gebhart/patrepeval huggingface dataset:
Prevalence of Periodontitis in Adults in the United States: 2009 and 2010 (2012)

This study estimated the prevalence, severity, and extent of periodontitis in the adult U.S. population, with data from the 2009 and 2010 National Health and Nutrition Examination Survey (NHANES) cycle. Estimates were derived from a sample of 3,742 adults aged 30 years and older, of the civilian non-institutionalized population, having 1 or more natural teeth. Attachment loss (AL) and probing depth (PD) were measured at 6 sites per tooth on all teeth (except the third molars). Over 47% of the sample, representing 64.7 million adults, had periodontitis, distributed as 8.7%, 30.0%, and 8.5% with mild, moderate, and severe periodontitis, respectively. For adults aged 65 years and older, 64% had either moderate or severe periodontitis. Eighty-six and 40.9% had 1 or more teeth with AL ≥ 3 mm and PD ≥ 4 mm, respectively. With respect to extent of disease, 56% and 18% of the adult population had 5% or more periodontal sites with ≥ 3 mm AL and ≥ 4 mm PD, respectively. Periodontitis was highest in men, Mexican Americans, adults with less than a high school education, adults below 100% Federal Poverty Levels (FPL), and current smokers. This survey has provided direct evidence for a high burden of periodontitis in the adult U.S. population.
Simple Fabrication of Asymmetric High-Aspect-Ratio Polymer Nanopillars by Reusable AAO Templates (2011)

We present a simple method of utilizing anodized aluminum oxide (AAO) as a reproducible template for fabricating high-aspect-ratio uniformly bent polymeric nanopillars that can be used as a physical adhesive. It is shown how to achieve straight high-aspect-ratio nanopillars with concepts of the work of adhesion and lateral collapse between polymer pillars without serious damage to the master template. With the support of manufacturing polymeric nanopillars from the reusable AAO, a simple route to asymmetric dry adhesive nanopillars bent by residual stresses was demonstrated.
Characteristics of triple-negative breast cancer (2010)

TNBC and BBC are not the same disease entity. The TNBBC subtype shows the largest homogeneity in terms of tumour development, prognosis and clinical intervention options.
The Vertical Replacement-Gate (VRG) MOSFET: a 50-nm vertical MOSFET with lithography-independent gate length (2003)

We have fabricated and demonstrated a new device called the Vertical Replacement-Gate (VRG) MOSFET. This is the first MOSFET ever built that combines (1) a gate length controlled precisely through a deposited film thickness, independently of lithography and etch, and (2) a high-quality gate oxide grown on a single-crystal Si channel. In addition to this unique combination, the VRG-MOSFET includes a self-aligned S/D formed by solid source diffusion (SSD) and small parasitic overlap, junction, and S/D capacitances. The drive current per /spl mu/m of coded width is significantly higher than that of advanced planar MOSFETs because each rectangular device pillar (with a thickness of minimum lithographic dimension) contains two MOSFETs driving in parallel. All of this is achieved using current manufacturing methods, materials, and tools, and competitive devices with 50-nm gate lengths (L/sub G/) have been demonstrated without advanced lithography.
Autologous bone marrow transplantation in B-cell non-Hodgkin's lymphoma: very low treatment-related mortality in 100 patients in sensitive relapse. (1990)

One hundred patients with B-cell non-Hodgkin's lymphoma (NHL) in sensitive relapse or incomplete first remission underwent high-dose chemoradiotherapy and anti-B-cell monoclonal antibody (MAb)-treated autologous bone marrow transplantation (ABMT). These patients demonstrated good performance status with a Karnofsky score of 80% or greater. The majority of these patients had one or more adverse prognostic features including a failure to achieve a complete remission (CR) with conventional combination chemotherapy (37 patients), bone marrow infiltration (69 patients), a history of extranodal disease other than bone marrow infiltration (42 patients), and histologic conversion (18 patients). At the time of ABMT, only 52 patients were in CR; however, all patients achieved a minimal disease state following conventional intensive therapy. Moreover, at the time of marrow harvest, 37 of these patients had histologic evidence of lymphoma cells infiltrating the marrow. Following high-dose ablative therapy, two acute in-hospital treatment-related deaths were observed. Two late deaths were observed, not due to recurrent lymphoma. Of the remaining 96 patients, 61 are in unmaintained CR with a median follow-up of 13 months. Kaplan-Meier actuarial analysis predicts 50% probability of disease-free survival (DFS) at 37.8 months. This very low treatment-related mortality provides the rationale to apply high-dose therapy and ABMT as consolidative therapy for patients in first remission who are at high risk for relapse following conventional therapy.
Characterization of a Rhodospirillum rubrum plasmid: loss of photosynthetic growth in plasmidless strains (1983)

