gebhart/patrepeval huggingface dataset:
Estimating future hepatitis C morbidity, mortality, and costs in the United States (2000)

Our results confirm prior Centers for Disease Control and Prevention projections and suggest that HCV may lead to a substantial health and economic burden over the next 10 to 20 years.
[Model study on CO2 removal by photobioreactor]. (2006)

The key point of study on CO2 removal by microalgae cultured in a photobioreactor is to improve CO2 removal capability. In this paper, a model of air-lift photobioreactor was developed by combination of conditions including the velocity of flow, the degree of mixing, the gas-liquid mass transfer and the rate of photosynthesis, and two corresponding simplified methods, such as time discretization and lumped parameters were put forward. Using a method of lumped parameters, the model for simulation of time course of DO, pH in the column air-lift photobioreactor and prediction of CO2, O2 concentrations in the outlet gas under different CO2 concentration in the aeration gas was thoroughly discussed. Experimental data were also used to verify the model which could potentially be applied to rational design of the photobioreactor, high-density culture of microalgae and efficient removal of CO2.
FDTD verification of deep-set brain tumor hyperthermia using a spherical microwave source distribution (1996)

Although use of noninvasive microwave hyperthermia to treat cancer is problematic in many human body structures, careful selection of the source electric field distribution around the entire surface of the head can generate a tightly focused global power density maximum at the deepest point within the brain. An analytic prediction of the optimum volume field distribution in a layered concentric head model based on summing spherical harmonic modes is derived and presented. This ideal distribution is then verified using a three-dimensional finite difference time domain (FDTD) simulation with a discretized, MRI-based head model excited by the spherical source. The numerical computation gives a very similar dissipated power pattern as the analytic prediction. This study demonstrates that microwave hyperthermia can theoretically be a feasible cancer treatment modality for tumors in the head, providing a well-resolved "hot-spot" at depth without overheating any other healthy tissue.
Bacteriorhodopsin mutants containing single substitutions of serine or threonine residues are all active in proton translocation. (1991)

To study their role in proton translocation by bacteriorhodopsin, 22 serine and threonine residues presumed to be located within and near the border of the transmembrane segments have been individually replaced by alanine or valine, respectively. Thr-89 was substituted by alanine, valine, and aspartic acid, and Ser-141 by alanine and cysteine. Most of the mutants showed essentially wild-type phenotype with regard to chromophore regeneration and absorption spectrum. However, replacement of Thr-89 by Val and of Ser-141 by Cys caused striking blue shifts of the chromophore by 100 and 80 nm, respectively. All substitutions of Thr-89 regenerated the chromophore at least 10-fold faster with 13-cis retinal than with all-trans retinal. The substitutions at positions 89, 90, and 141 also showed abnormal dark-light adaptation, suggesting interactions between these residues and the retinylidene chromophore. Proton pumping measurements revealed 60-75% activity for mutants of Thr-46, -89, -90, -205, and Ser-226, and about 20% for Ser-141----Cys, whereas the remaining mutants showed normal pumping. Kinetic studies of the photocycle and of proton release and uptake for mutants in which proton pumping was reduced revealed generally little alterations. The reduced activity in several of these mutants is most likely due to a lower percentage of all-trans retinal in the light-adapted state. In the mutants Thr-46----Val and Ser-226----Ala the decay of the photointer-mediate M was significantly accelerated, indicating an interaction between these residues and Asp-96 which reprotonates the Schiff base. Our results show that no single serine or threonine residue is obligatory for proton pumping.
New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays (2010)

This report describes a number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens. The compounds identified by such substructural features are not recognized by filters commonly used to identify reactive compounds. Even though these substructural features were identified using only one assay detection technology, such compounds have been reported to be active from many different assays. In fact, these compounds are increasingly prevalent in the literature as potential starting points for further exploration, whereas they may not be.
Deletion of the Paired α5(IV) and α6(IV) Collagen Genes in Inherited Smooth Muscle Tumors (1993)

