gebhart/patrepeval huggingface dataset:
Effects of cool storage on survival and function of intrastriatal ventral mesencephalic grafts (1991)

Ongoing clinical trials with fetal tissue transplants in Parkinson's disease would be facilitated by an effective tissue storage technique that would allow for temporal separation of the procurement of the fetal donor tissue and implantation surgery. In order to develop such a method, we grafted rat or human fetal ventral mesencephalic tissue to the dopamine-depleted striatum of rats either directly, or following pregraft refrigeration in a 'hibernation' medium at 4 °C. Rat tissue transplants were found to normalize amphetamine-induced circling behavior at 6 weeks post-transplantation after having been hibernated for either 2 or 5 days. The number of tyrosine hydroxylase immunoreactive neurons in these hibernated grafts did not differ significantly from that found in matched grafts of fresh tissue. Hibernation for 10 days resulted both in an absence of functional effects and in decreases of graft survival down to 10-20% of control values. Volume assessment of fresh and hibernated grafts prepared from human fetal tissue revealed no adverse effects of a 3 day hibernation interval at 3 weeks after transplantation into immunosuppressed rats. The results indicate that hibernation of neural tissue may be a convenient and simple tool, which can help to guarantee tissue availability at the planned time of implantation in patients and facilitate transport and bacteriological examination. Furthermore, the method offers a simple means which permits prolonged exposure of the neural tissue to trophic factors and specific markers prior to grafting in experimental animals.
In Vivo Imaging of the Bronchial Wall Microstructure Using Fibered Confocal Fluorescence Microscopy (2006)

Endoscopic FCFM represents a minimally invasive method to study specific basement membrane alterations associated with premalignant bronchial lesions in vivo. The technique may also be useful to study the bronchial wall remodeling in nonmalignant chronic bronchial diseases.
Evidence of negative bias temperature instability in 4H-SiC metal oxide semiconductor capacitors (2007)

Generation lifetimes and interface state densities of n-type 4H-SiC metal oxide semiconductor (MOS) capacitors are characterized by using the pulsed MOS capacitor technique. A decrease in lifetime and increase in interface state density occurs when the devices are negatively biased at 400°C. This behavior is consistent with an effect seen in Si∕SiO2 devices known as negative bias temperature instability. A portion of the lifetime degradation caused by this effect can be recovered by removing the negative bias as well as by positively biasing the device.
Efficient frequency domain analysis of large nonlinear analog circuits (2002)

In this paper, we present a new implementation of the harmonic balance method which extends its applicability to circuits 2-3 orders of magnitude larger than was previously practical. The results reported here extend our previous work which only considered large circuits operating in a mildly nonlinear regime. The new implementation is based on quadratically convergent Newton methods and is able to simulate general nonlinear circuits. The significant efficiency improvement is achieved by use of Krylov subspace methods and a problem-specific preconditioner for inverting the harmonic balance Jacobian matrix. The analysis of radio-frequency mixers, implemented in integrated circuit technology, is an important application of our new method. We describe the theory behind the method, then report performance results on a complete receiver design using detailed transistor models.
Near-Infrared Microspectroscopic Analysis of Rat Skin Tissue Heterogeneity in Relation to Noninvasive Glucose Sensing (2009)

Distribution of the chemical components of rat skin is significant relative to the dimensions of noninvasive glucose sensing. Chemical distribution maps reveal that variations in the chemical composition of the skin samples are on the same length scale as the fiber-optic probe used to collect noninvasive near-infrared spectra. Analysis of variance between tissue slices collected for one animal and analysis of variations between animals indicate that animal-to-animal variation for all four chemical components is significantly higher than variations between samples for a given animal. These findings justify the collection and interpretation of near-infrared microspectroscopic maps of human skin to establish chemical heterogeneity and its impact on noninvasive glucose sensing for the management of diabetes.
Purification of zymogen to plasminogen activator from human glioblastoma cells by affinity chromatography with monoclonal antibody (1982)

