gebhart/patrepeval huggingface dataset:
Stem Cells (2004)

Regenerative medicine and emerging biotechnologies stand to revolutionize the practice of medicine. Advancements in stem cell biology, including embryonic and postnatal somatic stem cells, have made the prospect of tissue regeneration a potential clinical reality. Short of reproductive cloning, these same technologies, properly used, could allow for the creation of replacement tissue for the deficient host. To provide a concise review for surgeons on the current science and biology of stem cells, we surveyed the scientific literature, MEDLINE, and relevant political headlines that illuminate the stem cell discussion; the issues are summarized in this review. Building on this conceptual framework, the related issues of clinical promise and the political debate enveloping this emerging technology are examined. A basic understanding of stem cell biology is paramount to stay informed of this emerging technology and the national debate.
Approximate minimum-time trajectories for 2-link flexible manipulators (1989)

Powell's nonlinear programming code, VF02AD, was used to generate approximate minimum-time tip trajectories for 2-link semi-rigid and flexible manipulator movements in the horizontal plane. The manipulator is modeled with an efficient finite-element scheme for an n-link, m-joint system with horizontal-plane bending only. Constraints on the trajectory include boundary conditions on position and energy for a rest-to-rest maneuver, straight-line tracking between boundary positions, and motor torque limits. Trajectory comparisons utilize a change in the link stiffness, EI, to transition from the semi-rigid to flexible case. Results show the level of compliance necessary to excite significant modal behavior. Quiescence of the final configuration is examined with the finite-element model.
Binding of the nicotinic acetylcholine receptor to SH2 domains of Fyn and Fyk protein tyrosine kinases. (1994)

The nicotinic acetylcholine receptor (AChR) is phosphorylated on tyrosine both in vitro and in vivo. To identify the protein tyrosine kinase that phosphorylates the receptor, we have previously cloned and characterized two protein tyrosine kinases, Fyn and Fyk, that are highly expressed in Torpedo electric organ, a tissue enriched in the AChR. Both kinases were shown by coimmunoprecipitation to be specifically associated with the AChR. In this study, we examined the molecular basis for the interaction of Fyn and Fyk with the AChR using fusion proteins containing the SH2 domains of the two kinases as affinity reagents. The AChR bound specifically and in a protein concentration-dependent manner to the SH2 domain fusion proteins of Fyn and Fyk. Quantitation of the association revealed that the binding of the AChR to Fyn and Fyk SH2 domain fusion proteins was to a single class of saturable high affinity sites. In addition, the association of the AChR with the SH2 domain fusion proteins was dependent on tyrosine phosphorylation of the AChR and was mediated by the delta subunit of the receptor. Furthermore, upon dissociation of the AChR into subunits, the delta subunit coimmunoprecipitated with both Fyn and Fyk. These data suggest that the association of the AChR with Fyn and Fyk is mediated by an interaction of the tyrosine-phosphorylated delta subunit of the receptor with the SH2 domains of the protein tyrosine kinases.
Isolated norovirus GII.7 strain within an extended GII.4 outbreak (2010)

Noroviruses are a major cause of viral gastroenteritis and have been detected with increasing prevalence in recent years. Currently, two main genogroups GI and GII with an increasing number of subtypes are differentiated. Because of a high genetic variability new variants emerge constantly allowing epidemiological tracing of viruses from year to year and location to location. A 282 bp sequence at the 5'end of the capsid gene was analyzed in isolates originating from the University hospital, Technische Universität München. Phylogenetic analysis was based on 20 GII positive samples from an outbreak in March/April 2006 and 8 samples from the following winter season 2006-2008. In the initial outbreak two distinct genotypes were identified. The GII.4 strain 2006a found in the majority of outbreaks in 2006 worldwide was isolated from all but two patients. These two individuals were infected with a GII.7 strain clustering mainly with isolates from Asia. Of note, they excreted noroviral RNA for 81 and 27 days, respectively. Longitudinal analysis of an extended 1381 bp sequence revealed positive selection in the P2 domain. The variant was very similar to GII.7 strains isolated in 1990 and 1994 suggesting slow evolution with evidence of recombination according to the SimPlot analysis. Strains found in the following years 2006-2008 clustered around the isolate GII.4 2006b, characterized in the spring of 2006 and reaching a high prevalence in 2006-2007. The results provide an insight into norovirus evolution at a University hospital over 3 years and describe intraindividual evolution within a patient infected chronically.
Quantum Computations and Images Recognition (1997)

