gebhart/patrepeval huggingface dataset:
Classification with Asymmetric Label Noise: Consistency and Maximal\n Denoising (2013)

In many real-world classification problems, the labels of training examples\nare randomly corrupted. Most previous theoretical work on classification with\nlabel noise assumes that the two classes are separable, that the label noise is\nindependent of the true class label, or that the noise proportions for each\nclass are known. In this work, we give conditions that are necessary and\nsufficient for the true class-conditional distributions to be identifiable.\nThese conditions are weaker than those analyzed previously, and allow for the\nclasses to be nonseparable and the noise levels to be asymmetric and unknown.\nThe conditions essentially state that a majority of the observed labels are\ncorrect and that the true class-conditional distributions are "mutually\nirreducible," a concept we introduce that limits the similarity of the two\ndistributions. For any label noise problem, there is a unique pair of true\nclass-conditional distributions satisfying the proposed conditions, and we\nargue that this pair corresponds in a certain sense to maximal denoising of the\nobserved distributions.\n Our results are facilitated by a connection to "mixture proportion\nestimation," which is the problem of estimating the maximal proportion of one\ndistribution that is present in another. We establish a novel rate of\nconvergence result for mixture proportion estimation, and apply this to obtain\nconsistency of a discrimination rule based on surrogate loss minimization.\nExperimental results on benchmark data and a nuclear particle classification\nproblem demonstrate the efficacy of our approach.\n
Functional implications of the localization and activity of acid-sensitive channels in rat peripheral nervous system (2002)

Acid-sensitive ion channels (ASIC) are proton-gated ion channels expressed in neurons of the mammalian central and peripheral nervous systems. The functional role of these channels is still uncertain, but they have been proposed to constitute mechanoreceptors and/or nociceptors. We have raised specific antibodies for ASIC1, ASIC2, ASIC3, and ASIC4 to examine the distribution of these proteins in neurons from dorsal root ganglia (DRG) and to determine their subcellular localization. Western blot analysis demonstrates that all four ASIC proteins are expressed in DRG and sciatic nerve. Immunohistochemical experiments and functional measurements of unitary currents from the ASICs with the patch-clamp technique indicate that ASIC1 localizes to the plasma membrane of small-, medium-, and large-diameter cells, whereas ASIC2 and ASIC3 are preferentially in medium to large cells. Neurons coexpressing ASIC2 and ASIC3 form predominantly heteromeric ASIC2-3 channels. Two spliced forms, ASIC2a and ASIC2b, colocalize in the same population of DRG neurons. Within cells, the ASICs are present mainly on the plasma membrane of the soma and cellular processes. Functional studies indicate that the pH sensitivity for inactivation of ASIC1 is much higher than the one for activation; hence, increases in proton concentration will inactivate the channel. These functional properties and localization in DRG have profound implications for the putative functional roles of ASICs in the nervous system.
B7-H4 Induces Donor-Specific Tolerance in Mouse Islet Allografts (2011)

Negative cosignaling molecules play an important role in regulating T-cell responses to alloantigen stimulation. We recently reported that adenoviral-mediated transduction of islet allografts with B7-H4 inhibits allograft rejection. In this study, we investigate the mechanism for B7-H4-induced prolongation of mouse islet allograft survival. Streptozotocin-induced diabetic C57BL/6 mice were rendered normoglycemic by renal subcapsular implants of B7-H4-transduced BALB/c islets. Grafts and spleens were removed after days 2, 10, and 60 (n = 8 each) for characterization of kinetics of Foxp3 and interleukin 10 (IL-10) expression. Mixed lymphocyte reaction (MLR) was done at day 60. Ten mice were subjected to nephrectomy at 60 days and then five were implanted with secondary BALB/c islets and five were given third-party CBA/J islets. An increase in Foxp3 and IL-10 mRNA expression was detected in recipients' spleens at day 60 and this was associated with increased quantities of Foxp3(+) cells. Splenocytes at day 60 showed hyporesponsiveness during MLR to alloantigen stimulation. Proliferation was partially restored after CD25(+) T-cell depletion. Secondary BALB/c islets survived for 79 ± 29 days compared with 21 ± 3.6 days for CBA/J islets (p < 0.001). Local expression of B7-H4 induces long-term unresponsiveness to donor-specific alloantigens, and is associated with T regulatory cells, suggesting the development of tolerance.
A Prospective Follow-up Study of Alcoholic Violent Offenders and Fire Setters (1996)