Incorporation of the serine protease active site reagent diisopropyl fluorophosphate (DFP) into a plasminogen activator with an Mr of approximately 52000 released from cultured human glioblastoma cells was strongly enhanced by incubation with plasmin. This observation led to the isolation of an inactive form of the enzyme from serum-free conditioned culture fluid by affinity chromatography on a column of a Sepharose-bound monoclonal antibody raised against urokinase. An 831-fold purification was obtained with a yield of 41%. The purified molecule was homogeneous as evaluated by polyacrylamide gel electrophoresis with sodium dodecyl sulfate (NaDodSO4), having one stainable band under nonreducing as well as reducing conditions with an Mr of approximately 52000. It was unable to activate plasminogen, but catalytic amounts of plasmin converted it into active enzyme. After NaDodSO4-polyacrylamide gel electrophoresis, the active enzyme showed one band under nonreducing conditions, but after reduction, two bands with Mr values of approximately 20000 and 32000 were observed. The active enzyme incorporated [3H]DFP into the approximately Mr 32000 band, while no incorporation was observed into the inactive form. These findings show that the Mr 52000 human plasminogen activator exists in a proenzyme form consisting of a single polypeptide chain that by proteolysis between half-cystine residues is converted into the active enzyme consisting of two chains with molecular weights of approximately 20000 and 32000, the active site being on the latter chain. The results are consistent with the active form of the enzyme being identical with the higher molecular weight form of urokinase, and together with recent observations that a murine plasminogen activator is released from sarcoma virus transformed cells as an inactive proenzyme, they suggest that zymogens to plasminogen activators are of more general occurrence.
Acidity Generated by the Tumor Microenvironment Drives Local Invasion (2013)

The pH of solid tumors is acidic due to increased fermentative metabolism and poor perfusion. It has been hypothesized that acid pH promotes local invasive growth and metastasis. The hypothesis that acid mediates invasion proposes that H(+) diffuses from the proximal tumor microenvironment into adjacent normal tissues where it causes tissue remodeling that permits local invasion. In the current work, tumor invasion and peritumoral pH were monitored over time using intravital microscopy. In every case, the peritumoral pH was acidic and heterogeneous and the regions of highest tumor invasion corresponded to areas of lowest pH. Tumor invasion did not occur into regions with normal or near-normal extracellular pH. Immunohistochemical analyses revealed that cells in the invasive edges expressed the glucose transporter-1 and the sodium-hydrogen exchanger-1, both of which were associated with peritumoral acidosis. In support of the functional importance of our findings, oral administration of sodium bicarbonate was sufficient to increase peritumoral pH and inhibit tumor growth and local invasion in a preclinical model, supporting the acid-mediated invasion hypothesis. Cancer Res; 73(5); 1524-35. ©2012 AACR.
Lens and Wedge Absorption Cells for FT-IR Spectroscopy (1985)

New cell geometries for extending the dynamic range of FT-IR absorption spectroscopy are described. These are variants of the stepped multiple thickness cells described before, in which the cell thickness varies continuously with location. Either homogeneous wedge or lenslike cells are used. The resulting distortion of the cell's photometric linearity can be straightened out computationally. However, the change in the measured energy levels drastically increases the dynamic range of the measurement for a given tolerable relative error in absorbance. The theoretical behavior of the cells is analyzed, and their photometric distortion and dynamic range calculated. The experimental realization of one of them is used to show the usefulness and limitations of the procedure.
A Novel Secure H.264 Transcoder using Selective Encryption (2007)

In digital broadcast TV systems, video data is normally encrypted before transmission. For in-home redistribution, it is often necessary to transcode the bitstream to achieve optimum utilization of available bandwidth. If a signal is decrypted before transcoding and re-encrypted, this may lead to a security loophole. This paper presents a solution in the form of a novel H.264 selective encryption algorithm that encrypts sign bits of transform coefficients and motion vectors to allow secure transcoding without decryption. The performance of this system is compared with I-frame encryption. The results show that sign encryption is more secure than I-frame encryption and has a lower complexity. A hybrid system using a modified transcoder and sign encryption is found to give an optimal compromise between security and transcoding performance.
Synthesis of Iodoalkylacylates and Their Use in the preparation ofS-Alkyl Phosphorothiolates (1995)

