gebhart/patrepeval huggingface dataset:
Conformal Geometry and Its Applications on 3D Shape Matching, Recognition, and Stitching (2007)

Three-dimensional shape matching is a fundamental issue in computer vision with many applications such as shape registration, 3D object recognition, and classification. However, shape matching with noise, occlusion, and clutter is a challenging problem. In this paper, we analyze a family of quasi-conformal maps including harmonic maps, conformal maps, and least-squares conformal maps with regards to 3D shape matching. As a result, we propose a novel and computationally efficient shape matching framework by using least-squares conformal maps. According to conformal geometry theory, each 3D surface with disk topology can be mapped to a 2D domain through a global optimization and the resulting map is a diffeomorphism, i.e., one-to-one and onto. This allows us to simplify the 3D shape-matching problem to a 2D image-matching problem, by comparing the resulting 2D parametric maps, which are stable, insensitive to resolution changes and robust to occlusion, and noise. Therefore, highly accurate and efficient 3D shape matching algorithms can be achieved by using the above three parametric maps. Finally, the robustness of least-squares conformal maps is evaluated and analyzed comprehensively in 3D shape matching with occlusion, noise, and resolution variation. In order to further demonstrate the performance of our proposed method, we also conduct a series of experiments on two computer vision applications, i.e., 3D face recognition and 3D nonrigid surface alignment and stitching.
Mouse cells transformed by bovine papillomavirus contain only extrachromosomal viral DNA sequences. (1981)

The viral DNA sequences in mouse C127 cells transformed by bovine papillomavirus type 1 (BPV-1) virions, by full-length linear BPV-1 DNA, or by a defined transforming subgenomic DNA segment of BPV-1 were examined by reassociation kinetics and blot hybridization. In all cases, the transformed cells contained multiple copies of BPV-1 DNA, present exclusively as supercoiled or nicked circular extrachromosomal molecules or as a slowly migrating complex of circular viral DNA molecules. In the transformed cell lines established from cells transfected with full-length linear BPV-1 DNA, there was recircularization of the input DNA which in some cases resulted in the loss of the restriction site used in the linearization of the DNA. In the transformed cell lines established with the defined subgenomic segment there was circularization of the DNA accompanied by the acquisition of new sequences or duplication and rearrangement of the BPV-1 sequences. In contrast to other well-studied virus transformation systems, no integration of the BPV-1 genome into the host chromosome could be detected under conditions sensitive enough to detect 0.1-0.2 viral genome equivalent. It was concluded that maintenance of transformation may be mediated by nonintegrated viral DNA.
First Cr(III)−SNS Complexes and Their Use as Highly Efficient Catalysts for the Trimerization of Ethylene to 1-Hexene (2003)

Cr(III) complexes of tridentate SNS ligands have been prepared and evaluated as catalysts for ethylene trimerization, with several giving very high activity and excellent selectivity toward 1-hexene when activated with methylaluminoxane. The new complexes illustrate the potential of sulfur-based ligands on early transition metals for catalysis.
A 12 megabase restriction map at the cystic fibrosis locus (1989)

We have constructed a physical map of the chromosomal region containing the cystic fibrosis locus using seven DNA markers and pulsed-field gel electrophoresis methods. The map includes cleavage sites for 8 rare-cutting restriction enzymes and spans over 12 megabases (Mb) of DNA, with one unlinked probe covering an additional 5 Mb. To our knowledge, this is the largest segment of human DNA which has been restriction-mapped to date. We can identify thirteen putative HTF islands spaced at intervals of 0.3-3.2 Mb. The region between loci D7S8 and MET, where the CF gene lies, includes 1.4-1.9 Mb of DNA.
The frequency of influenza and bacterial coinfection: a systematic review and meta‐analysis (2016)

The frequency of coinfection in the published studies included in this review suggests that although providers should consider possible bacterial coinfection in all patients hospitalized with influenza, they should not assume all patients are coinfected and be sure to properly treat underlying viral processes. Further, high heterogeneity suggests additional large-scale studies are needed to better understand the etiology of influenza bacterial coinfection.
Utilization of the skin attachment model to determine the antibacterial efficacy of potential carcass treatments (1997)

