gebhart/patrepeval huggingface dataset:
Two Naturally Occurring Mutations on FVII Gene (S363I-W364C) Altering Intrinsic Catalytic Activity (2002)

Factor VII (FVII) requires the cleavage of an internal peptide bond and the association with tissue factor (TF) to attain its fully active FVIIa conformation. This event alone leaves FVIIa in a zymogen-like state of relatively low specific activity. The TF-induced allosteric enhancement of FVIIa's activity contributes to the procoagulant activity of the complex. We have characterized two naturally occurring mutations (S363I - W364C) on FVII gene. Both homozygous patients for each mutation have a normal FVII: Ag level associated to an undetectable FVII coagulant activity. The patient carrying the allele 364C had a more severe hemorrhagic diathesis than the S363I mutant. To understand the mechanism of these deficiency, in vitro expression analysis with further biochemical characterization of recombinant proteins of both mutants FVII-363I, FVII-364C and wild type (WTFVII) FVII constructs were done. The results recapitulated the patients' plasma data with normal Ag level and no detectable coagulant activity. The D-F-Pip-R-pNA and CH(3)SO(2)-D-CHA-A-But-R chromogenic substrates were used to evaluate the amidolytic activity of WT and mutant FVII in presence and absence of recombinant tissue factor (rTF). Binding of FVII to rTF by a solid phase binding assay was done using recombinant human rTF. The results of amidolytic assays showed that rTF enhances 28 fold the value of the specificity of constant (kcat/K(m)) in WT but no activity was detectable in either mutant constructs under any condition. The equilibrium dissociation constant of rTF-FVIIa interaction showed Kd equal to 4.4 +/- 0.2nM, 4.9 +/- 0.5nM and 6 +/- 0.9 of WT, 363I and 364C FVII forms, respectively. The K(d) values of the non activated forms were equal to 24.7 +/- 3.3, 24.4 +/- 3.1 and 20.6 +/- 4nM, respectively. These data demonstrate that, compared to the WT form, FVII-363I and FVII-364C have no significant affinity change for TF and that the detrimental effect of these two mutations is attributable to the loss of an efficient catalytic machinery in the FVII molecule causing a severe deficiency of coagulant activities.
C-Terminal Peptide of Fusarium heterosporum Lipase Is Necessary for Its Increasing Thermostability (1998)

Saccharomyces cerevisiae bearing a lipase cDNA from Fusarium heterosporum produced two lipases, A and B. Lipase B was significantly more stable to temperature than lipase A, but their optimum temperatures were similar. Lipase B was composed of one polypeptide (301 amino acids), and lipase A was composed of two polypeptides (275 and 26 amino acids) generated by the cleavage between Arg275 and Asp276 with a trypsin-like protease. It was suggested that the C-terminal peptide (26 amino acids) tightened the lipase structure when bound to the catalytic domain (275 amino acids) through a peptide bond. The tight structure was loosened by cleavage of the C-terminal peptide, even though the peptide interacted noncovalently with the catalytic domain, possibly through charged amino acids, in which it is rich. Deletion of the C-terminal peptide greatly decreased the lipase production by the recombinant S. cerevisiae, although its transcriptional level was the same as that of cells carrying the wild-type gene. These facts suggested that the C-terminal peptide affected the lipase production in the post-transcriptional step.
Optimum beamforming using transmit antenna arrays (2003)

Transmit beamforming is a powerful means of increasing capacity in systems in which the transmitter is equipped with an antenna array, especially in systems in which receive beamforming is not available, as is typical in the base-to-mobile downlink in a cellular communication system. In this paper, the problem of transmit beamforming is formulated as one of minimizing the power radiated by the base station, subject to satisfying quality of service requirements at the mobiles. For a single cell system, a global minimum is shown to exist, and an iterative algorithm that converges to it is provided. The solution extends to accommodate receive beamforming at the mobiles. It also extends to provide a mechanism for space-time transmit filtering, which exploits the differences between the temporal as well as the spatial channels between the base station and different mobiles. Finally, a system with multiple source-destination pairs (e.g., in an ad hoc network) is considered. An iterative algorithm that outputs a convergent sequence of feasible points with monotonically decreasing costs is provided for this case.
Steganalysis by Subtractive Pixel Adjacency Matrix (2010)

