gebhart/patrepeval huggingface dataset:
Periostin, a matrix protein, is a novel biomarker for idiopathic interstitial pneumonias (2010)

Idiopathic interstitial pneumonias (IIPs) are histopathologically classified into several types, including usual interstitial pneumonia (UIP), nonspecific interstitial pneumonia (NSIP) and cryptogenic organising pneumonia (COP). We investigated whether periostin, a matrix protein, could be used as a biomarker to assess histopathological types of IIPs. We performed immunohistochemical analyses in each histopathological type of IIP, examined serum levels of periostin in IIP patients and analysed the relationship between serum levels of periostin and the pulmonary functions in patients with idiopathic pulmonary fibrosis (IPF). Periostin was strongly expressed in lungs of UIP and fibrotic NSIP patients, whereas expression of periostin was weak in the lungs of cellular NSIP and COP patients, as well as in normal lungs. Serum levels of periostin in IPF were significantly higher than those of healthy subjects and COP patients. Furthermore, periostin levels in IPF patients were inversely correlated with their pulmonary functions. Thus, we have found that periostin is a novel component of fibrosis in IIP. Periostin may be a potential biomarker to distinguish IIP with fibrosis.
Tricalcium phosphate and glutaraldehyde crosslinked gelatin incorporating bone morphogenetic protein—A viable scaffold for bone tissue engineering (2005)

Bone defects caused by various etiologies must be filled with suitable substances to promote bone repair. Autogenous iliac crest graft is most frequently used, but is often associated with morbidities. Several bone graft substitutes have been developed to provide osteoconductive matrices as well as to enhance osteoinductivity. A tricalcium phosphate and glutaraldehyde crosslinked gelatin (GTG) scaffold, incorporated with bone morphogenetic proteins (BMPs), was developed to provide an alternative mean of bone tissue engineering. This study investigated differences between GTG and BMP-4 immobilized GTG (GTG-BMP) scaffolds on neonatal rat calvaria osteoblast activities. The GTG scaffold possessed an average pore size of 200 microm and a porosity of 75%. HE staining revealed uniform cell distribution throughout the scaffold 24 h post cell seeding. Alkaline phosphatase (ALP) activity of the GTG samples increased initially and then stabilized at 3 weeks postseeding. ALP activity of the GTG-BMP samples was similar to that of the GTG samples in the second and third weeks, but it continued increasing and became significantly greater than that of the GTG samples by the fourth week. Gla-type osteocalcin (Gla-OC) activity of the GTG-BMP samples was initially lower, but also became significantly greater than that of the GTG samples by the fourth week. An HE stain revealed greater numbers of attached cells and a richer matrix deposits in the GTG-BMP samples. A von Kossa stain showed larger mineralizing nodules, in greater numbers, after 4 weeks of in vitro cultivation. These findings suggest that the GTG scaffold provides an excellent porous structure, conductive to greater cell attachment and osteoblast differentiation, and that utility can be significantly enhanced by the inclusion of BMPs. A GTG-BMP scaffold holds promise as a superior bioactive material for bone tissue engineering.
Linear optical controlled-NOT gate in the coincidence basis (2002)

We describe the operation and tolerances of a nondeterministic, coincidence basis, quantum controlled-NOT gate for photonic qubits. It is constructed solely from linear optical elements and requires only a two-photon source for its demonstration. Its success probability is $1/9.$
Comparison of three rapid detection systems for type A influenza virus on tracheal swabs of experimentally and naturally infected birds (2004)

