gebhart/patrepeval huggingface dataset:
Influence of the maternal vaginal microbiota on the oral microbiota of the newborn. (1998)

The present study was conducted on 50 expectant mothers and the newborns, with the aim of observing if any, the relationship, acquisition and survival of the maternal vaginal microbiota to the oral microflora after birth. The oral cavity was sterile in 6% of the newborns. The differences between the counts of S. aureus, Klebsiella, Lactobacillus, Ps. aeruginosa and Veillonella sp. in the mother and in the child were of statistical significance. No statistically significant difference was observed between the counts of S. epidermidis in the mother and in the child. Of the microorganisms present at birth, only S. epidermidis persisted in the oral cavity. At the end of the observation period, S. salivarius was the predominant oral microorganism.
Interactive Visual Graph Analytics on the Web (2021)

We present a web-based network visual analytics platform called GraphVis that combines interactive visualizations with analytic techniques to reveal important patterns and insights for sense making, reasoning, and decision-making. The platform is designed with simplicity in mind and allows users to visualize and explore networks in seconds with a simple drag-and-drop of a graph file into the web browser. GraphVis is fast and flexible, web-based, requires no installation, while supporting a wide range of graph formats as well as state-of-the-art visualization and analytic techniques. In particular, the multi-level network analysis engine of GraphVis gives rise to a variety of new possibilities for exploring, analyzing, and understanding complex networks interactively in real-time. Finally, we also highlight other key aspects including filtering, querying, ranking, manipulating, exporting, partitioning (community/role discovery), as well as tools for dynamic network analysis and visualization, interactive graph generators (including two new block model approaches), and a variety of multi-level network analysis and statistical techniques.
Molecular cytogenetic abnormalities in multiple myeloma and plasma cell leukemia measured using comparative genomic hybridization (1997)

Comparative genomic hybridization (CGH) was used to identify recurrent regions of DNA sequence loss and gain in 21 multiple myeloma (MM) and plasma cell leukemia (PCL) primary tumor specimens and cell lines. Multiple regions of non-random sequence loss and gain were observed in 8/8 primary advanced stage tumors and 13/13 cell lines. Identification of sequence copy number changes was facilitated by statistical analyses that reduce subjectivity associated with identification of copy number changes and by requiring that sequence changes are visible using both red- and green-labeled tumor DNA. Loss of sequence on 13q and 14q and gain of sequence on 1q and chromosome 7 occurred in 50-60% of the population. In general, cell lines carry more and larger regions of sequence gain and loss than primary tumors. Regions of sequence copy number change that recur among MM cell lines and primary tumors include, in order of prevalence, enh(1q12qter), dim(13), enh(7), enh(3q22q29), enh(11q13.3qter), dim(14q11.2q31), enh(8q21qter), enh(3p25pter), dim(17p11.2p13), and dim(6q22.1q23). Population distributions of genome-wide changes in primary tumors reveal "hot-spots" of sequence loss from 13q12.1-q21, 13q32-q34, 14q11.2-q13, and 14q23-q31. Genomic changes detected using CGH are consistent with those identified using banding analyses, although recurrent involvement of additional regions of the genome are also evident. A higher prevalence of genomic changes is visible using CGH compared to banding. Identification of recurrent regions of sequence gain and loss provides opportunities to identify regions of the genome that may be involved in the malignant phenotype and/or disease progression.
Characterization of the role of EGF-A of low density lipoprotein receptor in PCSK9 binding (2013)

Proprotein convertase subtilisin kexin-like 9 (PCSK9) promotes the degradation of low density lipoprotein receptor (LDLR) and plays an important role in regulating plasma LDL-cholesterol levels. We have shown that the epidermal growth factor precursor homology domain A (EGF-A) of the LDLR is critical for PCSK9 binding at the cell surface (pH 7.4). Here, we further characterized the role of EGF-A in binding of PCSK9 to the LDLR. We found that PCSK9 efficiently bound to the LDLR but not to other LDLR family members. Replacement of EGF-A in the very low density lipoprotein receptor (VLDLR) with EGF-A of the LDLR promoted the degradation of the mutant VLDLR induced by PCSK9. Furthermore, we found that PCSK9 bound to recombinant EGF-A in a pH-dependent manner with stronger binding at pH 6.0. We also identified amino acid residues in EGF-A of the LDLR important for PCSK9 binding. Mutations G293H, D299V, L318D, and L318H reduced PCSK9 binding to the LDLR at neutral pH without effect at pH 6.0, while mutations R329P and E332G reduced PCSK9 binding at both pH values. Thus, our findings reveal that EGF-A of the LDLR is critical for PCSK9 binding at the cell surface (neutral pH) and at the acidic endosomal environment (pH 6.0), but different determinants contribute to efficient PCSK9 binding in different pH environments.
Determination of the integral refractive index of cells in suspension by digital holographic phase contrast microscopy (2008)