The gene encoding alpha 6(IV) collagen, COL4A6, was identified on the human X chromosome in a head-to-head arrangement and within 452 base pairs of the alpha 5(IV) collagen gene, COL4A5. In earlier studies, intragenic deletions of COL4A5 were detected in a subset of patients with Alport syndrome (AS), a hereditary defect of basement membranes. In some families, AS cosegregates with diffuse leiomyomatosis (DL), a benign smooth muscle tumor diathesis. Here it is shown that patients with AS-DL harbor deletions that disrupt both COL4A5 and COL4A6. Thus, type IV collagen may regulate smooth muscle differentiation and morphogenesis.
Neurocognition in PTSD: Treatment Insights and Implications (2016)

Post-traumatic stress disorder (PTSD) is classified as a traumatic stress-related condition and is most often discussed in terms of emotional dysfunction. However, given that cognitive and emotional processes are intricately intertwined, implemented by overlapping brain networks, and effectively integrated in at least some of the same regions (e.g., prefrontal cortex, for a review, see Crocker et al. 2013), an abundance of literature now highlights the key role that cognitive functioning plays in both the development and maintenance (or exacerbation) of PTSD symptoms (Aupperle et al. 2012a; Verfaellie et al. 2012). Findings from this body of work detail objective impairment in neuropsychological function in those with PTSD (Brandes et al. 2002; Hayes et al. 2012a; Koenen et al. 2001). Yet despite the impact of neurocognition on PTSD treatment engagement and success (e.g., Haaland et al. 2016; Nijdam et al. 2015) and conversely, the role of PTSD treatment in normalizing cognitive dysfunction, a much smaller literature exists on neurocognitive changes following treatment for PTSD. Even aside from its role in treatment, cognitive functioning in PTSD has significant implications for daily functioning for individuals with this disorder, as cognition is predictive of school achievement, obtaining and maintaining employment, job advancement, maintaining relationships, greater wealth, and better health and quality of life (e.g., Diamond and Ling 2016).
Cancer vaccine: learning lessons from immune checkpoint inhibitors (2017)

Cancer vaccines have been exclusively studied all through the past decades, and have made exceptional achievements in cancer treatment. Few cancer vaccines have been approved by the US Food and Drug Administration (FDA), for instance, Provenge, which was approved for the treatment of prostate carcinoma in 2012. Moreover, more recently, T-VEC got approval for the treatment of melanoma. While, the overall therapeutic effects of cancer vaccines have been taken into consideration as below expectations, low antigenicity of targeting antigen and tumor heterogeneity are the two key limiting barriers encountered by the cancer vaccines. Nonetheless, recent developments in cancer immune-therapies together with associated technologies, for instance the unparalleled achievements bagged by immune checkpoint inhibitor based therapies and neo-antigen identification tools, envisage potential improvements in cancer vaccines in respect to the treatments of malignancies. This review brings forth measures for the purpose of refining therapeutic cancer vaccines by learning lessons from the success of PD-1 inhibitor based immune-therapies.
An acoustic-phonetic-based speaker adaptation technique for improving speaker-independent continuous speech recognition (1994)

A new speaker adaptation technique is proposed for improving speaker-independent continuous speech recognition based on a decomposition of spectral variation sources. In this technique, the spectral variations are separated into two categories, one acoustic and the other phone-specific, where each variation source is modeled by a linear transformation system. The technique consists of two sequential steps: first, acoustic normalization is performed, and second, phone model parameters are adapted. Experiments of speaker adaptation on the TIMIT database using short calibration speech (5 s per speaker) have shown significant performance improvement over the baseline speaker-independent continuous speech recognition, where the recognition system uses Gaussian mixture density based hidden Markov models of phone units. For a vocabulary size of 853 and test set perplexity of 104, the recognition word accuracy has been improved from 86.9% for the baseline system to 90.5% after adaptation, corresponding to an error reduction of 27.5%. On a more difficult test set that contains an additional variation source due to recording channel mismatch, a more significant performance improvement has been obtained: for the same vocabulary and a test set perplexity of 101, the recognition word accuracy has been improved from 65.4% for the baseline to 86.0% after adaptation, corresponding to an error reduction of 59.5%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Steiner tree optimization for buffers. Blockages and bays (2002)