This paper presents a method for detection of steganographic methods that embed in the spatial domain by adding a low-amplitude independent stego signal, an example of which is least significant bit (LSB) matching. First, arguments are provided for modeling the differences between adjacent pixels using first-order and second-order Markov chains. Subsets of sample transition probability matrices are then used as features for a steganalyzer implemented by support vector machines. The major part of experiments, performed on four diverse image databases, focuses on evaluation of detection of LSB matching. The comparison to prior art reveals that the presented feature set offers superior accuracy in detecting LSB matching. Even though the feature set was developed specifically for spatial domain steganalysis, by constructing steganalyzers for ten algorithms for JPEG images, it is demonstrated that the features detect steganography in the transform domain as well.
REQUIREMENT FOR C5a IN LUNG VASCULAR INJURY FOLLOWING THERMAL TRAUMA TO RAT SKIN (1997)

Previous studies in rats have shown that deep second degree dermal burns, involving 28-30% of total body surface area, result in systemic complement activation, appearance in plasma of chemotactic activity, sequestration of blood neutrophils in lung capillaries, and development of neutrophil-dependent dermal vascular and lung vascular injury. Although blockade of complement activation or depletion of complement before skin burns has resulted in significant attenuation of tissue injury both locally and distally (in lung), a role for C5a in these events is unclear. In the following studies, we demonstrate the presence of C5a and neutrophil chemotactic activity in serum and in lung homogenates after thermal injury. C5a has also been found in bronchoalveolar lavage fluids of thermally injured animals. Treatment of animals with a polyclonal neutralizing rabbit antibody to rat C5a was lung protective. The protective effects of the antibody (anti-C5a) were associated with diminished vascular permeability changes, as well as reduced tissue build-up of myeloperoxidase. Anti-C5a also prevented up-regulation of lung vascular ICAM-1 (intercellular adhesion molecule-1) in skin-burned rats. These observations indicate that C5a is essential for development of neutrophil accumulation and vascular permeability increases in distant (lung) organs after thermal trauma to skin. The protective effects of anti-C5a in lung, appear to be related to prevention of up-regulation of vascular ICAM-1. Accordingly, C5a may represent a target for clinical approaches in the treatment of organ injury following thermal trauma.
Blue-light generation by quasi-phase-matched frequency doubling in thermally poled optical fibers (1995)

Periodically patterned second-order nonlinearities are created in optical fibers by thermal poling in vacuo. Cw quasi-phase-matched frequency conversion to the blue is demonstrated. The measured bandwidth, 0.78 nm cm, is close to the theoretical prediction.
Shortest path first with emergency exits (1990)

Under heavy and dynamic traffic, the SPF routing algorithm often suffers from wild oscillation and severe congestion, and results in degradation of the network performance. In this paper, we present a new routing algorithm (SPF-EE) which attempts to eliminate the problems associated with the SPF algorithm by providing alternate paths as emergency exits. With the SPF-EE algorithm, traffic is routed along the shortest-paths under normal condition. However, in the presence of congestion and resource failures, the traffic can be dispersed temporarily to alternate paths without route re-computation. Simulation experiments show that the SPF-EE algorithm achieves grater throughput, higher responsiveness, better congestion control and fault tolerance, and substantially improves the performance of routing in a dynamic environment.
Possibilities for the digital baton as a general-purpose gestural interface (1997)

This paper describes issues and results from the design and use of the Digital Baton, a new interface for real-time gestural control. Its construction was originally motivated by the need for a new instrument on which to perform computer music, and it was designed to replicate as closely as possible the feel of a traditional conducting baton. However, it has unexpectedly become a model for the design of new interfaces and digital objects, and is currently being used to record data for analysis in gesture-recognition research. Some preliminary results and future research areas are discussed at the end.
Current situation of Panitumumab, Matuzumab, Nimotuzumab and Zalutumumab (2007)

