gebhart/patrepeval huggingface dataset:
Simian T-Cell Leukemia Virus (STLV) Infection in Wild Primate Populations in Cameroon: Evidence for Dual STLV Type 1 and Type 3 Infection in Agile Mangabeys ( Cercocebus agilis ) (2004)

Three types of human T-cell leukemia virus (HTLV)-simian T-cell leukemia virus (STLV) (collectively called primate T-cell leukemia viruses [PTLVs]) have been characterized, with evidence for zoonotic origin from primates for HTLV type 1 (HTLV-1) and HTLV-2 in Africa. To assess human exposure to STLVs in western Central Africa, we screened for STLV infection in primates hunted in the rain forests of Cameroon. Blood was obtained from 524 animals representing 18 different species. All the animals were wild caught between 1999 and 2002; 328 animals were sampled as bush meat and 196 were pets. Overall, 59 (11.2%) of the primates had antibodies cross-reacting with HTLV-1 and/or HTLV-2 antigens; HTLV-1 infection was confirmed in 37 animals, HTLV-2 infection was confirmed in 9, dual HTLV-1 and HTLV-2 infection was confirmed in 10, and results for 3 animals were indeterminate. Prevalences of infection were significantly lower in pets than in bush meat, 1.5 versus 17.0%, respectively. Discriminatory PCRs identified STLV-1, STLV-3, and STLV-1 and STLV-3 in HTLV-1-, HTLV-2-, and HTLV-1- and HTLV-2-cross-reactive samples, respectively. We identified for the first time STLV-1 sequences in mustached monkeys (Cercopithecus cephus), talapoins (Miopithecus ogouensis), and gorillas (Gorilla gorilla) and confirmed STLV-1 infection in mandrills, African green monkeys, agile mangabeys, and crested mona and greater spot-nosed monkeys. STLV-1 long terminal repeat (LTR) and env sequences revealed that the strains belonged to different PTLV-1 subtypes. A high prevalence of PTLV infection was observed among agile mangabeys (Cercocebus agilis); 89% of bush meat was infected with STLV. Cocirculation of STLV-1 and STLV-3 and STLV-1-STLV-3 coinfections were identified among the agile mangabeys. Phylogenetic analyses of partial LTR sequences indicated that the agile mangabey STLV-3 strains were more related to the STLV-3 CTO604 strain isolated from a red-capped mangabey (Cercocebus torquatus) from Cameroon than to the STLV-3 PH969 strain from an Eritrean baboon or the PPA-F3 strain from a baboon in Senegal. Our study documents for the first time that (i) a substantial proportion of wild-living monkeys in Cameroon is STLV infected, (ii) STLV-1 and STLV-3 cocirculate in the same primate species, (iii) coinfection with STLV-1 and STLV-3 occurs in agile mangabeys, and (iv) humans are exposed to different STLV-1 and STLV-3 subtypes through handling primates as bush meat.
Evidence of Genetic Diversity Underlying Rh D−, Weak D (Du), and Partial D Phenotypes as Determined by Multiplex Polymerase Chain Reaction Analysis of the RHD Gene (1997)

The human blood group Rh antigens are expressed by proteins encoded by a pair of highly homologous genes located at chromosome 1p34-36. One of the genes (RHCE) encodes Rh CcEe antigens, while the other (RHD) the D antigen. Point mutations in the RHCE gene generate the C/c and E/e polymorphisms, while it has been shown that an RHD gene deletion can generate the D-negative phenotype. We have analyzed intron 4 of the RHCE and RHD genes and have defined the site of an RHD-specific deletion located in this intron. Using a multiplex RHD typing assay, which combines a reverse polymerase chain reaction (PCR) primer, which straddles this RHD-specific sequence, and a pair of primers located in exon 10 of the RHD gene, we have analyzed 357 different genomic DNA samples derived from individuals expressing D+, D-, weak D, and partial D phenotypes. Of these, we have noted a significant discordance with our multiplex PCR assay in the D- phenotypes dCcee and dccEe (which have been previously described) and weak D phenotypes. Our results suggest that in five serologically D- individuals we have identified an apparently intact RHD gene. Sequence analysis of transcripts obtained from one of these individuals (of phenotype dCCee) illustrates the presence of full-length RHD transcripts, which have a point mutation at nucleotide 121 (C --> T), which generates an in-frame stop codon (Gln41Stop). Thus, we describe a different molecular basis for generating the D- phenotype to the complete RHD gene deletion described previously. We also show that there are discordances with serotype and the multiplex assay in weak D and partial D phenotypes, indicating that the underlying molecular basis can be heterogeneous. Existing Rh D PCR assays assume the complete absence of the RHD gene in D- phenotypes. We describe a different molecular basis for generating the D- phenotype to the complete RHD gene deletion described previously.
Molecular mechanisms of antibiotic resistance (2011)

