gebhart/patrepeval huggingface dataset:
Determination of Kinetic Rate Constants for the Binding of Inhibitors to HIV-1 Protease and for the Association and Dissociation of Active Homodimer (1994)

Association and dissociation rate constants for a competitive inhibitor of HIV-1 protease were determined by a novel method employing a pair of integrated rate equations. This method, termed the paired progress curve method, is both rapid and reproducible. Progress curves, taken at a single concentration of inhibitor, are analyzed simultaneously to determine association and dissociation rate constants, the concentration of active sites, and the catalytic rate constant. The method is applied to BILA 398, a compound for which the cocrystal structure with HIV-2 protease has been reported recently [Tong, L., et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8387-8391]. This compound exhibited an association constant of 1.6 x 10(7) M-1 s-1 and a dissociation constant of 1.0 x 10(-4) s-1 corresponding to a binding affinity constant of 6.4 x 10(-12) M. During the course of the analysis, nonlinearity was observed in control reactions containing enzyme and substrate only. This was subsequently shown to be due to a reversible inactivation process resulting from enzyme dilution. Integrated rate equations were developed on the basis of the dissociation of active dimeric enzyme during dilution and a reassociation of dilute monomers following the addition of substrate. The equations were modeled to the data, yielding a dissociation constant of 1.9 x 10(-3) s-1 and an association constant of 9.2 x 10(5) M-1 s-1 for the monomer-dimer interconversion process. This corresponds to an equilibrium constant of 4 x 10(-9) M for the dimerization of HIV-1 protease.
Identification of a locus which shows no genetic recombination with the autosomal dominant polycystic kidney disease gene on chromosome 16. (1990)

The major site for mutations leading to autosomal dominant polycystic kidney disease (ADPKD) is at the PKD1 locus, previously mapped to 16p13. Three additional probes have now been mapped within an existing array of genetic markers flanking this locus. One of these, CMM65b (D16S84), shows no recombination with PKD1 in 201 informative meioses. The others, Fr3-42 (D16S21) and EKMDA2 (D16S83), are shown to be the closest telomeric flanking markers. Somatic cell hybrids containing derivative chromosome 16s were used to construct a physical map of the region. Cosmid overlap cloning of the D16S84 region allowed a t(16;1) translocation breakpoint to be mapped at the molecular level, orientating the extended D16S84 locus with respect to the chromosome. The new markers and physical map described here provide an improved framework for attempts to clone the PKD1 region and to identify polycystic kidney disease mutations.
Persistence of recombinant adenovirus in vivo is not dependent on vector DNA replication (1997)

Recombinant adenovirus vectors represent an efficient means of transferring genes into many different organs. The first-generation E1-deleted vector genome remains episomal and, in the absence of host immunity, persists long-term in quiescent tissues such as the liver. The mechanism(s) which allows for persistence has not been established; however, vector DNA replication may be important because replication has been shown to occur in tissue culture systems. We have utilized a site-specific methylation strategy to monitor the replicative fate of E1-deleted adenovirus vectors in vitro and in vivo. Methylation-marked adenovirus vectors were produced by the addition of a methyl group onto the N6 position of the adenine base of XhoI sites, CTCGAG, by propagation of vectors in 293 cells expressing the XhoI isoschizomer PaeR7 methyltransferase. The methylation did not affect vector production or transgene expression but did prevent cleavage by XhoI. Loss of methylation through viral replication restores XhoI cleavage and was observed by Southern analysis in a wide variety of, but not all, cell culture systems studied, including hepatoma and mouse and macaque primary hepatocyte cultures. In contrast, following liver-directed gene transfer of methylated vector in C57BL/6 mice, adenovirus vector DNA was not cleaved by XhoI and therefore did not replicate, even after a period of 3 weeks. Although replication may occur in some tissues, these results show that stabilization of the vector within the target tissue prior to clearance by host immunity is not dependent upon replication of the vector, demonstrating that the input transduced DNA genomes were the persistent molecules. This information will be useful for the design of optimal adenovirus vectors and perhaps nonviral episomal vectors for clinical gene therapy.
Hybridization Properties of Oligodeoxynucleotide Pairs Bridged by Polyarginine Peptides (1996)

