gebhart/patrepeval huggingface dataset:
Decreased Prevalence of Heparin-Induced Thrombocytopenia with Low-Molecular-Weight Heparin and Related Drugs (2004)

Heparin-induced thrombocytopenia (HIT) Type II represents a disease spectrum associated with a high risk of thrombosis leading to limb loss and death. The pathophysiology of HIT is based on the development of antibodies to the heparin-platelet factor 4 (PF4) complex. Unfractionated heparin (UFH) is heterogeneous in molecular chain length and degree of sulfation accounting in part, for, the heterogeneity of HIT antibodies. Because of its smaller size, low-molecular-weight heparin (LMWH) does not interact with PF4 and platelets as efficiently as does UFH. This translates into a lower risk of immune sensitization with LMWH than with UFH treatment. LMWH is less likely than UFH to cause antibody generation and thus patients do not develop clinical HIT at the same frequency with LMWH as with UFH treatment. The antibodies generated by LMWH treatment are more often immunoglobulin A (IgA) and IgM as opposed to IgG antibodies, which are associated with symptomatic clinical HIT generated by exposure to UFH. However, platelet activation/aggregation can occur from LMWHs in the presence of most pre-existing HIT antibodies that had been generated from UFH exposure, although the response is less than that caused by UFH plus HIT antibody. With the expanded use of LMWH, the frequency of clinical HIT may naturally decline, given that LMWHs are less likely to generate HIT antibody.
Light‐induced nuclear import of phytochrome‐A:GFP fusion proteins is differentially regulated in transgenic tobacco and Arabidopsis (2000)

Phytochromes (phy) are a family of photoreceptors that control various aspects of light-dependent plant development. Phytochrome A (phyA) is responsible for the very low fluence response (VLFR) under inductive light conditions and for the high irradiance response (HIR) under continuous far-red light. We have recently shown that nuclear import of rice phyA:GFP is regulated by VLFR in transgenic tobacco. The import is preceded by very fast, light-induced formation of sequestered areas of phyA:GFP in the cytosol. Here we report that expression of the Arabidopsis phyA:GFP fusion protein in phyA-deficient Arabidopsis plants complements the mutant phenotype. In these transgenic Arabidopsis lines, both light-dependent cytosolic formation of sequestered areas of the phyA:GFP as well as VLFR or HIR-mediated nuclear import of the fusion protein was observed. By contrast, light-dependent nuclear import of the same fusion protein was induced only by continuous far-red light (HIR) but not by pulses of far-red light (VLFR) in transgenic tobacco. These results demonstrate that photoregulation of intracellular partitioning of the Arabidopsis phyA:GFP differs significantly in different genetic backgrounds.
Urea Cycle Disorders (2010)

The urea cycle is a series of steps required to generate urea from nitrogen produced by protein catabolism. The cycle was first described in 1932 by Krebs and Henseleit (Krebs and Henseleit 1932). Six enzymes and two transporters are necessary for urea cycle activity. Specific deficiencies have been described with each of these. The process converts nitrogen from ammonia and aspartate into urea, which is freely excreted by the kidney (Brusilow 1995). Embedded within the urea cycle is the nitric oxide cycle. Nitric oxide is generated from arginine by nitric oxide synthase (NOS), producing citrulline (Scaglia et al. 2004). The entire urea cycle is present only in the liver. The proximal cycle (N-acetylglutamate synthase [NAGS], carbamyl phosphate synthetase [CPS], ornithine transcarbamylase [OTC]) is also present in the intestinal tract, whereas the distal cycle (argininosuccinic acid synthase [ASS], argininosuccinic acid lyase [ASL], arginase [ARG]) is active in the kidney. The most common of the urea cycle disorders (UCDs) is ornithine transcarbamylase deficiency, which is inherited in an X-linked manner. All of the others are autosomal recessive. The overall incidence of all urea cycle disorders is estimated at between 1/10,000 to 1/25,000, although patients with incomplete deficiency are likely significantly more common (Nagata, Matsuda et al. 1991). When the urea cycle function is absent or diminished, either by direct enzymatic deficiency or by secondary inhibition of the proximal four steps, nitrogen accumulates in the form of toxic ammonium. In null activity patients, this typically presents in the first days of life with hyperammonemia, resulting in central nervous system (CNS) dysfunction with overwhelming encephalopathy and coma, brain edema, seizures, and potentially death, with severe long-term neurodevelopmental sequelae if not rapidly reversed. The differential diagnosis of severe hyperammonemia includes organic acidemias, herpes-related hepatitis, and other disorders of liver function. Respiratory alkalosis and hyperventilation is classically seen in UCDs, although if encephalopathy progresses, apneas and acidosis may be seen (Burton 1998). If not recognized and reversed immediately, this may progress to fatal cerebral edema and herniation. There are multiple postulated mechanisms for ammonia-related neurotoxicity.
Effect of epidermal growth factor receptor tyrosine kinase inhibition on epithelial proliferation in normal and premalignant breast. (2002)

