gel permeation chromatography, and disaccharide analysis of heparinase-catalyzed depolymerized heparin. The in vitro functional activities of these heparins have also been determined. The goal of this study is to establish the structural and functional similarities and potential differences between bovine and porcine heparins. Porcine and bovine heparins have structural and compositional similarities and differences.
Matrix Metalloproteinase 9 Is a Mediator of Epidermal Growth Factor–Dependent E-Cadherin Loss in Ovarian Carcinoma Cells (2008)

Epidermal growth factor (EGF) receptor (EGFR) is frequently elevated in epithelial ovarian cancer, and E-cadherin expression is often reduced in advanced disease. In this study, we investigated a mechanism by which EGFR activation promotes disruption of adherens junctions through induction of matrix metalloproteinase 9 (MMP-9). We show that EGFR activation down-modulates E-cadherin, and broad spectrum MMP inhibition ameliorates EGF-stimulated junctional disruption and loss of E-cadherin protein. MMP-9 involvement in EGF-dependent down-regulation of E-cadherin was determined by siRNA specifically directed against MMP-9. Furthermore, treatment with recombinant MMP-9 or transient expression of MMP-9 is sufficient to reduce E-cadherin levels in differentiated ovarian tumor cells. Stable overexpression of MMP-9 led to a loss of E-cadherin and junctional integrity, and promoted a migratory and invasive phenotype. Thus, elevated MMP-9 protein expression is sufficient for junctional disruption and loss of E-cadherin in these cells. The associations between EGFR activation, MMP-9 expression, and E-cadherin were investigated in human ovarian tumors and paired peritoneal metastases wherein immunohistochemical staining for activated (phospho) EGFR and MMP-9 colocalized with regions of reduced E-cadherin. These data suggest that regulation of MMP-9 by EGFR may represent a novel mechanism for down-modulation of E-cadherin in ovarian cancer.
SPARC (BM-40, Osteonectin) Inhibits the Mitogenic Effect of Vascular Endothelial Growth Factor on Microvascular Endothelial Cells (1998)

SPARC (secreted protein, acidic and rich in cysteine) is a matricellular protein that modulates cell adhesion and proliferation and is thought to function in tissue remodeling and angiogenesis. In this study, we demonstrate that SPARC inhibits DNA synthesis by >90% in human microvascular endothelial cells (HMEC) stimulated by the endothelial cell mitogen vascular endothelial growth factor (VEGF). Peptides derived from SPARC domain IV, which contains a disulfide-bonded EF-hand sequence and binds to endothelial cells, mimicked the effect of native SPARC. The inhibition was also observed with a peptide from the follistatin-like domain II, whereas peptides from SPARC domains I and III had no effect on VEGF-stimulated DNA synthesis. The inhibition of HMEC proliferation was mediated in part by the binding of VEGF to SPARC. The binding of 125I-VEGF to HMEC was reduced by SPARC and SPARC peptides from domain IV in a concentration-dependent manner. In a radioimmune precipitation assay, peptides from SPARC domains II and IV each competed with native SPARC for its binding to VEGF. It has been reported that VEGF stimulates the tyrosine phosphorylation and activation of mitogen-activated protein kinases Erk1 and Erk2. We now show that SPARC reduces this phosphorylation in VEGF-stimulated HMEC to levels of unstimulated controls. SPARC thus modulates the mitogenic activity of VEGF through a direct binding interaction and reduces the association of VEGF with its cell-surface receptors. Moreover, an additional diminution of VEGF activity by SPARC is accomplished through a reduction in the tyrosine phosphorylation of mitogen-activated protein kinases.
Improved Procedures for Bromopropadiene and Iodopropadiene (1991)

Abstract Pure bromopropadiene, BrCH═C═CH2, and the corresponding iodo compound have been obtained with reasonable yields by removing the propargyl halide present in the equilibrium mixtures resulting from treatment of the propargyl halide with CuBr or CuI, with a limited amount of diethylamine.
Direct visualization of plasmid DNA in bacterial cells (1992)