The present paper reports of the comparison between three rapid virus detection systems and virus isolation (VI) from pooled tracheal swabs collected from naturally and experimentally infected birds with a low pathogenicity avian influenza virus of the H7N3 subtype. The relative sensitivity, specificity and agreement (K value) were calculated for a commercial antigen capture enzyme immunoassay (AC-EIA) and for two nucleic acid detection tests, a one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and a real-time RT-PCR (RRT-PCR), both targeting the M gene. The results indicate that in experimentally infected turkeys VI was positive from the pooled tracheal swabs collected from day 3 to day 10. One-step RT-PCR was able to detect influenza RNA from samples collected from day 3 to day 12, while RRT-PCR amplified influenza RNA in swabs collected from day 3 to day 15. The AC-EIA test yielded positive results between day 5 and day 10 post-infection. On field samples, the K value between the AC-EIA and VI tests was 0.82. Compared with VI, the relative sensitivity of this test was 88.9% (CI95 = 85.2-92.6) and the relative specificity was 95.7% (CI95 = 93.7-97.7). The K value between the RT-PCR and VI tests was 0.88. Compared with virus isolation, the relative sensitivity of the one-step RT-PCR was 95.6% (CI95 = 93.1-98.0) and the relative specificity was 96.3% (CI95 = 94.4-98.1). The K value between the RRT-PCR and VI tests was 0.92. Compared with virus isolation, the relative sensitivity and specificity of RRT-PCR was 93.3% (CI95 = 90.4-96.3) and 98.4% (CI95 = 97.2-99.6), respectively. Generally speaking, comparison between virus isolation, the AC-EIA test and the two nucleic acid detection methods indicated excellent agreement. Data obtained from both experimental and field study suggest a higher sensitivity of the PCR-based methods compared with the AC-EIA. The economical and practical implications of using one of the rapid tests as an alternative to VI during an avian influenza epidemic are discussed.
Prognosis Versus Actual Outcome. IV. The Effectiveness of Clinical Parameters and IL‐1 Genotype in Accurately Predicting Prognoses and Tooth Survival (1999)

Knowledge of the patient's IL-1 genotype and smoking status will improve the clinician's ability to accurately assign prognosis and predict tooth survival. Clinical implications are as follows. Investigators were unable to judge which patients would be IL-GP or negative based on their clinical presentation or family history of tooth loss due to periodontal disease. Since periodontal diseases are multifactorial, knowledge of the patient's genotype is more important in predicting future risk than explaining past disease. Knowledge of IL-1 genotype status would be important in developing a treatment plan and predicting tooth survival for a new patient who smokes and presents with periodontal disease, especially if restorative care is needed. Knowledge of a maintenance patient's IL-1 status would help target therapy for non-responding areas; one would be less likely to take a "wait and see approach" with IL-1GP patients. IL-1 positive non-smokers can be successfully treated and maintained over long periods of time.
Combination of a Bispecific Antibody and Costimulatory Antibody-Ligand Fusion Proteins for Targeted Cancer Immunotherapy (2012)

Initiation of a tumor-directed immune response and appropriate modulation of its progress are key issues in cancer immunotherapy. Combinatorial strategies addressing both aspects might therefore be especially suitable. Here, we report a targeted approach combining a bispecific antibody with 2 costimulatory antibody-ligand fusion proteins. According to the concept, the bispecific antibody (scDbFAP×CD3) retargets T cells in a MHC-independent manner to tumor cells, providing an artificial first signal that allows the costimulatory antibody-ligand fusion proteins (B7.2-Db and scFv-4-1BBL) likewise targeted to the tumor cells to modulate the T-cell response. In our model system, the target cells coexpress the fibroblast activation protein (FAP) and endoglin as antigens. ScDbFAPCD3 and B7.2-Db are targeted to FAP although by different antibody moieties, whereas scFv-4-1BBL is directed against endoglin. ScDbFAPCD3-induced T-cell stimulation could be enhanced by the addition of either B7.2-Db or scFv-4-1BBL and even further by the combination of both as shown in terms of cytokine release (interleukin-2/interferon γ), proliferation and activation marker expression (CD25). By combined costimulation, overall T-cell population strongly increased in activation-experienced memory phenotype accompanied by a decrease in naive phenotype. ScFv-4-1BBL-mediated costimulation of naive CD8+ T cells promoted the expansion and development of cytotoxic T cells with strong effector potential. Thus, combining a bispecific antibody with antibody-ligand fusion protein-mediated CD28 and 4-1BB costimulation in a targeted approach shows great potential to generate and shape an immune response at the tumor site. Therefore, the adaptation of this approach to other immune modulatory ligands and tumor-relevant targets seems to be promising.
Designing information gathering robots for human-populated environments (2015)

Advances in mobile robotics have enabled robots that can autonomously operate in human-populated environments. Although primary tasks for such robots might be fetching, delivery, or escorting, they present an untapped potential as information gathering agents that can answer questions for the community of co-inhabitants. In this paper, we seek to better understand requirements for such information gathering robots (InfoBots) from the perspective of the user requesting the information. We present findings from two studies: (i) a user survey conducted in two office buildings and (ii) a 4-day long deployment in one of the buildings, during which inhabitants of the building could ask questions to an InfoBot through a web-based interface. These studies allow us to characterize the types of information that InfoBots can provide for their users.
Color variation with electroluminescent organic semiconductors in multimode resonant cavities (1994)