A single plasmid of 55 kilobases was found in crude cell lysates of each of nine strains of Rhodospirillum rubrum. Restriction endonuclease analysis showed identical fragment patterns with a given nuclease for all plasmids except one, for which an additional EcoRI site was observed. Elimination of the plasmid required that the cells be passaged several times in 25 mM calcium-containing medium, followed by at least two passages under photosynthetic growth conditions in low-calcium medium before treatment with ethyl methanesulfonate. The resulting plasmidless mutants only grew aerobically and were all incapable of pigment formation and photosynthetic growth, suggesting that plasmid DNA is required for photosynthetic competence in R. rubrum.
SPARC antagonizes the effect of basic fibroblast growth factor on the igration of bovine aortic endothelial cells (1992)

Migration of endothelial cells is requisite to wound repair and angiogenesis. Since the glycoprotein SPARC (secreted protein, acidic and rich in cysteine) is associated with remodeling, cellular migration, and angiogenesis in vitro, we questioned whether SPARC might influence the motility of endothelial cells. In this study we show that, in the absence of serum, exogenous SPARC inhibits the migration of bovine aortic endothelial cells induced by bFGF. Similar results were obtained from two different assays, in which cell migration was measured in a Boyden chamber and in monolayer culture after an experimental wound. Without bFGF, the migration of endothelial cells was unaffected by SPARC. The inhibitory effect of SPARC on cell motility was dose-dependent, required the presence of Ca2+, was mimicked by synthetic peptides from the N- and C-terminal Ca(2+)-binding domains of the protein, and was not seen in the presence of serum. Modulation of the activities of secreted and cell-associated proteases, including plasminogen activators and metalloproteinases, appeared not to be responsible for the effects that we observed on the motility of endothelial cells. Moreover, a molecular interaction between SPARC and bFGF was not detected, and SPARC did not interfere with the binding of bFGF to high-affinity receptors on endothelial cells. Finally, in culture medium that contained serum, SPARC inhibited the incorporation of [3H]-thymidine into newly synthesized DNA, both in the absence and presence of bFGF. However, DNA synthesis was not affected by SPARC when the cells were plated on gelatin or fibronectin in serum-free medium. We propose that the combined action of a serum factor and SPARC regulates both endothelial cell proliferation and migration and coordinates these events during morphogenetic processes such as wound repair and angiogenesis.
Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production (2010)

Our results confirm that glucose fermentations among the tested strains are effective even at high solids loading (18% by weight). However, xylose consumption in the lignocellulosic hydrolysate is the major bottleneck affecting overall yield, titer or rate of the process. In comparison, Saccharomyces cerevisiae 424A(LNH-ST) is the most relevant strains for industrial production for its ability to ferment both glucose and xylose from undetoxified and unsupplemented hydrolysate from AFEX-pretreated corn stover at high yield.
Expression of Fc mu receptors by human T lymphocytes: effects of enzymes, metabolic inhibitors, and X-irradiation. (1981)

Abstract The expression of Fcµ receptors by purified human peripheral blood T lymphocytes during culture was studied using a rosette technique with rabbit IgM antibody-coated ox erythrocytes (EOx-IgM). Unbound Fcµ receptors were not detected on freshly isolated purified T cells before or after treatment with 50 U/ml neuraminidase (Vibrio comma). Optimal detection of unbound receptors required culture of viable T cells for 24 hr at 37°C in RPMI-1640 medium with FCS, or in Iscove’s medium without FCS. Freshly isolated T cells treated with sodium azide did not express Fcµ receptors, nor did T cells cultured at 4°C. A reduced number of T cells expressed Fcµ receptors after incubation in RPMI-1640 medium without FCS. A direct influence of T cell protein synthesis on Fcµ receptor expression is likely, since T cells cultured with puromycin or cycloheximide or briefly treated with actinomycin D or mitomycin C prior to culture displayed parallel temporal inhibition of EOx-IgM rosette formation and 3H-leucine incorporation. Freshly isolated T cells irradiated with 500 to 5000 R before culture also displayed parallel temporal inhibition of EOx-IgM rosette formation and 3H-leucine incorporation. No impairment of optimal EOx-IgM rosette formation occurred in control T lymphocytes cultured for 24 hr then treated with metabolic inhibitors or x-irradiation before rosetting, which suggests that their effects did not directly influence the receptor-ligand interaction itself. However, treatment of these cultured control T cells with trypsin or IgM but not neuraminidase before rosetting subsequently decreased these cells’ EOx-IgM rosette formation. These findings suggest the expression of Fcµ receptors by cultured T cells as detected by EOx-IgM rosette formation is critically dependent on intracellular events, principally protein synthesis, whereas the interaction of receptor and ligand leading to rosette formation is principally dependent on the absence of a competitive ligand, i.e., unbound IgM.
Single- and multiple-wavelength operation of acoustooptically tuned semiconductor lasers at 1.3 mu m (1989)