A digital holographic microscopy method for the determination of the integral refractive index of living cells in suspension is presented. Therefore, digital holographic phase contrast images of trypsinized cells in suspension are recorded. Afterwards, the cell radius and the integral cellular refractive index are determined by fitting of a two dimensional model. The applied algorithm requires only information about the refractive index of the suspension medium and the scale of the microscopic imaging system. The fitting algorithm is characterized on simulated phase data and digital holographic phase contrast images of beads. Results obtained from living human pancreas tumor cells demonstrate the applicability of the method for cell characterization.
A 110-amino Acid Region within the A1-domain of Coagulation Factor VIII Inhibits Secretion from Mammalian Cells (1995)

Factor VIII is the coagulation factor deficient in the X-chromosome-linked bleeding disorder hemophilia A. Factor VIII is homologous to blood coagulation factor V, both having a domain structure of A1-A2-B-A3-C1-C2. Previous transfection studies demonstrated that factor VIII is 10-fold less efficiently expressed than the homologous coagulation factor, factor V. The inefficient expression correlated with interaction of the factor VIII primary translation product with the protein chaperonin BiP in the lumen of the endoplasmic reticulum. In contrast, factor V was not detected in association with BiP and was secreted efficiently. To determine whether specific amino acid sequences within factor VIII inhibit secretion, we have studied the secretion of factor VIII deletion and factor VIII/factor V chimeric proteins upon transient transfection of COS-1 monkey cells. A chimeric factor VIII protein that contained the A1- and A2-domains of factor V was secreted with a similar efficiency as wild-type factor V, whereas the complementary chimera having the A1- and A2-domains of factor VIII was secreted with low efficiency, similar to wild-type factor VIII. These results suggested that sequences within the A1- and A2-domains were responsible for the low secretion efficiency of factor VIII. Secretion of A1-domain-deleted factor VIII was increased approximately 10-fold compared to wild-type factor VIII or A2-domain-deleted factor VIII. Expression of the factor VIII A1-domain alone did not yield secreted protein, whereas expression of the factor VIII A2-domain alone or the factor V A1-domain or A2-domain alone directed synthesis of secreted protein. Secretion of a hybrid in which the carboxyl-terminal 110 amino acids of the A1-domain were replaced by homologous sequences from the factor V A1-domain was also increased 10-fold compared to wild-type factor VIII, however, the secreted protein was not functional and the heavy and light chains were not associated. These results localize a 110-amino acid region within the A1-domain that inhibits factor VIII secretion. This region is clustered with multiple short peptide sequences that have potential to bind BiP.
Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines (2013)

Pneumonic plague is a highly virulent infectious disease with 100% mortality rate, and its causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror agent. Currently, there is no FDA approved vaccine against plague. The polymeric bacterial capsular protein F1, a key component of the currently tested bivalent subunit vaccine consisting, in addition, of low calcium response V antigen, has high propensity to aggregate, thus affecting its purification and vaccine efficacy. We used two basic approaches, structure-based immunogen design and phage T4 nanoparticle delivery, to construct new plague vaccines that provided complete protection against pneumonic plague. The NH₂-terminal β-strand of F1 was transplanted to the COOH-terminus and the sequence flanking the β-strand was duplicated to eliminate polymerization but to retain the T cell epitopes. The mutated F1 was fused to the V antigen, a key virulence factor that forms the tip of the type three secretion system (T3SS). The F1mut-V protein showed a dramatic switch in solubility, producing a completely soluble monomer. The F1mut-V was then arrayed on phage T4 nanoparticle via the small outer capsid protein, Soc. The F1mut-V monomer was robustly immunogenic and the T4-decorated F1mut-V without any adjuvant induced balanced TH1 and TH2 responses in mice. Inclusion of an oligomerization-deficient YscF, another component of the T3SS, showed a slight enhancement in the potency of F1-V vaccine, while deletion of the putative immunomodulatory sequence of the V antigen did not improve the vaccine efficacy. Both the soluble (purified F1mut-V mixed with alhydrogel) and T4 decorated F1mut-V (no adjuvant) provided 100% protection to mice and rats against pneumonic plague evoked by high doses of Y. pestis CO92. These novel platforms might lead to efficacious and easily manufacturable next generation plague vaccines.
Treatment of the Infected Hip Replacement (2004)