The using of quantum parallelism is often connected with consideration of quantum system with huge dimension of space of states. The n-qubit register can be described by complex vector with 2^n components (it belongs to n'th tensor power of qubit spaces). For example, for algorithm of factorization of numbers by quantum computer n can be about a few hundreds for some realistic applications for cryptography. The applications described further are used some other properties of quantum systems and they do not demand such huge number of states. The term "images recognition" is used here for some broad class of problems. For example, we have a set of some objects V_i and function of "likelihood": F(V,W) &lt; F(V,V) = 1 If we have some "noisy" or "distorted" image W, we can say that recognition of W is V_i, if F(W,V_i) is near 1 for some V_i.
Deprotonative Metalation Using Ate Compounds: Synergy, Synthesis, and Structure Building (2007)

Historically, single-metal organometallic species such as organolithium compounds have been the reagents of choice in synthetic organic chemistry for performing deprotonation reactions. Over the past few years, a complementary new class of metalating agents has started to emerge. Owing to a variable central metal (magnesium, zinc, or aluminum), variable ligands (both in their nature and number), and a variable second metallic center (an alkali metal such as lithium or sodium), "ate" complexes are highly versatile bases that exhibit a synergic chemistry which cannot be replicated by the homometallic magnesium, zinc, or aluminum compounds on their own. Deprotonation accomplished by using these organometallic ate complexes has opened up new perspectives in organic chemistry with unprecedented reactivities and sometimes unusual and unpredictable regioselectivities.
Application and Commercialization of Flow Cytometrically Sex‐Sorted Semen (2008)

The current technology to sort X and Y chromosome bearing sperm population requires individual identification and selection of spermatozoa in a modified high-speed flow cytometer. For farm animal species, the technology is capable of producing sexed sperm at greater than 90% purity. However, only in the bovine, the technology has reached a developmental level that allows its commercial application. Meanwhile, the demand for female calves has grown rapidly, which encourages the demand for sex-sorted semen from high genetic value bulls. The success of the technology will depend mainly on the fertilizing capacity of the sorted spermatozoa, as this is the most affecting and economically relevant factor. To date, fertility is still variable and is quite dependent on post-sort processing. New processing techniques are under investigation and will likely be able to improve the fertility rates after AI with sex-sorted semen. It is of great importance to select the right bulls and to test the sorted samples on a routine basis. In addition to the demand for sex-sorted semen by the cattle industry, there is also a significant demand expressed by pig farmers. However, it is still unknown if the use of sex-sorted semen through commercial pig AI will be economically feasible. For the pig, the combination of in vitro fertilization with sexed semen and non-surgical embryo transfer is an alternative that merits further scientific attention. Recent developments in ovine AI and ET will make it very likely that commercial sheep industry will adopt the sexing technology in their breeding concepts.
The Effects of Chocolate and Chocolate by-product Consumption on Wild and Domestic Animals (2012)

Modern, high-yield cocoa plantations have a negative impact on biodiversity, and there is a pressing need for financial incentives to encourage use of less destructive farming systems.


The use of low-value cocoa by-products, particularly cocoa husk, in animal feed has potential economic benefits for many cocoa-producing countries.


Inclusion of chocolate and its by-products in animal feed has led to fatal toxicity in pigs, poultry, cattle, and horses.