The range of possibilities in controlling the color of an organic semiconductor based light emitter diode (LED) by incorporating the active layers in a multimode Fabry–Pérot cavity is demonstrated. The combination of carefully designed multimode microcavities and electroluminescent organic semiconductors makes possible the realization of mixed colors such as white, purple, etc. with a single LED. The parameters affecting the color include the total optical thickness of the device and the position of the electromagnetic-field antinodes with respect to the location of the emitting dipoles. The electrical characteristics and quantum efficiency of such devices are also reported.
A Method for Evaluating Volt-VAR Optimization Field Demonstrations (2014)

In a regulated business environment, a utility must be able to validate that deployed technologies provide quantifiable benefits to the end-use customers. While there are well established procedures for determining the benefits derived from the deployment of traditional technologies, the same procedures do not exist for many emerging technologies. Volt-VAR Optimization is an example of an emerging technology that is being deployed across the nation without a standardized method for determining system performance and benefits. This paper will present a method for the evaluation, and quantification of benefits, for field deployments of Volt-VAR Optimization technologies. In addition to presenting the methodology, the paper will present a summary of results, and observations, from two separate Volt-VAR Optimization field evaluations using the presented method.
Inhibition of CXCR4 by CTCE-9908 inhibits breast cancer metastasis to lung and bone (2009)

Metastasis occurs, in part, due to tumor cell responses to chemokine secretion by ectopic organs or tissues. SDF-1 is constitutively expressed in tissues where metastases frequently develop while breast carcinoma cells express the receptor for SDF-1, CXCR4, which is correlated with increased bone metastasis and poor overall survival. We hypothesized that treatment with a CXCR4 antagonist, CTCE-9908, would decrease incidence of bone and lung metastasis. Treatment with CTCE-9908 (25 mg/kg) began the day prior to or the day of intravenous or intracardiac tumor cell inoculation of MDA-MB-231 human breast carcinoma cells expressing enhanced green fluorescent protein (GFP) into athymic mice. After 5 or 8 weeks (i.c. and i.v. injections, respectively), the presence of fluorescent foci at metastatic sites was assessed. Somewhat surprisingly, CTCE-9908 treatment did not decrease incidence of metastasis as hypothesized. However, CTCE-9908 did decrease metastatic burden (i.e., size of metastases) in all organs examined (lungs, bone, heart, liver, kidneys, pancreas and spleen). Based upon this and other studies, the use of CTCE-9908 is promising as an adjuvant therapy for metastatic disease.
DNA gene fusion vaccines against cancer. (2002)

The ability of DNA vaccination to induce effective immune responses has been shown in a range of preclinical disease models. However, the potency of DNA vaccines must be further improved for their use in patients. DNA fusion vaccine strategies, whereby target antigens are genetically linked to immuno-enhancing molecules, are currently being explored. The ease of DNA manipulation has allowed incorporation of a wide variety of molecules able to promote antigen uptake, processing and presentation by professional antigen-presenting cells, to provide critical CD4 T-cell help and to activate more effective immune effector pathways. These strategies are particularly important for cancer vaccines to increase their immunogenicity and to overcome tolerance.
Antibodies Against B7-DC with Differential Binding Properties Exert Opposite Effects (2012)

Programmed cell death 1 (PD-1) is an immunoregulatory receptor on T cells that binds two ligands, B7-H1 and B7-DC. Although accumulating reports suggest a critical role for the B7-H1:PD-1 pathway in peripheral tolerance, the actual involvement of B7-DC has not been well confirmed. Here, we established a new MAb against mouse B7-DC (MIH37) and compared its functional properties with a previously established anti-B7-DC MAb (TY25). Binding analyses using flow cytometry demonstrated that MIH37 showed an approximately four-fold higher binding affinity to B7-DC and stronger inhibitory effects on B7-DC:PD-1 binding. In contrast to the effects of TY25, treatment with MIH37 at both sensitization and challenge inhibited hapten-induced contact hypersensitivity reactions. Furthermore, the addition of MIH37 inhibited OVA-specific T cell responses in vitro. The inhibitory effects of MIH37 were counteracted by co-blockade with PD-1 and absent in PD-1-deficient mice, suggesting PD-1-dependent action of MIH37. Our present results suggest that greater complexities of PD-1-mediated functions are induced via ligand binding for controlling immunity and tolerance.
Requirements for identity management in next generation networks (2004)