Abstract Synthesis of iodoalkylacylates 3a-f and use of 3 c in the preparation of an oligonucleoside phosphorothiate prodrug analog 5 is described.
International Variation in Histologic Grading Is Large, and Persistent Feedback Does Not Improve Reproducibility (2003)

Histologic grading systems are used to guide diagnosis, therapy, and audit on an international basis. The reproducibility of grading systems is usually tested within small groups of pathologists who have previously worked or trained together. This may underestimate the international variation of scoring systems. We therefore evaluated the reproducibility of an established system, the Banff classification of renal allograft pathology, throughout Europe. We also sought to improve reproducibility by providing individual feedback after each of 14 small groups of cases. Kappa values for all features studied were lower than any previously published, confirming that international variation is greater than interobserver variation as previously assessed. A prolonged attempt to improve reproducibility, using numeric or graphical feedback, failed to produce any detectable improvement. We then asked participants to grade selected photographs, to eliminate variation induced by pathologists viewing different areas of the slide. This produced improved kappa values only for some features. Improvement was influenced by the nature of the grade definitions. Definitions based on "area affected" by a process were not improved. The results indicate the danger of basing decisions on grading systems that may be applied very differently in different institutions.
Diversified Latent Variable Models (2018)

Latent variable model is a common probabilistic framework which aims to estimate the hidden states of observations. More specifically, the hidden states can be the position of a robot, the low dimensional representation of an observation. Meanwhile, various latent variable models have been explored, such as hidden Markov models (HMM), Gaussian mixture model (GMM), Bayesian Gaussian process latent variable model (BGPLVM), etc. Moreover, these latent variable models have been successfully applied to a wide range of fields, such as robotic navigation, image and video compression, natural language processing. So as to make the learning of latent variable more efficient and robust, some approaches seek to integrate latent variables with related priors. For instance, the dynamic prior can be incorporated so that the learned latent variables take into account the time sequence. Besides, some methods introduce inducing points as a small set representing the large size latent variable to enhance the optimization speed of the model. Though those priors are effective to facilitate the robustness of the latent variable models, the learned latent variables are inclined to be dense rather than diverse. This is to say that there are significant overlapping between the generated latent variables. Consequently, the latent variable model will be ambiguous after optimization. Clearly, a proper diversity prior play a pivotal role in having latent variables capture more diverse features of the observations data. In this thesis, we propose diversified latent variable models incorporated by different types of diversity priors, such as single/dual diversity encouraging prior, multi-layered DPP prior, shared diversity prior. Furthermore, we also illustrate how to formulate the diversity priors in different latent variable models and perform learning, inference on the reformulated latent variable models.
Thrombospondin exerts an antiangiogenic effect on cord formation by endothelial cells in vitro. (1991)

The response of endothelial cells to angiogenic stimuli has been shown to be influenced by the extracellular microenvironment. We tested whether thrombospondin, an extracellular matrix protein, modulated the spontaneous formation of cords by endothelial cells in vitro. Despite continued proliferation, a decrease in secreted thrombospondin was detected in cord-containing, as compared with subconfluent, cultures of both aortic and microvascular endothelial cells. Consistent with this trend, mRNA levels of thrombospondin decreased by factors of 16 in aortic and 60 in microvascular cultures that contained endothelial cords. Since thrombospondin was immunolocalized to fibrillar arrays that appeared to be associated with endothelial cords, we added anti-thrombospondin IgG to cord-forming cultures to limit the availability of the protein during this process. In the presence of anti-thrombospondin antibodies, there was a 33-50% increase in cord formation. These results suggest that thrombospondin is an inhibitor of angiogenesis in vitro and are consistent with its proposed roles as a destabilizer of endothelial cell focal contacts and as an inhibitor of endothelial cell proliferation.
Joint congestion control, contention control and resource allocation in wireless networks (2008)

