gebhart/patrepeval huggingface dataset:
Endoscopic Cholecystectomy (1991)

We analyzed our initial 381 endoscopic cholecystectomies with particular emphasis on postoperative complications. The rate of conversion to open cholecystectomy was 3%. A technical complication occurred in 2% and a non-technical complication in 4%, for a total complication incidence of 6%. There were three postoperative fatalities (0.9%). Two fatal technical complications consisted of unrecognized intestinal injuries at the time of endoscopic cholecystectomy that were obvious when the abdomen was opened. One patient died of a cerebrovascular accident. Nonfatal technical complications included five bile leaks that required treatment. There were no common bile duct injuries, but excessive caution to prevent common bile duct injury may have contributed to the high incidence of bile leaks. Examination of the case numbers of the technical complications and conversion to open cholecystectomy suggests that the learning curve is real and somewhat prolonged, and that a willingness to convert to open cholecystectomy is necessary if technical complications are to be avoided.
Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles (1990)

Coulombic interactions between charges on the surface of proteins contribute to stability. It is difficult, however, to estimate their importance by protein engineering methods because mutation of one residue in an ion pair alters the energetics of many interactions in addition to the coulombic energy between the two components. We have estimated the interaction energy between two charged residues, Asp-12 and Arg-16, in an alpha-helix on the surface of a barnase mutant by invoking a double-mutant cycle involving wild-type enzyme (Asp-12, Thr-16), the single mutants Thr----Arg-16 and Asp----Ala-12, and the double mutant Asp----Ala-12, Thr----Arg-16. The changes in free energy of unfolding of the single mutants are not additive because of the coulombic interaction energy. Additivity is restored at high concentrations of salt that shield electrostatic interactions. The geometry of the ion pair in the mutant was assumed to be the same as that in the highly homologous ribonuclease from Bacillus intermedius, binase, which has Asp-12 and Arg-16 in the native enzyme. The ion pair does not form a hydrogen-bonded salt bridge, but the charges are separated by 5-6 A. The mutant barnase containing the ion pair Asp-12/Arg-16 is more stable than wild type by 0.5 kcal/mol, but only a part of the increased stability is attributable to the electrostatic interaction. We present a formal analysis of how double-mutant cycles can be used to measure the energetics of pairwise interactions.
GENETICS OF RETROVIRAL INTEGRATION (1992)

Today the retroviral integration reaction is probably understood, both in terms of its genetics and chemistry, in as much detail as any eukaryotic recombination process. That understanding is in part due to its high efficiency (for it can be induced to occur synchronously in every cell of a culture); to its simplicity (for there is only one major protein player); to its accessibility (for the viral genome has provided all the cis- and trans-acting players); and to its willingness to perform well in vitro, ultimately with purified components. The process has thus made the classic transition from a phenomenon to be studied genetically to a reaction that can also be studied biochemically. The next advances in our understanding of the process of retroviral integration are likely to center on chemical issues. Some basic enzymological issues need to be addressed: we need to determine the oligomeric state of the native IN protein; its state when bound to linear viral DNA; the residues at the active site; the residues involved in sequence-specific recognition of DNA; and the points of contact between IN monomers. Much of this information will follow from detailed mutagenesis of expressed IN genes. A crucial step will be the determination of the structure of the IN protein at atomic resolution through X-ray diffraction analysis of protein crystals, a project underway in several laboratories. That structure may immediately suggest how the enzyme contacts and joins two DNA molecules, and will enormously facilitate the design and interpretation of mutational studies. It seems plausible that we can understand the IN protein as a machine as well as any nuclease or recombinase. A significant number of larger biological questions about integration remain unanswered and will require genetic approaches. What is the true structure of the preintegration complex in the cytoplasm? How does the complex enter the nucleus, and obtain access to the host DNA? Why, at least for most viruses in most cells, does integration depend on cell division? Why does efficient expression of the viral DNA to form progeny viral RNA and proteins depend on integration? How are target sites for integration on the host genome selected, and why are there "hot spots" for insertion? Are there host proteins that facilitate or participate in the integration reaction itself, and what are those proteins? Are any of those proteins involved in site selection?(ABSTRACT TRUNCATED AT 400 WORDS)
XPS and SEM detection of surface changes on 64 ureteral stents after human usage (1998)