Identity management will become crucial to the success of Next Generation Networks (NGN). However, until now very little research has been done in this field. This paper presents the requirements for identity management in NGN which are currently being investigated by our research group. Our analysis is based on the characteristics and requirements of NGN architectures, services, network operators, end users, identity management requirements for web services, recent standardization efforts by various bodies, etc.
Resistance-related mutations in the HIV-1 protease gene of patients treated for 1 year with the protease inhibitor ritonavir (ABT-538) (1996)

Long-term treatment with ritonavir is associated with the emergence of multiple mutations in the HIV-1 protease gene. The mutations L10I, I54V, L63P, A71V, V82A/F and I84V correspond to known drug-resistance mutations for ritonavir and other protease inhibitors. Phenotypic resistance to ritonavir was detected in a majority of ritonavir-treated patients at 1 year of treatment. In addition, long-term ritonavir treatment selects for cross-resistance to the protease inhibitors indinavir and saquinavir. This argues against sequential therapy with several protease inhibitors. Delayed resistance in one patient was accompanied with a prolonged increase in CD4 cell count and decrease in viral load suggesting a temporary benefit of treatment.
A double‐blind randomized controlled trial of oxytocin nasal spray in Prader Willi syndrome (2014)

Individuals with Prader-Willi syndrome (PWS) have a significant reduction in the number of oxytocin-producing neurons (42%) in the hypothalamic paraventricular nucleus. A number of animal studies and observations of humans show that lesions in this region can produce PWS-like symptoms. Given the evidence for potential oxytocin deficiency, we tested the effects of a course of intranasal oxytocin on PWS symptoms. Thirty individuals with PWS aged 12-30 years participated in an 18-week randomized double-blind placebo-controlled crossover trial. Participants received 8 weeks of oxytocin and 8 weeks of placebo with a minimum 2-week washout period. The first 11 participants received the following oxytocin doses: 24 IU (twice daily) B.I.D for participants 16 years and over and 18 IU B.I.D for participants 13-15 years. The dose was increased for the remaining 18 participants to 40 IU B.I.D for participants 16 years and over and 32 IU B.I.D for 13-15 years. Measures used to assess changes were standardized well-accepted measures, including the Developmental Behavior Checklist-Monitor, Parent, Teacher, and Adult; The Yale-Brown Obsessive Compulsive Scale; The Dykens Hyperphagia questionnaire; Reading The Mind in the Eyes Test; Epworth Sleepiness Scale and the Movie Stills. Oxytocin had little impact on any measure. The only significant difference found between the baseline, oxytocin, and placebo measures was an increase in temper outbursts (P = 0.023) with higher dose oxytocin. The lack of effect of oxytocin nasal spray may reflect the importance of endogenous release of oxytocin in response to exogenous oxytocin.
IC–P–025: Regional network pattern of MRI gray matter volume in Alzheimer's dementia (2006)

