gebhart/patrepeval huggingface dataset:
The Gibbs-Donnan near-equilibrium system of heart (1990)

The gradients of the major inorganic ions across the plasma membrane of heart were examined to determine the factors controlling the extent and direction of the changes induced during injury, certain diseases, and electrolyte disturbances. The ionic environment was altered by changing only the concentration of inorganic phosphate, [sigma Pi]o, from 0 to 1.2 to 5 mM in the Krebs-Henseleit buffer perfusing working rat hearts. Raising [sigma Pi]o from 1.2 to 5 mM resulted in a decrease in total Mg2+ content and calculated free cytosolic [Mg2+] from 0.44 to 0.04 mM, conversion of 4 mmol of MgATP2- to ATP4- and a decrease in measured intracellular [Cl-]i from 41 to 16 mM. At all levels of [sigma Pi]o, both the [Na+]i and [K+]i were invariant at about 3 mM and 130 mM, respectively, as was the energy of hydrolysis of the terminal phosphate bond of sigma ATP, delta GATP Hydr, of -13.2 kcal/mol. The relationship maintained between the ions on both sides of the plasma membrane by the 3Na+/2K(+)transporting ATPase (EC 3.6.1.37) and an open K+ channel was: (formula; see text) The energy of the gradients of the other inorganic ions across the plasma membrane, delta G[ion]o/i, exhibited three distinct quanta of energy derived from the prime quantum of delta GATP Hydr of -13.2 kcal/mol. The second quantum was about one-third of delta GATP Hydr or +/- 4.4 kcal/mol and comprised the delta G[Na+]o/i, delta G[Mg2+]o/i, and delta G[HPO42-]o/i. These results indicated near-equilibrium was achieved by the reactants of the 3Na+/2K(+)-ATPase, the K+ channel, the Na(+)-Pi co-transporter, and a postulated net Mg2+/H2PO4- exchanger. The third quantum was one-third of delta G[Na+]o/i or about +/- 1.5 kcal/mol and comprised delta G[H+]o/i, delta G[HCO3-]o/i, and delta G[Cl-]o/i. The delta G[K+]o/i was 0, indicating near-equilibrium between the chemical energy of [K+]o/i and the E across the plasma membrane of -83 mV. It is concluded that the gradients of the major inorganic ions across the plasma membrane and the potential across that membrane constitute a Gibbs-Donnan equilibrium system catalyzed by transport enzymes sharing common substrates. The chemical and electrical energies of those gradients are equal in magnitude and opposite in sign to the chemical energy of ATP hydrolysis.
Biochemistry: The Molecular Basis of Life (2002)

Biochemistry: The Molecular Basis of Life, Fourth Edition, is the ideal text for students who do not specialize in biochemistry but require a strong grasp of essential biochemical principles for their future careers. NEW! Online Homework System from Sapling Learning. Oxford University Press has partnered with Sapling Learning to produce an online homework and instructional solution for the McKee & McKee Biochemistry: The Molecular Basis of Life textbook. The text that presents the coverage you need with the relevance your students want is now available with the most powerful online homework system in the industry. The relationship between Oxford University Press and Sapling Learning is based on: *Creating the highest-quality content *Providing unparalleled customer service to you and your students *Offering the McKee/Sapling Learning package at the most affordable price Visit http: //www.saplinglearning.com/college/oxford-university-pre ss-us to learn more about Sapling Learning and how pairing this incredible system with McKee & McKee's Biochemistry: The Molecular Basis of Life will help improve your instruction and your students' learning. NEW TO THE FOURTH EDITION: * Increased relevance: Features brand-new Biochemistry in Perspective essays that show students how biochemical principles will be applied in their future scientific careers * Enhanced problem-solving: Includes twice as many problems as the previous edition, spanning a wider range of difficulty and equipping students with stronger skills in critical thinking * Greater currency: Covers the latest scholarship on such topics as macromolecular crowding, systems biology, and protein-folding diseases, to keep students up to date and poised for further study * Improved illustrations: Includes more than sixty new figures to better help students visualize complex biochemical processes and understand the impact of these processes on the living state ADDITIONAL RESOURCES TO AID YOU IN YOUR COURSE: COMPANION WEBSITE www.oup.com/us/mckee Contains a wide range of interactive study aids for students and password-protected assessment resources for instructors Student Resources * Multiple-choice quizzes that comprise over 600 questions to help students ace their exams * Over 300 interactive 3-D models of molecules in tutorial and quiz format, to help students identify important biomolecules and grasp their basic structural principles Instructor Resources (available to adopters of the text and password-protected) * All illustrations from the text available in electronic format for download into lecture presentations * Comprehensive Test Bank that includes over 700 questions in editable Word files for easy customization (available only on the Instructor's Resource CD-ROM: contact your Oxford University Press sales representative for details) * All Biochemistry in Perspective essays from the text, including favorites from past editions Student Study Guide and Solutions Manual (ISBN 9780195342925) Provides solutions to all of the exercises not included in the back of the book, as well as helpful study tips and further explanations of key concepts
PatchDock and SymmDock: servers for rigid and symmetric docking (2005)

Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.
Human cytomegalovirus (HCMV) immediate-early enhancer/promoter specificity during embryogenesis defines target tissues of congenital HCMV infection (1995)

Congenital human cytomegalovirus (HCMV) infection is a common cause of deafness and neurological disabilities. Many aspects of this prenatal infection, including which cell types are infected and how infection proceeds, are poorly understood. Transcription of HCMV immediate-early (IE) genes is required for expression of all other HCMV genes and is dependent on host cell transcription factors. Cell type-specific differences in levels of IE transcription are believed to underlie differences in infection permissivity. However, DNA transfection experiments have paradoxically suggested that the HCMV major IE enhancer/promoter is a broadly active transcriptional element with little cell type specificity. In contrast, we show here that expression of a lacZ gene driven by the HCMV major IE enhancer/promoter -524 to +13 segment is restricted in transgenic mouse embryos to sites that correlate with known sites of congenital HCMV infection in human fetuses. This finding suggests that the IE enhancer/promoter is a major determinant of HCMV infection sites in humans and that transcription factors responsible for its regulation are cell type-specifically conserved between humans and mice. The lacZ expression patterns of these transgenic embryos yield insight into congenital HCMV pathogenesis by providing a spatiotemporal map of the sets of vascular, neural, and epithelial cells that are likely targets of infection. These transgenic mice may constitute a useful model system for investigating IE enhancer/promoter regulation in vivo and for identifying factors that modulate active and latent HCMV infections in humans.
Ichthyophthiriasis in carp, Cyprinus carpio L.: fate of parasites in immunized fish (1992)

Abstract. The host‐parasite relationship between O‐group carp and the ciliatc Ichthyophthirius multifiliis Fouquet was investigated, with the specific aim of characterizing the fate of parasites encountering immunized fish. Carp were immunized by repeated controlled infections; immunized fish and control fish naive to I. multifiliis were then infected in the caudal fin epidermis by a single controlled exposure to theronts, which were applied in a droplet suspension to the tail surface. The number of parasites present within the caudal fin was monitored over a subsequent 5‐day period by means of in situ parasite mapping. Results indicated that, contrary to previous reports, theronts penetrated the skin of immunized fish in numbers comparable to those of fish receiving a primary infection. However, the majority of parasites which penetrated immune skin did not complete normal development; 79% of the parasites which had initially penetrated the immune skin were not relocated within 2h of exposure, and since no parasite material was detected at penetration sites, it was concluded that these parasites had prematurely exited the skin rather than been killed in situ. Subsequently, these sites became populated by leucocytes, predominantly macrophages, and the infiltrations continued for up to 5 days after the initial exposure. In contrast, at sites where mature trophonts had exited the skin of fish following a primary infection, more diffuse leucocytic infiltrations were recorded, and these were predominated by neutrophils. Differences in the response to parasite exit from immunized and previously unexposed control fish skin are discussed, with particular reference to the mode of protection and the fate of parasites encountering immune fish.
New approaches towards the synthesis of the side-chain of mycolactones A and B (2005)