EGFR overexpression usually correlates with a more advanced disease stage, a poorer prognosis and a worse chemotherapy response. EGFR expression increase has been observed in many tumours. For all the aforementioned reasons, EGFR inhibition can be considered an attractive approach in cancer treatment. One strategy has been receptor inhibition of extracellular domain using monoclonal antibodies. Cetuximab is the most developed one and there is plenty information on the literature about its current status. In this review we focus on other EGFR monoclonal antibodies under clinical development. The more developed one is Panitumumab. Its clinical development is taking place very quickly and it has mainly been studied in colorectal cancer showing promising results. There are also other interesting drugs such as Matuzumab, Nimotuzumab and Zalutumumab.
A prospective study of unexplained visible abdominal bloating. (1994)

Patients whose primary complaint is visible abdominal bloating have greater increases in girth but not weight during bloating episodes than the normal daily fluctuations seen in healthy controls. They have weak abdominal muscles and frequently have recently gained weight. They are not more likely to have constipation, irritable bowel syndrome or obesity than patients whose primary complaint is something other than bloating.
Synthesis and structural characterization of amino-functionalized polysaccharides (2008)

Abstract A variety of carbohydrates, in particular polysaccharides can be subjected to chemical modification to obtain derivatives with amphiphilic properties, which enable biochemical or biological reactions at the polymer surface. In the present work, a polydisperse maltodextrin mixture of average molecular weight 3000 was coupled with 1,6-hexamethylenediamine (HMD) via reductive amination reaction. Resulting products were characterized by thermal analysis and positive nanoelectrospray quadrupole time-of-flight (Q-TOF) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Both thermal analysis and MS screening confirmed the formation of the HMD-polysaccharide coupling products. Moreover, HMD-linked polysaccharide chains containing 2 to 26 glucose building blocks were identified by nanoESI Q-TOF MS. MS/MS fragmentation using collision-induced dissociation (CID) at low ion acceleration energies provided strong evidence for HMD-maltodextrin linkage formation and the set of sequence ions diagnostic for the composition and structure of a HMD-linked chain containing 18 glucose residues.
Post-translational Modifications of Endothelin Receptor B from Bovine Lungs Analyzed by Mass Spectrometry (1998)

A new mild experimental approach for isolation of peptide membrane receptors and subsequent analysis of post-translational modifications is described. Endothelin receptors A and B were isolated on oligo(dT)-cellulose using N-(epsilon-maleimidocaproyloxy)succinimide endothelin coupled to a protected (dA)-30-mer. This allowed a one-step isolation of the receptor from oligo(dT)-cellulose via variation solely of salt concentration. The identity of the receptor was confirmed by direct amino acid sequencing of electroblotted samples or by using antibodies against ETA and ETB receptors. The method used here is very fast, requires only very mild elution conditions and, for the first time, gave both ETA and ETB receptors concurrently in very good yield. Following enzymatic in-gel digestion, MALDI, and electrospray ion trap mass spectrometric analysis of the isolated endothelin B receptor showed phosphorylation at Ser-304, -418, -438, -439, -440, and -441. Further phosphorylation at either Ser-434 or -435 was observed. The endothelin B receptor is also palmitoylated at Cys residues 402 and 404. Phosphorylation of Ser304 may play a role in Hirschsprung's disease.
Clostridium difficile -Associated Diarrhea: Epidemiology, Risk Factors, and Infection Control (1997)

Abstract Objectives: To evaluate the effectiveness of specific infection control measures on the incidence of Clostridium difficile -associated diarrhea (CDAD) and to identify risk factors for its development. Setting: 370-bed, tertiary-care teaching hospital with approximately 12,000 to 15,000 admissions per year. Methods: Several infection control measures were implemented in 1991 and 1992, and the attack rates of CDAD were calculated quarterly. Antibiotic use for 1988 through 1993 was analyzed. A case-control study was conducted from January 1992 to December 1992 to identify risk factors for acquisition of CDAD. Results: From 1989 to 1992, the attack rate of CDAD increased from 0.49% to 2.25%. An increase in antibiotic use preceded the rise in the incidence of CDAD in 1991. Despite implementation of various infection control measures, the attack rate decreased to 1.32% in 1993, but did not return to baseline. Ninety-two cases and 78 controls (patients with diarrhea but with negative toxin assay) were studied. By univariate analysis, history of prior respiratory tract infections (odds ratio [OR], 3.6; 95% confidence interval [CI 95 ], 1.2-10.4), the number of antibiotics, and the duration of exposure to second-generation cephalosporins (OR, 3.55; CI 95 , 1.47-9.41) and to ciprofloxacin (OR, 7.27; CI 95 , 1.13-166.0) were related significantly to the development of CDAD. By stepwise logistic regression analysis, only exposure to antibiotics and prior respiratory tract infections ( P =.0001 and .0203, respectively) were found to be significant. Conclusion: Antibiotic pressure might have contributed to failure of infection control measures to reduce the incidence of CDAD to baseline.
Computationally designed liver-specific transcriptional modules and hyperactive factor IX improve hepatic gene therapy (2014)