Ureteral stents are commonly implanted to assist the postsurgery flow of urine from the kidney to the bladder. We hypothesized that different surface compositions of stent material could result in different conditioning film depositions and potentially altered receptivity to bacterial biofilms. Using XPS, three types of ureteral stents recovered from 64 patients were found to have adsorbed conditioning films that altered the surface composition of the devices. Elements associated with encrustation (calcium, magnesium and phosphorus) were found on 69% of the silicone latex stents, 44% of the low surface energy (LSe) devices, and 38% of the carbon-rich stents. No statistical difference was found in relation to patient gender, stent type, duration of implantation, and encrustation deposition. The composition of the film suggested that the nature of the underlying material did not significantly alter the elements that adsorbed. Thus, devices may take on a similar surface coat within days, and perhaps hours, of exposure to the host. With respect to dense encrustations, fewer appeared on the LSe devices. SEM confirmed the presence and nature of the film crystals and showed bacterial biofilms adherent to devices and encrustations in three patients who had received prophylactic trimethoprim compared to one on ciprofloxacin. In conclusion, although encrustation deposition and biofilm formation on ureteral stents is not unique to Cook devices, the human model and surface science test systems described here are invaluable to evaluate biomaterials used in patients. Unless biomaterials undergo rigorous analysis in vivo, including true assessment of the outcome of prophylactic antibiotic usage, clinicians will be unable to accurately select the best device and management strategy for a given patient.
Large Sample Properties of Matching Estimators for Average Treatment Effects (2005)

Matching estimators for average treatment effects are widely used in evaluation research despite the fact that their large sample properties have not been established in many cases. The absence of formal results in this area may be partly due to the fact that standard asymptotic expansions do not apply to matching estimators with a fixed number of matches because such estimators are highly nonsmooth functionals of the data. In this article we develop new methods for analyzing the large sample properties of matching estimators and establish a number of new results. We focus on matching with replacement with a fixed number of matches. First, we show that matching estimators are not N1/2-consistent in general and describe conditions under which matching estimators do attain N1/2-consistency. Second, we show that even in settings where matching estimators are N1/2-consistent, simple matching estimators with a fixed number of matches do not attain the semiparametric efficiency bound. Third, we provide a consistent estimator for the large sample variance that does not require consistent nonparametric estimation of unknown functions. Software for implementing these methods is available in Matlab, Stata, and R.
On the use of multiple constant multiplication in polyphase FIR filters and filter banks (2004)

Multiple constant multiplication (MCM) has been shown to be an efficient way to reduce the number of additions and subtractions in FIR filter implementations. However, for polyphase decomposed FIR filters and filter banks, the problem can be formulated in three different ways. Either as one MCM block with all coefficients, one MCM block for each subfilter, or as a matrix MCM block. In this work we compare the approaches in terms of complexity, both for the MCM blocks and for the remaining hardware, such as structural additions and delay elements.
Splitting of a Cooper Pair by a Pair of Majorana Bound States (2008)

We propose a method to probe the nonlocality of a pair of Majorana bound states by crossed Andreev reflection, which is the injection of an electron into one bound state followed by the emission of a hole by the other (equivalent to the splitting of a Cooper pair). We find that, at sufficiently low excitation energies, this nonlocal scattering process dominates over local Andreev reflection involving a single bound state. As a consequence, the low-temperature and low-frequency fluctuations deltaI(i) of currents into the two bound states i=1, 2 are maximally correlated: deltaI_1deltaI_2[over ]=deltaI_i(2).[over ].
Tissue engineered meat- Future meat (2011)

Current meat production methods have many health, environmental and other problems associated with them like high risk of infectious animal diseases, nutrition-related diseases, resource use and environmental pollution through green house gas emissions, decrease in the fresh water supply, erosion and subsequent habitat and biodiversity loss (Asner et al., 2004; Savadogo et al., 2007) besides the use of farm animals and non-sustainable meat supply. A new approach to produce meat and thereby reducing these risks is probably feasible with existing tissue engineering techniques and has been proposed as a humane, safe and environmentally beneficial alternative to slaughtered animal flesh. The growing demand for meat and the shrinking resources available to produce it by current methods also demand a new sustainable production system. In vitro meat production system ensures sustainable production of a new chemically safe and disease free meat besides reducing the animal suffering significantly. This review discusses the requirements that need to be met to increase the feasibility of in vitro meat production, which includes finding an appropriate stem cell source, their growth inside a bioreactor and providing essential cues for proliferation and differentiation.
	
	Key words: In vitro meat, tissue engineering, future meat substitute.
Optical biosensors for cell adhesion (2009)