The factors controlling epithelial proliferation in ductal carcinoma in situ (DCIS) are unclear. Antiestrogens are effective in the prevention of the majority of estrogen receptor-positive, but not estrogen receptor (ER)-negative breast cancers, which suggests that other factor(s) are promoting proliferation in ER-negative DCIS. Mutated or overexpressed tyrosine kinases are frequently associated with tumor development. Epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is involved with mitogenesis and is expressed in ER-negative DCIS. We hypothesized that EGFR is central in driving proliferation in ER-negative/EGFR-positive DCIS. The purpose of this study was to establish whether the EGFR tyrosine kinase inhibitor (EGFR-TKI), ZD1839 (Iressa), can reduce epithelial proliferation and increase apoptosis in EGFR-positive DCIS. Breast tissue from 16 women undergoing surgery for DCIS were implanted into 16-32 immunosuppressed mice/experiment (8 xenografts/mouse). Treatment commenced 2 weeks after implantation and consisted of once daily oral gavage with ZD1839 at doses ranging from 10 to 200 mg/kg for 14-28 days; appropriate controls were present. Xenografts were removed on days 14, 21, 28, and 42 after implantation and then assessed for proliferation (LI) by Ki67 immunostaining and apoptosis index (AI) by morphology. All Ps reported are two-sided. Overall, a 56% reduction in epithelial proliferation was seen with Iressa in EGFR-positive DCIS. EGFR-TK inhibition compared with vehicle controls resulted in a fall in Geometric Mean Labeling Index (LI) after 14 days (day 28) of treatment both in ER-negative/EGFR-positive DCIS [6.5% interquartile range (IQR, 3.8-11.1) versus 13.9% (IQR, 12.0-16.3%); F(1,3) = 103; P = 0.002] and ER-positive/EGFR-positive DCIS [4.6% (IQR, 3.9-5.2%) versus 11.7% (IQR, 9.2-15.5); F(1,2) = 32.3; P = 0.03]. EGFR-TK inhibition had similar effects on the "at risk" normal breast epithelium adjacent to DCIS in the treated epithelium LI day 28 [ZD1839 2.2% (IQR, 1.7-3.3%) compared with control 3.8% (IQR, 2.4-5.4%); F(1,14) = 29.2; P = 0.00009] and in addition increased epithelial apoptotic index at day 21 [ZD1839 0.38 (0.23-0.83) compared with control 0.19 (0.1-0.25); F(1,6) = 12.2; P = 0.013]. The effect on epithelial proliferation was still significant after 28 days of treatment [for both DCIS (F1,29) = 24; P = 0.039 and normal breast F(1,6) = 47.3; P = 0.0005]. EGFR-TK inhibition with ZD1839 offers a novel approach to the treatment of EGFR-positive DCIS, regardless of ER status, and provides a potential new chemopreventative approach in patients at high risk of breast cancer.
MOBILE NODE AUTHENTICATION PROTOCOL FOR PROXY MOBILE (2009)