The development of the next-generation gene therapy vectors for hemophilia requires using lower and thus potentially safer vector doses and augmenting their therapeutic efficacy. We have identified hepatocyte-specific transcriptional cis-regulatory modules (CRMs) by using a computational strategy that increased factor IX (FIX) levels 11- to 15-fold. Vector efficacy could be enhanced by combining these hepatocyte-specific CRMs with a synthetic codon-optimized hyperfunctional FIX-R338L Padua transgene. This Padua mutation boosted FIX activity up to sevenfold, with no apparent increase in thrombotic risk. We then validated this combination approach using self-complementary adenoassociated virus serotype 9 (scAAV9) vectors in hemophilia B mice. This resulted in sustained supraphysiologic FIX activity (400%), correction of the bleeding diathesis at clinically relevant, low vector doses (5 × 10(10) vector genomes [vg]/kg) that are considered safe in patients undergoing gene therapy. Moreover, immune tolerance could be induced that precluded induction of inhibitory antibodies to FIX upon immunization with recombinant FIX protein.
Acute Bronchitis (2006)

A 40-year-old man with no underlying lung disease has a 7-day history of cough that is now productive of purulent sputum and mild shortness of breath with exertion. He reports no paroxysms of cough and no contact with ill persons in his community. He does not appear to be in distress. His temperature is 37°C, his pulse 84 beats per minute, and his respiratory rate 17 breaths per minute. On auscultation of the lungs, no rales are heard; scattered wheezes are heard in the lung bases. How should he be evaluated and treated?
Defective natural killer cytotoxicity and polymorphonuclear leukocyte antibody-dependent cellular cytotoxicity in patients with LFA-1/OKM-1 deficiency. (1984)

Four children with an immunodeficiency involving the absence of leukocyte membrane glycoproteins reacting with anti-LFA-1 and OKM-1 monoclonal antibodies were unable to mediate adherence-dependent leukocyte functions. Even with normal Fc receptor function, their PMN-ADCC and MC-NKC were markedly deficient. Single cell analysis demonstrated deficient antibody-mediated PMN-target cell adherence. Monoclonal antibodies against LFA-1 and OKM-1 reproduced this immunodeficiency in leukocytes from normal adults. LFA-1/OKM-1 mediates a PMN-target cell adhesive step.
Chromosome Y Regulates Survival Following Murine Coxsackievirus B3 Infection (2012)

Coxsackievirus B3 (CVB3) contributes to the development of myocarditis, an inflammatory heart disease that predominates in males, and infection is a cause of unexpected death in young individuals. Although gonadal hormones contribute significantly to sex differences, sex chromosomes may also influence disease. Increasing evidence indicates that Chromosome Y (ChrY) genetic variants can impact biological functions unrelated to sexual differentiation. Using C57BL/6J (B6)-ChrY consomic mice, we show that genetic variation in ChrY has a direct effect on the survival of CVB3-infected animals. This effect is not due to potential Sry-mediated differences in prenatal testosterone exposure or to differences in adult testosterone levels. Furthermore, we show that ChrY polymorphism influences the percentage of natural killer T cells in B6-ChrY consomic strains but does not underlie CVB3-induced mortality. These data underscore the importance of investigating not only the hormonal regulation but also ChrY genetic regulation of cardiovascular disease and other male-dominant, sexually dimorphic diseases and phenotypes.
143 Spinal Cord Astrocytomas (2013)