Traditional congestion control protocols assume that each link provides a fixed capacity, while it is not always the case in wireless networks which have shared and variable medium. In this paper, we incorporate variable link capacity as a function of resource allocated, and random-access interference model dependent on physical location, in addition to congestion control, into the network utility maximization framework. Despite non-convexity and non-separability of the primal formulation, we transform the problem and apply a two-level dual based decomposition for solving it. We then propose practical algorithm and prove their convergence to the globally optimum. By collaboratively optimization of transmission rate at the transport layer, link persistence probability at the media-access control layer, and allocated resource at the physical layer, our algorithm can improve the system performance which is further demonstrated by numerical results.
A new classification of head injury based on computerized tomography (1991)

✓ A new classification of head injury based primarily on information gleaned from the initial computerized tomography (CT) scan is described. It utilizes the status of the mesencephalic cisterns, the degree of midline shift in millimeters, and the presence or absence of one or more surgical masses. The term “diffuse head injury” is divided into four subgroups, defined as follows: Diffuse Injury I includes all diffuse head injuries where there is no visible pathology; Diffuse Injury II includes all diffuse injuries in which the cisterns are present, the midline shift is less than 5 mm, and/or there is no high- or mixed-density lesion of more than 25 cc; Diffuse Injury III includes diffuse injuries with swelling where the cisterns are compressed or absent and the midline shift is 0 to 5 mm with no high- or mixed-density lesion of more than 25 cc; and Diffuse Injury IV includes diffuse injuries with a midline shift of more than 5 mm and with no high- or mixed-density lesion of more than 25 cc. There is a direct relationship between these four diagnostic categories and the mortality rate. Patients suffering diffuse injury with no visible pathology (Diffuse Injury I) have the lowest mortality rate (10%), while the mortality rate in patients suffering diffuse injury with a midline shift (Diffuse Injury IV) is greater than 50%. When used in conjunction with the traditional division of intracranial hemorrhages (extradural, subdural, or intracerebral), this categorization allows a much better assessment of the risk of intracranial hypertension and of a fatal or nonfatal outcome. This more accurate categorization of diffuse head injury, based primarily on the result of the initial CT scan, permits specific subsets of patients to be targeted for specific types of therapy. Patients who would appear to be at low risk based on a clinical examination, but who are known from the CT scan diagnosis to be at high risk, can now be identified.
Insulin - Like Growth Factor System 과 성장 , 대사 및 영양과의 관계 (2000)

The insulin-like growth factor (IGF) system comprises of IGF-I and IGF-II ligands, two types of IGF receptor, six species of IGF-binding protein (IGFBP) and a `secondary IGFBP`. In this communication, roles of the IGF system components as related to growth and metabolic control systems are reviewed, with a special emphasis on circulating IGFs and IGFBPs. It has been rigorously demonstrated, by studies involving transgenic and gene targeting animal models and also ablation and replacement or direct injection/infusion, that IGF-I stimulates fetal growth and development independently of growth hormone and also plays an intermediary role in growth hormone-stimulated somatic growth in postnatal animals. IGF-II also plays a similar role in fetal growth, but its role in postnatal animals is less than clear. IGFs also have an insulin-like activity in metabolic control of the carbohydrate, protein and fat as well as in the maintenance of glucose homeostasis as an auxiliary agent of insulin. IGFBPs, in general, play a modulatory role in these actions of the IGF. The IGF activity is suppressed under conditions of restricted energy and/or protein intake, which appears to be partly mediated by insulin. Unlike growth hormone, however, nutrition plays more of a permissive role than a regulatory role in the expression of IGF system components. Unfortunately, above information has been obtained mostly from clinical trials and also from studies in the rat as an animal model, although farm animal species are superior to the rat as an animal model in many aspects. More basic and interdisciplinary studies of the IGF system in farm animals as an alternative animal model and economic species are awaited.
TL1A-induced NF-κB Activation and c-IAP2 Production Prevent DR3-mediated Apoptosis in TF-1 Cells (2003)