Two experiments (EXP), utilizing the skin attachment model (SAM), were conducted to determine the bactericidal activity of six potential carcass disinfectants [EXP 1: 20, 400, and 800 ppm sodium hypochlorite; EXP 2: 5% acetic acid (AA), 8% trisodium phosphate (TSP), and 1% sodium metabisulfite (SS)] during simulated scalder (50 C for 2 min), chiller (0 C for 60 min), or post-process dip (23 C for 15 s) application. Efficacies of treatments were determined against populations of Salmonella typhimurium that were "loosely" or "firmly" attached to chicken breast skin (10 cm diameter). For comparison, activity of the six disinfectants was also determined against S. typhimurium in aqueous suspension. All disinfectants except SS reduced numbers of freely suspended S. typhimurium by > or = 4.5 log10 cfu/mL. The sodium metabisulfite did not reduce populations of salmonellae. In both EXP, there were disinfectant by application interactions (P < 0.05) on activity against loosely and firmly attached cells. Sodium hypochlorite at 20 ppm had little activity regardless of application, whereas higher levels were more effective (P < 0.001), particularly in the chiller application, in which loosely and firmly attached populations were reduced by 2.3 to 2.5 and 1.3 to 1.9 log10 cfu per skin, respectively. In EXP 2, SS showed no activity regardless of application. Trisodium phosphate was similarly effective (reduction by 1.2 to 1.8 log10 cfu per skin) in all applications (P > 0.05). In contrast, AA activity was affected by the application method (P < 0.05). Against loosely attached cells, AA was most effective in the chiller application (2.5 log10 reduction), whereas against firmly attached cells, AA was effective only in the scalder application (2.0 log10 reduction). Attachment of S. typhimurium to poultry skin apparently increased the ability of the bacteria to resist various disinfectants, and efficacy was influenced by extent of attachment of bacteria to skin and method of disinfectant application.
Tumour-stroma interactions: Phenotypic and genetic alterations in mammary stroma: implications for tumour progression (2001)

In addition to the well documented role of cytokines in mediating tissue-level interactions, it is now clear that matrix macromolecules fulfil a complementary regulatory function. Data highlighted in the present review extend the repertoire of matrix signalling mechanisms, (1) introducing the concept of 'matrikines', these defined as proteinase-generated fragments of matrix macromolecules that display cryptic bioactivities not manifested by the native, full-length form of the molecule, and (2) indicating that a previously identified motogenic factor (migration stimulating factor [MSF]) produced by foetal and cancer patient fibroblasts is a genetically generated truncated isoform of fibronectin, which displays bioactivities cryptic in all previously identified fibronectin isoforms. These observations are discussed in the context of the contribution of a 'foetal-like' stroma to the progression of breast cancer.
Molecular Imaging in Tracking Tumor-Specific Cytotoxic T Lymphocytes (CTLs) (2014)

Despite the remarkable progress of adoptive T cell therapy in cancer treatment, there remains an urgent need for the noninvasive tracking of the transfused T cells in patients to determine their biodistribution, viability, and functionality. With emerging molecular imaging technologies and cell-labeling methods, noninvasive in vivo cell tracking is experiencing impressive progress toward revealing the mechanisms and functions of these cells in real time in preclinical and clinical studies. Such cell tracking methods have an important role in developing effective T cell therapeutic strategies and steering decision-making process in clinical trials. On the other hand, they could provide crucial information to accelerate the regulatory approval process on the T cell therapy. In this review, we revisit the advances in tracking the tumor-specific CTLs, highlighting the latest development in human studies and the key challenges.
Calculating three‐dimensional changes in protein structure due to amino‐acid substitutions: The variable region of immunoglobulins (1986)

A procedure (coupled perturbation procedure, CPP) is introduced as a specific method for calculating the detailed three-dimensional structure of a protein molecule which has a number of amino-acid substitutions relative to some previously determined "parent" protein structure. The accuracy of the procedure is tested by calculating the conformation of a region of the human immunoglobulin fragment Fab Kol based on the analogous region of the human immunoglobulin fragment Fab New. Both structures have previously been determined crystallographically. The calculated model is accurate to the extent that both of the sequence differences in the region are modeled correctly and that conformational changes in a number of nearby residues are correctly identified. CPP is shown to give better results than other commonly used modeling procedures when applied to the same problem.
Nested quantization and Slepian-Wolf coding: a Wyner-Ziv coding paradigm for i.i.d. sources (2003)