Among male alcoholic violent offenders and fire setters, low CSF 5-HIAA and HVA concentrations are strongly associated with a family history positive for paternal violence and alcoholism, while low fasting plasma cholesterol concentration is associated with a family history positive for paternal alcoholism. Recidivist violent offenders and fire setters are predicted by low CSF 5-HIAA and MHPG concentrations and a developmental history positive for early paternal absence from and presence of brothers in the family of origin.
Regulation of chromosomally mediated multiple antibiotic resistance: the mar regulon (1997)

Free access1 October 1997 Share on Regulation of chromosomally mediated multiple antibiotic resistance: the mar regulonAuthors: M N Alekshun, S B LevyAuthors Info & AffiliationsDOI: https://doi.org/10.1128/AAC.41.10.2067 PDF/EPUB
TRIPSTAR: prioritizing oral triptan treatment attributes in migraine management (2004)

Migraine can be associated with severe pain and is often very disabling. Optimal treatment should provide rapid and sustained, complete pain relief, be well tolerated and restore normal function. The seven commercially available triptans show differences in performance on individual treatment attributes. The TRIPSTAR multiattribute decision model compares the profiles of the oral triptans, using efficacy and tolerability data weighted for importance, to identify if measurable differences are clinically relevant. Application of the TRIPSTAR model was demonstrated at the Migraine Trust International Symposium 2002, where delegates collectively prioritized treatment attributes according to the needs of a specific patient case history. The TRIPSTAR model identified the preferred triptans for this patient. These three triptans, almotriptan 12.5 mg, eletriptan 80 mg and rizatriptan 10 mg, standout in a triptan meta-analysis, three TRIPSTAR surveys and in a demonstration of the TRIPSTAR model at a symposium in the USA. Taken together the findings suggest that some differences amongst triptans may be relevant in clinical practice.
Treatment of a wound infection in a patient with mantle cell lymphoma (2001)

This case study examines the impact of a severe wound infection on a patient undergoing chemotherapy for the treatment of mantle cell lymphoma. The study illustrates how life threatening an infection can become in a patient whose body is compromised as a consequence of both disease and chemotherapy treatment. A number of specialist products were required in order to overcome the infection, debride and heal the wound. These included larval therapy, vacuum-assisted closure and Leptospermum honey. While this case study focuses on the successful outcome of one particular patient it aims to raise awareness of the role of specialist products, both old and new, in improving healing rates of complex wounds.
CRISPR-Cas Immunity against Phages: Its Effects on the Evolution and Survival of Bacterial Pathogens (2013)

Clustered regularly interspaced short palindromic repeats (CRISPR) loci are arrays of short repeats separated by equally short “spacer” sequences [1]–[3]. Along with the CRISPR-associated (cas) genes, they encode an adaptive immune system of archaea and bacteria that protects the cell against viral infection [4]. Remarkably, this system is capable of inserting a short piece of an infecting viral genome as a spacer in the CRISPR array [4], [5] (Figure 1A). The spacer sequence is transcribed and processed to generate a small antisense RNA (the CRISPR RNA or crRNA) (Figure 1B) [6] that is used as a guide for the recognition and destruction of the invader in subsequent infections (Figure 1C) [7]. Thus, spacer acquisition immunizes the bacterium and its progeny against the virus from which it was taken. Because spacers are incorporated in sequential order, CRISPR loci reflect the history of viral infection of the host. Cas proteins participate in all the different steps of this pathway, namely the insertion of spacer sequences into the CRISPR array [8], [9], the biogenesis of crRNAs [10], [11], and the destruction of the infecting viral genome [12], [13].



Figure 1

The CRISPR immunity pathway.