Planar optical waveguides offer an ideal substratum for cells on which to reside. The materials from which the waveguides are made--high refractive index transparent dielectrics--correspond to the coatings of medical implants (e.g., the oxides of niobium, tantalum, and titanium) or the high molecular weight polymers used for culture flasks (e.g., polystyrene). The waveguides can furthermore be modified both chemically and morphologically while retaining their full capability for generating an evanescent optical field that has its greatest strength at the interface between the solid substratum and the liquid phase with which it is invariably in contact (i.e., the culture medium bathing the cells), decaying exponentially perpendicular to the interface at a rate controllable by varying the material parameters of the waveguide. Analysis of the perturbation of the evanescent field by the presence of living cells within it enables their size, number density, shape, refractive index (linked to their constitution) and so forth to be determined, the number of parameters depending on the number of waveguide lightmodes analyzed. No labeling of any kind is necessary, and convenient measurement setups are fully compatible with maintaining the cells in their usual environment. If the temporal evolution of the perturbation is analyzed, even more information can be obtained, such as the amount of material (microexudate) secreted by the cell while residing on the surface. Separation of parallel effects simultaneously contributing to the perturbation of the evanescent field can be accomplished by analysis of coupling peak shape when a grating coupler is used to measure the propagation constants of the waveguide lightmodes.
Novel GLP‐1 mimetics developed to treat type 2 diabetes promote progenitor cell proliferation in the brain (2011)

One of the symptoms of diabetes is the progressive development of neuropathies. One mechanism to replace neurons in the CNS is through the activation of stem cells and neuronal progenitor cells. We have tested the effects of the novel GLP-1 mimetics exenatide (exendin-4; Byetta) and liraglutide (NN2211; Victoza), which are already on the market as treatments for type 2 diabetes, on the proliferation rate of progenitor cells and differentiation into neurons in the dentate gyrus of brains of mouse models of diabetes. GLP-1 analogues were injected subcutaneously for 4, 6, or 10 weeks once daily in three mouse models of diabetes: ob/ob mice, db/db mice, or high-fat-diet-fed mice. Twenty-four hours before perfusion, animals were injected with 5'-bromo-2'-deoxyuridine (BrdU) to mark dividing progenitor cells. By using immunohistochemistry and stereological methods, the number of progenitor cells or doublecortin-positive young neurons in the dentate gyrus was estimated. We found that, in all three mouse models, progenitor cell division was enhanced compared with nondiabetic controls after chronic i.p. injection of either liraglutide or exendin-4 by 100-150% (P < 0.001). We also found an increase in young neurons in the DG of high-fat-diet-fed mice after drug treatment (P < 0.001). The GLP-1 receptor antagonist exendin(9-36) reduced progenitor cell proliferation in these mice. The results demonstrate that GLP-1 mimetics show promise as a treatment for neurodegenerative diseases such as Alzheimer's disease, because these novel drugs cross the blood-brain barrier and increase neuroneogenesis.
Palladium-Catalyzed Cross-Coupling Substitution (2003)

For Abstract see ChemInform Abstract in Full Text.
A Neurotropic Virus Isolated from the Blood of a Native of Uganda (1940)

SummaryA neurotropic virus was isolated from the blood of an African woman with fever. The serum taken at the time of illness contained no demonstrable neutralizing antibodies against the virus, whereas convalescent serum taken 3 months later neutralized strongly.The virus has a particle size of approximately 21 to 31 mµ.The virus is pathogenic for mice by intracerebral, intranasal, and intraperitoneal inoculations. It is slightly, if at all, pathogenic for mice by subcutaneous inoculation. It induces encephalitis and causes death when introduced intracerebrally in rhesus monkeys. It causes fever without obvious illness in African monkeys (Cercopithecus ethiops centralis) and induces the formation of neutralizing antibodies. It is not pathogenic for rabbits and guinea pigs, but induces the formation of antibodies.Neutralization tests with this virus and appropriate immune sera may be carried out either by intracerebral or by intraperitoneal inoculation. Immunologically the agent is related to the virus of Japanese B encephalitis and perhaps also to the virus of louping ill.The lesions induced by the virus are essentially limited to the central nervous system and are apparently different from the lesions induced by other known neurotropic viruses pathogenic for man.
Longer-term effects of cardiac resynchronization therapy on mortality in heart failure [the CArdiac REsynchronization-Heart Failure (CARE-HF) trial extension phase] (2006)

The benefits of CRT observed in the main trial persist or increase with longer follow-up. Reduction in mortality was due to fewer deaths both from worsening heart failure and from sudden death.
A rapid method for characterizing transgenic mice. (1990)

Utilisation de la technique PCR pour identifier des souris transgeniques porteuses du gene de l'antigene T du SU40. Cette technique permet de prelever de faibles quantites d'echantillon par rapport au Southern blot
Biocatalytic and semisynthetic studies of the anticancer tobacco cembranoids (2007)

Historically, tobacco use was primarily recreational and has been smoked in cigarettes, cigars and pipes, as well as smokeless forms of consumption, all of which are associated with adverse health effects. However, recent scientific investigations indicate that tobacco also contains several diverse secondary metabolites that may provide potential health benefits in the treatment of cancer and neurodegenerative diseases. Specifically, the leaf and flower of Nicotiana tabacum contain high amounts of the key flavor ingredient, cembranoids. Tobacco alpha- and beta-2,7,11-cembratriene-4,6-diols display potent anticancer activity. These compounds have also been found to inhibit phorbol ester-stimulated (32)P(i) incorporation into phospholipids, induction of Epstein-Barr virus early antigen and protein phosphorylation. This review focuses on the biocatalytic and semisynthetic studies of tobacco cembanoids and their anticancer activity.
Using integrity constraints to provide intensional answers to relational queries (1989)