Theobromine is the main toxin responsible for accidental poisoning in domestic and wild animals. Horses, pigs, chickens, and dogs are particularly sensitive.


Chocolate is one of the most common causes of accidental poisoning in dogs.


Chocolate toxicity is rarely encountered in wildlife, but it does occur. Chocolate has been used to poison coyotes.
Multiple signal transduction pathways activated through the T cell receptor for antigen. (1991)

The T cell receptor for antigen (TCR) is a multichain complex on the surface of T lymphocytes which binds peptide antigen and transduces a transmembrane signal leading to IL-2 secretion. Engagement of the TCR leads to activation of a tyrosine phosphorylation pathway and a phospholipase C (PLC) pathway leading to activation of protein kinase C (PCK). Currently available data suggest that the primary event in signal transduction is tyrosine kinase activation, since when this pathway is inhibited, PLC activation is blocked and there is no production of IL-2. The nature of the tyrosine kinase which initiates the signaling cascade is currently unknown. The CD4/CD8 associated kinase p56lck clearly plays a role in tyrosine phosphorylation, but it is clearly not the only tyrosine kinase involved. Studies demonstrating physical association of p59lyn with the TCR implicate fyn as an important candidate for the TCR tyrosine kinase. The protein tyrosine phosphatase CD45 also plays a critical early role in signal transduction since in cells where it is deficient, neither tyrosine kinase activation nor later signaling events are seen. The importance of the PLC/PKC pathway is illustrated by the fact that activation of this pathway alone may lead to IL-2 production. However, there may also be other mechanisms which can generate an IL-2 response. Two proteins known to be involved in growth regulation--p21ras and c-raf--have now been shown to be downstream targets of the PLC/PKC pathway.
Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-Å structure of the ternary complex (2009)

Factor (f) IXa is a critical enzyme for the formation of stable blood clots, and its deficiency results in hemophilia. The enzyme functions at the confluence of the intrinsic and extrinsic pathways by binding to fVIIIa and rapidly generating fXa. In spite of its importance, little is known about how fIXa recognizes its cofactor, its substrate, or its only known inhibitor, antithrombin (AT). However, it is clear that fIXa requires extensive exosite interactions to present substrates for efficient cleavage. Here we describe the 1.7-A crystal structure of fIXa in its recognition (Michaelis) complex with heparin-activated AT. It represents the highest resolution structure of both proteins and allows us to address several outstanding issues. The structure reveals why the heparin-induced conformational change in AT is required to permit simultaneous active-site and exosite interactions with fIXa and the nature of these interactions. The reactive center loop of AT has evolved to specifically inhibit fIXa, with a P2 Gly so as not to clash with Tyr99 on fIXa, a P4 Ile to fit snugly into the S4 pocket, and a C-terminal extension to exploit a unique wall-like feature of the active-site cleft. Arg150 is at the center of the exosite interface, interacting with AT residues on beta-sheet C. A surprising crystal contact is observed between the heparin pentasaccharide and fIXa, revealing a plausible mode of binding that would allow longer heparin chains to bridge the complex.
Effect of modern analgesic drugs (tramadol, pentazocine, and buprenorphine) on the bile duct sphincter in man. (1986)

Modern narcotic analgesic drugs, such as tramadol, pentazocine, and buprenorphine share similarities of molecular structure with morphine which is widely believed to cause spasm of the bile duct sphincter and so impede bile flow. This study assessed the effects of intravenously administered analgesics on bile duct sphincter motor activity measured by ERCP manometry. Ten minutes after pentazocine injection the duration of contractions and baseline pressure of the bile duct sphincter rose from 6.2 +/- 0.2 to 8.2 +/- 0.27 s and from 5.1 +/- 0.6 to 8.8 +/- 0.4 mmHg respectively. Tramadol, buprenorphine and saline showed no such effect. These data indicated that the effects of such drugs on bile duct sphincter function can be safely assessed by ERCP manometry and that pentazocine adversely affects the bile duct sphincter, whilst tramadol and buprenorphine do not. We consider therefore that pentazocine is not the premedication of first choice for endoscopic procedures involving the sphincter of Oddi and should also be avoided in patients with pancreatic and biliary disorders.
Visibility Computation for Efficient Walkthrough of Complex Environments (1996)