Selection of the suitable treatment method for an infected hip arthroplasty requires careful assessment of patient-related variables and expected treatment goals. The basic treatment options include antibiotic suppression, open debridement, resection arthroplasty, arthrodesis, reimplantation of another prosthesis, and amputation. Successful treatment of infection requires complete debridement of all infected and foreign material and appropriate antimicrobial therapy. When possible, the preferred treatment approach is insertion of another prosthesis with a delayed reconstructive treatment technique. Patients now are presenting with an increasing incidence of resistant organisms and severe bone loss, which increases the difficulty of treatment.
Dispersion of carbon nanotubes by photo- and thermal-responsive polymers containing azobenzene unit in the backbone (2010)

Photo- and thermal-responsive polymers containing azobenzene units in the main chain have been utilized as removable dispersants for single-walled carbon nanotubes (SWNTs) in organic solvents. Intermolecular interactions between SWNTs and the polymers are reversibly controllable by tuning the trans-cis composition.
Detection of C polysaccharide in Streptococcus pneumoniae in the sputa of pneumonia patients by an enzyme-linked immunosorbent assay (1985)

The pneumococcal C polysaccharide (PnC) is species specific and believed to be a cell wall component of all pneumococcal types. A sandwich enzyme-linked immunosorbent assay (ELISA) for detection of PnC in sputa has been developed by using a monoclonal antiphosphorylcholine antibody and a polyclonal rabbit anti-PnC antiserum in the test system. A 1-year study of adult hospitalized patients with community-acquired pneumonia was performed. A total of 147 patients with clinical and radiological evidence for pneumonia were accepted for the study. Of these, 105 patients provided a sputum sample upon admission to the ward. The sputa were cultured semiquantitatively as well as tested for the presence of antigen. Of the sputum samples from patients with Streptococcus pneumoniae, 27 of 33 (accounting for a sensitivity of 82%) were positive in the ELISA test. Of the sputum samples from patients with pneumonia of some other known or suspected etiology, 32 of 34 (accounting for a specificity of 94%) were negative. In addition, 7 sputum samples from 31 patients with pneumonia of unknown etiology were positive. The ELISA test described here is in our opinion a sensitive and specific test for detecting PnC from S. pneumoniae in sputa from patients with untreated pneumonia.
Tag-based vision: assisting 3D scene analysis with radio-frequency tags (2003)

Radio frequency (RF) tags are growing popular for many industrial applications such as product tracking and security. We investigate the benefit of RF tagging in an application of 3D object registration from single view. We present a machine vision system that uses a RF Tag device to detect objects prior to locating them visually. The tag system consists of a tag reader that can interrogate, and receive radio signals from, tags attached on objects and characterizing them. Laying the basis of an object model database shared on a network, we perform a knowledge-based recognition task where the information retrieved from the database query serves as the prior. The recognition algorithm used is a matching with projective invariants. Our architecture is a prototype that prefigures tag based applications where physical and logic representations of objects are combined.
Infection of Ciliated Cells by Human Parainfluenza Virus Type 3 in an In Vitro Model of Human Airway Epithelium (2004)

