gebhart/patrepeval huggingface dataset:
A two-option Approach to Solving the Decision problem of Regeneration (2004)

Real option theory has for some decades been used in forest economics to analyse decision problems which involve irreversible and stochastic decisions. One such decision is when to harvest a stand and with what species to regenerate. The latter decision can be postponed for some time, making a species change possible if favoured by the value development or if regeneration of the present species is unsuccessful. This problem is analysed here as extension of the traditional two-option problem, by involving several stochastic elements.
for Optimal Boundary & Region Segmentation of Objects in N-D Images (2001)

In this paper we describe a new technique for general purpose interactive segmentation of N-dimensional images. The user marks certain pixels as “object” or “background” to provide hard constraints for segmentation. Additional soji constraints incorporate both boundary and region information. Graph cuts are used to find the globally optimal segmentation of the N-dimensional image. The obtained solution gives the best balance of boundary and region properties among all segmentations satishing the constraints. The topology o$our segmentation is unrestricted and both “object” and “background” segments may consist of several isolatedparts. Some experimental results are presented in the context ofphotohideo editing and medical image segmentation. We also demonstrate an interesting Gestalt example. A fast implementation of our segmentation method is possible via a new mar-$ow algorithm in [2].
Cross-Linking in Adhesive Quinoproteins:  Studies with Model Decapeptides (2000)

Mytilus edulis foot protein-1 (mefp1) is a major component of the byssus, an adhesive holdfast in mussels. The recent report of 5, 5'-di(dihydroxyphenyl-L-alanine) (diDOPA) cross-links in byssus [McDowell et al. (1999) J. Biol. Chem. 274, 20293] has raised questions about the relationship of these to mefp1. About 80% of the primary structure of mefp1 consists of a tandemly repeated consensus sequence Ala(1)-Lys(2)-Pro(3)-Ser(4)-Tyr(5)-Pro(6)-Pro(7)-Thr(8)-Tyr(9)-Lys(10 ) with varying degrees of posttranslational hydroxylation to hydroxyprolines in positions 3, 6, and 7 and to DOPA in positions 5 and 9. Six natural or synthetic variants of this decapeptide were subjected to oxidation by tyrosinase or periodate. DOPA is the only residue to suffer losses in all oxidized peptides. Moreover, using MALDI TOF mass spectrometry, oxidized decapeptides all showed evidence of multimer formation and a mass loss of 6 Da per coupled pair of peptides. Multimer formation was inhibited by addition of DOPA-like o-diphenols, but addition of simple amines such as free Lys had no effect. The results are consistent with aryloxy coupling to diDOPA followed by reoxidation to diDOPA quinone. There are subtle but noteworthy variations, however, in multimer formation among the peptide congeners. Decapeptides with Pro(3) modified to trans-4-hydroxyproline do not form multimers beyond dimers; they also exhibit significant Lys losses following oxidation of DOPA. Moreover, in Ala-Lys-Hyp-Ser-Tyr-DiHyp-Hyp-Thr-DOPA-Lys, Tyr appears to be protected from oxidation by tyrosinase.
Preparation and Characterization of New Room Temperature Ionic Liquids (2002)

A new series [C(n)O(m )mim][X] of imidazolium cation-based room temperature ionic liquids (RTILs), with ether and alcohol functional groups on the alkyl side-chain has been prepared. Some physical properties of these RTILs were measured, namely solubility in common solvents, viscosity and density. The solubility of LiCl, HgCl(2) and LaCl(3) in room temperature ionic liquids was also determined. The features of the solid-liquid phase transition were analysed, namely the glass transition temperature and the heat capacity jump associated with the transition from the non-equilibrium glass to the metastable supercooled liquid. These properties were compared with those reported for the 1-n-alkyl-3-methylimidazolium [C(n )mim][X] series. While the density and solid-liquid phase transition properties are similar for both series, the new RTILs present a considerably lower viscosity and an increased ability to dissolve HgCl(2) and LaCl(3) (up to 16 times higher).
Wave-equation tomography (1992)

