gebhart/patrepeval huggingface dataset:
Broken intramedullary nails. (1988)

Between 1962 and 1987, we treated fifty-six patients for sixty broken intramedullary nails, using a custom-made hook to extract the distal fragment of the nail. The charts and radiographs of all of the patients were reviewed. Thirty-nine of the nails had been inserted in a fresh fracture, which usually was comminuted; eight had been used for fixation of an osteotomy; nine, for fixation of a non-union; and four, for treatment of a pathological fracture. Several small-diameter intramedullary nails broke at the site of the fracture or non-union. In contrast, the sites of breakage in the interlocking nails were the interlocking holes and the welded junction of the top insertional portion and the proximal slot. Many of the breakages were in patients who had an unstable fracture pattern. The interval between insertion and breakage ranged from one to 120 months.
Pharmacologic C5-Complement Suppression Reduces Blood Loss During On-Pump Cardiac Surgery (2005)

Pexelizumab administration inhibits complement-dependent hemolytic activity and is associated with a reduction in postoperative chest tube drainage in patients undergoing cardiac surgery requiring cardiopulmonary bypass. Further, clinical studies are needed to assess the value of complement attenuation in this setting.
Uncoupling conformational change from GTP hydrolysis in a heterotrimeric G protein α-subunit (2004)

Heterotrimeric G protein alpha (G alpha) subunits possess intrinsic GTPase activity that leads to functional deactivation with a rate constant of approximately 2 min(-1) at 30 degrees C. GTP hydrolysis causes conformational changes in three regions of G alpha, including Switch I and Switch II. Mutation of G202-->A in Switch II of G alpha(i1) accelerates the rates of both GTP hydrolysis and conformational change, which is measured by the loss of fluorescence from Trp-211 in Switch II. Mutation of K180-->P in Switch I increases the rate of conformational change but decreases the GTPase rate, which causes transient but substantial accumulation of a low-fluorescence G alpha(i1).GTP species. Isothermal titration calorimetric analysis of the binding of (G202A)G alpha(i1) and (K180P)G alpha(i1) to the GTPase-activating protein RGS4 indicates that the G202A mutation stabilizes the pretransition state-like conformation of G alpha(i1) that is mimicked by the complex of G alpha(i1) with GDP and magnesium fluoroaluminate, whereas the K180P mutation destabilizes this state. The crystal structures of (K180P)G alpha(i1) bound to a slowly hydrolyzable GTP analog, and the GDP.magnesium fluoroaluminate complex provide evidence that the Mg(2+) binding site is destabilized and that Switch I is torsionally restrained by the K180P mutation. The data are consistent with a catalytic mechanism for G alpha in which major conformational transitions in Switch I and Switch II are obligate events that precede the bond-breaking step in GTP hydrolysis. In (K180P)G alpha(i1), the two events are decoupled kinetically, whereas in the native protein they are concerted.
Stereoelective polymerization of d,l-lactide using N-heterocyclic carbene based compounds (2004)

A new Zn alkoxide catalyst supported by an N-heterocyclic carbene rapidly polymerizes D,L-lactide (D,L-LA) to heterotactic enriched poly(lactide)(PLA), while the free carbene and analogs instead yield highly isotactic enriched PLA.
Category theory for the sciences (2015)

Category theory was invented in the 1940s to unify and synthesize different areas in mathematics, and it has proven remarkably successful in enabling powerful communication between disparate fields and subfields within mathematics. This book shows that category theory can be useful outside of mathematics as a rigorous, flexible, and coherent modeling language throughout the sciences. Information is inherently dynamic; the same ideas can be organized and reorganized in countless ways, and the ability to translate between such organizational structures is becoming increasingly important in the sciences. Category theory offers a unifying framework for information modeling that can facilitate the translation of knowledge between disciplines. Written in an engaging and straightforward style, and assuming little background in mathematics, the book is rigorous but accessible to non-mathematicians. Using databases as an entry to category theory, it begins with sets and functions, then introduces the reader to notions that are fundamental in mathematics: monoids, groups, orders, and graphs -- categories in disguise. After explaining the big three concepts of category theory -- categories, functors, and natural transformations -- the book covers other topics, including limits, colimits, functor categories, sheaves, monads, and operads. The book explains category theory by examples and exercises rather than focusing on theorems and proofs. It includes more than 300 exercises, with selected solutions. Category Theory for the Sciences is intended to create a bridge between the vast array of mathematical concepts used by mathematicians and the models and frameworks of such scientific disciplines as computation, neuroscience, and physics.
It’s Time to Bring Dendritic Cell Therapy to Type 1 Diabetes (2013)