Over the past decade, resistance to antibiotics has emerged as a crisis of global proportion. Microbes resistant to many and even all clinically approved antibiotics are increasingly common and easily spread across continents. At the same time there are fewer new antibiotic drugs coming to market. We are reaching a point where we are no longer able to confidently treat a growing number of bacterial infections. The molecular mechanisms of drug resistance provide the essential knowledge on new drug development and clinical use. These mechanisms include enzyme catalyzed antibiotic modifications, bypass of antibiotic targets and active efflux of drugs from the cell. Understanding the chemical rationale and underpinnings of resistance is an essential component of our response to this clinical challenge.
Suppression of interleukin 1alpha and interleukin 1beta in human limbal epithelial cells cultured on the amniotic membrane stromal matrix (2001)

AM stromal matrix markedly suppresses lipopolysaccharide induced upregulation of both IL-1alpha and IL-1beta. These data may explain in part the effect of AM transplantation in reducing ocular surface inflammation, underscoring the unique feature of the AM as a substrate for tissue engineering.
Peptide growth factors stimulate macrophage colony-stimulating factor in murine stromal cells (1991)

Bone marrow stromal cells influence hematopoiesis through cell-cell interaction and release of hematopoietic growth factors. Macrophage colony-stimulating factor (M-CSF) is constitutively produced by several murine and human stromal cell lines and is induced by inflammatory mediators such as interleukin-1 alpha or tumor necrosis factor-alpha (TNF-alpha) in a variety of mesenchymal cells. Other potentially important regulatory molecules such as platelet-derived growth factor (PDGF) and basic fibroblast growth factor (bFGF), released by activated monocytes in response to inflammation, stimulate the growth of human stromal cells. However, the effect of these peptide mitogens on M-CSF expression in stromal cells has not been explored. In this study, we used TC-1 murine bone marrow-derived stromal cells that constitutively secrete M-CSF to determine the effect of PDGF and bFGF on cell proliferation and M-CSF gene expression. PDGF and bFGF, but not TNF- alpha, were potent mitogens for the TC-1 cells. Similar to mouse L cells, TC-1 murine stromal cells constitutively expressed two major mRNA transcripts of 4.4 and 2.2 kb that hybridized to a murine M-CSF cDNA. PDGF, bFGF, and TNF-alpha markedly stimulated the steady-state expression of M-CSF mRNA with different time-course kinetics. The increased expression of M-CSF mRNA was associated with enhanced secretion of M-CSF as determined by radioimmunoassay. These findings suggest that PDGF, bFGF, and TNF-alpha may regulate hematopoiesis indirectly through release of M-CSF by stromal cells and may modulate, at least in part, the hematopoietic response to inflammation.
Palettes of Vaccines and Immunostimulatory Monoclonal Antibodies for Combination (2009)

Various monoclonal antibodies (mAb) target immune system molecules to enhance immunity by costimulating T cells (i.e., CD137, OX40, CD40, GITR) or interfering in coinhibitory signals (i.e., CTLA-4, PD-1). These powerful agents can be guided by cancer vaccines to enhance immunity against tumor but not self tissues. Clinically powerful therapeutic synergies are at hand.
Derivative-free optimization: a review of algorithms and comparison of software implementations (2012)

