gebhart/patrepeval huggingface dataset:
Third Molar Development in the Estimation of Chronologic Age in American Blacks as Compared With Whites* (2007)

Third molar (M3) development determined from dental radiographs in American blacks (African Americans; n=637) aged 14-24 years was contrasted against American whites (n=563) from a previous study using the method of Demirjian et al. Differences were assessed using descriptive statistics and the parametric proportional hazards model. For each developmental stage, the probability of an individual being at least 18 years old was evaluated. As in other M3 studies, there were highly significant modal differences, but the age ranges at each stage overlapped considerably. Black-white differences were highly significant with developmental stages occurring in blacks a year or so earlier. Gender differences also varied significantly, both with increasing age and between races. The empirical likelihood that an African American male with fully developed M3's is at least 18 years old is 93% and that for African American female is 84%. Corresponding risks for whites are 90% and 93%.
A first-in-human phase 1 study of a hepcidin monoclonal antibody, LY2787106, in cancer-associated anemia (2017)

ClinicalTrial.gov, NCT01340976.
Design of Antisense RNA Constructs for Downregulation of the Acetone Formation Pathway of Clostridium acetobutylicum (2003)

We investigated the effect of antisense RNA (asRNA) structural properties on the downregulation efficacy of enzymes in the acetone-formation pathway (acetoacetate decarboxylase [AADC] and coenzyme A-transferase [CoAT]) of Clostridium acetobutylicum strain ATCC 824. First, we generated three strains, C. acetobutylicum ATCC 824 (pADC38AS), 824(pADC68AS), and 824(pADC100AS), which contain plasmids that produce asRNAs of various lengths against the AADC (adc) transcript. Western analysis showed that all three strains exhibit low levels of AADC compared to the plasmid control [ATCC 824(pSOS95del)]. By using computational algorithms, the three different asRNAs directed toward AADC, along with previously reported clostridial asRNAs, were examined for structural features (free nucleotides and components). When the normalized metrics of these structural features were plotted against percent downregulation, only the component/nucleotide ratio correlated well with in vivo asRNA effectiveness. Despite the significant downregulation of AADC in these strains, there were no concomitant effects on acetone formation. These findings suggest that AADC does not limit acetone formation and, thus, we targeted next the CoAT. Using the component/nucleotide ratio as a selection parameter, we developed three strains [ATCC 824 (pCTFA2AS), 824(pCTFB1AS), and 824(pCOAT11AS)] which express asRNAs to downregulate either or both of the CoAT subunits. Compared to the plasmid control strain, these strains produced substantially low levels of acetone and butanol and Western blot analyses showed significantly low levels of both CoAT subunits. These results show that CoAT is the rate-limiting enzyme in acetone formation and strengthen the hypothesis that the component/nucleotide ratio is a predictive indicator of asRNA effectiveness.
Accelerated telomere shortening and telomerase activation in Fanconi's anaemia (1999)

Fanconi's anaemia (FA) is an autosomal recessive disorder characterized by progressive bone marrow failure that often evolves towards acute leukaemia. FA also belongs to a group of chromosome instability diseases. Because telomeres are directly involved in chromosomal stability and in cell proliferation capacity, we examined telomere metabolism in peripheral blood mononuclear cells (PBMC). Telomere length was significantly shorter in 54 FA patient samples, compared to 51 controls (P<0.0001). In addition, mean telomere terminal restriction fragment lengths (TRF) in nine heterozygous patient samples did not differ from those of controls. In 14 samples from FA patients with severe aplastic anaemia (SFA), telomere length was significantly shorter than in 22 samples of age-matched FA patients with moderate haematological abnormalities (NSFA) (P<0.001). However, no correlation was found between TRF length and the presence of bone marrow clonal abnormalities in 16 additional, separately analysed, patient samples. Sequential measurement of TRF in six FA patients showed an accelerated rate of telomere shortening. Accordingly, telomere shortening rate was inversely correlated with clinical status. Telomerase, the enzyme that counteracts telomere shortening, was 4.8-fold more active in 25 FA patients than in 15 age-matched healthy controls. A model for the FA disease process is proposed.
Future of Early Detection of Lung Cancer: The Role of Mouse Models (2005)