An intensionalanswer to a query is a set of characterizations of the set of database values that satisfy the query (the extensional answer). Intensional answers provide users with additional insight into the nature of standard extensional answers. In this paper we describe a method that applies database constraints to generate intensional answers. These intensional answers characterize the extensional answers in two ways: (1) with constraints that are applicable to the extensional answer, and (2) with database views that are contained entirely in the extensional answer. Our method is to represent the definitions of constraints in special “meta-relations”, and extend standard algebraic operators to these relations. When a query is presented to the database system, it is performed both on the actual relations, resulting in an extensional answer, and on the meta-relations, resulting in definitions of constraints that apply to the extensional answer, as well as database views that are contained entirely in the extensional answer. These definitions are translated into an intensional answer that accompanies the extensional answer.
Population Biology of Lymphocytes: The Flight for Survival (2000)

In this essay we suggest that the primary goal of the cells of the immune system is to ensure their own growth and survival. In adults, in steady-state conditions, the number and distribution of lymphocyte populations is under homeostatic control. New lymphocytes that are continuously produced in primary and secondary lymphoid organs must compete with resident cells for survival. We discuss recent findings supporting lymphocyte survival as a continuous active process and implicating cognate receptor engagement as fundamental survival signals for both T and B lymphocytes. The conflict of survival interests between different cell types gives rise to a pattern of interactions that mimics the behavior of complex ecological systems. In their flight for survival and in response to competition, lymphocytes use different survival signals within different ecological niches during cell differentiation. This is the case for T and B lymphocytes and also for naive and memory/activated T and B cells. We discuss how niche differentiation allows the co-existence of different cell types and guarantees both repertoire diversity and efficient immune responses.
Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans (2014)

The CRISPR RNA-guided Cas9 nuclease gene-targeting system has been successfully used for genome editing in a variety of organisms. Here, we report the use of dual sgRNA-guided Cas9 nuclease to generate knockout mutants of protein coding genes, noncoding genes, and repetitive sequences in C. elegans. Co-injection of C. elegans with dual sgRNAs results in the removal of the interval between two sgRNAs and the loss-of-function phenotype of targeted genes. We sought to determine how large an interval can be eliminated and found that at least a 24 kb chromosome segment can be deleted using this dual sgRNA/Cas9 strategy. The deletion of large chromosome segments facilitates mutant screening by PCR and agarose electrophoresis. Thus, the use of the CRISPR/Cas9 system in combination with dual sgRNAs provides a powerful platform with which to easily generate gene knockout mutants in C. elegans. Our data also suggest that encoding multiple sgRNA sequences into a single CRISPR array to simultaneously edit several sites within the genome may cause the off-target deletion of chromosome sequences.
Multiple-Play Bandits in the Position-Based Model (2016)

Sequentially learning to place items in multi-position displays or lists is a task that can be cast into the multiple-play semi-bandit setting. However, a major concern in this context is when the system cannot decide whether the user feedback for each item is actually exploitable. Indeed, much of the content may have been simply ignored by the user. The present work proposes to exploit available information regarding the display position bias under the so-called Position-based click model (PBM). We first discuss how this model differs from the Cascade model and its variants considered in several recent works on multiple-play bandits. We then provide a novel regret lower bound for this model as well as computationally efficient algorithms that display good empirical and theoretical performance.
Prostate cancer cells use genetic and epigenetic mechanisms for progression to androgen independence (2006)

Studies on the genetic basis of prostate cancer (PCa) have lead to mixed results with the only consensus being that PCa is a complex disease. Our goal was to gain insight into potential events involved in the acquisition of the androgen-refractory phenotype in PCa cells regardless of DNA-change dependence. To this end, we examined two LNCaP PCa cell line models of progression-one developed in vivo and one developed in vitro-using molecular cytogenetic and microarray gene expression analyses and extended this investigation of specific events into PCa tumors. The chromosomal changes observed in both in vivo and in vitro androgen-independent cell lines are similar to those seen in PCa during tumor progression. Correspondingly, gene expression analysis showed significant heterogeneity in the genes expressed among androgen-independent cells, but with some common gene expression changes that correlated with the acquired androgen-independent phenotype. Thus, growth conditions under which the cells progress appeared to impact the mechanisms used for progression, albeit within tumor-type-specific pathways. Our findings suggest that a dynamic and adaptable combination of epigenetic and DNA-change-dependent events can be used by PCa cells for the acquisition of the androgen-independent phenotype. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.