Type 1 diabetes (T1D) is an autoimmune disease that results from a deficient induction or maintenance of tolerance to islet β-cell antigens, allowing the eventual T-cell–mediated destruction of insulin-producing β-cells within the pancreatic islets (1). Under homeostatic conditions, immune tolerance is established by various subsets of antigen-presenting cells (APCs) with tolerance-inducing/maintaining (tolerogenic) functions and reinforced by other cells with suppressor and immunomodulatory properties. T-cell tolerance manifests itself through elimination (deletion), inactivation (anergy), or suppression of self-reactive T cells (Fig. 1 A ). These functions may be performed by a variety of tolerogenic APCs (Table 1), some of which have the ability to induce/boost regulatory T cells (Tregs) and/or B cells (Bregs). Genetic and environmental factors that vary among different individuals contribute to the development of T1D, in part by impacting mechanisms of tolerance (Fig. 1 B ). Therefore, a major goal for the prevention and/or reversal of T1D is to restore effective and durable tolerance to either prevent further destruction of remaining islet β-cells, help islet β-cell regeneration, or protect islet transplants and obviate the use of nonspecific immunosuppressive drugs. The approach reviewed here consists of developing a personalized therapy using the patient’s own cells manipulated to perform as tolerogenic APCs (Fig. 1 C ). In this review, we will explain why dendritic cells (DCs) are the tolerogenic cells of choice to fulfill the goal of restoring immune tolerance in T1D as part of a potentially powerful and safe cellular immunotherapy, the next generation of therapies (2). We will present the clinical considerations and challenges ahead and the plans to address them, taking into account lessons learned from animal models such as the NOD mouse.



Figure 1 
Tolerance to β-cell antigens: induction, loss, and restoration. A : Tolerance to β-cell antigens is induced and maintained by tolerogenic cells comprised of migratory DCs transporting antigens from peripheral to lymphoid …
A sequence-profile-based HMM for predicting and discriminating β barrel membrane proteins (2002)

We develop a HMM model, which can predict the topology of beta barrel membrane proteins using, as input, evolutionary information. The model is cyclic with 6 types of states: two for the beta strand transmembrane core, one for the beta strand cap on either side of the membrane, one for the inner loop, one for the outer loop and one for the globular domain state in the middle of each loop. The development of a specific input for HMM based on multiple sequence alignment is novel. The accuracy per residue of the model is 83% when a jack knife procedure is adopted. With a model optimisation method using a dynamic programming algorithm seven topological models out of the twelve proteins included in the testing set are also correctly predicted. When used as a discriminator, the model is rather selective. At a fixed probability value, it retains 84% of a non-redundant set comprising 145 sequences of well-annotated outer membrane proteins. Concomitantly, it correctly rejects 90% of a set of globular proteins including about 1200 chains with low sequence identity (<30%) and 90% of a set of all alpha membrane proteins, including 188 chains.
Effect of sodium chloride on transport of bacteria in a saturated aquifer material (1991)

Determinations were made of the influence of NaCl concentration, cell density, and flow velocity on the transport of Pseudomonas sp. strain KL2 through columns of aquifer sand under saturated conditions. A pulse-type boundary condition was used. The experiments were conducted by using 0.3-m-long Plexiglas columns with an internal diameter of 0.05 m. When a 1-h pulse of a 0.01 M NaCl solution containing 10(8) cells per ml was added at a flow rate of 10(-4) m s-1, the bacterial density in the effluent never exceeded 2.2% of the density of cells added, and only 1.5% of the bacteria passed through the aquifer material. In contrast, when the bacteria were applied in distilled water, the relative cell density in the effluent approached 100%, and 60% of the bacteria were transported through the aquifer solids. Under these conditions, the breakthrough of Pseudomonas sp. strain KL2 was slower than chloride. When the flow rate was 2.0 x 10(-4) m s-1, the cell density in the effluent reached 7.3% of that added in 0.01 M NaCl solution, but only 3.9% of the bacteria were transported through the aquifer particles. On the other hand, the density in the effluent approached 100% of that added in deionized water, and 77% of the added bacteria were recovered. When the density of added cells was 10(9) cells per ml at a flow rate of 10(-4) m s-1, the densities in the effluent reached 70 and 100% of those added in salt solution and deionized water, respectively, and 44 and 57% of the bacteria were transported through the aquifer solids.(ABSTRACT TRUNCATED AT 250 WORDS)
Fixed points of polynomial maps. Part II. Fixed point portraits (1993)