The hybridization properties of a series of probes, based on two 9mer oligodeoxynucleotides (designated as I and II) having an appended oligoarginine chain (Rn) to produce peptide-oligonucleotide conjugates or peptide-bridged oligonucleotide pairs (e.g. Rn-I or II-Rn-I), were investigated. For the double-linked probes, we found that the peptide bridge induces the two 9mers to bind complementary single-stranded DNA or RNA targets with substantially enhanced thermal stability. The resulting hybrid with complementary DNA was found to assume a 1:1 complex in the B conformation as judged by UV mixing curves and CD spectroscopy. Complexes of single or double-linked probes with complementary RNA exhibited sensitivity to RNase H digestion. The influence of the identity and chirality of the repeating unit in the bridge, the length of the bridge, the gap size and the salt concentration on the hybridization properties of this new class of oligonucleotide probes was also studied. Our data reveal that these compounds exhibit properties that should prove useful in the development of antisense strategies.
Forensic classification of imaging sensor types (2007)

Digital images can be captured or generated by a variety of sources including digital cameras and scanners. In many cases it is important to be able to determine the source of a digital image. Methods exist to authenticate images generated by digital cameras or scanners, however they rely on prior knowledge of the image source (camera or scanner). This paper presents methods for determining the class of the image source (camera or scanner). The method is based on using the differences in pattern noise correlations that exist between digital cameras and scanners. To improve the classification accuracy a feature vector based approach using an SVM classifier is used to classify the pattern noise.
Information Services for Greater Driving Enjoyment (1998)

&lt;div class="htmlview paragraph"&gt;A prototype navigation system with cellular phone access to an information service center was constructed and evaluated. Center personnel can also operate the system remotely, in addition to providing traffic information and information for more enjoyable travel. Real-time conversation with a center operator is also possible. The system was rated positively by most of the subjects, especially the real-time voice service. This paper describes the car navigation market and cellular phone market in Japan, the system configuration, evaluation results and possible solutions to problems in the system. It also touches on the outlook for future car navigation systems and information services.&lt;/div&gt;
Interaction of Plasma Kallikrein with the C1 Inhibitor (1970)

Abstract The development of a hemolytic assay for the measurement of the inhibitor of the activated first component of complement (C1̄INH) and the isolation of a functionally pure preparation of plasma kallikrein have permitted the following observations: The C1̄INH inhibits the enzymatic activity of purified human plasma kallikrein on TAMe and on its natural substrate kininogen. The interaction of C1̄INH and kallikrein proceeds in a fashion similar to the interaction of this inhibitor and the first component of complement. The reaction follows a second order kinetics, resulting in the formation of an inactive stoichiometric complex of C1̄INH and kallikrein. The finding that C1̄INH acts effectively against both the activated first component of complement and plasma kallikre in is consistent with the view that the absence of this control step may be responsible for the episodic activation of C1 as well as the elaboration of the pathogenic peptide in patients with hereditary angioedema (HAE).
Drop-on-Demand Single Cell Isolation and Total RNA Analysis (2011)

Technologies that rapidly isolate viable single cells from heterogeneous solutions have significantly contributed to the field of medical genomics. Challenges remain both to enable efficient extraction, isolation and patterning of single cells from heterogeneous solutions as well as to keep them alive during the process due to a limited degree of control over single cell manipulation. Here, we present a microdroplet based method to isolate and pattern single cells from heterogeneous cell suspensions (10% target cell mixture), preserve viability of the extracted cells (97.0±0.8%), and obtain genomic information from isolated cells compared to the non-patterned controls. The cell encapsulation process is both experimentally and theoretically analyzed. Using the isolated cells, we identified 11 stem cell markers among 1000 genes and compare to the controls. This automated platform enabling high-throughput cell manipulation for subsequent genomic analysis employs fewer handling steps compared to existing methods.
siRNA delivery by a transferrin‐associated lipid‐based vector: a non‐viral strategy to mediate gene silencing (2007)