Early detection represents one of the most promising approaches to improving lung cancer survival. To date, no screening strategies have been shown to decrease mortality from the disease. Furthermore, no reliable circulating biomarkers of lung cancer have been identified that allow early diagnosis. With the advent of gene targeting technology, new genetically engineered mouse models of lung cancer closely recapitulate the pathobiology of human disease. These mouse models have enabled novel approaches to early detection, including the identification of cancer-associated serum markers using proteomic technologies and the development of new molecular imaging tools. The application of innovative technologies to accurate mouse models promises to accelerate the discovery of new molecular targets and imaging biomarkers for the early detection of lung cancer.
The Association Rate Constant for Heme Binding to Globin Is Independent of Protein Structure (1996)

Rate constants for CO-heme binding to 35 different recombinant apomyoglobins and several other apoproteins were measured in an effort to understand the factors governing heme affinity and the velocity of the association reaction. Surprisingly, the rate constant for the binding of monomeric heme is approximately 1 x 10(8) M-1 s-1 regardless of the structure or overall affinity of the apoprotein for iron-porphyrin. Major differences between the proteins are reflected primarily in the rates of dissociation of the prosthetic group. Slow phases observed in the reaction of CO heme with excess apomyoglobin result from formation of nonspecific heme-protein complexes which must dissociate before heme can bind specifically in the heme pocket. Once the specific heme-globin complex is formed, the heme pocket rapidly collapses around the porphyrin, simultaneously forming the bond between the proximal His93 and the heme iron atom. The overall affinity of sperm whale apomyoglobin for hemin is approximately 1 x 10(14) M-1. Nonspecific hydrophobic interactions between the porphyrin and the apolar heme cavity account for a factor of 10(5)-10(7). Covalent bond formation between Fe3+ and His93(F8) provides an additional factor of 10(3)-10(4). Specific interactions with conserved amino acids in the heme pocket contribute the final factor of 10(3)-10(4).
The potential impact of percutaneous pulmonary valve stent implantation on right ventricular outflow tract re-intervention (2005)

Preliminary data suggests that percutaneous pulmonary valve implantation provides a promising additional and complementary approach to a successful surgical programme. Both approaches are safe with acceptable levels of morbidity and low mortality. With current technology the aneurysmal outflow tract remains a problem for the percutaneous approach. Follow-up remains too short, at present, to prove longevity of the percutaneous conduit.
Chemical‐shift artifact correction scheme using echo‐time encoding technique (1985)

An investigation has been undertaken to study the effects of chemical shift on NMR image obtained by the projection reconstruction technique. Mathematical simulation studies indicate that chemical shift causes blurring in NMR images regardless of the image reconstruction technique. A systematic study of such artifacts is presented and possible correction schemes are proposed. Exemplary results with and without correction of the chemical-shift artifact and pulse schemes employed for projection reconstruction are presented. The present chemical-shift correction scheme is basically the same as a spectroscopic imaging technique such as the existing 4-D NMR imaging method except that the encoding steps required can be reduced substantially in the case of modest spectroscopic resolution.
A functional role for vimentin intermediate filaments in the metabolism of lipoprotein-derived cholesterol in human SW-13 cells. (1992)

Numerous studies have indicated that cytoplasmic intermediate filaments (cIFs) can associate with cellular lipids. To determine if these interactions might have functional consequences, we have studied the lipid metabolism of human SW-13 adrenal tumor cell lines that either contain vimentin-type cIFs (vim+) or lack any detectable cIF network (vim-). Although there were no significant differences in phospholipid or glyceride synthesis, vim- cell lines had elevated levels of cholesterol synthesis and decreased cholesterol esterification, compared with vim+ cells. These differences in cholesterol synthesis and esterification were found to be due to an impaired ability of vim- cells to utilize low density lipoprotein (LDL)-derived cholesterol, although receptor-mediated endocytosis of LDL and the capacity of these cells to esterify endogenously produced cholesterol were not affected. Expression of a mouse vimentin cDNA in stably transfected cell lines, derived from vim- cells, restored the capacity of these cells to utilize LDL cholesterol. The uptake and metabolism of [3H]cholesterol linoleate-loaded LDL showed that the impaired ability of vim- cells to esterify LDL cholesterol was not associated with an accumulation of cellular free cholesterol but rather an increase in the appearance of [3H]cholesterol in the culture medium. These studies indicate that in SW-13 cells, the intracellular movement of LDL-derived cholesterol from the lysosome to the site of esterification is a vimentin-dependent process.
The activity of the tissue inhibitors of metalloproteinases is regulated by C-terminal domain interactions: A kinetic analysis of the inhibition of gelatinase A (1993)