Abstract This paper addresses the solution of bound-constrained optimization problems using algorithms that require only the availability of objective function values but no derivative information. We refer to these algorithms as derivative-free algorithms. Fueled by a growing number of applications in science and engineering, the development of derivative-free optimization algorithms has long been studied, and it has found renewed interest in recent time. Along with many derivative-free algorithms, many software implementations have also appeared. The paper presents a review of derivative-free algorithms, followed by a systematic comparison of 22 related implementations using a test set of 502 problems. The test bed includes convex and nonconvex problems, smooth as well as nonsmooth problems. The algorithms were tested under the same conditions and ranked under several criteria, including their ability to find near-global solutions for nonconvex problems, improve a given starting point, and refine a near-optimal solution. A total of 112,448 problem instances were solved. We find that the ability of all these solvers to obtain good solutions diminishes with increasing problem size. For the problems used in this study, , , and are better, on average, than other derivative-free solvers in terms of solution quality within 2,500 function evaluations. These global solvers outperform local solvers even for convex problems. Finally, , , and show superior performance in terms of refining a near-optimal solution.
The cellular phenotype conditions Btk for cell survival or apoptosis signaling (2000)

Bruton's agammaglobulinemia tyrosine kinase (Btk) was identified as the gene mutated in X-linked agammaglobulinemia. Btk is involved in B-cell receptor signaling and B cell ontogeny as the disease is characterized by a block in B-cell development. Cell proliferation and apoptosis are integral parts of B-cell development. We have demonstrated that overexpression of Btk in HeLa cells led to apoptosis, whereas in B cells, en dogenous levels of Btk protected the cells from apoptosis. We suggest a dual role for Btk in apoptosis and cell survival. We further propose that the phenotype of the cell may direct Btk for either cell survival or apoptosis. Our model is in line with the general feature of mammalian cells that have the inherent property to die unless the survival signals are triggered. The interplay between survival and apoptotic signaling is regulated by cell sur face receptors, cytoplasmic and nuclear regulatory molecules. These regu latory molecules may be simple unidirectional regulators or bidirectional regulators such as Btk. The different molecules involved in these pathways bring about an orchestrated signal depending on the phenotype of the cell, and a cell type-specific biological response is achieved that decides the fate of the cell.
Neural Networks and Adaptive Nonlinear Control of Agile Antiair Missiles (2000)

Research has shown that neural networks can be used to improve on approximate dynamic inversion for control ofuncertainnonlinearsystems.Inonearchitecture,theneuralnetworkadaptively cancelsinversionerrorsthrough on-linelearning. Suchlearning isaccomplishedby asimpleweightupdaterulederived from Lyapunov theory,thus assuring the stability of the closed-loop system. This methodology is reviewed and extended to incorporate an important classof neural networkswith onesigmoidal hidden layer. An agileantiair-missile autopilot is subsequently designed using this control scheme. A control law based on approximate inversion of the nonlinear dynamics is presented. This control system is augmented by the addition of a neural network with on-line learning. Numerical results from a nonlinear agile antiair-missile simulation demonstrate the effectiveness of the resulting autopilot.
Adenovirus-Mediated Interleukin-10 Gene Transfer Inhibits Post-Transplant Fibrous Airway Obliteration in an Animal Model of Bronchiolitis Obliterans (1998)

Bronchiolitis obliterans, a form of chronic allograft rejection characterized by progressive fibrous obliteration of the airways, is the major obstacle limiting prolonged survival of lung transplant recipients. To date, no effective therapy against this fatal complication exists. Interleukin-10 (IL-10), an anti-inflammatory and immunosuppressive cytokine, inhibits various T cell and antigen-presenting cell functions. We examined the effect of IL-10 in an animal model for bronchiolitis obliterans. A heterotopic tracheal transplant model was used. IL-10 was administered to the recipient either in its recombinant form by osmotic minipump or by adenoviral-mediated IL-10 gene transfer (Ad5E1mIL-10). Successful gene transfection and expression was confirmed by measuring circulating IL-10 protein. Tracheal allografts were assessed histologically based on a scoring system. IL-10 administration (in recombinant form or by gene transfer) inhibited the development of fibrous airway obliteration 3 weeks after transplantation in comparison to untreated controls (p < 0.05). This was demonstrated only if the delivery was initiated 5 days after transplantation and not if it was started at the time of transplantation. A single administration of the gene construct was sufficient to achieve the desired effect. We have shown that IL-10 can prevent the development of airway fibro-obliteration in this model. Gene transfection at a site distant from a graft can be used to produce a desired effect on the graft. IL-10 may be of major importance in the control of post-transplant bronchiolitis obliterans. The timing of its administration is critical and further studies are required to determine the mechanisms underlying the observed effects of IL-10.
Mutational analysis of the conserved cysteine-rich region of the human immunodeficiency virus type 1 Tat protein (1990)