Cationic liposomes associated with Tf form stable siRNA lipoplexes with reduced toxicity and enhanced specific gene knockdown activity compared to conventional lipoplexes. Thus, such formulations may constitute efficient delivery systems for therapeutic siRNA applications.
Faithful Chromosome Transmission Requires Spt4p, a Putative Regulator of Chromatin Structure in Saccharomyces cerevisiae (1996)

A chromosome transmission fidelity (ctf) mutant, s138, of Saccharomyces cerevisiae was identified by its centromere (CEN) transcriptional readthrough phenotype, suggesting perturbed kinetochore integrity in vivo. The gene complementing the s138 mutation was found to be identical to the S. cerevisiae SPT4 gene. The s138 mutation is a missense mutation in the second of four conserved cysteine residues positioned similarly to those of zinc finger proteins, and we henceforth refer to the mutation of spt4-138. Both spt4-138 and spt4 delta strains missegregate a chromosome fragment at the permissive temperature, are temperature sensitive for growth at 37 degrees C, and upon a shift to the nonpermissive temperature show an accumulation of large budded cells, each with a nucleus. Previous studies suggest that Spt4p functions in a complex with Spt5p and Spt6p, and we determined that spt6-140 also causes missegregation of a chromosome fragment. Double mutants carrying spt4 delta 2::HIS3 and kinetochore mutation ndc10-42 or ctf13-30 show a synthetic conditional phenotype. Both spt4-138 and spt4 delta strains exhibit synergistic chromosome instability in combination with CEN DNA mutations and show in vitro defects in microtubule binding to minichromosomes. These results indicate that Spt4p plays a role in chromosome segregation. The results of in vivo genetic interactions with mutations in kinetochore proteins and CEN DNA and of in vitro biochemical assays suggest that Spt4p is important for kinetochore function.
[Cholestatic liver disease in children]. (2002)

Cholestatic liver disease constitutes a large part of chronic liver diseases during infancy. It is caused either by extrahepatic disorders (obstruction) or by intrahepatic cholestasis (functional). The differential diagnosis should be done as early as possible because the delayed surgical therapy in extrahepatic cholestasis has a very bad prognosis. Intrahepatic cholestasis may be caused by a broad spectrum of different disorders such as congenital infection, endocrine, chromosomal abnormalities or inborn errors of metabolism. Familial clustering is typical for the Byler's disease, Alagille's syndrome, PFIC, errors of bile acid synthesis or alpha-1-ATD. The established diagnosis allows to start etiological treatment: dietary--in metabolic diseases, antibiotics--in bacterial infections, antiviral--in viral infections etc. To lower bile acids level pharmacological treatment (UDCA) or surgical procedures (hepatoportoenterostomy, partial biliary diversion) should be performed. In progressive cholestasis the only effective therapy is liver transplantation.
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine (2013)

The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (https://www.hgmd.cf.ac.uk) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.
The clinical course of fistulating Crohn's disease (2003)

Healing is usually achieved. However, morbidity is great and healing is slow. Proctectomy is required in one-fifth of patients, and perineal healing is often slow. Defining the perianal fistula anatomy as complex or simple determines the likelihood of healing and the type of surgical approach required.
Autoclaved liquid medium for propagation of Treponema hyodysenteriae (1986)

Three liquid media that differ slightly in composition but not in the method of preparation were developed for the propagation of Treponema hyodysenteriae and Treponema innocens. The three media are unique in that all components are sterilized by autoclaving before use. These media supported better growth of T. hyodysenteriae than did previously used liquid media.
A virtual sensor for room detection (2003)