We are now going to the 4G network and in the 4G network environment, there are so many devices connected to the Internet while they move. We have protocol that can support movement of communicating node without any disruption of their connection status named Mobile IP(MIP). But, the major problem of this MIP is too heaviness of the protocol for small mobile nodes. So, IETF now propose PMIP to solve this problem. But, there is no way to authenticate the mobile node in PMIP. In this paper, we propose updated version of one-time key based authentication protocol for PMIPv6[Song (2008)] and show the extended results of analysis. With our proposed protocol, we can give a lot of securing features to current PMIPv6. Keywords: AAA; Proxy MIP; Security. 1.
EGFL7: a unique angiogenic signaling factor in vascular development and disease (2011)

EGFL7 is a secreted angiogenic factor that is highly conserved in vertebrates. Most secreted angiogenic signaling molecules, including VEGF and fibroblast growth factor-2, are mainly expressed by non-endothelial cell types such as fibroblasts. In contrast, EGFL7 is unique because it is almost exclusively expressed by and acts on endothelial cells. Egfl7 expression is highest when the endothelium is in an active, proliferating state. This factor acts as a chemoattractant for endothelial cells and binds to components of the extracellular matrix. In vivo, Egfl7 is important for regulating tubulogenesis in zebrafish and for controlling vascular patterning and integrity in mice. Its function in blood vessel development is mediated, at least in part, through modulation of Notch signaling. In this review, we summarize the findings that support a role for Egfl7 in developmental and postnatal angiogenesis and describe the EGFL7-signaling pathways that underlie these processes. In addition, we discuss a potential role for EGFL7 in vascular repair and its possible use as a therapeutic target for treatment of hypoxia-induced injury. Finally, we consider EGFL7 action during tumorigenesis and its potential as an antiangiogenic agent.
Increased levels of uric acid predict haemodynamic compromise in patients with heart failure independently of B-type natriuretic peptide levels: Figure 1 (2007)

Heart failure is a leading cause of mortality in the USA and Europe, and the ability to predict prognosis is essential for optimal allocation of treatments. Biomarkers offering prognostic information in patients with heart failure have recently entered practice. Although B-type natriuretic peptide (BNP) is an established biomarker,1 uric acid may also have prognostic value.2,3

Increases in BNP results primarily from increasing cardiac filling pressures, whereas increases in uric acid are associated with increased vascular tone4 and depressed myocardial contractility via increased xanthine oxidase activity.5 Thus, uric acid, like BNP, could be associated with haemodynamic compromise in heart failure. We tested the hypothesis that increased uric acid levels are associated with worsening haemodynamic compromise in patients with heart failure independent of BNP.

Study patients were referred for right heart catheterisation between 1 January 2003 and 1 July 2004. Right atrial, pulmonary arterial and pulmonary capillary wedge (PCW) pressures were measured using a balloon-tipped, flow-directed catheter. Cardiac output was determined by thermodilution. Heart transplant recipients or patients currently receiving synthetic human BNP were excluded. Uric acid and N-terminal proBNP (NT-proBNP) levels were drawn during the right heart catheterisation. The study was approved by the Johns Hopkins Institutional Review Board.

Patients were divided into groups on the basis of the median serum uric acid and NT-proBNP levels: low uric acid and low NT-proBNP (n = 27), high uric acid and low NT-proBNP (n = 24), low uric acid and high NT-proBNP (n = 22), and high uric acid and high NT-proBNP (n = 33). We compared haemodynamic parameters between groups using linear …
Complex structure of knobs and centromeric regions in maize chromosomes. (2000)