We constructed a human recombinant parainfluenza virus type 3 (rPIV3) that expresses enhanced green fluorescent protein (GFP) and used this virus, rgPIV3, to characterize PIV3 infection of an established in vitro model of human pseudostratified mucociliary airway epithelium (HAE). The apical surface of HAE was highly susceptible to rgPIV3 infection, whereas only occasional cells were infected when virus was applied to the basolateral surface. Infection involved exclusively ciliated epithelial cells. There was little evidence of virus-mediated cytopathology and no spread of the virus beyond the ciliated cell types. Infection of ciliated cells by rgPIV3 was sensitive to a neuraminidase specific for alpha2-6-linked sialic acid residues, but not to a neuraminidase that cleaves alpha2-3- and alpha2-8-linked sialic acid residues. This provided evidence that rgPIV3 utilizes alpha2-6-linked sialic acid residues for initiating infection, a specificity also described for human influenza viruses. The PIV3 fusion (F) glycoprotein was trafficked exclusively to the apical surface of ciliated cells, which also was the site of release of progeny virus. F glycoprotein localized predominately to the membranes of the cilial shafts, suggesting that progeny viruses may bud from cilia per se. The polarized trafficking of F glycoprotein to the apical surface also likely restricts its interaction with neighboring cells and could account for the observed lack of cell-cell fusion. HAE derived from cystic fibrosis patients was not more susceptible to rgPIV3 infection but did exhibit limited spread of virus due to impaired movement of lumenal secretions due to compromised function of the cilia.
The acidic amino-terminal region of herpes simplex virus type 1 alpha protein ICP27 is required for an essential lytic function (1993)

The herpes simplex virus type 1 (HSV-1) alpha protein ICP27 regulates the transition between the delayed-early and late phases of the viral infection. Previous genetic analyses have suggested that the important functional domains of ICP27 map to its carboxyl-terminal half. One striking feature of the primary sequence of ICP27, however, is an extremely acidic region near its amino terminus. To determine whether this region is required for ICP27 function, we deleted the sequences in the ICP27 gene which encode it (codons 12 through 63). In transient expression assays, the deletion mutant was unable to efficiently repress the expression of a cotransfected reporter gene or to efficiently complement the growth of d27-1, an HSV-1 ICP27 null mutant. These results suggested that the acidic region of ICP27 is involved in a regulatory function required for lytic growth. To test this possibility further, we introduced the mutant allele into the HSV-1 genome by marker transfer. Two independently derived isolates of the mutant virus, designated d1-2a and d1-2b, were recovered and analyzed. Both isolates were defective for growth in Vero cells, exhibiting a 100-fold reduction in virus yield compared with the wild-type infection. Vero cells infected with the d1-2 isolates showed a three- to eightfold reduction in viral DNA replication, a moderate reduction in the expression of viral gamma genes, and a delay in the repression of beta genes. The phenotype of the d1-2 isolates differs substantially from the phenotypes of previously isolated ICP27 mutants, which show much more severe defects in viral gene expression. Our results demonstrate that the amino-terminal half of ICP27 participates in its regulatory activities in both infected and transfected cells.
The Liver as an Immunological Organ (2006)

The liver is a unique anatomical and immunological site in which antigen-rich blood from the gastrointestinal tract is pressed through a network of sinusoids and scanned by antigen-presenting cells and lymphocytes. The liver's lymphocyte population is selectively enriched in natural killer and natural killer T cells which play critical roles in first line immune defense against invading pathogens, modulation of liver injury and recruitment of circulating lymphocytes. Circulating lymphocytes come in close contact to antigens displayed by endothelial cells, Kupffer cells and liver resident dendritic cells in the sinusoids. Circulating lymphocytes can also contact hepatocytes directly, because the sinusoidal endothelium is fenestrated and lacks a basement membrane. This unique anatomy of the liver may facilitate direct or indirect priming of lymphocytes, modulate the immune response to hepatotrophic pathogens and contribute to some of the unique immunological properties of this organ, particularly its capacity to induce antigen-specific tolerance.
Signal Transduction in Responses to UV-B Radiation (2009)

UV-B radiation is a key environmental signal that initiates diverse responses in plants that affect metabolism, development, and viability. Many effects of UV-B involve the differential regulation of gene expression. The response to UV-B depends on the nature of the UV-B treatment, the extent of adaptation and acclimation to UV-B, and interaction with other environmental factors. Responses to UV-B are mediated by both nonspecific signaling pathways, involving DNA damage, reactive oxygen species, and wound/defense signaling molecules, and UV-B-specific pathways that mediate photomorphogenic responses to low levels of UV-B. Importantly, photomorphogenic signaling stimulates the expression of genes involved in UV-protection and hence promotes plant survival in UV-B. Photomorphogenic UV-B signaling is mediated by the UV-B-specific component UV RESISTANCE LOCUS8 (UVR8). Both UVR8 and CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) are required for UV-B-induced expression of the ELONGATED HYPOCOTYL5 (HY5) transcription factor, which plays a central role in the regulation of genes involved in photomorphogenic UV-B responses.
Ion Exchange and Thermal Stability of MCM-41 (1995)