Distribution of CRISPR-Cas Loci among Bacterial Pathogens
In spite of the unique role that CRISPR-Cas loci play in antiviral defense, they are not universal. To date, the CRISPR database [14], a webtool that determines the presence of CRISPR arrays in completed genomes, indicates that 119/141 archaeal (84%) and 1012/2113 bacterial (48%) genomes contain CRISPR loci. In bacteria, there are species in which all strains have CRISPR loci, some in which only some strains have these loci, and species without strains having CRISPR loci. Therefore it is not possible to determine unequivocally that lack of CRISPR in certain strains or species is due to loss of these loci. However, because CRISPR sequences are spread thorough horizontal gene transfer [15], [16] and can be easily lost [17]–[20], it has been hypothesized recently that CRISPR are in a constant state of flux and can appear and disappear depending on the selective forces of the environment [20]. The same type of uneven distribution is found when we look at the presence of CRISPR loci in bacterial pathogens in the CRISPR database (http://crispr.u-psud.fr/crispr/).
Computer-assisted surgery (1990)

Computer-assisted surgery (CAS), a new navigation aid for skull-base surgery, is discussed. The system described combines 3-D coordinate measurement techniques, voxel processing methods, and pseudo-3-D image presentations to support preoperative planning of therapy, path-finding during the operation itself, and postoperative therapy control. The surgeon employs a hand-guided electromechanical 3-D-coordinate digitizer to locate points of interest within the operative field. The coordinates measured this way are correlated with a voxel model of the object gained by a preceding computed-tomography examination. With a prototype system the accuracy of this method has proven to be better than +or-1 mm. The system has been successfully applied in more than 60 ear-nose-throat operations and four neurosurgical procedures. The computer hardware and integration of the system into an experimental picture archiving and communication system are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the O-chain polysaccharide of the phenol-phase soluble lipopolysaccharide of Escherichia coli 0:157:H7 (1986)

The phenol-phase soluble lipopolysaccharide isolated from Escherichia coli 0:157 by the hot phenol-water extraction procedure was shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, periodate oxidation, methylation, and 13C and 1H nuclear magnetic resonance studies to be an unbranched linear polysaccharide with a tetrasaccharide repeating unit having the structure: (formula; see text) The serological cross-reactivity of E. coli 0:157 with Brucella abortus, Yersinia enterocolitica (serotype 0:9), group N Salmonella, and some other E. coli species can be related immunochemically to the presence of 1,2-glycosylated N-acylated 4-amino-4, 6-dideoxy-alpha-D-mannopyranosyl residues in the O-chains of their respective lipopolysaccharides.
Guide to CO2 Separations in Imidazolium-Based Room-Temperature Ionic Liquids (2009)

Room-temperature ionic liquids (RTILs) are nonvolatile, tunable solvents that have generated significant interest across a wide variety of engineering applications. The use of RTILs as media for CO2 separations appears especially promising, with imidazolium-based salts at the center of this research effort. The solubilities of gases, particularly CO2, N2, and CH4, have been studied in a number of RTILs. Process temperature and the chemical structures of the cation and anion have significant impacts on gas solubility and gas pair selectivity. Models based on regular solution theory and group contributions are useful to predict and explain CO2 solubility and selectivity in imidazolium-based RTILs. In addition to their role as a physical solvent, RTILs might also be used in supported ionic liquid membranes (SILMs) as a highly permeable and selective transport medium. Performance data for SILMs indicates that they exhibit large permeabilities as well as CO2/N2 selectivities that outperform many polymer membranes. Furthermore, the greatest potential of RTILs for CO2 separations might lie in their ability to chemically capture CO2 when used in combination with amines. Amines can be tethered to the cation or the anion, or dissolved in RTILs, providing a wide range of chemical solvents for CO2 capture. However, despite all of their promising features, RTILs do have drawbacks to use in CO2 separations, which have been overlooked as appropriate comparisons of RTILs to common organic solvents and polymers have not been reported. A thorough summary of the capabilities—and limitations—of imidazolium-based RTILs in CO2-based separations with respect to a variety of materials is thus provided.
Specific Labeling of Cell Surface Proteins with Chemically Diverse Compounds (2004)