In many virtual reality applications as well as general computer graphics we need to consider large numbers of objects to render one image. In many cases rendering can be preceded by a culling phase that employs simple mechanisms to reject most of the objects. As a result, only a very small portion of the model has to go through the time-consuming process of hidden object removal. We report on such a culling mechanism that is based on regular space subdivision into cells followed by cell classification into interior, exterior, and wall cells. A special cell-to-cell visibility algorithm is then activated between every two nonexterior cells. Only the objects in the potentially visible set of cells are actually submitted to the hidden object removal algorithm. We report on the implementation of the algorithm and its performance for walkthrough of various environments.
[Association between polymorphisms of CYP17 and CYP3A4 genes and intrahepatic cholestasis of pregnancy in Chengdu]. (2006)

The T/C polymorphism of CYP17 gene is not associated with the risk of ICP in Chengdu. There are not -290A/G polymorphism of CYP3A4 gene among pregnunt women in Chengdu.
Ad hoc On-Demand Distance Vector (AODV) Routing (2003)

The Ad hoc On-Demand Distance Vector (AODV) routing protocol is intended for use by mobile nodes in an ad hoc network. It offers quick adaptation to dynamic link conditions, low processing and memory overhead, low network utilization, and determines unicast routes to destinations within the ad hoc network. It uses destination sequence numbers to ensure loop freedom at all times (even in the face of anomalous delivery of routing control messages), avoiding problems (such as counting to infinity) associated with classical distance vector protocols.
Radial cytoarchitecture and patterns of cortical connectivity in autism (2009)

To explain the pattern of preserved and superior abilities found in autism spectrum disorders, a hypothesis has emerged, which assumes that there is a developmental bias towards the formation of short-range connections. This would result in excessive activity and overconnectivity within susceptible local networks. These networks might become partially isolated and acquire novel functional properties. In turn, this would affect the formation of long-range circuits and systems governing top-down control and integration. Despite many tantalizing clues, mechanisms relating pathogenesis and altered cell function to the 'disconnection' of integrative and focal activity remain obscure. However, recent post-mortem studies of brains of individuals with autism have shown characteristic differences in the morphometry of radial cell minicolumns, which add credence to the connectivity hypothesis.
Intramyocardial Transplantation of Autologous Endothelial Progenitor Cells for Therapeutic Neovascularization of Myocardial Ischemia (2003)

These favorable outcomes encourage future clinical trials of catheter-based, intramyocardial transplantation of autologous CD34+ MNCs in the setting of chronic myocardial ischemia.
The Multiway Relay Channel (2012)

The multiuser communication channel, in which multiple users exchange information with the help of a relay terminal, termed the multiway relay channel (mRC), is introduced. In this model, multiple interfering clusters of users communicate simultaneously, such that the users within the same cluster wish to exchange messages among themselves, i.e., each user multicasts its message to all the other users in its own cluster. It is assumed that the users cannot receive each other's signals directly. Hence, the relay terminal in this model is the enabler of communication. In particular, restricted encoders are considered, such that the encoding function of each user depends only on its own message and the received signal is used only for decoding the messages of the other users in the cluster. Achievable rate regions and an outer bound are characterized for the Gaussian mRC, and their comparison is presented in terms of the exchange rate, the symmetric rate point in the capacity region in a symmetric Gaussian mRC scenario. It is shown that the compress-and-forward (CF) protocol achieves exchange rates within a constant bit offset of the optimal exchange rate, independent of the power constraints of the terminals in the network. A finite bit gap between the exchange rates achieved by the CF and the amplify-and-forward protocols is also shown. The two special cases of the mRC, the full data exchange model, in which every user wants to receive messages of all other users, and the pairwise data exchange model which consists of multiple two-way relay channels, are investigated in detail. In particular for the pairwise data exchange model, in addition to the proposed random coding-based achievable schemes, a nested lattice coding-based scheme is also presented and is shown to achieve exchange rates within a constant bit gap of the exchange capacity.
Organo- and Water-Dispersible Graphene Oxide−Polymer Nanosheets for Organic Electronic Memory and Gold Nanocomposites (2010)