We recently identified TL1A, an endothelium-derived T cell costimulator and a ligand for tumor necrosis factor receptor superfamily members DR3 and decoy receptor 3. To elucidate the signaling events triggered by TL1A-DR3 interaction and to understand the molecular mechanisms regulating DR3-mediated apoptosis, we have studied the effect of TL1A and an agonistic DR3 monoclonal antibody in human erythroleukemic TF-1 cells, which express DR3 endogenously. TL1A induced the formation of a DR3 signaling complex containing TRADD, TRAF2, and RIP and activated the NF-kappaB and the ERK, JNK, and p38 mitogen-activated protein kinase pathways. However, TL1A or an agonistic DR3 monoclonal antibody did not induce apoptosis in these cells nor were there detectable levels of FADD or procaspase-8 seen in the signaling complex. Interestingly, DR3-mediated apoptosis was induced in TF-1 cells in the presence of a NF-kappaB pathway-specific inhibitor but not in the presence of mitogen-activated protein kinase inhibitors, either alone or in combination, suggesting that DR3-induced NF-kappaB activation was responsible for resistance to apoptosis in these cells. Consistent with this, we found that TL1A significantly increased the production of c-IAP2, a known NF-kappaB-dependent anti-apoptotic protein, and that the NF-kappaB inhibitor or cycloheximide prevented its synthesis. Furthermore, inhibition of c-IAP2 production by RNA interference significantly sensitized TF-1 cells to TL1A-induced apoptosis. Our study identifies a molecular mechanism by which TL1A and DR3 regulate cell fate in TF-1 cells.
Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice (2014)

Our results indicate that the agricultural trait could be purposely modified by sgRNA:Cas9-induced gene targeting. CRISPR-Cas9 system could be exploited as a powerful tool for trait improvements in crop breeding.
The structure of carbamoyl phosphate synthetase determined to 2.1 Å resolution (1999)

Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As isolated from Escherichia coli, the enzyme is an alpha,beta-heterodimer consisting of a small subunit that hydrolyzes glutamine and a large subunit that catalyzes the two required phosphorylation events. Here the three-dimensional structure of carbamoyl phosphate synthetase from E. coli refined to 2.1 A resolution with an R factor of 17.9% is described. The small subunit is distinctly bilobal with a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. As observed in those enzymes belonging to the alpha/beta-hydrolase family, the active-site nucleophile, Cys269, is perched at the top of a tight turn. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain. Both the carboxyphosphate and carbamoyl phosphate synthetic components bind Mn2+ADP. In the carboxyphosphate synthetic component, the two observed Mn2+ ions are both octahedrally coordinated by oxygen-containing ligands and are bridged by the carboxylate side chain of Glu299. Glu215 plays a key allosteric role by coordinating to the physiologically important potassium ion and hydrogen bonding to the ribose hydroxyl groups of ADP. In the carbamoyl phosphate synthetic component, the single observed Mn2+ ion is also octahedrally coordinated by oxygen-containing ligands and Glu761 plays a similar role to that of Glu215. The carboxyphosphate and carbamoyl phosphate synthetic components, while topologically equivalent, are structurally different, as would be expected in light of their separate biochemical functions.
Study of the “molten globule” intermediate state in protein folding by a hydrophobic fluorescent probe (1991)

Binding of the hydrophobic fluorescent probe, 1-anilino-naphthalene-8-sulfonate (ANS), to synthetic polypeptides and proteins with a different structural organization has been studied. It has been shown that ANS has a much stronger affinity to the protein "molten globule" state, with a pronounced secondary structure and compactness, but without a tightly packed tertiary structure as compared with its affinity to the native and coil-like proteins, or to coil-like, alpha-helical, or beta-structural hydrophilic homopolypeptides. The possibility of using ANS for the study of equilibrium and kinetic molten globule intermediates is demonstrated, with carbonic anhydrase, beta-lactamase, and alpha-lactalbumin as examples.