INTRODUCTION: There are currently no clear treatment guidelines for the management of spinal cord astrocytomas. Additionally there is no conclusive evidence for the surgical resection of these tumors, with some studies even demonstrating worse survival with surgery. However, most studies have examined patients treated prior to the routine use of magnetic resonance imaging and advanced microsurgical techniques. In this study, the authors have examined the effect of resection on survival and neurological outcome in a modern cohort of patients with spinal cord astrocytomas. METHODS: A retrospective review was performed of patients with spinal cord astrocytomas treated at the Duke University Medical Center from 1992 to 2012. Univariate and multivariate analyses were utilized to identify variables associated with survival. RESULTS: A total of 46 consecutive patients were identified and included in the analysis, most of whom had low grade tumors (63.0%). The majority of patients (67.4%) underwent surgical resection, with the remaining only receiving biopsy. Of those who underwent resection, only 12.5% of patients underwent gross total resection, all of whom had low grade astrocytomas. Of all patients, 30.7% worsened compared to their preoperative baseline. The occurrence of worsening increased with high tumor grade (52.9% vs 27.6%, P = .086) and an increased extent of resection (66.7% vs 18.8%, P = .0069). Resection did not provide a survival benefit compared to biopsy alone (P = .53). Multivariate analysis revealed high grade histology (HR: 11.3; 95%CI: 2.41-53.2; P = .0021), tumor dissemination (HR:4.24;95%CI:1.22-14.8; P = .023), and an increasing number of tumor involved levels (HR:1.31;95%CI:0.99-1.74;P = .058) to be associated with worse survival. CONCLUSION: As surgical intervention is associated with a higher rate of neurological complications and lacks a clear benefit, the resection of spinal cord astrocytomas should be reserved for select cases and should be utilized sparingly. Synthes Skull Base Surgery Award
Management of asthma in children. (1994)

Management of chronic asthma has changed significantly in recent years. Most of the changes in management are the result of an increased recognition of the importance of the inflammatory component in the pathogenesis and treatment of asthma. The National Heart, Lung, and Blood Institute issued guidelines for the management of asthma in 1991. Beta agonists, cromolyn and nedocromil are mainstays of treatment in patients with mild to moderate asthma. Inhaled steroids are useful in the treatment of patients with moderate to severe asthma. Nonpharmacologic management of asthma includes avoidance of allergens and irritants, the use of peak flow meters, and patient and family education.
Chemical structures of the core regions of Campylobacter jejuni serotypes O:1, O:4, O:23, and O:36 lipopolysaccharides (1993)

Complete structures, including the location of N-acetylneuraminic acid (Neu5Ac) residues, were assigned for the core regions of Campylobacter jejuni serotypes O:1, O:4, and O:23 and O:36 lipopolysaccharides (LPS). In continuation of earlier studies, structure determinations of liberated oligosaccharides and, where necessary, of intact LPS, were by 1H-NMR spectroscopy, Smith degradation, chromium trioxide and enzymic degradations, in conjunction with methylation studies supported by fast-atom-bombardment mass spectrometry and linkage analyses by gas chromatography/mass spectrometry. It was concluded on the basis of the following structures, in which each was linked 1-->5 to a terminal 3-deoxy-D-manno-octulosonic acid residue, that the core regions with qualitatively similar sugar compositions showed serotypic differences in one or more of their sequences, linkage types, and anomeric configurations: [formula: see text] [corrected]. The outer regions of each structure carry Neu5Ac residues linked 2-->3 to available beta-D-Galp residues and show striking similarities with various glycosphingolipids of the ganglioside family. However, Neu5Ac epitopes are not apparently involved in determining serospecificity.
Optimizing the Performance of Remote Phosphor LEDs (2008)

The accuracy of results from Monte Carlo ray-tracing analysis significantly depends on the input values of the optical properties of the various package components. One important piece of input information is the phosphor particle MFP (mean-free-path), which is not easily determined. This study introduced a method to determine the MFP by matching the experimental results with optical ray-tracing analysis at a wavelength beyond the phosphor excitation range. Using these experiment values for MFP in an optical ray-tracing analysis of a white LED package showed an excellent match with measured results for light output and chromaticity.