Alzheimer's disease (AD) is characterized by reductions in brain volume measured by magnetic resonance imaging (MRI), with temporal lobe structures preferentially affected early. To investigate the regional pattern of gray matter atrophy throughout the brain in AD, we used a multivariate model of regional covariance with voxel–based morphometry (VBM) to identify networks of gray matter volume that distinguish AD from healthy aging. Ten otherwise healthy patients with probable AD [NINDS–ADRDA criteria; mean±s.d. age=65±9 years; 6M/4F; Mini–Mental State Exam (MMSE)=16.1±6.3] were compared to 15 age–matched, healthy controls [age=63±8 years; 10M/5F; MMSE=29.5±0.7] with T1–weighted volumetric MRI scans. Statistical parametric mapping (SPM2) was used with optimized VBM to produce smoothed maps of gray matter volume. We used a form of principal component analysis, the Scaled Subprofile Model (SSM) on a voxel–basis, to identify patterns of regional interactions in gray matter that distinguished the AD patients from healthy controls. SSM analysis for the two groups combined identified a linear combination of five component patterns whose subject scores were highly predictive of group membership (R2adj=0.85, p<0.000001). The combined pattern indicated that the AD patients differed from controls with less gray matter in bilateral hippocampal, lateral temporal, and parietal/precuneus regions with relative preservation in small areas that included bilateral prefrontal cortex and right cerebellum. In the AD group, memory performance was best characterized by a linear combination of four of these five component patterns (R2adj=0.66, p<0.05), with poorer memory associated with less gray matter in bilateral hippocampal and parietal/precuneus areas with relative preservation in small areas that included bilateral prefrontal and left basal ganglia regions. AD patients differ from healthy elderly in a regionally distributed network pattern of gray matter atrophy that includes brain regions known to be preferentially affected in AD. Further, the expression of such gray matter networks is associated with individual differences in cognitive dysfunction. Multivariate network analysis of MRI VBM with SSM may aid early detection, assist in tracking disease progression, and potentially help in the evaluation of treatments for AD.
Mammalian DNA ligase II is highly homologous with vaccinia DNA ligase. Identification of the DNA ligase II active site for enzyme-adenylate formation. (1994)

Mammalian cells contain three biochemically distinct DNA ligases. In this report we describe the purification of DNA ligase II to homogeneity from bovine liver nuclei. This enzyme interacts with ATP to form an enzyme-AMP complex, in which the AMP moiety is covalently linked to a lysine residue. An adenylylated peptide from DNA ligase II contains the sequence, Lys-Tyr-Asp-Gly-Glu-Arg, which is homologous to the active site motif conserved in ATP-dependent DNA ligases. The sequences adjacent to this motif in DNA ligase II are different from the comparable sequences in DNA ligase I, demonstrating that these enzymes are encoded by separate genes. The amino acid sequences of 15 DNA ligase II peptides exhibit striking homology (65% overall identity) with vaccinia DNA ligase. These peptides are also homologous (31% overall identity) with the catalytic domain of mammalian DNA ligase I, indicating that the genes encoding DNA ligases I and II probably evolved from a common ancestral gene. Since vaccinia DNA ligase is not required for DNA replication but influences the ability of the virus to survive DNA damage, the homology between this enzyme and DNA ligase II suggests that DNA ligase II may be involved in DNA repair.
Hypercholesterolemia Impairs Endothelium-Dependent Relaxation of Rabbit Corpus Cavernosum Smooth Muscle (1991)

The majority of cases of impotence are associated with vascular risk factors such as diabetes, hypercholesterolemia, hypertension and smoking. These factors induce impairment of endothelium-dependent relaxation of blood vessels in man and in experimental animals. In this study the effects of hypercholesterolemia on the reactivity of rabbit corpus cavernosum smooth muscle strips to endothelium-dependent and endothelium-independent agents were investigated. New Zealand White rabbits (n = 14) were randomly divided into control and treatment groups. The control group (n = 7) received a regular diet while the treatment group (n = 7) was fed a diet of 0.5% cholesterol and 4% peanut oil for 10 weeks. Animals were then sacrificed and the corporal tissue studied in organ chambers for isometric tension measurement. Tissue was contracted with phenylephrine and concentration-dependent relaxation to acetylcholine, in the presence and absence of indomethacin, and to nitroprusside were examined. Blood level of cholesterol in the cholesterol-fed group was significantly higher compared to the control group. Contractions to phenylephrine were similar in both groups. Hypercholesterolemia, however, inhibited relaxation to acetylcholine but did not alter relaxation to nitroprusside, a cyclic guanosine monophosphate (cGMP)-dependent, direct smooth muscle dilator. Indomethacin enhanced the relaxations to acetylcholine in both control and cholesterol-fed groups but did not correct the difference in the relaxation to acetylcholine between both groups. It is concluded that hypercholesterolemia impairs endothelium-mediated relaxation of rabbit corpus cavernosum smooth muscle. The mechanism for the endothelial dysfunction does not appear to involve alteration in cyclooxygenase products of arachidonate or the cGMP-dependent relaxation of corporal smooth muscle. Impairment of endothelium-dependent relaxation of corporal smooth muscle may contribute to the pathophysiology of impotence associated with hypercholesterolemia in man.