The specific and covalent labeling of fusion proteins with synthetic molecules opens up new ways to study protein function in the living cell. Here we present a novel method that allows for the specific and exclusive extracellular labeling of proteins on the surfaces of live cells with a large variety of synthetic molecules including fluorophores, protein ligands, or quantum dots. The approach is based on the specific labeling of fusion proteins of acyl carrier protein with synthetic molecules through post-translational modification catalyzed by phosphopantetheine transferase. The specificity and versatility of the labeling should allow it to become an important tool for studying and manipulating cell surface proteins and for complementing existing approaches in cell surface engineering.
Extrahepatic secreted complement C3 contributes to circulating C3 levels in humans (1996)

The majority of complement protein C3 is synthesized by the liver, but many other cell types produce small amounts of functionally active C3. The overall contribution of such extrahepatic C3 production to the total circulating C3 level is unknown. Bone marrow and extrahepatic C3 productions were quantified in bone marrow transplant (BMT) and liver transplant (LT) recipients, respectively, where a mismatch for the C3 allotypes distinguished by the mAb HAV 4-1 had occurred. In the BMT group, donor-derived C3 was detected by ELISA and immunoblotting techniques. It contributed to 0.1 to 2.6% of the total circulating C3 during the immediate post-BMT period in response to inflammatory stimuli. Cell culture and immunostaining techniques demonstrated that monocytes were the source of the C3. By 6 wk following BMT, donor-derived C3 levels had decreased to below the detection limit of the assays. By contrast in the LT group, total extrahepatic C3 levels were higher (3.1-5.7% of the total circulating C3) and remained stable for up to 1 yr post-LT. This study demonstrates that extrahepatic derived C3 forms a larger proportion of the circulating C3 levels than was considered previously and that in the resting state, most of this extrahepatically derived C3 comes from nonmyeloid sources. In addition, monocytes, which in the resting state contribute negligible amounts of C3, have the potential when stimulated to contribute significantly to the total systemic C3 pool. These findings highlight the importance of locally secreted complement proteins.
Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology (2017)

Whole-cell patch-clamp electrophysiological recording is a powerful technique for studying cellular function. While in vivo patch-clamp recording has recently benefited from automation, it is normally performed "blind," meaning that throughput for sampling some genetically or morphologically defined cell types is unacceptably low. One solution to this problem is to use two-photon microscopy to target fluorescently labeled neurons. Combining this with robotic automation is difficult, however, as micropipette penetration induces tissue deformation, moving target cells from their initial location. Here we describe a platform for automated two-photon targeted patch-clamp recording, which solves this problem by making use of a closed loop visual servo algorithm. Our system keeps the target cell in focus while iteratively adjusting the pipette approach trajectory to compensate for tissue motion. We demonstrate platform validation with patch-clamp recordings from a variety of cells in the mouse neocortex and cerebellum.
Regulation of autoinducer production in Salmonella typhimurium (1999)

Salmonella typhimurium strain LT2 secretes an organic signalling molecule that can be assayed by its ability to activate one of two specific quorum-sensing systems in Vibrio harveyi. Maximal activity is produced during mid- to late exponential phase when S. typhimurium is grown in the presence of glucose or other preferred carbohydrates. The signal is degraded by the onset of stationary phase or when the carbohydrate is depleted from the medium. Presumably, quorum sensing in S. typhimurium is operational during periods of rapid, nutrient-rich growth. Protein synthesis is required for degradation of the activity, suggesting that a complex regulatory circuitry controls signal production and detection in S. typhimurium. Increased signalling activity is observed if, after growth in the presence of glucose, S. typhimurium is transferred to a high-osmolarity (0.4 M NaCl) or to a low-pH (pH 5.0) environment. Degradation of the signal is induced by conditions of low osmolarity (0.1 M NaCl). High osmolarity and low pH are two conditions encountered by S. typhimurium cells when they undergo the transition to a pathogenic existence inside a host organism, suggesting that quorum sensing may have a role in the regulation of virulence in S. typhimurium.
A Genetic Algorithm for Cost Estimating Turned Parts in an Interactive DFM Environment (2003)