Abstract The relation between ray-trace and diffraction tomography is usually obscured by formulation of the two methods in different domains: the former in space, the latter in wavenumber. Here diffraction tomography is reformulated in the space domain, under the title of wave-equation tomography. With this transformation, wave-equation tomography projects monochromatic, scattered wavefields back over source-receiver wavepaths, just as ray-trace tomography projects traveltime delays back over source-receiver raypaths. Derived under the Born approximation, these wavepaths are wave-theoretic backprojection patterns for reflected energy; derived under the Rytov approximation, they are wave-theoretic back-projection patterns for transmitted energy.Differences between ray-trace and wave-equation tomography are examined through comparison of wavepaths and raypaths, followed by their application to a transmission-geometry, synthetic data set. Rytov wave-equation tomography proves superior to ray-trace tomography in dealing with geometrical frequency dispersion and finite-aperture data, but inferior in robustness. Where ray-trace tomography assumes linear phase delay and inverts the arrival time of one well-understood event, wave-equation tomography accommodates scattering and inverts all of the signal and noise on an infinite trace simultaneously. Interpreted through the uncertainty relation, these differences lead to a redefinition of Rytov wavepaths as monochromatic raypaths, and of raypaths as infinite-bandwidth wavepaths (Rytov wavepaths averaged over an infinite bandwidth).The infinite-bandwidth and infinite-time assumptions of ray-trace and Rytov, wave-equation tomography are reconciled through the introduction of bandlimited raypaths (Rytov wavepaths averaged over a finite bandwidth). A compromise between rays and waves, bandlimited raypaths are broad backprojection patterns that account for the uncertainty inherent in picking traveltimes from bandlimited data.
Pharmacological basis for a novel therapeutic strategy based on the use of aquated cisplatin. (1997)

In pursuit of a strategy for increasing delivery of platinum drugs to tumors, we compared the cytotoxicity, extent of cellular uptake, and DNA platination of native cisplatin (DDP) and aquated cisplatin (aqDDP) in human head and neck carcinoma UMSCC10b cells. AqDDP was 1. 8-fold more toxic than DDP when tested against UMSCC10b cells in vitro. At high concentrations, aqDDP uptake was 3-fold more rapid than that of DDP; uptake of DDP and aqDDP was nonsaturable up to a concentration of 1600 micrometer. AqDDP produced 6.4-fold more platination of DNA than did DDP at the same concentration, suggesting that once inside the cell, aqDDP was 2-fold more effective at producing adducts in DNA than the native drug. Despite the paradox that aqDDP, which contains some charged species, entered the cell more rapidly than did neutral native DDP at high concentrations, studies on the effect of temperature, ATP depletion, and sulfhydryl group blockade did not provide evidence for uptake of aqDDP via a channel or transporter. AqDDP was more nephrotoxic to mice than DDP; however, s.c. administration of sodium thiosulfate protected against this toxicity and permitted a 7-fold escalation of aqDDP dose. These studies provide the preclinical basis for a novel therapeutic strategy based on the regional intraarterial or intracavitary administration of aqDDP in combination with a systemic neutralizing agent.
Unsupervised Learning of Noisy-Or Bayesian Networks (2013)

This paper considers the problem of learning the parameters in Bayesian networks of discrete variables with known structure and hidden variables. Previous approaches in these settings typically use expectation maximization; when the network has high treewidth, the required expectations might be approximated using Monte Carlo or variational methods. We show how to avoid inference altogether during learning by giving a polynomial-time algorithm based on the method-of-moments, building upon recent work on learning discrete-valued mixture models. In particular, we show how to learn the parameters for a family of bipartite noisy-or Bayesian networks. In our experimental results, we demonstrate an application of our algorithm to learning QMR-DT, a large Bayesian network used for medical diagnosis. We show that it is possible to fully learn the parameters of QMR-DT even when only the findings are observed in the training data (ground truth diseases unknown).
Evolution and ecology of antibiotic resistance genes (2007)

A new perspective on the topic of antibiotic resistance is beginning to emerge based on a broader evolutionary and ecological understanding rather than from the traditional boundaries of clinical research of antibiotic-resistant bacterial pathogens. Phylogenetic insights into the evolution and diversity of several antibiotic resistance genes suggest that at least some of these genes have a long evolutionary history of diversification that began well before the 'antibiotic era'. Besides, there is no indication that lateral gene transfer from antibiotic-producing bacteria has played any significant role in shaping the pool of antibiotic resistance genes in clinically relevant and commensal bacteria. Most likely, the primary antibiotic resistance gene pool originated and diversified within the environmental bacterial communities, from which the genes were mobilized and penetrated into taxonomically and ecologically distant bacterial populations, including pathogens. Dissemination and penetration of antibiotic resistance genes from antibiotic producers were less significant and essentially limited to other high G+C bacteria. Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations.
Microbiota Dynamics in Patients Treated with Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection (2013)