Indoor environments typically consist of sets of connected room-like spaces. We present a local technique that uses range data to detect these spaces during navigation. Our technique includes two parts: segmentation, which isolates room-like spaces and detects when the robot has entered a new one; and feature extraction, which associates each space with a set of geometric features useful for navigation or recognition. Many such features can be considered: here we propose a new method to compute width and length of a rectangular room in a way which is largely invariant with respect to the configuration of the furniture. We report experimental results that show the performance of our technique, and hint at a possible use of this technique for coarse localization on a topological map.
Design of ZnO/SiO/sub 2//Si monolithic integrated programmable SAW filter (2002)

In this paper the design of a ZnO/SiO/sub 2//Si monolithic integrated programmable SAW filter is suggested. The input SAW interdigital transducer (IDT) and tap delay lines (TDL) are fabricated on ZnO/SiO/sub 2/ structure. A NMOS-DMOS sampling, weighting, controlling and summing integrated circuit is designed compatibly in SiO/sub 2//Si structure. This IC can control the IDT and TDL by programmable weighting signal to realize the shift of the central frequency of bandpass of this SAW filter.
Technology for Proton Therapy (2009)

The technology that is used for the production and delivery of therapeutic proton beams is reviewed. Increased interest in this treatment modality has inspired a new generation of technology development and research into methods that will make proton treatment facilities more widely available (less expensive) and more efficient. Proton beam therapy has been in use for more than 40 years; it remains a treatment modality of interest because it provides a highly conformal dose distribution to a wide variety of disease sites and the potential for improving clinical outcomes. Recent advances in beam scanning technology may represent the ultimate in external beam radiotherapy dose conformality and treatment delivery efficiency. We describe how this new technology can be integrated into a proton therapy facility.
Histomorphometry of human sinus floor augmentation using a porous β‐tricalcium phosphate: a prospective study (2004)

Tricalcium phosphate (TCP) has been historically a well-accepted material for bone augmentation. We examined the use of a porous beta-TCP (100%) in a split mouth model for sinus floor augmentation. Five patients were treated bilaterally, receiving 1-2 mm-sized beta-TCP particles (Cerasorb) on one side (test side) and autologous chin bone particles on the other (control) side. Four other patients were treated with a unilateral sinus floor augmentation using 100% beta-TCP (no controls). Biopsies of the augmented sites were taken at 6 months. Histomorphometry measurements were carried out in order to quantify bone augmentation at test and control sides. The average bone volume (BV) formed in the augmented sinus at the control side was 41% (32-56%) and 17% (9-27%) in the test side when all nine patients were included (statistically significant, P=0.04). When only the five bilateral patients were included, mean BV of the test side was 19% (13-27%), which was also significantly different from the control side (P=0.009). Osteoid formation tended to be higher in the test side biopsies (1.3%) than in the controls (0.3%) (marginally significant, P=0.1), indicating ongoing bone formation in the TCP material. The amount of lamellar bone at the test side was less than half the amount in the control side, indicating that remodelling had only recently started in the TCP-augmented side. The resorption surface, however, did not differ significantly between the two sides. These histological results indicate that Cerasorb is an acceptable bone substitute material for augmentation of the maxillary sinus. Due to the osteoconductive, but not osteoinductive properties of this material, the rate of bone formation is somewhat delayed in comparison to autologous bone.
Synthesis and applications of Rhodamine derivatives as fluorescent probes (2009)

Rhodamine dyes are widely used as fluorescent probes owing to their high absorption coefficient and broad fluorescence in the visible region of electromagnetic spectrum, high fluorescence quantum yield and photostability. A great interest in the development of new synthetic procedures for preparation of Rhodamine derivatives has arisen in recent years because for most applications the probe must be covalently linked to another (bio)molecule or surface. In this critical review the strategies for modification of Rhodamine dyes and a discussion on the variety of applications of these new derivatives as fluorescent probes are given (108 references).
Akt Activation Suppresses Chk2-Mediated, Methylating Agent–Induced G2 Arrest and Protects from Temozolomide-Induced Mitotic Catastrophe and Cellular Senescence (2005)