Electronic tuning of a 1.3- mu m InGaAsP semiconductor laser over a wavelength range of 0.083 mu m (83 nm) using an acoustooptic filter in an external cavity configuration is discussed. Both single- and multiple-wavelength operation were achieved. Chirping modes of the cavity were eliminated by placing a second acoustooptic filter inside the cavity. Linearity of the chirping modes was verified experimentally.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Methods for evaluating the progression of osteoarthritis. (2000)

This article discusses methods for evaluating the progression of osteoarthritis through dynamic functional imaging as opposed to current static techniques. Comparison is made between static and dynamic methods of evaluating knee alignment. The correlation between dynamic knee moments during gait and bone mineral content is discussed. Knee loading is considered in terms of high tibial osteotomy, knee braces, pain, and non-steroidal anti-inflammatory drugs. New image-processing techniques for quantitating cartilage loss are described, and computational methods for generating true three-dimensional (3-D) maps of cartilage thickness are developed. Finally, new approaches to cross-correlate magnetic resonance images with kinematic measurements are described. These new techniques promise to become powerful diagnostic tools to detect and characterize pathological load distributions across articular cartilage.
De novo formation of several features of a centromere following introduction of a Y alphoid YAC into mammalian cells (1994)

The DNA sequence requirements for mammalian centromere function have been investigated by re-introducing human YAC clones containing either centromeric or non-centromeric sequences into hamster and human cells. All YACs integrated into the host chromosomes. In most cell lines produced by spheroplast fusion into hamster cells, intact copies of the YAC and a large amount of yeast DNA were found. Cell lines produced by lipofection into human cells usually contained simple structures without yeast DNA. YACs containing Y alphoid DNA reformed several of the properties of a centromere, including a cytogenetically visible constriction, CREST antiserum binding and disruption of anaphase chromosome movement. In contrast, YACs containing non-centromeric sequences produced none of these results. This work suggests that a few hundred kb of alphoid DNA is sufficient to reconstitute several important features of a centromere.
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007)

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.
Syntheses of 2-deoxo-2-phenyl-5-deazaflavins and 3-phenyl-5-deazaflavins and their use in the oxidation of benzyl alcohol and benzylamine. (1980)

Treatment of 6-(N-alkylanilino)-2-phenylpyrimidin-4 (3H)-ones, which were prepared by the condensation of 6-chloro-2-phenylpyrimidin-4 (3H)-one with N-alkylanilines, with the Vilsmeier reagent (dimethylformamide-phosphoryl chloride) gave the corresponding 10-alkyl-2-deoxo-2-phenyl-5-deazaflavins (III) in excellent yields. Heating of 6-chloro-5-formyl-3-phenyluracil with N-alkylanilines in dimethylformamide gave the corresponding 10-alkyl-3-phenyl-5-deazaflavins (VI) in a single step. The abilities of the 5-deazaflavins (III) and (VI) thus obtained to oxidize benzyl alcohol and benzylamine were compared, and some automatic recycling of the oxidation reactions was observed. The reaction of compounds III with benzylamine exceptionally gave the adducts, 5-benzylamino-2-deoxo-2-phenyl-5-deazaflavins.
IL-6 mediates hypoferremia of inflammation by inducing the synthesis of the iron regulatory hormone hepcidin (2004)

Hypoferremia is a common response to systemic infections or generalized inflammatory disorders. In mouse models, the development of hypoferremia during inflammation requires hepcidin, an iron regulatory peptide hormone produced in the liver, but the inflammatory signals that regulate hepcidin are largely unknown. Our studies in human liver cell cultures, mice, and human volunteers indicate that IL-6 is the necessary and sufficient cytokine for the induction of hepcidin during inflammation and that the IL-6-hepcidin axis is responsible for the hypoferremia of inflammation.
Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri (2013)