Clostridium difficile causes antibiotic-associated diarrhea and pseudomembraneous colitis and is responsible for a large and increasing fraction of hospital-acquired infections. Fecal microbiota transplantation (FMT) is an alternate treatment option for recurrent C. difficile infection (RCDI) refractory to antibiotic therapy. It has recently been discussed favorably in the clinical and scientific communities and is receiving increasing public attention. However, short- and long-term health consequences of FMT remain a concern, as the effects of the transplanted microbiota on the patient remain unknown. To shed light on microbial events associated with RCDI and treatment by FMT, we performed fecal microbiota analysis by 16S rRNA gene amplicon pyrosequencing of 14 pairs of healthy donors and RCDI patients treated successfully by FMT. Post-FMT patient and healthy donor samples collected up to one year after FMT were studied longitudinally, including one post-FMT patient with antibiotic-associated relapse three months after FMT. This analysis allowed us not only to confirm prior reports that RCDI is associated with reduced diversity and compositional changes in the fecal microbiota, but also to characterize previously undocumented post-FMT microbiota dynamics. Members of the Streptococcaceae, Enterococcaceae, or Enterobacteriaceae were significantly increased and putative butyrate producers, such as Lachnospiraceae and Ruminococcaceae were significantly reduced in samples from RCDI patients before FMT as compared to post-FMT patient and healthy donor samples. RCDI patient samples showed more case-specific variations than post-FMT patient and healthy donor samples. However, none of the bacterial groups were invariably associated with RCDI or successful treatment by FMT. Overall microbiota compositions in post-FMT patients, specifically abundances of the above-mentioned Firmicutes, continued to change for at least 16 weeks after FMT, suggesting that full microbiota recovery from RCDI may take much longer than expected based on the disappearance of diarrheal symptoms immediately after FMT.
Two mouse monoclonal antibodies detecting two different epitopes of an activated lymphocyte antigen on adult T-cell leukemia cells. (1985)

Mouse monoclonal antibodies were produced against MT-2 cell line derived from adult T-cell leukemia or human T-cell leukemia virus-rich fraction therefrom. Two IgG1 antibodies, Ta60a and Ta60b, were found to be reactive not only with cell lines derived from adult T-cell leukemia or cutaneous T-cell lymphomas, but also with activated peripheral blood lymphocytes, suggesting the similarity of Ta60 antigen group to Tac antigen which is present on interleukin 2 receptor. Thus, the relationship among these antigens was studied. Two Ta60 antibodies and Tac antibody immunoprecipitated the molecule with almost identical electrophoretic mobility, approximately a Mr 60,000 antigen from [3H]glucosamine-labeled activated peripheral blood lymphocytes or MT-2, MT-1, or ATN-1 cells from adult T-cell leukemia and a Mr 53,000 antigen from HUT-102 cells derived from cutaneous T-cell lymphomas. Further, Tac antibody was found to immunoprecipitate Ta60b molecule on 125I-labeled MT-2 cells by sequential immunoprecipitation, indicating that these two epitopes are on the same molecule. Antibody binding inhibition assays with either 3H-labeled Ta60a or Ta60b antibody demonstrated that Ta60a and Tac are the same epitope, but different from Ta60b. Thus, at least two epitopes were demonstrated to be present on interleukin 2 receptor molecule. However, Ta60b antibody showed almost no blocking effects on proliferation of an interleukin-2-dependent cell line, whereas Ta60a antibody did. Various hematopoietic tumor cells were typed with these two antibodies, but the results with Ta60b antibody were described, because they showed a similar specificity. Ta60b antibody reacted with all adult T-cell leukemia cases, but did not react with T-cell acute lymphoblastic leukemia, lymphoblastic lymphoma, or mature T-cell lymphoma. Interestingly, 3 of 12 acute myeloblastic leukemia and 2 of 5 chronic myelocytic leukemia in blastic crisis showed positive reactions. One-third of B-cell chronic lymphocytic leukemia and B-cell lymphoma as well as a few B-cell lines were also weakly reactive with this antibody. A part of the results with direct tests was confirmed by the absorption tests. The results obtained demonstrated the presence of Ta60b on a certain fraction of malignant hematopoietic cells of other than T-cell origin.
Biochemical, immunological, and functional aspects of the growth-suppressor/oncoprotein p53. (1992)