Pharmacologic inhibition of the DNA signal transducers Chk1 and p38 blocks G2 arrest and sensitizes glioblastoma cells to chemotherapeutic methylating agent-induced cytotoxicity. Because Akt pathway activation has been suggested to also block G2 arrest induced by DNA-damaging agents and because glioma cells frequently have high levels of Akt activation, we examined the contribution of the Akt pathway to methylating agent-induced G2 arrest and toxicity. U87MG human glioma cells containing an inducible Akt expression construct were incubated with inducing agent or vehicle, after which the cells were exposed to temozolomide and assayed for activation of the components of the G2 arrest pathway and survival. Temozolomide-treated control cells activated the DNA damage signal transducers Chk1, Chk2, and p38, leading to Cdc25C and Cdc2 inactivation, prolonged G2 arrest, and loss of clonagenicity by a combination of senescence and mitotic catastrophe. Temozolomide-treated cells induced to overexpress Akt, however, exhibited significantly less drug-induced Cdc25C/Cdc2 inactivation and less G2 arrest. Akt-mediated suppression of G2 arrest was associated not with alterations in Chk1 or p38 activation but rather with suppression of Chk2 activation and reduced recruitment of Chk2 to sites of damage in chromatin. Unlike bypass of the G2 checkpoint induced by pharmacologic inhibitors of Chk1 or p38, however, Akt-induced bypass of G2 arrest suppressed, rather than enhanced, temozolomide-induced senescence and mitotic catastrophe. These results show that whereas Akt activation suppresses temozolomide-induced Chk2 activation and G2 arrest, the overriding effect is protection from temozolomide-induced cytotoxicity. The Akt pathway therefore represents a new target for the sensitization of gliomas to chemotherapeutic methylating agents such as temozolomide.
Siah Proteins: Novel Drug Targets in the Ras and Hypoxia Pathways (2009)

The Siah (seven in absentia homolog) family of RING-domain proteins are components of ubiquitin ligase complexes, targeting proteins for proteasomal degradation. Siah family members have been reported to function in Ras, estrogen, DNA-damage, and hypoxia response pathways. Although earlier reports implicated Siah proteins as tumor suppressors, recent studies in mouse models have shown that Siah inhibition impairs tumor growth and metastasis. Given their central role in oncogenic and angiogenic pathways, Siah proteins are attractive novel therapeutic targets in cancer.
Epidemic Meningococcemia and Purpura Fulminans with Induced Protein C Deficiency (1993)

Patients with epidemic infections caused by Neisseria meningitidis serogroup C were studied to assess the relationship of abnormal coagulation parameters to prognosis. Patients were categorized into stages within the first hour of observation according to severity of illness. During the epidemic years 1986 through 1991, 113 patients with bacteriologically proven N. meningitidis infection were observed, 15 of whom died. Purpura fulminans was seen in 28 patients, of whom 14 (50%) died. Among the 14 surviving patients who had purpura fulminans, 10 suffered gangrene with deforming autoamputation secondary to the dermal microvascular thrombosis and hemorrhagic necrosis. Evaluation of the induced diffuse intravascular coagulation in 59 patients included studies of the naturally occurring anticoagulants, focusing on protein C and protein S. The magnitude of the declining levels of protein C, the degree of thrombocytopenia, and the presence of fibrin split products are directly related to the clinical severity of the illness (P = .0053). Thus, in individuals with severe disease expression, the risk of purpura fulminans with death or deformity was significantly increased when the platelet count was < 50,000 cells/mm3 (P = .0001) and protein C levels were low (P = .0158). The immaturity of the protein C system in children who are < 4 years of age may contribute to the rapid and more frequent pathogenesis of purpura fulminans. Therapy directed at replacement of the naturally occurring anticoagulants, such as protein C, may ultimately improve the prognosis for individuals with purpura fulminans.