The strains of Xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly all X. axonopodis pv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1(s)) strains have been observed to be resistant to Cp2 (Cp2(r)) and vice versa. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to the Siphoviridae. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3'-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that of Xanthomonas phage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologically Escherichia coli T7-like phages of Podoviridae. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection of X. axonopodis pv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.
8×256Gbps Virtual-Carrier Assisted WDM Direct-Detection Transmission over a Single Span of 200km (2017)

We demonstrate 8×215Gbps net-data-rate WDM transmissions at 1550nm with virtual carriers over a record span length of 200km, in which each channel was detected by a single photodiode with either Kramers-Kronig detection or a low-complexity interference cancellation scheme.
Synthesis and Biological Evaluations of 3-Substituted Indolin-2-ones:  A Novel Class of Tyrosine Kinase Inhibitors That Exhibit Selectivity toward Particular Receptor Tyrosine Kinases (1998)

3-Substituted indolin-2-ones have been designed and synthesized as a novel class of tyrosine kinase inhibitors which exhibit selectivity toward different receptor tyrosine kinases (RTKs). These compounds have been evaluated for their relative inhibitory properties against a panel of RTKs in intact cells. By modifying the 3-substituted indolin-2-ones, we have identified compounds which showed selective inhibition of the ligand-dependent autophosphorylation of various RTKs at submicromolar levels in cells. Structure-activity analysis for these compounds and their relative potency and selectivity to inhibit particular RTKs has determined that (1) 3-[(five-membered heteroaryl ring)methylidenyl]indolin-2-ones are highly specific against the VEGF (Flk-1) RTK activity, (2) 3-(substituted benzylidenyl)indolin-2-ones containing bulky group(s) in the phenyl ring at the C-3 position of indolin-2-ones showed high selectivity toward the EGF and Her-2 RTKs, and (3) the compound containing an extended side chain at the C-3 position of the indolin-2-one (16) exhibited high potency and selectivity when tested against the PDGF and VEGF (Flk-1) RTKs. Recent published crystallographic data for two of these 3-substituted indolin-2-ones provides a rationale to suggest that these compounds may bind in the ATP binding pocket of RTKs. The structure-activity analysis supports the use of subsets of these compounds as specific chemical leads for the development of RTK-specific drugs with broad application for the treatment of human diseases.
Normal and Abnormal Biology of the beta-Amyloid Precursor Protein (1994)

Few macromolecules have become the object of more intense chemical and biological scrutiny in recent years than has the l3-amyloid precursor protein. This highly conserved and widely expressed integral membrane protein is the focus of a rapidly growing number of studies aimed at its characterization by protein chemical, molecular biological , cell biological , and neuroanatomical methods. The principal reason for this attention is clear. The early promise that a 39-43 residue fragment of I3APP, the amyloid l3-protein (AI3), might play a central role in the pathogenesis of Alzheimer's disease has increasingly been borne out. Although there is still substantial debate about exactly when AI3 becomes involved in Alzheimer's disease and how attractive a therapeutic target it represents , accumulating evidence now points to an early and sometimes causative role in the pathogenetic cascade. I3APP has become a compelling example of the phenomenon of research that begins with a strictly disease-oriented focus giving rise to novel insights about the normal biology of a whole family of macromolecules, in this case about the processing of certain cell surface, single membrane-spanning polypeptides. Here, I review recent information about the normal structure and function of I3APP and how its AI3 fragment contributes to Alzheimer's disease. Such
US FDA-approved therapeutic antibodies with high-concentration formulation: summaries and perspectives (2021)

Thirty four (34) of the total US FDA approved 103 therapeutic antibody drugs, accounts for one third of the total approved mAbs, are formulated with high protein concentration (100 mg/mL or above) which are the focus of this article. The highest protein concentration of these approved mAbs is 200 mg/mL. The dominant administration route is subcutaneous (76%). Our analysis indicates that it may be rational to implement a platform formulation containing polysorbate, histidine and sucrose to accelerate high concentration formulation development for antibody drugs. Since 2015, the FDA approval numbers are significantly increased which account for 76% of the total approval numbers, i.e., 26 out of 34 highly concentrated antibodies. Thus, we believe that the high concentration formulations of antibody drugs will be the future trend of therapeutic antibody formulation development, regardless of the challenges of highly concentrated protein formulations.