New approaches towards the synthesis of the C1'-C16' side-chain of mycolactones A and B from Mycobacterium ulcerans are reported. Chiral building block 4 (Fig. 2) with the correct stereochemistry was obtained starting from naturally occurring monosaccharides, i.e. D-glucose or L-rhamnose. The polyunsaturated moiety 3 was synthesized in only 3 steps from 2,4-dimethylfuran. The building blocks were connected through a Sonogashira coupling resulting in the fast and convergent assembly of an 8,9-dehydro analogue 2 of the side-chain of mycolactones A and B. The synthesis of 1 is at this stage hampered by the lack of a selective partial hydrogenation protocol for alkynes embedded in a conjugated system. Alternative strategies involving palladium catalyzed sp2-sp2 coupling between C7' and C8' or C9' and C10' (Fig. 1) were also explored.
Microbial synthesis, physical properties, and biodegradability of polyhydroxyalkanoates (1995)

Abstract Poly(( R )‐3‐hydroxybutyrate), P(3HB), is produced by Alcaligenes eutrophus from fructose or butyric acid. The kinetics and mechanism of P(3HB) biosynthesis are presented. Four types of copolymers, poly(3‐hydroxybutyrate‐ co ‐3‐hydroxyvalerate), poly (3‐hydroxybutyrate‐ co ‐3‐hydroxypropionate), poly (3‐hydroxybutyrate‐ co ‐3‐hydroxyhexanoate), and poly (3‐hydroxybutyrate‐ co ‐4‐hydroxybutyrate), are produced by several bacterial strains from various carbon substrates. These microbial polyesters are biodegradable thermoplastics whose physical properties can be regulated by varying the molecular structure and composition of copolymers.
Transparent, near-infrared organic photovoltaic solar cells for window and energy-scavenging applications (2011)

We fabricate near-infrared absorbing organic photovoltaics that are highly transparent to visible light. By optimizing near-infrared optical-interference, we demonstrate power efficiencies of 1.3±0.1% with simultaneous average visible transmission of &amp;gt;65%. Subsequent incorporation of near-infrared distributed-Bragg-reflector mirrors leads to an increase in the efficiency to 1.7±0.1%, approaching the 2.4±0.2% efficiency of the opaque cell, while maintaining high visible-transparency of &amp;gt;55%. Finally, we demonstrate that a series-integrated array of these transparent cells is capable of powering electronic devices under near-ambient lighting. This architecture suggests strategies for high-efficiency power-generating windows and highlights an application uniquely benefiting from excitonic electronics.
Analysis of p60 and p80 tumor necrosis factor-alpha receptor messenger RNA and protein in human placentas. (1993)

Tumor necrosis factor-alpha (TNF), a pleiotrophic, multifunctional polypeptide factor, has been reported in both normal and infected human placentas. To identify potential targets for this cytokine, the cells in early and late gestation placentas and extraplacental membranes that express the two TNF receptor (TNF-R) genes, p60 and p80, were identified by using in situ hybridization and immunocytochemistry. Gestation-related, cell lineage-specific differences in steady-state levels of p60 and p80 TNF-R messenger RNA were observed. p60 TNF-R messenger RNA predominated at both early and late stages of gestation, being high in both mesenchymal and trophoblastic cell lineages. By contrast, p80 TNF-R messenger RNA was abundant only in intermittent stretches of first trimester syncytiotrophoblast and term placental mesenchymal cells. Overall, intensities of the TNF-R hybridization signals were stronger in term than in first trimester tissues. Transcription of the two TNF-R genes was confirmed by Northern blot hybridization. Translation was verified in all samples by immunohistology using polyclonal antibodies specific for the receptor proteins. p60 and p80 TNF-R proteins were identified both intracellularly and in maternal and fetal blood. Because TNF-Rs exist in both membrane-bound and soluble forms, the results of this study are consistent with the postulate that placental TNF-R have two critical functions: 1) modulation of TNF utilization by specific placental cell lineages during the course of pregnancy; and 2) protection against excessive TNF produced during infections.
Graft Selection in Anterior Cruciate Ligament Reconstruction (2005)