The cloning and expression of the full-length tissue inhibitor of metalloproteinase 2 (TIMP-2), delta 187-194TIMP-2, and delta 128-194TIMP-2 and the purification of these inhibitors and a cleaved version of TIMP-2 lacking nine C-terminal amino acids (delta 186-194TIMP-2) are described. The mechanism of inhibition of gelatinase A by the TIMPs was investigated by comparing the kinetics of association of TIMP-1, TIMP-2, the C-terminal deletions, and the mutants of both TIMPs which consisted of the N-terminal domain only. The full-length TIMPs inhibited gelatinase A rapidly with association constants of 3.2 x 10(6) M-1 s-1 for TIMP-1 and 2.1 x 10(7) M-1 s-1 for TIMP-2 at I = 0.2. The C-terminal peptide of TIMP-2 is proposed to exist as an exposed "tail" responsible for binding to progelatinase A and for increasing the rate of inhibition of active gelatinase A through electrostatic interactions with the C-terminal domain of the enzyme. The C-terminal domains of both TIMP-1 and TIMP-2 participate in low-affinity interactions with the C-terminal domain of gelatinase A which increase the rate of association by a factor of about 100 in both cases.
Structure of a factor VIII C2 domain–immunoglobulin G4κ Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII (2001)

The development of an immune response to infused factor VIII is a complication affecting many patients with hemophilia A. Inhibitor antibodies bind to antigenic determinants on the factor VIII molecule and block its procoagulant activity. A patient-derived inhibitory immunoglobulin G4kappa antibody (BO2C11) produced by an immortalized memory B-lymphocyte cell line interferes with the binding of factor VIII to phospholipid surfaces and to von Willebrand factor. The structure of a Fab fragment derived from this antibody complexed with the factor VIII C2 domain was determined at 2.0 A resolution. The Fab interacts with solvent-exposed basic and hydrophobic side chains that form a membrane-association surface of factor VIII. This atomic resolution structure suggests a variety of amino acid substitutions in the C2 domain of factor VIII that might prevent the binding of anti-C2 inhibitor antibodies without significantly compromising the procoagulant functions of factor VIII.
Separation and Purification of Recombinant Thymosin Alpha 1 and Interferon alfacon-1 Fusion Protein (2009)

BACKGROUND: It demonstrated that combined application of thymosin α1 (TM-α1) and interferon (IFN) can enhance the antiviral activity of IFN.
OBJECTIVE: To obtain recombinant fusion protein of TM-α1 and consensus IFNα(IFNα-con) with double activity of antiviral activity and immunity enhancement.
DESIGN, TIME AND SETTING: The in vitro contrast experiment was conducted in the Biochemical Laboratory of Research Institute of Medicine, Chongqing K.E.W Pharmaceutical Co., Ltd. from March 2003 to December 2004.
MATERIALS: The fusion gene fragment (TM-α1+IFNα-con) was synthesized by Shanghai Sangon Biological Engineering Technology And Service Co., Ltd, WISH cell, and vesicular stomatitis virus (VSV) was purchased from Institute of Biochemistry and Cell Biology, commercial products of IFNα1b, IFNα2a and TM-α1 was served as reference substance.
METHODS: The preference for E. coli of fusion sequence coding TM-α1 and IFNα-con were cloned into expression vector of pET-22b(+) and expressed in BL21(DE3)-Codon plus-RP-X, which was purified by precipitation of (NH4)2SO4, hydrophobic interaction chromatography, anion-exchange chromatography, cation-exchange chromatography and molecular exclusion chromatography. The antiviral activity of fusion protein was tested by cytopathic-effect inhibition assay, and effect of fusion protein on lymphocyte proliferation was tested by cell proliferative assay.
MAIN OUTCOME MEASURES: The specific activity of fusion protein and its biological activity in promoting lymphocyte proliferation.
RESULTS: The fusion protein was expressed as a soluble form, accounting for over 20% of the total cell protein in E. coli, which approached 96% after purification. The antiviral activity of fusion protein was superior to IFNα1b and IFNα2a. However, the activity of fusion protein for promoting lymphocyte proliferation was similar to TM-α1.
CONCLUSION: The fusion protein of TM-α1 and IFNα-con expressed in E. coli has both effects on anti-virus and promoting lymphocyte proliferation.
Nonaqueous Biocatalytic Degradation of a Nerve Gas Mimic (1995)