Buffer insertion is essential for achieving timing closure. This work studies buffer insertion under two types of constraints: (i) avoiding blockages, and (ii) inserting buffers into pre-determined buffer bay regions. We propose a general Steiner tree routing problem to drive this application and present a maze-routing based heuristic. We show that this approach leads to useful solutions on industry designs.
A statistical approach to risk mitigation in computational markets (2007)

We study stochastic models to mitigate the risk of poor Quality-of-Service (QoS) in computational markets. Consumers whopurchase services expect both price and performance guarantees. They need to predict future demand to budget for sustained performance despite price fluctuations. Conversely, providers need to estimate demand to price future usage. The skewed and bursty nature of demand in large-scale computer networks challenges the common statistical assumptions of symmetry, independence, and stationarity. This discrepancy leads to under estimation of investment risk. We confirm this non-normal distribution behavior in our study of demand in computational markets.
Antigen recognition by H-2-restricted cytolytic T lymphocytes is not mediated by two independent receptors. (1984)

Detergent-solubilized murine cytolytic T lymphocytes (CTL) clones were incorporated into Sendai virus-containing synthetic liposomes. When these liposomes were then fused with other CTL clones possessing a different non-cross-reacting specificity, the fusion products were observed to lyse target cells recognized by both parental CTL clones. This method was then used with two H-2-restricted CTL clones of different, non-cross-reacting specificities (anti-H-2b-H-Y or anti-H-2b Moloney leukemia virus). Once again, the fusion products were found to be lytic against both target cells recognized by the parental clones, but in no instance was there any observable lysis of target cells bearing the same nominal antigen in the context of different H-2 molecules. These results provide strong evidence that antigen recognition by H-2-restricted CTL is not mediated by two independent antigen receptors.
Prevention of nitrate tolerance with angiotension converting enzyme inhibitors. (1991)

This study demonstrates that ACE inhibitors may prevent nitrate tolerance to long-term nitrate therapy.
[A primary study of criterion for source identification of gastrointestinal tumor sample with Identifiler multiplex system]. (2011)

Criteria I and criteria II were powerful for distinguishing tumor sample from an unrelated individual or a full sibling of the patient with tumor, respectively, when the Identifiler system was adopted for source identification of gastrointestinal tumor sample.
Influence of electric fields on the excitability of granule cells in guinea‐pig hippocampal slices. (1981)

1. Monosynaptic evoked potentials were recorded from the granule cell layer of slices of guinea-pig hippocampus maintained in vitro. Current pulses of 25-250 msec duration were passed across the slices, between gross electrodes in the bathing liquid. 2. Polarizing current modified the excitability of the granule cells as judged by changes in their population discharge during postsynaptic responses. All durations of polarization had at least qualitatively similar effects. Conventional current from dendrites to cell bodies increased excitability (and vice versa). This is consistent with altered membrane potential of a spike trigger zone, at or close to the granule cell bodies, imposed by the fraction of polarizing current which flows intracellularly. 3. In some experiments polarization also affected the presynaptic volley and (hence?) the synaptic potential. When this occurred it was in the wrong sense to explain the concomitant changes in population spike. 4. Focal polarization, where currents were applied across the cell body layer between a small electrode on the mid or outer dendritic regions and a remote gross electrode, altered granule cell excitability in the same direction as in (2). Thus conventional current injected at the dendritic electrode increased excitability. 5. The smallest effect polarizing currents caused extracellular voltage gradients of 5-10 mV/mm, which is less than occurs in this tissue during synchronous activation of the neurons or during seizure activity. Therefore such field potentials could increased the synchrony of discharge of the granule cells.
Optical Imaging of Spontaneous Breast Tumors Using Protease Sensing ‘Smart’ Optical Probes (2005)