The Tat transactivator protein of human immunodeficiency virus type 1 contains a highly conserved cysteine-rich region, containing seven cysteines from residues 22 through 37. To investigate the importance of noncysteine residues in this region of the Tat protein, we have carried out a mutational analysis, in most cases substituting a single alanine for the wild-type noncysteine residue. Alanine substitution of residue 23, 24, 46, or 47 had no effect on Tat activity in plasmid transfection assays. In contrast, alanine substitutions of all eight noncysteines analyzed, from residues 26 through 41, significantly reduced the activity of the Tat protein, in some cases as drastically as mutations in cysteine residues. The results demonstrate that the precise sequence of the cysteine-rich region is crucial for a fully functional Tat protein.
Some forms of tinnitus may involve the extralemniscal auditory pathway (1992)

It has previously been shown that the click-evoked responses recorded from the intracranial portion of the eighth nerve in patients with incapacitating tinnitus are not abnormal, nor is the latency of peak III of the click-evoked brainstem auditory-evoked potentials significantly altered; however, the latency of peak V is slightly (but significantly) shortened in comparison to that of patients with the same degree of hearing loss but no tinnitus. In this study the hypothesis that the extralemniscal auditory system is involved in the generation of tinnitus is tested. We made use of the fact that neurons of the extralemniscal auditory system also receive input from the somatosensory system, and that stimulation of the somatosensory system can influence the processing of auditory information in the extralemniscal system. In 4 of 26 patients with mild-to-severe tinnitus whose median nerve was stimulated electrically, the tinnitus increased noticeably during stimulation, in 6 the intensity of the tinnitus decreased noticeably, and in the remaining 16 there was no noticeable change in the tinnitus. In some of the patients the character of the tinnitus changed in a complex way. There were no significant differences in hearing thresholds in these three groups of patients. Electrical stimulation of the median nerve in 12 individuals with normal hearing who did not have tinnitus either had no effect on the loudness of sounds or it caused a slight increase in the loudness.
Portable orientation estimation device based on accelerometers, magnetometers and gyroscope sensors for sensor network (2003)

In this paper, we developed a portable orientation estimating device equipped with the Bluetooth network module. Accelerometers and magnetometers are used to measure absolute orientation against the Earth. Gyroscope sensors are used to measure the local angular velocity. By integrating the measured absolute orientation with the local angular velocity using an unscented Kalman filter (UKF), the stability and robustness of estimating absolute orientation are improved over either sensor alone. Since this device has the Bluetooth module, we can easily construct sensor networks.
Improved Constructions for Universal Re-encryption. (2003)

Golle et al recently introduced universal re-encryption, defining it as re-encryption by a player who does not know the key used for the original encryption, but which still allows an intended player to recover the plaintext. Universal re-encryption is potentially useful as part of many information-hiding techniques, as it allows any player to make ciphertext unidentifiable without knowing the key used. Golle et al’s techniques for universal re-encryption are reviewed, and an improved hybrid universal re-encryption construction which permits indefinite re-encryptions with better efficiency and an almost-optimally small increase in file size is presented. Some implementational issues and optimisations are discussed.
Ge MOS characteristics with CVD HfO/sub 2/ gate dielectrics and TaN gate electrode (2004)

In this paper, we report for the first time Ge MOS characteristics with ultra thin rapid thermal CVD HfO/sub 2/ gate dielectrics and TaN gate electrode. Using the newly developed pre-gate cleaning and NH/sub 3/-based Ge surface passivation, the TaN/HfO/sub 2//Ge gate stack with EOT of 12.9 /spl Aring/ exhibits excellent leakage current density of 6 mA/cm/sup 2/ @Vg=1V and interface state density (D/sub it/) of 8/spl times/10/sup 10//cm/sup 2/-eV. Both D/sub it/ and CV hysteresis of Ge MOS are improved significantly with NH/sub 3/ surface treatment. We also study the effects of post-deposition anneal and investigate the conduction mechanism of TaN/HfO/sub 2//Ge gate stack.
A group synchronization mechanism for stored media in multicast communications (2002)