This paper presents a method for the optimization of machining parameters, essential for the determination of an economical operating point for multi-pass turning operations. Optimal selection of cutting parameters such as the number of passes, depth of cuts, cutting speeds and feed rates are critical to process planning and cost optimization. This in turn creates a crossing point between product design and manufacturing. Generally, machining models are complex since they are highly non-linear. This research utilizes genetic algorithms as an optimization technique in order to maximize the accuracy of results, the computational achievement, and to minimize the influence of initial conditions and part geometry. A new approach that uses conventional turning process modeling along with genetic algorithms to rapidly search and optimize the feasible workspace is considered. The total production cost minimization is achieved by adding together the minimum cost of each roughing pass and the final finishing pass. In addition, the preventive tool replacement policy used in practice is incorporated. Finally, the results obtained for test cases are evaluated and compared.
Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis (2000)

Bacillus anthracis is one of the most genetically homogeneous pathogens described, making strain discrimination particularly difficult. In this paper, we present a novel molecular typing system based on rapidly evolving variable-number tandem repeat (VNTR) loci. Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. In our system, fluorescently labeled PCR primers are used to produce PCR amplification products from eight VNTR regions in the B. anthracis genome. These are detected and their sizes are determined using an ABI377 automated DNA sequencer. Five of these eight loci were discovered by sequence characterization of molecular markers (vrrC(1), vrrC(2), vrrB(1), vrrB(2), and CG3), two were discovered by searching complete plasmid nucleotide sequences (pXO1-aat and pXO2-at), and one was known previously (vrrA). MLVA characterization of 426 B. anthracis isolates identified 89 distinct genotypes. VNTR markers frequently identified multiple alleles (from two to nine), with Nei's diversity values between 0.3 and 0.8. Unweighted pair-group method arithmetic average cluster analysis identified six genetically distinct groups that appear to be derived from clones. Some of these clones show worldwide distribution, while others are restricted to particular geographic regions. Human commerce doubtlessly has contributed to the dispersal of particular clones in ancient and modern times.
Evaluation of Cyclophosphamide/GVAX Pancreas Followed by Listeria-Mesothelin (CRS-207) with or without Nivolumab in Patients with Pancreatic Cancer (2020)

Although the study did not meet its primary endpoint of improvement in OS of Arm A over Arm B, the OS was comparable with standard therapy. Objective responses and immunologic changes in the tumor microenvironment were evident.
Effects of low oxygen concentrations and metabolic inhibitors on proteoglycan and protein synthesis rates in the intervertebral disc (1999)

The intervertebral disc is the largest asvacular structure in the body; consequently, there are steep gradients in O2 concentration, with PO2 falling to as low as 1% O2 in the centre of the disc. We investigated the effect of O2 concentration on the rates of O2 consumption, lactate production, and sulphate and proline incorporation in bovine caudal discs. We also investigated the effects of metabolic inhibitors of energy production pathways on tracer incorporation. Samples from the outer annulus and nucleus pulposus were incubated for 24 hours in 1-21% O2. Rates were measured during the last 4 hours of incubation. As O2 concentration was reduced from 10 to 1% O2, O2 consumption rates fell by around 75% and lactate production rates almost doubled; the bovine discs thus showed a positive progressive Pasteur effect. Incorporation rates of [3H]proline and [35S]sulphate were lowest at 1% O2. In the nucleus, but not in the outer annulus, the rate of [35S]incorporation peaked at 5% O2, where it was 30% greater than at 21% O2 and 150% greater than at 1% O2. The competitive glycolysis inhibitor 2-deoxyglucose, the oxidative phosphorylation uncoupler 2,4-dinitrophenol, and the oxidative phosphorylation inhibitor sodium azide all markedly reduced sulphate incorporation. These results, together with previous measurements of CO2 production rates, suggest that a functionally significant fraction of the disc's energy is supplied by oxidative phosphorylation. However, low levels of PO2, 2,4-dinitrophenol, and sodium azide have been reported to reduce sulphate incorporation in articular cartilage, a tissue that derives its energy almost entirely from glycolysis.
Non-viral eNOS gene delivery and transfection with stents for the treatment of restenosis (2010)

These results support the hypothesis that a potent non-viral gene vector encoding for eNOS coated onto a stent can inhibit restenosis through inhibition of smooth muscle cell growth and promotion of a healthy endothelium.