FRI and FMT using "smart" protease sensing probes permits detection of experimental spontaneous breast cancers. Because the expression levels of various proteases correlate with patient outcome, this technique may not only help to detect, but also to differentiate breast cancers noninvasively.
Overexpression of Human poly(ADP‐Ribose) Polymerase in Transfected Hamster Cells Leads to Increased Poly(ADP‐Ribosyl)ation and Cellular Sensitization to γ irradiation (1997)

Poly(ADP-ribosyl)ation is a posttranslational modification of nuclear proteins catalyzed by poly(ADP-ribose) polymerase (PARP), an enzyme which uses NAD+ as substrate. Binding of PARP to DNA single-strand or double-strand breaks leads to enzyme activation. Inhibition of poly(ADP-ribose) formation impairs the cellular recovery from DNA damage. Here we describe stable transfectants of the Chinese hamster cell line CO60 that constitutively overexpress human PARP (COCF clones). Immunofluorescence analysis of gamma-irradiation-stimulated poly(ADP-ribose) synthesis revealed consistently larger fractions of cells positive for this polymer in the COCF clones than in control clones, which failed to express human PARP. HPLC-based quantitative determination of in vivo levels of poly(ADP-ribose) confirmed this result and revealed that the basal polymer levels of undamaged cells were significantly higher in the COCF clones. The COCF clones were sensitized to the cytotoxic effects of gamma irradiation compared with control transfectants and parental cells. This effect could not be explained by depletion of cellular NAD+ or ATP pools. Together with the well-known cellular sensitization by inhibition of poly(ADP-ribosyl)ation, our data lead us to hypothesize that an optimal level of cellular poly(ADP-ribose) accumulation exists for the cellular recovery from DNA damage.
A 3D audio coding technique based on extracting the distance parameter (2014)

This paper presents a compression technique to improve the quality of three-dimensional (3D) audio produced by multiple loudspeaker channels or by headphone. The approach is based on extracting the side information of spatial sound sources within the three-dimensional space when capturing the sound sources. Different from other compression technique, the distances of sound sources are included in the side information. The separated signals of different sound sources are downmixed into one mono or stereo audio signal with the side information. The resulting downmixed signal is then compressed with traditional audio coder, resulting in a better perceptual quality of 3D audio by adding the distance parameter in the side information, and maintaining a low bit rates comparable with directional audio coding (DirAC).
Immunogenicity/Hypersensitivity of Biologics (2013)

This continuing education course was designed to provide an overview of the immunologic mechanisms involved in immunogenicity and hypersensitivity reactions following administration of biologics in nonclinical toxicity studies, the methods used to determine whether such reactions are occurring, and the associated clinical and anatomic pathology findings. Hypersensitivity reactions have classically been divided into type I, II, III, and IV reactions; type I and III reactions are those most often observed following administration of biologics. A variety of methods can be used to detect these reactions. Antemortem methods include hematology; detection of antidrug antibodies, circulating immune complexes and complement fragments, and immunoglobulin E in serum; tests for serum complement activity; and evaluation of complement receptor 1 on erythrocytes. Postmortem methods include routine light microscopy and electron microscopy, which can demonstrate typical findings associated with hypersensitivity reactions, and immunohistochemistry, which can detect the presence of immune complexes in tissues, including the detection of the test article. A final determination of whether findings are related to a hypersensitivity reaction in individual animals or across the entire study should rely on the overall weight of evidence, as findings indicative of these reactions are not necessarily consistent across all affected animals.
Electrochemical Fabrication of 3D Microperiodic Porous Materials (2001)

3D periodic microstructures of high-refractive index materials(see Figure), in particular the II–VI semiconductors CdS and CdSe, have been synthesized by electrodeposition through silica- or polystyrene-based colloidal assemblies. The highest refractive index contrast is achieved after removal of the silica or polystyrene templates with HF or toluene, respectively.
A new treatment for obstructive sleep apnea syndrome by electrical stimulation of submental region. (1988)