The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat x maize crosses enables us to analyze the structure and composition of individual maize chromosomes via the isolation and characterization of chromosome-specific cosmid clones. Restriction fragment fingerprinting, sequencing, and in situ hybridization were applied to discover a new family of knob associated tandem repeats, the TR1, which are capable of forming fold-back DNA segments, as well as a new family of centromeric tandem repeats, CentC. Analysis of knob and centromeric DNA segments revealed a complex organization in which blocks of tandemly arranged repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration/association of certain retrotransposable elements into knobs or centromere regions as well as for integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. DNA hybridization to a blot panel of eight individual maize chromosome addition lines revealed that CentC, TR1, and 180-bp tandem repeats are found in each of these maize chromosomes, but the copy number of each can vary significantly from about 100 to 25,000. In situ hybridization revealed variation among the maize chromosomes in the size of centromeric tandem repeats as well as in the size and composition of knob regions. It was found that knobs may be composed of either 180-bp or TR1, or both repeats, and in addition to large knobs these repeated elements may form micro clusters which are detectable only with the help of in situ hybridization. The association of the fold-back elements with knobs, knob polymorphism and complex structure suggest that maize knob may be consider as megatransposable elements. The discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes.
Presenilin-1 and -2 Are Molecular Targets for γ-Secretase Inhibitors (2000)

Presenilins are integral membrane protein involved in the production of amyloid beta-protein. Mutations of the presenilin-1 and -2 gene are associated with familial Alzheimer's disease and are thought to alter gamma-secretase cleavage of the beta-amyloid precursor protein, leading to increased production of longer and more amyloidogenic forms of A beta, the 4-kDa beta-peptide. Here, we show that radiolabeled gamma-secretase inhibitors bind to mammalian cell membranes, and a benzophenone analog specifically photocross-links three major membrane polypeptides. A positive correlation is observed among these compounds for inhibition of cellular A beta formation, inhibition of membrane binding and cross-linking. Immunological techniques establish N- and C-terminal fragments of presenilin-1 as specifically cross-linked polypeptides. Furthermore, binding of gamma-secretase inhibitors to embryonic membranes derived from presenilin-1 knockout embryos is reduced in a gene dose-dependent manner. In addition, C-terminal fragments of presenilin-2 are specifically cross-linked. Taken together, these results indicate that potent and selective gamma-secretase inhibitors block A beta formation by binding to presenilin-1 and -2.
Glycosyl-phosphatidylinositol/inositol phosphoglycan: a signaling system for the low-affinity nerve growth factor receptor. (1991)

Nerve growth factor (NGF) exerts a variety of actions during embryonic development. At the early stages of inner ear development, NGF stimulates cell proliferation, an effect mediated through low-affinity receptors. We have studied the possibility that the glycosyl-phosphatidylinositol/inositol phosphoglycan (glycosyl-PtdIns/IPG) system is involved in transmitting this NGF signal. Endogenous glycosyl-PtdIns was characterized in extracts of cochleovestibular ganglia (CVGs) that incorporated [3H]glucosamine, [3H]galactose, [3H]myristic acid, and [3H]palmitic acid. Incubation of CVG with NGF produced a rapid and transient hydrolysis of glycosyl-PtdIns. Hydrolysis was complete at 100 ng/ml, and the half-maximal effect occurred at 25 ng/ml, overlapping with the concentration dependence of the mitogenic effect of NGF. An IPG was isolated from embryonic extracts. It had biological effects similar to those reported for the insulin-induced IPG in other tissues. It exerted a powerful mitogenic effect on CVG, comparable to that of NGF. Both the IPG- and NGF-induced cell proliferation were blocked by anti-IPG antibodies that recognized the endogenous IPG on a silica plate immunoassay. These results show that CVG possesses a fully active glycosyl-PtdIns/IPG signal transduction system and that the proliferative effects associated with NGF binding to low-affinity receptors require IPG generation.
Identification and purification of a bacterial ice-nucleation protein. (1986)