The cellular phosphoprotein p53 was initially discovered in a variety of in vitro transformed and tumor-derived cell lines. Later on, p53 was also found in normal, nontransformed cells albeit at very low levels. Inhibition of p53 functions by microinjection of anti-p53 antibodies prevented quiescent cells from reentering the cell cycle after serum stimulation, indicating that p53 might somehow be involved in the regulation of cell proliferation. After detection of p53-specific mRNAs, the gene was discovered in diverse species ranging from fish and frog to man. Knowing the p53 DNA sequence, it became clear that mutant forms of p53 had immortalizing and, in cooperation with other oncogenes, transforming activities. On the other hand, wild-type p53 could suppress oncogene-mediated transformation. It seems clear now that wild-type p53 is a tumor suppressor. Moreover, analysis of p53 from many types of human tumors indicates that the p53 gene is a very frequent target for mutational alterations. Because the biochemical consequences of these alterations are not yet clear, it is not understood yet on the molecular level how p53 can act as an oncogenic protein, on one hand, and as a growth-suppressor protein on the other hand. Therefore, the present review aims to summarize the biochemical and immunological properties of p53 and to address some biological activities of p53 in order to allow more insight into how p53 might be regulated within the cell or how p53 might regulate cell proliferation.
Nebulised hypertonic saline for cystic fibrosis (2005)

Nebulised hypertonic saline improves mucociliary clearance in short-term clinical trials and appears to increase lung function compared to control. In comparison to recombinant deoxyribonuclease it may be less effective at improving lung function after three months. Currently there is insufficient evidence to support the use of hypertonic saline as routine treatment for people with cystic fibrosis.
Dietary Factors That Promote or Retard Inflammation (2006)

Inflammation plays a pivotal role in all stages of atherosclerosis. Cardiovascular risk factors and metabolic syndrome are typified by low-grade inflammation. Intervention trials convincingly demonstrate that weight loss reduces biomarkers of inflammation, such as C-reactive protein (CRP) and interleukin (IL)-6. Limited studies have shown that certain dietary factors; oleic acid, alpha-linolenic acid, and antioxidants RRR-alpha-alpha tocopherol, reduce biomarkers of inflammation. Most of the studies with fish oil supplementation have shown null effects, and conflicting results have been reported with saturated and trans fatty acids, cholesterol, and soy intake. Much further research is needed to define the role of individual dietary factors on the biomarkers of inflammation and the mechanism of the anti-inflammatory effects of weight loss.
RNA-SeQC: RNA-seq metrics for quality control and process optimization (2012)

See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.
Development and validation of flow cytometric measurement for parasitaemia using autofluorescence and YOYO-1 in rodent malaria (2007)

An automated flow cytometric (FCM) detection method has been developed and validated with a simple diagnostic procedure in parasitized erythrocytes of Plasmodium berghei-infected rats using the nucleic acid-binding fluorescent dye YOYO-1. High levels of reticulocytes were detected during the course of the infection, ranging from 1.2-51.2%, but any RNA potentially confounding the assay could be removed by digestion with RNAse. The cell counts of uninfected, infected, and nucleated cells occurred with high precision. The cells were divided into different populations according to their physical or chemical properties but various factors within the assay such as cell fixation, RNA digestion, and compensation required optimization. In this study, FCM greatly simplified and accelerated parasite detection, with a mean precision of 4.4%, specificity of 98.9% and accuracy of 101.3%. The detection and quantitation limits in the assay were 0.024% and 0.074% parasitaemia, respectively. Overall, the parasite counts by FCM measurement correlated highly (r2=0.954-0.988) with the parasitaemia measured by light microscopical analysis when animals treated with suppressive, clearance, and curative doses of novel antimalarial drugs were examined. The lower levels of parasitaemia (30%) detected by microscopy compared to FCM may be related to a number of schizonts externally attached to the erythrocyte membranes that normally would not be included in microscopy counting. Lower sampling error and reliable identification of rodent erythrocyte parasites based on the principles of FCM have replaced the traditional blood smear in our laboratory.
Bactericidal action of ofloxacin, sulbactam-ampicillin, rifampin, and isoniazid on logarithmic- and stationary-phase cultures of Mycobacterium tuberculosis (1996)