10.1021/jp102640s
Pbx-Hox Heterodimers Recruit Coactivator-Corepressor Complexes in an Isoform-Specific Manner (1999)

Homeobox (hox) proteins have been shown to regulate cell fate and segment identity by promoting the expression of specific genetic programs. In contrast to their restricted biological action in vivo, however, most homeodomain factors exhibit promiscuous DNA binding properties in vitro, suggesting a requirement for additional cofactors that enhance target site selectivity. In this regard, the pbx family of homeobox genes has been found to heterodimerize with and thereby augment the DNA binding activity of certain hox proteins on a subset of potential target sites. Here we examine the transcriptional properties of a forced hox-pbx heterodimer containing the pancreas-specific orphan homeobox factor pdx fused to pbx-1a. Compared to the pdx monomer, the forced pdx-pbx1a dimer, displayed 10- to 20-fold-higher affinity for a consensus hox-pbx binding site but was completely unable to bind a hox monomer recognition site. The pdx-pbx dimer stimulated target gene expression via an N-terminal trans-activation domain in pdx that interacts with the coactivator CREB binding protein. The pdx-pbx dimer was also found to repress transcription via a C-terminal domain in pbx-1a that associates with the corepressors SMRT and NCoR. The transcriptional properties of the pdx-pbx1 complex appear to be regulated at the level of alternative splicing; a pdx-pbx polypeptide containing the pbx1b isoform, which lacks the C-terminal extension in pbx1a, was unable to repress target gene expression via NCoR-SMRT. Since pbx1a and pbx1b are differentially expressed in endocrine versus exocrine compartments of the adult pancreas, our results illustrate a novel mechanism by which pbx proteins may modulate the expression of specific genetic programs, either positively or negatively, during development.
Drusen proteome analysis: An approach to the etiology of age-related macular degeneration (2002)

Drusen are extracellular deposits that accumulate below the retinal pigment epithelium on Bruch's membrane and are risk factors for developing age-related macular degeneration (AMD). The progression of AMD might be slowed or halted if the formation of drusen could be modulated. To work toward a molecular understanding of drusen formation, we have developed a method for isolating microgram quantities of drusen and Bruch's membrane for proteome analysis. Liquid chromatography tandem MS analyses of drusen preparations from 18 normal donors and five AMD donors identified 129 proteins. Immunocytochemical studies have thus far localized approximately 16% of these proteins in drusen. Tissue metalloproteinase inhibitor 3, clusterin, vitronectin, and serum albumin were the most common proteins observed in normal donor drusen whereas crystallin was detected more frequently in AMD donor drusen. Up to 65% of the proteins identified were found in drusen from both AMD and normal donors. However, oxidative protein modifications were also observed, including apparent crosslinked species of tissue metalloproteinase inhibitor 3 and vitronectin, and carboxyethyl pyrrole protein adducts. Carboxyethyl pyrrole adducts are uniquely generated from the oxidation of docosahexaenoate-containing lipids. By Western analysis they were found to be more abundant in AMD than in normal Bruch's membrane and were found associated with drusen proteins. Carboxymethyl lysine, another oxidative modification, was also detected in drusen. These data strongly support the hypothesis that oxidative injury contributes to the pathogenesis of AMD and suggest that oxidative protein modifications may have a critical role in drusen formation.