The protein product of a gene (inaZ) responsible for ice nucleation by Pseudomonas syringae S203 has been identified and purified after overexpression in Escherichia coli. The amino acid composition and the N-terminal sequence of the purified, denatured protein corresponded well with that predicted from the sequence of the inaZ gene. The product of inaZ was also found to be the major component in preparations of ice-nucleating, proteinaceous particles, obtained after extraction with and gel filtration in a mixture of urea and the nondenaturing detergent octyl beta-D-thioglucopyranoside. The activity of these preparations in the absence of added lipid implies that the protein participates directly in the nucleation process.
Dielectric Loaded Antennas (2005)

Abstract Dielectric media affect the wave propagation by their reflective index. Their use in antennas can provide a number of diverse benefits. In applications such as high‐gain antennas, they influence the phase of the propagating waves, and thus influence the direction and gain of the transmitted waves. Lens antennas are typical examples that can be used alone, or in conjunction with other antennas, such as horn and microstrip antennas, to enhance their gain. In other applications like dielectric loaded horns and waveguides the use of dielectric inside them controls the excitation of various modes and thus the performance of the horns. Hybrid and multimode horns are examples that can improve the horn performance for reflector feed applications. Similarly, dielectric resonator antennas can control and improve the radiation performance by controlling the excitation and the phase of the wave propagating through them. Dielectrics being non‐conducting can also be used to insulate and, thus, isolate the antennas from living tissues, in medical treatment and studies. Large permittivity of some dielectrics reduces the signal wavelength and in areas of small antennas can be used to reduce the antenna dimensions. Finally, the dielectric permittivity also influences the wave impedance and can be used to match the impedance of antennas to the radiation media and enhance their gain. This article provides a brief review of some of these applications.
Guidelines for the optimal design of miRNA-based shRNAs (2016)

RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA.
Graded Structures for All-ceramic Restorations (2010)

One failure mode of all-ceramic restorations is radial cracking at the cementation surface, from occlusally induced flexure of the stiffer ceramic layer(s) on the softer dentin underlayer. We hypothesize that such failure may be substantially mitigated by an appropriate grading of elastic modulus through the ceramic thickness. In this study, we fabricated graded structures by infiltrating glass into zirconia plates, with resulting diminished modulus in the outer surfaces. The plates were then bonded to a polymeric base and subjected to flexure by contact loading until fracture. Comparison of infiltrated specimens with non-infiltrated controls showed a significant increase in the fracture loads, by a factor of nearly 2. Finite element analysis revealed the cause of increase in the load-bearing capacity to be diminished tensile stresses within the lower-modulus graded zone, corresponding to an increase in material strength. The results confirmed that suitably graded structures can be highly beneficial in the design of next-generation all-ceramic restorations.
Integrin-associated Protein Is a Ligand for the P84 Neural Adhesion Molecule (1999)

P84 (also known as SHPS-1, BIT, and SIRP) is a heterophilic adhesive membrane protein involved in receptor tyrosine kinase signaling that is found at synapses in the mammalian central nervous system and in non-neural tissues. We have identified a binding partner for P84 using an expression cloning strategy. Here we report that integrin-associated protein (IAP/CD47) is a predominant binding partner of P84. Immunohistochemistry reveals a virtually identical distribution of P84 and IAP in a variety of adult brain regions. Because IAP has been implicated in cell signaling in cells of the immune system, P84 and IAP represent a heterophilic binding pair that is likely to be involved in bi-directional signaling at the synapse and in other tissues.
Geometric signal processing and applications to brain mapping (2002)

Discusses spatial transformation techniques for multidimensional image registration. Examples from brain mapping are given. The authors illustrate the problem by reviewing point matching, which is the 'gold standard' in this area. The point matching formulation is not adequate for all applications, and they describe various extensions and generalizations. One important issue is multi-set registration, others are more general nonlinear models, as well as the problems of registration on the basis of intensity data and when the geometrical objects to be registered are curves, surfaces, or volumes. This leads to many interesting problems that deserve further study. Finally, the authors discuss the accuracy in registration.