The ideal graft for use in anterior cruciate ligament reconstruction should have structural and biomechanical properties similar to those of the native ligament, permit secure fixation and rapid biologic incorporation, and limit donor site morbidity. Many options have been clinically successful, but the ideal graft remains controversial. Graft choice depends on surgeon experience and preference, tissue availability, patient activity level, comorbidities, prior surgery, and patient preference. Patellar tendon autograft, the most widely used graft source, appears to be associated with an increased incidence of anterior knee pain compared with hamstring autograft. Use of hamstring autograft is increasing. Quadriceps tendon autograft is less popular but has shown excellent clinical results with low morbidity. Improved sterilization techniques have led to increased safety and availability of allograft, although allografts have a slower rate of incorporation than do most types of autograft. No graft has clearly been shown to provide a faster return to play. However, in general, patellar tendon autografts are preferable for high-performance athletes, and hamstring autografts and allografts have some relative advantages for lower-demand individuals. No current indications exist for synthetic ligaments.
PNA Clamping Techniques for the Determination of Oncogene Mutations (2003)

Activating point mutations of the ras and p53 type can be used as genetic markers to screen for the presence of neoplastic cells in human tissue (1,2). The high frequency of activating K-ras and p53 mutations found in most solid tumors and the fact that a large percentage of these are found within a relatively small number of so-called “hotspot” positions has encouraged the development of PCR techniques which at the same time provide a high degree of sensitivity.
<title>Chiral effects in trioxadecalin-derived liquid crystals</title> (1998)

The chiral effects displayed by trioxadecalin derived liquid crystals are summarized. All these mesogenic properties depend strongly on small changes in the molecular structure. It is therefore possible to obtain a wide array of different chiral effects like helix inversions, blue phases, TGB<SUB>A</SUB> phase, S<SUB>C*</SUB> phase to name only some of them by changing only a small part of the molecule, meanwhile the basic mesogenic core is kept constant. In addition the mesogenic properties of new trioxadecalins are described, that have been obtained by a new synthetic pathway.
Existence of a mannitol hydrate during freeze‐drying and practical implications (1999)

We report thermal and crystallographic evidence for a previously unknown mannitol hydrate that is formed in the process of freeze-drying. The mannitol hydrate was produced by freeze-drying pure mannitol solutions (1-4% w/v) using the following cycle: (1) equilibration at -5 degreesC for 1 h; (2) freezing at -40 degreesC; (3) primary drying at -10 degreesC for 15 h; and (4) secondary drying at 10 degreesC for 2 h and then 25 degreesC for 5 h. This crystal form was also observed upon freeze-drying in the presence of sorbitol (1% w/v). The mannitol hydrate showed a distinct X-ray powder diffraction pattern, low melting point, and steplike desolvation behavior that is characteristic of crystalline hydrates. The mannitol hydrate was found to be metastable, converting to anhydrous polymorphs of mannitol upon heating and exposure to moisture. The amount of the mannitol hydrate varied significantly from vial to vial, even within the same batch. The formation of mannitol hydrate has several potential consequences: (1) reduced drying rate; (2) redistribution of the residual hydrate water during accelerated storage to the amorphous drug; and (3) vial-to-vial variation of the moisture level.
Iron-Related Proteins (2009)

These findings suggest that iron and iron-related proteins might be promising candidate urine biomarkers to identify HIV-infected children at risk of developing HIVAN and HIV-HUS. Moreover, based on the results of previous studies, we speculate that the release or accumulation of iron in the kidney of HIV-infected children may contribute to the rapid progression of their renal disease, and could become a new therapeutic target against HIVAN and HIV-HUS.
Polynomial curb detection based on dense stereovision for driving assistance (2010)