The bactericidal actions of ofloxacin and sulbactam-ampicillin, alone and in combination with rifampin and isoniazid, on exponential-phase and stationary-phase cultures of a drug-susceptible isolate of Mycobacterium tuberculosis were studied in vitro. In exponential-phase cultures, all drugs were bactericidal, with the higher concentrations of ofloxacin (5 micrograms/ml) and sulbactam-ampicillin (15 micrograms of ampicillin per ml) being as bactericidal as 1 microgram of isoniazid per ml or 1 microgram of rifampin per ml. In two-drug combinations, both drugs increased the levels of activity of isoniazid and rifampin and were almost as bactericidal as isoniazid-rifampin; they also appeared to increase the level of activity of isoniazid-rifampin in three-drug combinations. In contrast, ofloxacin and sulbactam-ampicillin had little bactericidal activity against stationary-phase cultures and were less active than isoniazid or rifampin alone. Furthermore, in two-drug or three-drug combinations, they did not increase the level of activity of isoniazid, rifampin, or isoniazid-rifampin. These findings suggest that ofloxacin and sulbactam-ampicillin are likely to be most useful in the early stages of treatment and in preventing the emergence of resistance to other drugs but are unlikely to be effective as sterilizing drugs helping to kill persisting lesional bacilli.
Comparative Study of Microepineurial Anastomoses with the Use of CO2 Laser and Suture Techniques in Rat Sciatic Nerves: Part 1 (1985)

The possibility of utilizing the CO2 laser for neural anastomoses was investigated in a rat sciatic nerve model. One nerve in each animal was acutely divided and anastomosed using 10-0 nylon epineurial sutures, while the opposite side was joined by "welding" the opposed nerve ends together with CO2 laser pulses. The surgical incisions were reexplored 60 days postoperatively, action potentials were recorded across the anastomoses, and the nerves were removed for light and electron microscopy. The operative patency rate in the suture group was 100%, compared to 87% in the laser group. Among those animals with bilaterally intact nerves, action potentials could be recorded across the anastomotic site in 78% of the sutured preparations and in 85% of nerves spot-welded with the CO2 laser. Morphological studies showed a greater degree of scar tissue formation and constriction in the anastomotic zone of the nerves joined by sutures than was present in laser-treated animals. We believe these preliminary observations suggest that the CO2 laser may have a role to play in peripheral nerve surgery. Further study of this technique is warranted.
Lymphohematopoietic Engraftment in Minimally Myeloablated Hosts (1998)

The concept that myeloablation to open space was a prerequisite for marrow stem cell engraftment has been challenged by studies showing high rates of engraftment in nonmyeloablated mice (Stewart et al,Blood 81:2566, 1993; Quesenberry et al, Blood Cells20:97, 1994; Brecher et al, Blood Cells 5:237, 1979; Saxe et al, Exp Hematol 12:277, 1984; and Wu et al, Exp Hematol21:251, 1993). However, relatively large numbers of marrow cells were necessary to achieve high long-term donor percentages. We have demonstrated, using a BALB/c male/female marrow transplant model and detecting male DNA in host tissues by Southern blot or fluorescent in situ hybridization, that exposure to doses of irradiation that cause minimal myeloablation (50 to 100 cGy) leads to very high levels of donor chimerism, such that relatively small numbers of marrow cells (10 to 40 million) can give donor chimerism in the 40% to 100% range. Studies of radiation sensitivity of long-term engrafting cells have shown that 100 cGy, although not myelotoxic, is stem cell toxic, and indicate that the final host:donor ratios are determined by competition between host and donor stem cells. These data indicate that low levels of irradiation should be an effective approach to nontoxic marrow transplantation in gene therapy or in attempts to create allochimerism to treat such diseases as cancer, sickle cell anemia, or thalassemia.