A new paradigm for Wyner-Ziv coding of i.i.d. sources is proposed that consists of nested quantization and Slepian-Wolf coding. The former plays the role of quantization with side information (at the decoder) and the latter lossless coding with side information. The proposed Slepian-Wolf coded nested quantization (SWC-NQ) framework generalizes the classic source coding approach of quantization and lossless/entropy coding. The main thrust is to treat Wyner-Ziv coding as a source-channel coding problem in which the side information is taken into account in the channel coding component via binning. For Gaussian sources with MSE measure, assuming nested lattice quantization with ideal Slepian-Wolf coding and high rate, we establish system performance bounds of SWC-NQ similar to those in classic source coding, showing that 1-D/2-D nested lattice quantization performs 1.53/1.36 dB worse than the Wyner-Ziv distortion-rate function D/sub WZ/{R). Using nested lattices in higher dimensions or nested trellis-coded quantization (TCQ) could possibly approach D/sub WZ/(R) even further. We implement 1-D and 2-D nested lattice quantization, together with irregular low-density parity-check (LDPC) codes for Slepian-Wolf coding, obtaining performance close to the corresponding theoretical limits.
Wavelength-division-multiplexing and -demultiplexing by using a substrate-mode grating pair (1992)

We present theoretical and experimental studies of a novel substrate-mode grating pair structure for wavelength-division-multiplexing/demultiplexing applications. Normally incident coupling and on-axis output imaging with this device provide easier alignment with coupled optical fibers. We have designed and fabricated wavelength-division-multiplexing devices that are implemented by polarization-insensitive high-efficiency (> 85%) substrate-mode holograms. Three-channel demultiplexing experiments have also been successfully demonstrated with the limited available wavelength range of our diode-laser system.
Homeostasis of memory T cells (2006)

The pool of memory T cells is regulated by homeostatic mechanisms to persist for prolonged periods at a relatively steady overall size. Recent work has shown that two members of the common gamma chain (gammac) family of cytokines, interleukin-7 (IL-7) and IL-15, govern homeostasis of memory T cells. These two cytokines work in conjunction to support memory T-cell survival and intermittent background proliferation. Normal animals contain significant numbers of spontaneously arising memory-phenotype (MP) cells, though whether these cells are representative of true antigen-specific memory T cells is unclear. Nevertheless, it appears that the two types of memory cells do not display identical homeostatic requirements. For antigen-specific memory CD8+ T cells, IL-7 is primarily important for survival while IL-15 is crucial for their background proliferation. For memory CD4+ T cells, IL-7 has an important role, whereas the influence of IL-15 is still unclear.
HIV-1 Viral Load Assays for Resource-Limited Settings (2006)

Resources vary signifi cantly by country. Human resources and infrastructure that might be readily available in major cities, such as trained personnel, clean water, and electricity, may not be found in more rural areas. Reference laboratories that have the personnel, equipment, and infrastructure to perform CD4 cell counts and viral load testing may lack the resources to purchase the kits. Thus, what works for one country, or even for one city within a country, may not apply in all resource-limited settings. Options available to developing countries include performing the
Apoptosis Induced by the Kinase Inhibitor BAY 43-9006 in Human Leukemia Cells Involves Down-regulation of Mcl-1 through Inhibition of Translation (2005)