Mesoporous molecular sieve MCM-41 with a Si/Al ratio of 39 was obtained by hydrothermal synthesis with a gel composition of 6 SiO2:0.1 Al2O3:1 hexadecyltrimethylammonium chloride:0.25 dodecyltrimethylammonium bromide:0.25 tetrapropylammonium bromide:0.15 (NH4)(2)0:1.5 Na2O:300 H2O. The MCM-41 sample incorporating aluminum (AlMCM-41) was calcined in O-2 flow at 813 K and subsequently ion exchanged with Na+, K+, Ca2+, and Y3+. Th, ion exchange levels have been increased as high as 0.41 Na/Al, 0.36 K/A1, 0.37 Ca/A1 and 0.39 Y/A1, respectively. Hydrothermal stability of the ion exchanged A1MCM-41 materials has been investigated with X-ray powder diffraction pattern, BET specific surface area, and magic-angle spinning Al-27 NMR spectroscopy, after the samples were heated for 2 h at various temperatures in O-2 flow saturated with water vapor at room temperature. The hydrothermal stability of the AlMCM-41 has been found to extend to the following temperatures depending on ion exchange: Y3+ (1170 K) approximate to Ca2+ &gt; Na+ (1070 K) approximate to as calcined AlMCM-41 &gt; pure-silica MCM-41 (980 K)
Increased Serum Levels of Vascular Endothelial Growth Factor in Patients with Inflammatory Bowel Disease (1998)

Significantly increased VEGF serum levels were observed in patients with active Crohn's disease and ulcerative colitis, which suggests that VEGF has an important role in chronic inflammatory bowel disease. Its possible association with fistulas has yet to be determined.
Trellis-based optimization of MPEG-4 advanced audio coding (2000)

We outline a method to perform efficient low rate quantization for MPEG-4 advanced audio coding (AAC). The AAC bit stream consists of indices for quantized spectral coefficients as well as side information about quantizer step sizes and Huffman codebooks. The MPEG-4 Verification Model does not explicitly account for side information bits in its optimization and suffers from poor compression efficiency at low bit rates. We reformulate the encoding problem as one of optimal parameter selection, where the side information bits are taken into account, so as to minimize the noise to mask ratio for the given target bit rate. The optimal solution is determined by a dynamic programming procedure that efficiently searches through a trellis. This trellis-based optimization greatly improves the low bit rate performance of AAC and, consequently, the performance of a multi-layer AAC system. The resulting bit stream is standard-compatible, and additional complexity due to the proposed optimization is only incurred at the encoder.
Benign Recurrent Intrahepatic Cholestasis Type 2 in Siblings with Novel ABCB11 Mutations (2019)

Benign recurrent intrahepatic cholestasis (BRIC), a rare cause of cholestasis, is characterized by recurrent episodes of cholestasis without permanent liver damage. BRIC type 2 (BRIC2) is an autosomal recessive disorder caused by <i>ABCB11</i> mutations. A 6-year-old girl had recurrent episodes of jaundice. At two months of age, jaundice and hepatosplenomegaly developed. Liver function tests showed cholestatic hepatitis. A liver biopsy revealed diffuse giant cell transformation, bile duct paucity, intracytoplasmic cholestasis, and periportal fibrosis. An <i>ABCB11</i> gene study revealed novel compound heterozygous mutations, including c.2075+3A>G in IVS17 and p.R1221K. Liver function test results were normal at 12 months of age. At six years of age, steatorrhea, jaundice, and pruritus developed. Liver function tests improved following administration of phenylbutyrate and rifampicin. Her younger brother developed jaundice at two months of age and his genetic tests revealed the same mutations as his sister. This is the first report of BRIC2 confirmed by <i>ABCB11</i> mutations in Korean siblings.