A real-time algorithm for curb detection in traffic scenes, based on dense stereovision, is proposed. Curbs are modeled as cubic polynomial curves. 3D points from stereovision are transformed into a Digital Elevation Map (DEM), in order to have a compact representation of the 3D space. Curb points are detected as the cells of the DEM that present a specific height variation. Only curb points that are temporally persistent and non-occluded are considered. Relevant cubic polynomials are computed from the set of curb points by a RANdom SAmple Consensus (RANSAC) approach. For each relevant polynomial, the curb patch is extracted by analyzing the DEM along the polynomial curve. Finally, the vertical location and height of each curb are computed based on the local elevation data.
Distance learning with digital video (1995)

The use of emerging multimedia technologies in education will cause a major shift in the educational services paradigm that promises major advantages over present analog distance learning systems. However, the difficulties encountered with the simultaneous introduction of new services and new technologies often impede the accomplishment of set goals. A more prudent and feasible first step might well be to use the new technologies while following existing paradigms. Such a step will then facilitate the transition to new services that capitalize on the new technologies. Abiding by this principle, researchers at Stanford are developing a prototype on-line distance learning system based on recent advances in digital video compression, video servers, and multimedia networking to deliver live and stored video lectures and seminars to students at their desktops. For the sake of concreteness, we are designing this system with the Stanford University Instructional Television Network in mind, as a first step beyond existing video-based instructional services. The prototype system and extensions, however, are general enough to apply to other environments and application domains.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro growth inhibition of human small cell lung cancer by physalaemin. (1987)

Production and secretion of neuroendocrine peptides by small cell lung cancer (SCLC) has been detected in the past years. Most recently the role of bombesin as an autocrine/paracrine growth modifier has been demonstrated. We used the soft agarose clonogenic assay to evaluate the influence of other neuroendocrine peptides on the in vitro proliferation of SCLC cell lines. Neuroendocrine peptides tested were adrenocorticotropic hormone, arginine vasopressin, calcitonin, glucagon, kassinin, neurotensin, physalaemin, somatostatin, and substance P. Experiments were carried out in serum-free and serum-supplemented media with and without serum-free incubation periods. Our results indicated that the amphibian undecapeptide physalaemin inhibits the clonal and mass culture growth of SCLC cell lines at picomolar concentrations. All other neuroendocrine peptides failed to influence SCLC growth in the test systems used. These results suggest a growth regulating effect of physalaemin and a potential new form of neuroendocrine peptide therapy for SCLC.
Differential gene expression in colon carcinoma cells and tissues detected with a cDNA array (1999)

Expression of selected genes coding for proteins with defined cellular functions was analysed in human cell lines derived from normal colonic mucosa, non-mucinous colonic carcinomas and mucinous colonic carcinomas. Altered expression of 10 genes in colon carcinoma cells was found by using a cDNA array; 6 of these alterations (60%) were confirmed by Northern blotting or semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). Among these 6 genes, 3 transcription factors as well as the topoisomerase II alpha and the mitosis inhibitor WEE1Hu gene were significantly suppressed in the tumour cell lines. In addition, the gene coding for the cell cycle inhibitor p21 was overexpressed only in cell lines derived from mucinous carcinomas. The significant suppression of the kinase WEE1Hu gene in carcinoma cells of both phenotypes and the tendency of the mucinous phenotype to overexpress p21 protein were confirmed in human colon carcinoma tissues. Our data show that the cDNA array method permits a correct identification of changes in gene expression with a relatively high accuracy. The different expression of the p21 gene in the non-mucinous and mucinous carcinoma cells supports the hypothesis that these phenotypes may develop along different genetic pathways. The detection of WEE1Hu gene suppression in colon carcinoma cells and tissues suggests its potential role in tumourigenesis.