Douady, Hubbard and Branner have introduced the concept of a "limb" in the Mandelbrot set. A quadratic map f(z) = z 2 + c belongs to the p/q-limb if and only if there exist q external rays of its Julia set which land at a common fixed point of/, and which are permuted by/with combinatorial rotation number ^^Q/Z, p/q^O. (Compare Figure This note will make a similar analysis of higher degree polynomials by introducing the concept of the "fixed point portrait" of a monic polynomial map.
Glomerular basement membrane thickness in normal adults and its application to the diagnosis of thin basement membrane disease: an Indian study. (2005)

Microscopic hematuria of non-urologic origin warrants ultrastructural study of renal biopsy. Thinning and variations in the texture of glomerular basement membrane (GBM) are difficult to be recognized under light microscope; transmission electron microscope (TEM) therefore plays a vital role in identifying such changes. Ultrastructural morphometry is a valuable diagnostic aid when GBM is suspected of being abnormally thin. In an effort to determine the normal GBM thickness (GBMT) in Indian adults and to determine the cutoff value of GBMT for a diagnosis of thin basement membrane disease (TBMD), we determined GBM thickness in 25 normal adults. Postmortem biopsies of 25 normal adults (16 males and 9 females) aging between 18-58 years were included in the study. GBM thickness was determined through ultrastructural morphometry on accurately enlarged electron micrographs as harmonic mean of 50 orthogonal intercepts across the GBM in each case. Study revealed a mean GBM thickness of 321 nm with a standard deviation (SD) of 28 nm. Mean-2SD (321-56), that is 265 nm, was fixed as cutoff value of GBMT for the diagnosis of TBMD. A systematic split study of control subjects revealed thicker GBM (329+/-38 nm) in higher age group (35-60 years) as compared to GBMT (316+/-21 nm) in lower age group (18-30 years). Males in higher age group also revealed thicker GBM (males: 343+/-39 nm versus females: 300+/-12 nm). Ten patients with non-urologic hematuria and having GBMT<265 nm were diagnosed as cases of TBMD. Patients with TBMD revealed significantly attenuated GBM as compared to age and sex matched controls (214 +/- 40 nm versus 311 +/- 17 nm; p<0.0005). No overlap was observed in the distribution of GBMT in patients of TBMD and age and sex matched controls. Ultrastructural morphometry is the ultimate and appropriate method for diagnosing TBMD.
Degradation of Chemical Warfare Agents by Reactive Polymers (2008)

Nucleophilic hydrolysis of chemical warfare agents (CWA), S-2-(diisopropylamino)ethyl O-ethyl methylphosphonothioate (VX), O-pinacolyl methylphosphonofluoridate (soman, or GD), and isopropyl methylphosphonofluoridate (sarin, or GB) by polyacrylamidoxime (PANOx) and poly(N-hydroxyacrylamide) (PHA) has been demonstrated. The reactive PANOx and PHA were obtained by one-step oximation of polyacrylonitrile and polyacrylamide, respectively. The polymers were converted to their respective oximate salts at pH values greater than the pKa of oximate or amidoximate groups of 7.5 and 10.8, respectively. Although the PANOx and PHA exhibited spontaneous hydrolysis at ambient temperature and humidity, the conversion of the hydroxamate into the unreactive carboxylic groups was insignificant even at prolonged storage, so that the polymers maintained reactivity at ambient conditions. When exposed to ambient air or 100% humidity, the polymers imbibed up to 65 wt % water, which dramatically enhanced the polymer reactivity toward the CWA under study. The half-lives of VX in heterogeneous hydrolysis, which appeared to be pseudo-first-order in the polymer dispersions, were measured to be from 0.093 to 4.3 and 7.7 h in the presence of PANOx and PHA, respectively. The rates of hydrolytic activity of PANOx for VX exhibited a strong dependency on the degree of conversion of the amidoxime to amidoximate groups. The half-life of GB was less than 3 min. Only a minor presence of the toxic VX degradation product, S-[2-(diisopropylamino)ethyl]methylphonothioate (EA-2192), was detected in the course of degradation by the reactive polymers. The efficiency, ease of synthesis, and nontoxic nature of the PANOx and PHA polymers make them attractive materials in decontamination and as components of reactive barriers.
Integrated Management of Emergency Vehicle Fleet (2006)