Organophosphorus hydrolase has been shown to be an effective catalyst for the continuous decontamination of a nerve agent in a continuous gas phase reactor. Very small quantities of the enzyme are sufficient to enable detoxification of low concentrations of the nerve agent for extended periods of time. In the case where the nerve agent is at high concentrations (a liquid), the enzyme has also been shown to be active in biphasic mixtures of a solvent with water. The activity and specificity of the enzyme in both environments (continuous gas phase and biphasic mixture) obey classical models of enzyme kinetics. The activity of the enzyme in such extreme environments enables optimization of systems capable of continuous gas or liquid phase biocatalytic degradation of highly toxic chemicals.
Cytochrome P450 Protocols (2013)

Cytochromes P450 (CYPs) comprise a large superfamily of proteins that are of central importance in the detoxification or activation of a tremendous number of natural and synthetic hydrophobic xenobiot
Network Formation and Degradation Behavior of Hydrogels Formed by Michael-Type Addition Reactions (2004)

Hydrolytically labile poly(ethylene glycol)-based hydrogels are fabricated via a Michael-type addition reaction between unsaturated acrylate moieties and nucleophilic thiols. Although these gels offer the advantage of selective, in situ polymerization and potential as biocompatible matrixes for cell and protein encapsulation, a thorough understanding of the complex structure-property relationships that control the macroscopic behaviors of these cross-linked networks before and during hydrolytic degradation does not exist. Therefore, in this work, a novel theoretical model is presented to describe the formation and hydrolytic degradation of the step-polymerized gels. The model accounts for variations in hydrolysis kinetics as well as structural effects such as precursor functionality and the presence of primary cycles or other structural nonidealities that lower the cross-linking efficiency of the networks. Comparison of model predictions and experimental data validate this methodology for optimizing biomaterial design and reveal that structural nonidealities play a key role in determining the degradation behavior of real cross-linked systems. Decreasing precursor concentration and functionality during network formation generate high concentrations of network nonidealities that ultimately lead to higher initial swelling ratios and faster apparent rates of degradation.
Single-mode waveguide propagation and reshaping of sub-ps terahertz pulses in sapphire fibers (2000)

Waveguide propagation of sub-ps terahertz pulses in single-crystal sapphire fibers is reported. An incident THz pulse of approximately 0.6 ps duration undergoes considerable reshaping due to the absorptive and dispersive waveguide propagation, resulting in transmitted chirped pulse durations of 10–30 ps. Good agreement between theory and experiment is obtained by analyzing the propagation in terms of the single HE11 waveguide mode. The dominance of the single HE11 mode, despite the fiber dimensions allowing for multimode propagation, is attributed to the free-space to waveguide coupling.
A steady-state throughput analysis of cluster tools: dual-blade versus single-blade robots (1997)

An analysis of throughput in a cluster tool with a dual-blade robot operating in steady-state mode is presented. The analysis is based on a single-wafer serial processing cluster tool. Two types of schedules are distinguished, called transport-bound schedules and process-bound schedules. In a transport-bound schedule changes in process times do not affect the throughput of the cluster tool, and denotes the maximum throughput achievable in the cluster tool. In a process-bound schedule, the process time predominates the effect on the throughput. The analysis indicates that a dual-blade robot improves the throughput of the cluster tool over a single-blade robot under process-bound conditions. Under process-bound conditions, a cluster tool with a single-blade robot would need to double the speed of the robot, compared with a dual-blade robot of equivalent speed, to achieve similar throughput. Under transport-bound conditions, the throughput of the cluster tool is the same for both dual-blade and single-blade cluster tools.
Impact of UWB interference on IEEE 802.11a WLAN system (2010)