BAY 43-9006 is a kinase inhibitor that induces apoptosis in a variety of tumor cells. Here we report that treatment with BAY 43-9006 results in marked cytochrome c and AIF release into the cytosol, caspase-9, -8, -7, and -3 activation, and apoptosis in human leukemia cells (U937, Jurkat, and K562). Pronounced apoptosis was also observed in blasts from patients with acute myeloid leukemia. These events were accompanied by ERK1/2 inactivation and caspase-independent down-regulation of Mcl-1. Inducible expression of a constitutively active MEK1 construct did not prevent Mcl-1 down-regulation, suggesting that this event is not related to MEK/ERK pathway inactivation. Furthermore, BAY 43-9006 did not induce major changes in Mcl-1 mRNA levels monitored by real-time PCR or Mcl-1 promoter activity demonstrated by luciferase reporter assays, but it did enhance Mcl-1 down-regulation in actinomycin D-treated cells. Inhibition of protein synthesis by cycloheximide or proteasome function with MG132 and pulse-chase studies with [35S]methionine demonstrated that BAY 43-9006 did not diminish Mcl-1 protein stability, nor did it enhance Mcl-1 ubiquitination, but instead markedly attenuated Mcl-1 translation in association with the rapid and potent dephosphorylation of the eIF4E translation initiation factor. Finally, ectopic expression of Mcl-1 in leukemic cells markedly inhibited BAY 43-9006-mediated cytochrome c cytosolic release, caspase-9, -7, and -3 activation, as well as cell death, indicating that Mcl-1 operates upstream of cytochrome c release and caspase activation. Together, these findings demonstrate that BAY 43-9006 mediates cell death in human leukemia cells, at least in part, through down-regulation of Mcl-1 via inhibition of translation.
Investigations into tandem acoustic modeling for the Aurora task (2001)

In tandem acoustic modeling, signal features are first processed by a discriminantly-trained neural network, then the outputs of this network are treated as the feature inputs to a conventional distribution-modeling Gaussian-mixture model (GMM) speech recognizer.This arrangement achieves relative error rate reductions of 30% or more on the Aurora task, as well as supporting feature stream combination at the posterior level, which can eliminate more than 50% of the errors compared to the HTK baseline.In this paper, we explore a number of variations on the tandem structure to improve our understanding of its effectiveness.We experiment with changing the subword units used in each model (neural net and GMM), varying the data subsets used to train each model, substituting the posterior calculations in the neural net with a second GMM, and a variety of feature condition such as deltas, normalization and PCA rank reduction in the 'tandem domain' i.e. between the two models.All results are reported on the Aurora-2000 noisy digits task.
The Src Family Tyrosine Kinase Fyn Regulates Natural Killer T Cell Development (1999)

T lymphocytes express two Src tyrosine kinases, Lck and Fyn. While thymocyte and T cell subsets are largely normal in fyn(-/-) mice, animals lacking Lck have impaired T cell development. Here, it is shown that Fyn is required for the rapid burst of interleukin (IL)-4 and IL-13 synthesis, which occurs promptly after T cell receptor activation. The lack of cytokine induction in fyn mutant mice is due to a block in natural killer (NK) T cell development. Studies using bone marrow chimeras indicate that the defect behaves in a cell-autonomous manner, and the lack of NK T cells is probably not caused by inappropriate microenvironmental cues. Both NK T cells and conventional T cells express similar levels of Lck, implying that Fyn and Lck have distinct roles in regulating NK T cell ontogeny. The fyn mutation defines the first signaling molecule that is selectively required for NK T cell, but not for T lymphocyte or NK cell development.
Bounds on Error-Pattern Probabilities for Digital Communications Systems (1972)

An upper bound is obtained on the probability that a specified pattern of errors, caused by a combination of intersymbol interference and additive Gaussian noise, occurs in an amplitudemodulated digital data transmission system. The bound, which is a generalization of Saltzberg's upper bound for the probability of a single error, behaves as an exponential function of the signal-to-noise ratio and the overall channel impulse response. The exponent of the bound for a pair of errors is calculated for two "typical" channels and in each case is fairly close to twice the corresponding Saltzberg exponent for a single error.
A Novel Acyl-CoA Oxidase That Can Oxidize Short-chain Acyl-CoA in Plant Peroxisomes (1999)