The growing public concerns for safety and the advances in traffic management systems, that have made the availability of real-time traffic information a reality, have created an opportunity to build integrated decision support systems that can improve the coordination and sharing of information between agencies that are responsible for public safety and security and transportation agencies to provide more efficient Emergency Response Service. In an Emergency Response System, reduction of the duration of response time can yield substantial benefits. The response time plays a crucial role in minimizing the adverse impacts: fatalities and loss of property can be greatly reduced by reducing the response time for emergencies. In this dissertation, we have developed an integrated model that can assist emergency response fleet dispatchers in managing the fleet. This model can help reduce the response time and improve service level by specifically accounting for the following: Vehicle Deployment: given real-time information about the status of the emergency response fleet, traffic information and the status of emergency calls, select proper fleet assignment schemes that satisfy various operation requirements. Vehicle Routing: given real-time traffic information, provide real-time route guidance for drivers of dispatched vehicles. This goal is achieved by applying various shortest path algorithms into the solution procedure. Planning and Evaluation: given the status of the fleet and the frequency of emergency calls in various areas of a region, the model can help evaluate the performance of the current system and help plan for potential sites for the relocation of vehicles and allocate an appropriate fleet of vehicles to these sites. The vehicle deployment problem is formulated as an integer optimization problem. Since this problem has been shown to be NP-hard and because of the nature of emergency response, we developed heuristics which can provide quality solutions with short computational times. Several test algorithms are proposed to solve the emergency response vehicle deployment problem. Different methods for obtaining lower bounds for the value of objective function are analyzed in this dissertation. To evaluate the performance of the system under various scenarios, a simulation model is developed. The simulation system is calibrated based on real-world data. The results of simulation and analysis show the proposed system can effectively improve the emergency response service level. Application of this model in facility allocation illustrates its usage in other relevant operational scenarios.
Green Tea Extract Modulates Actin Remodeling via Rho Activity in an <i>In vitro</i> Multistep Carcinogenic Model (2005)

Alteration of actin polymerization and loss of actin filaments is a marker of cellular dedifferentiation and early malignant transformation. To study this phenomenon, an in vitro human urothelial model consisting of two cell lines, HUC-PC and MC-T11, were incorporated into the study design. These two cell lines have different malignant transformation potential. The effect of green tea extract (GTE), a potential anticancer agent, on actin remodeling was investigated. Upon exposure to the carcinogen 4-aminobiphenyl (4-ABP), the untransformed HUC-PC undergoes malignant transformation whereas the transformed MC-T11 progresses from noninvasive to invasive tumor. GTE induces actin polymerization in MC-T11 cells in a dose-responsive manner, but this effect is less obvious in the untransformed, more differentiated HUC-PC cells, which natively have higher actin polymerization status. In contrast, GTE antagonizes carcinogen 4-ABP induced actin depolymerization and stress fiber disruption in HUC-PC cells. In MC-T11 cells, GTE inhibits 4-ABP induced motility by increasing cell adhesion and focal adhesion complex formation. The effect of GTE on actin remodeling seems to be mediated by the stimulation of small GTP-binding protein Rho activity, because C3 exoenzyme, a specific inhibitor for Rho, blocks GTE-mediated Rho activation and stress fiber formation in MC-T11 cells. This study shows that GTE exerts an effect on cytoskeletal actin remodeling and provides further support for the use of GTE as a chemopreventive agent.
Anatomy of Herpes Simplex Virus DNA XII. Accumulation of Head-to-Tail Concatemers in Nuclei of Infected Cells and Their Role in the Generation of the Four Isomeric Arrangements of Viral DNA (1979)