The direct visualization of plasmid DNA inside Escherichia coli cells is demonstrated using phase-fluorescence microscopy of DAPI (4',6-diamidino-2-phenylindole)-stained bacteria. Small as well as large plasmids could be detected, both in minicells and in cells of larger size. For large plasmids, even single molecules appeared to be within the detection limit. The fluorescence generated from monomers of small plasmids was probably below this limit, and for these plasmids the observed signals may represent aggregates. The distribution of the fluorescence foci might reflect specific plasmid positioning during partition and/or replication.
Propulsion system design of electric and hybrid vehicles (1997)

There is a growing interest in electric and hybrid-electric vehicles due to environmental concerns. Efforts are directed toward developing an improved propulsion system for electric and hybrid-electric vehicles applications. This paper is aimed at developing the system design philosophies of electric and hybrid vehicle propulsion systems. The vehicles' dynamics are studied in an attempt to find an optimal torque-speed profile for the electric propulsion system. This study reveals that the vehicles' operational constraints, such as initial acceleration and grade, can be met with minimum power rating if the power train can be operated mostly in the constant power region. Several examples are presented to demonstrate the importance of the constant power operation. Operation of several candidate motors in the constant power region are also examined. Their behaviors are compared and conclusions are made.
The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypotheses (1993)

We have developed a computer program, called NEWLEAD, for the automatic generation of candidate structures conforming to the requirements of a given pharmacophore. The treatment consists in connecting the pharmacophoric pieces with spacers assembled from small chemical entities (atoms, chains, or ring moieties). We have tested the program on several sets of input fragments, each comprising selected functional groups obtained from the bioactive conformations of reference molecules. In addition to the expected solutions, the program can generate new structures that are chemically unrelated to the reference molecules. This provides an unbiased starting point for the design of new generations of lead structures. The concept used in this approach is presented and discussed. The present possibilities of the program are illustrated by some examples. The treatment is very fast, because only a few bonds are created between building blocks already having ideal geometries. The ability to generate rapidly a variety of molecules conforming to a three-dimensional pharmacophoric model makes NEWLEAD a useful tool with wide applicability in rational drug design, including the areas of molecular mimicry and peptidomimetism.
Preprocessing media to facilitate later insertion of a watermark (2003)

There are several watermarking applications that require the deployment of a very large number of watermark embedders. These consumer applications have severe budgetary constraints that limit the computation resources that are available. Under these circumstances, only simple embedding algorithms can be deployed, which have limited performance. In order to improve performance, we propose preprocessing the original media during content creation. A simple example of this procedure is described and experimental results confirm our assertions.
Metal Contact Engineering and Registration-Free Fabrication of Complementary Metal-Oxide Semiconductor Integrated Circuits Using Aligned Carbon Nanotubes (2011)

Complementary metal-oxide semiconductor (CMOS) operation is very desirable for logic circuit applications as it offers rail-to-rail swing, larger noise margin, and small static power consumption. However, it remains to be a challenging task for nanotube-based devices. Here in this paper, we report our progress on metal contact engineering for n-type nanotube transistors and CMOS integrated circuits using aligned carbon nanotubes. By using Pd as source/drain contacts for p-type transistors, small work function metal Gd as source/drain contacts for n-type transistors, and evaporated SiO(2) as a passivation layer, we have achieved n-type transistor, PN diode, and integrated CMOS inverter with an air-stable operation. Compared with other nanotube n-doping techniques, such as potassium doping, PEI doping, hydrazine doping, etc., using low work function metal contacts for n-type nanotube devices is not only air stable but also integrated circuit fabrication compatible. Moreover, our aligned nanotube platform for CMOS integrated circuits shows significant advantage over the previously reported individual nanotube platforms with respect to scalability and reproducibility and suggests a practical and realistic approach for nanotube-based CMOS integrated circuit applications.