Short-chain acyl-CoA oxidases are beta-oxidation enzymes that are active on short-chain acyl-CoAs and that appear to be present in higher plant peroxisomes and absent in mammalian peroxisomes. Therefore, plant peroxisomes are capable of performing complete beta-oxidation of acyl-CoA chains, whereas mammalian peroxisomes can perform beta-oxidation of only those acyl-CoA chains that are larger than octanoyl-CoA (C8). In this report, we have shown that a novel acyl-CoA oxidase can oxidize short-chain acyl-CoA in plant peroxisomes. A peroxisomal short-chain acyl-CoA oxidase from Arabidopsis was purified following the expression of the Arabidopsis cDNA in a baculovirus expression system. The purified enzyme was active on butyryl-CoA (C4), hexanoyl-CoA (C6), and octanoyl-CoA (C8). Cell fractionation and immunocytochemical analysis revealed that the short-chain acyl-CoA oxidase is localized in peroxisomes. The expression pattern of the short-chain acyl-CoA oxidase was similar to that of peroxisomal 3-ketoacyl-CoA thiolase, a marker enzyme of fatty acid beta-oxidation, during post-germinative growth. Although the molecular structure and amino acid sequence of the enzyme are similar to those of mammalian mitochondrial acyl-CoA dehydrogenase, the purified enzyme has no activity as acyl-CoA dehydrogenase. These results indicate that the short-chain acyl-CoA oxidases function in fatty acid beta-oxidation in plant peroxisomes, and that by the cooperative action of long- and short-chain acyl-CoA oxidases, plant peroxisomes are capable of performing the complete beta-oxidation of acyl-CoA.
Release of somatostatin and its role in the mediation of the anti‐inflammatory effect induced by antidromic stimulation of sensory fibres of rat sciatic nerve (1998)

1. The effect of antidromic stimulation of the sensory fibres of the sciatic nerve on inflammatory plasma extravasation in various tissues and on cutaneous vasodilatation elicited in distant parts of the body was investigated in rats pretreated with guanethidine (8 mg kg(-1), i.p.) and pipecuronium (200 microg kg(-1), i.v.). 2. Antidromic sciatic nerve stimulation with C-fibre strength (20 V, 0.5 ms) at 5 Hz for 5 min elicited neurogenic inflammation in the innervated area and inhibited by 50.3 +/- 4.67% the development of a subsequent plasma extravasation in response to similar stimulation of the contralateral sciatic nerve. Stimulation at 0.5 Hz for 1 h also evoked local plasma extravasation and inhibited the carrageenin-induced (1%, 100 microl s.c.) cutaneous inflammation by 38.5 +/- 10.0% in the contralateral paw. Excitation at 0.1 Hz for 4 h elicited no local plasma extravasation in the stimulated hindleg but still reduced the carrageenin-induced oedema by 52.1 +/- 9.7% in the paw on the contralateral side. 3. Plasma extravasation in the knee joint in response to carrageenin (2%, 200 microl intra-articular injection) was diminished by 46.1 +/- 12.69% and 40.9 +/- 4.93% when the sciatic nerve was stimulated in the contralateral leg at 0.5 Hz for 1 h or 0.1 Hz for 4 h, respectively. 4. Stimulation of the peripheral stump of the left vagal nerve (20 V, 1 ms, 8 Hz, 10 min) elicited plasma extravasation in the trachea, oesophagus and mediastinal connective tissue in rats pretreated with atropine (2 mg kg(-1), i.v.), guanethidine (8 mg kg(-1), i.p.) and pipecuronium (200 microg kg(-1), i.v.). These responses were inhibited by 37.8 +/- 5.1%, 49.7 +/- 9.9% and 37.6 +/- 4.2%, respectively by antidromic sciatic nerve excitation (5 Hz, 5 min) applied 5 min earlier. 5. Pretreatment with polyclonal somatostatin antiserum (0.5 ml/rat, i.v.) or the selective somatostatin depleting agent cysteamine (280 mg kg(-1), s.c.) prevented the anti-inflammatory effect of sciatic nerve stimulation (5 Hz, 5 min) on a subsequent neurogenic plasma extravasation of the contralateral paw skin. The inhibitory effect of antidromic sciatic nerve excitation on plasma extravasation in response to vagal nerve stimulation was also prevented by somatostatin antiserum pretreatment. 6. Cutaneous blood flow assessment by laser Doppler flowmetry indicated that antidromic vasodilatation induced by sciatic nerve stimulation was not inhibited by excitation of the sciatic nerve of the contralateral leg (1 Hz, 30 min) or by somatostatin (10 microg/rat, i.v.) injection. 7. Plasma levels of somatostatin increased more than 4 fold after stimulation of both sciatic nerves (5 Hz, 5 min) but the stimulus-evoked increase was not observed in cysteamine (280 mg kg(-1), s.c.) pretreated rats. 8. These results suggest that somatostatin released from the activated sensory nerve terminals mediates the systemic anti-inflammatory effect evoked by stimulating the peripheral stump of the sciatic nerve.