Loss of upper airway muscle tone during sleep has been thought to be responsible for obstructive apnea episodes. To examine the effect of electrical stimulation of the submental region on sleep apnea episodes, patients with obstructive sleep apnea syndrome were polysomnographically studied during all-night session with and without stimulation.
Intravitreal Sustained Release of VEGF Causes Retinal Neovascularization in Rabbits and Breakdown of the Blood– Retinal Barrier in Rabbits and Primates (1997)

Vascular endothelial growth factor (VEGF) has been identified as a possible mediator of retinal neovascularisation (NV), but it is not certain if VEGF alone is sufficient to cause retinal NV. We sought to investigate this issue by implanting ethylene-vinyl acetate copolymer pellets that slowly release VEGF into the vitreous cavity of rabbits and primates. Eyes were examined by indirect ophthalmoscopy, fundus photography, and fluorescein angiography and then animals were killed at various time points and immunocytochemical and ultrastructural evaluations were carried out. Seven days after implantation of a pellet containing 30 micrograms of human recombinant VEGF into the vitreous cavity of rabbits, retinal blood vessels became dilated and tortuous, and between days 14 and 21, retinal NV was noted in all eyes. Fluorescein angiography showed profuse leakage of dye from the anomalous vessels. Immunohistochemical staining for proliferating cell nuclear antigen (PCNA) showed positively staining nuclei in many of the endothelial cells of new blood vessels on the surface of the retina. Six eyes implanted with control pellets containing vehicle and two eyes implanted with pellets containing 30 micrograms of human serum albumin alone showed no retinal vascular abnormalities. Implantation of pellets containing 100 micrograms of VEGF into the vitreous cavity of primates resulted in iris NV and retinal vascular dilation and tortuosity very much like that seen in humans with ischemic retinopathies. Immunohistochemical staining for serum albumin showed widespread severe breakdown of the blood-retinal barrier (BRB). Histology showed dilated thin-walled retinal vessels, but unequivocal retinal NV could not be identified and staining for PCNA was negative. These findings indicate that sustained intravitreal release of VEGF causes widespread retinal vascular dilation and breakdown of the BRB. Retinal NV seems to require persistent high levels of VEGF at the retinal surface and can be achieved in rabbits providing a potentially useful model of retinal NV, but is difficult to achieve in primates. The extensive VEGF-induced disruption of the blood-retinal barrier suggests that VEGF antagonists may provide a new therapy for patients with ischemic retinopathies and macular edema.
Basal cell carcinoma – an in‐vivo model of human tumour microcirculation? (1999)

The role of angiogenesis in tumour growth and metastasis is well established. However, investigations of tumour microcirculation to date have used either biopsy material from human tumours, or animal models in vivo. We have studied the tumour microcirculation in vivo in human skin cancers using video-microscopy to examine 12 basal cell carcinomas (BCCs) on the head and neck of 11 patients, and compared the vessels with those seen in the peri-lesional skin, and in normal control skin on the opposite side of the body. The vessels seen within the BCCs were markedly abnormal qualitatively, forming bizarre, disorganized patterns. Quantitative analysis revealed that the mean diameter (+/-standard deviation) of the largest vessel was significantly greater within the BCC (0.086+/-0.029 mm) than that in the control skin (0.034+/-0.012 mm) (P<0.001). The area fraction, a measure of the area of tissue occupied by vessels, was increased highly significantly within the BCCs (0.158+/-0.038) compared with both peri-lesional skin (0.029+/-0.012) and control skin (0.027+/-0.010) (P<0.001). Length density, the length of blood vessel per unit area of tissue, was also highly significantly greater within the lesion (210.22+/-66.05 cm(-1)) compared to peri-lesional (27.10+/-15.67 cm(-1)) and control skin (28.27+/-15.81 cm(-1)) (P<0.001). This is the first study to have demonstrated that BCCs possess a distinct tumour microcirculation which can be observed directly, and assessed quantitatively. Prospective studies of tumour progression, possibly after intervention with angiogenesis inhibitors, are possible.