Previous reports (H. Delius and J. B. Clements, J. Gen. Virol. 33:125-134, 1976; G. S. Hayward, R. J. Jacob, S. C. Wadsworth, and B. Roizman, Proc. Natl. Acad. Sci. U.S.A. 72:4243-4247, 1975; B. Roizman, G. S. Hayward, R. Jacob, S. W. Wadsworth, and R. W. Honess, Excerpta Med. Int. Congr. Ser. 2:188-198, 1974) have shown that herpes simplex virus DNA extracted from virions accumulating in the cytoplasm of infected cells consists of four populations of linear molecules differing in the orientation of the covalently linked large (L) and small (S) components relative to each other. Together, these four isomeric arrangements of viral DNA display four different termini and four different L-S component junctions. In the studies reported in this paper, we analyzed with restriction endonucleases the newly replicated viral DNA shortly after the onset of viral DNA synthesis, the progeny DNA accumulating in the nuclei late in infection, and rapidly sedimenting DNA present in nuclei of infected cells at 8 h after infection. In each instance the nuclear viral DNA contained a decreased concentration of all four terminal fragments and an increase in the concentration of fragments spanning the junction of L and S components relative to the concentration of other DNA fragments. The results are consistent with the hypothesis that the viral DNA accumulating in the nuclei consists of head-to-tail concatemers arising from the replication of DNA by a rolling-circle mechanism. A model is presented for generation of all four isomeric arrangements of herpes simplex virus DNA from one arrangement based on excision and repair of unit length DNA from head-to-tail concatemers and known features of the sequence arrangement of viral DNA.
Real-time warning of biological-agent attacks with the Canadian Integrated Biochemical Agent Detection System II (CIBADS II) (1999)

The Gulf War highlighted the growing threat of military use of chemical and biological (CB) weapons. Since that time revelations about the size and scope of the offensive CB agent programs in the former Soviet Union, Iraq, and other nations have confirmed this assessment. Further, terrorist threats and incidents throughout the world in recent years have shown that there is a growing potential for the civilian use of CB weapons. Many countries have undertaken programs to develop improved defenses against CB agent use, focusing on more effective detection systems as the key to providing advanced warning of an attack or mitigating the effectiveness of an attack. Requirements for detection systems include real-time detection to provide warning in time to avoid exposure, near-real-time identification to identify agents in time to treat casualties, and collection of samples for independent verification of use to validate any response. The Canadian Integrated Biochemical Agent Detection System (CIBADS II) is the first system to combine reliable real-time detection with low support requirements and automated operation to enhance ease of deployment. A key element of the CIBADS II is the fluorescence aerodynamic particle sizer (FLAPS), which can distinguish particles that contain live organisms from most other respirable particles in air. The follow-on version of CIBADS II, called 4WARN, enhances the advantages of CIBADS II through the development of more effective alarm algorithms while reducing the size, weight, and power requirements of the system. The present article will summarize the results of over 100 releases of simulants at four sets of field trials (Dugway Proving Ground, Utah, and the Defence Research Establishment Suffield, Canada) where CIBADS II has reliably detected concentrations of simulants below 10 agent-containing particles per liter of air (ACPLA), with low false-alarm rates. It is able to discriminate releases of biological aerosols from normal background aerosols with the use of an automated alarm algorithm with an average response time of 15 s, and can avoid false alarms from fluctuations in background aerosol concentrations due to natural occurrences such as forest fires and human activity such as trucks passing by on the test site. In addition, data from the FLAPS provide previously unobtainable environmental information on the live biological content and variability in background aerosols. Our studies suggest that the background concentrations of biological particles at the sites tested can vary by over an order of magnitude, but are relatively constant as a proportion of the total background particles. These scientific data will be discussed in detail, as will the potential for use of CIBADS II and its components in the study of airborne biological organisms. © 1999 John Wiley & Sons, Inc. Field Analyt Chem Technol 3: 260–273, 1999