This paper proposes a group synchronization mechanism, which synchronizes slave destinations with the master destination, for stored media in multicast communications. At the master and slave destinations, intra-stream and inter-stream synchronization mechanisms which were proposed by the authors are employed to output the master media stream and slave media streams synchronously. We achieve group synchronization by adjusting the output timing of the master media stream at each slave destination to that at the master destination. We also deal with traffic control by media scaling and control of joining an in-progress multicast group. Furthermore, the paper presents experimental results using an ATM network. It shows the validity of the mechanism and illustrates the influence of parameters on the system performance.
On-chip CMOS-compatible optical signal processor (2012)

We propose and demonstrate an optical signal processor performing matrix-vector multiplication, which is composed of laser-modulator array, multiplexer, splitter, microring modulator matrix and photodetector array. 8 × 10⁷ multiplications and accumulations (MACs) per second is implemented at the clock at a clock frequency of 10 MHz. All functional units can be ultimately monolithically integrated on a chip with the development of silicon photonics and an efficient high-performance computing system is expected in the future.
Person Tracking with Audio-Visual Cues Using the Iterative Decoding Framework (2008)

Tracking humans in an indoor environment is an essential part of surveillance systems. Vision based and microphone array based trackers have been extensively researched in the past. Audio-visual tracking frameworks have also been developed. In this paper we consider human tracking to be a specific instance of a more general problem of information fusion in multimodal systems. Dynamic Bayesian networks have been the modeling technique of choice to build such information fusion schemes. The complexity and non-Gaussianity of distributions of the dynamic Bayesian networks for such multimodal systems have led to the use of particle filters as an approximate inference technique. In this paper we present an alternative approach to the information fusion problem. The iterative decoding algorithm is based on the theory of turbo codes and factor graphs used in communication systems. We modify and adapt the iterative decoding algorithm to do probabilistic inference for the problem of tracking humans in an indoor space, using multiple cameras and microphone arrays.
Identification and Characterization by Antisense Oligonucleotides of Exon and Intron Sequences Required for Splicing (1994)

Certain thalassemic human beta-globin pre-mRNAs carry mutations that generate aberrant splice sites and/or activate cryptic splice sites, providing a convenient and clinically relevant system to study splice site selection. Antisense 2'-O-methyl oligoribonucleotides were used to block a number of sequences in these pre-mRNAs and were tested for their ability to inhibit splicing in vitro or to affect the ratio between aberrantly and correctly spliced products. By this approach, it was found that (i) up to 19 nucleotides upstream from the branch point adenosine are involved in proper recognition and functioning of the branch point sequence; (ii) whereas at least 25 nucleotides of exon sequences at both 3' and 5' ends are required for splicing, this requirement does not extend past the 5' splice site sequence of the intron; and (iii) improving the 5' splice site of the internal exon to match the consensus sequence strongly decreases the accessibility of the upstream 3' splice site to antisense 2'-O-methyl oligoribonucleotides. This result most likely reflects changes in the strength of interactions near the 3' splice site in response to improvement of the 5' splice site and further supports the existence of communication between these sites across the exon.
Two‐Component 10—23 DNA Enzymes (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Organic Heterostructure Field-Effect Transistors (1995)

Organic field-effect transistors have been developed that function as either n-channel or p-channel devices, depending on the gate bias. The two active materials are alpha-hexathienylene (alpha-6T) and C(60). The characteristics of these devices depend mainly on the molecular orbital energy levels and transport properties of alpha-6T and C(60). The observed effects are not unique to the two materials chosen and can be quite universal provided certain conditions are met. The device can be used as a building block to form low-cost, low-power complementary integrated circuits.
Did Merck's Failed HIV Vaccine Cause Harm? (2007)

SEATTLE, WASHINGTON--
 AIDS researchers met here last week to explore an alarming finding: A vaccine candidate may actually have increased the risk of HIV infection in some study participants.