The objective of this paper is to assess the effects of multiple UWB devices emission on the IEEE 802.11a WLAN receiver. The data rates and SINR of WLAN is evaluated with and without the UWB interference. Approximate path loss model is used to calculate the UWB signal power that interferes with the WLAN system. The three dimensional hemispherical distribution of UWB tramsmitters around the victim WLAN receiver is considered. Based on this model, the analytical analysis to assess the effect of the multiple UWB devices emission on the IEEE 802.11a system is presented.
Changes in hypertension treatment and in congestive heart failure mortality in the United States. (1989)

The use of antihypertensive agents has increased in recent years and has been more marked among individuals in older age groups (65-74 years) than in middle-aged groups (45-54 years). Because hypertension is a strong risk factor for the development of congestive heart failure, more common use of antihypertensive agents would be expected to reduce the incidence of congestive heart failure. Examination of the national death statistics reveals decreases in congestive heart failure mortality at younger ages with mortality increases at older ages. The reasons for these divergent trends in congestive heart failure mortality in different ages and the apparent inconsistency with respect to the changes in the use of antihypertensive drugs are explored. We speculate that antihypertensive treatment does not completely prevent congestive heart failure but merely postpones its development by several decades.
Real-time, accurate depth of field using anisotropic diffusion and programmable graphics cards (2004)

Computer graphics cameras lack the finite depth of field (DOF) present in real world ones. This results in all objects being rendered sharp regardless of their depth, reducing the realism of the scene. On top of that, real-world DOF provides a depth cue, that helps the human visual system decode the elements of a scene. Several methods have been proposed to render images with finite DOF, but these have always implied an important trade-off between speed and accuracy. We introduce a novel anisotropic diffusion partial differential equation (PDE) that is applied to the 2D image of the scene rendered with a pin-hole camera. In this PDE, the amount of blurring on the 2D image depends on the depth information of the 3D scene, present in the Z-buffer. This equation is well posed, has existence and uniqueness results, and it is a good approximation of the optical phenomenon, without the visual artifacts and depth inconsistencies present in other approaches. Because both inputs to our algorithm are present at the graphics card at every moment, we can run the processing entirely in the GPU. This fact, coupled with the particular numerical scheme chosen for our PDE, allows for real-time rendering using a programmable graphics card.
Human Leptospirosis (1975)

Human leptospirosis is a subject of increasing interest. Although this disease was frequently associated with individuals whose occupation or geographic location placed them in close proximity to wild animals or farm animals, recent cases have been particularly prevalent in young children and adolescents in urban and suburban America. Many of the recent cases have been acquired from household pets, particularly from dogs or hamsters. In particular, healthy dogs who have been immunized with leptospiral organisms, thereby creating a significant risk for their owners. This article will review the pathophysiology, clincal manifestations, laboratory diagnosis, treatment, and prevention of leptospirosis in the modern era, with particular emphasis on a more complete understanding of the epidemiology of this disorder.
Helix propensities of short peptides: Molecular dynamics versus bioinformatics (2003)

Knowledge-based potential functions for protein structure prediction assume that the frequency of occurrence of a given structure or a contact in the protein database is a measure of its free energy. Here, we put this assumption to test by comparing the results obtained from sequence-structure cluster analysis with those obtained from long all-atom molecular dynamics simulations. Sixty-four eight-residue peptide sequences with varying degrees of similarity to the canonical sequence pattern for amphipathic helix were drawn from known protein structures, regardless of whether they were helical in the protein. Each was simulated using AMBER6.0 for at least 10 ns using explicit waters. The total simulation time was 1176 ns. The resulting trajectories were tested for reproducibility, and the helical content was measured. Natural peptides whose sequences matched the amphipathic helix motif with greater than 50% confidence were significantly more likely to form helix during the course of the simulation than peptides with lower confidence scores. The sequence pattern derived from the simulation data closely resembles the motif pattern derived from the database cluster analysis. The difficulties encountered in sampling conformational space and sequence space simultaneously are discussed.