gebhart/patrepeval huggingface dataset:
Human papillomavirus genotype detection and viral load in paired genital and urine samples from both females and males (2011)

The ability to detect type-specific high risk HPV (HR-HPV) infections in samples from females and males is important for monitoring the epidemiology of HPV and the impact of vaccination. Type-specific detection concordance between paired urine and genital samples from females (n = 264) undergoing routine colposcopy and males (n = 88) attending a genito-urinary medicine clinic was evaluated using an in-house genotyping assay. The overall inter-rater agreement (κ) was 0.781 for female pairs and 0.346 for male pairs. Female urine had sensitivity for detection of HPV16/18 and HR-HPV of 75% and 84%, respectively, while male urine had sensitivities of 13% and 28%, respectively. Genital samples had a higher HPV DNA copy number than urine although a small proportion (10%) of urine samples had a higher copy number than the corresponding genital sample. The proportion of females with normal cytology positive for HPV16/18 was 19%, increasing to 57% in moderate or severely dyskaryotic samples. The same trend was seen in the corresponding urine (19-43%) compounded by the reduced sensitivity of this sample type. The HPV16 viral load in female genital samples, but not in urine, was weakly associated with cervical disease stage. Despite reduced sensitivity, urine appears to be an appropriate surrogate sample for type-specific HPV detection in females for epidemiological objectives. The lower sensitivity and lack of association between viral load and disease stage in urine suggest that urine may not be useful for clinical management of HPV infection. The utility of urine for type-specific detection in males is less certain.
Expression of synaptic vesicle protein 2A in epilepsy-associated brain tumors and in the peritumoral cortex (2010)

Synaptic vesicle protein 2A (SV2A) has been identified as the binding site for the antiepileptic drug levetiracetam and is thought to decrease neuronal excitability. Since knockout of SV2A in mice leads to seizures, we hypothesized that a reduction in SV2A expression promotes seizure generation in epilepsy-associated brain tumors. We compared the SV2A expression and distribution in surgically removed tumor tissue (n = 63) and peritumoral cortex (n = 31) of patients with glial and glioneuronal tumors to normal control cortex obtained at autopsy in nonbrain tumor patients (n = 6). Additionally, we compared the SV2A expression and distribution in tumor patients with epilepsy (n = 39) with SV2A expression in tumor patients without epilepsy (n = 24). Immunohistochemistry in control cortex demonstrated strong and diffuse SV2A immunoreactivity (IR) throughout all cortical layers. Similar strong SV2A IR (with the same diffuse distribution pattern) was observed in the peritumoral cortical specimens in both patients with and without epilepsy. Modest SV2A IR was observed within the tumor area. The SV2A-positive cells detected within the tumor area were mainly entrapped neurons. Oligodendrogliomas and glioneuronal tumors displayed variable SV2A neuropil staining. In ganglioglioma (GG), strong SV2A IR was present along the dysplastic neuronal cell borders and processes. In both GG and dysembryoplastic neuroepithelial tumors, SV2A IR was occasionally observed within the neuronal perikarya. We found no differences in SV2A expression in the peritumoral cortex between the patients with and without epilepsy, which suggests that the role of SV2A in epileptogenesis in patients with glial tumors is questionable. The distinct pattern of SV2A IR in glioneuronal tumors suggests a redistribution of SV2A.
Strain Evolution in CoherentGe/SiIslands (2000)

Strain evolution of coherent Ge islands on Si(001) is measured using a newly developed transmission electron microscopy technique based on two-beam dark-field strain imaging. The strain measurements show that a metastable Ge island shape is involved in the shape transition between pyramids and domes; this shape is more readily observed for growth at 550 than 600 degrees C because of the slower rate at which islands cross the kinetic barrier between shapes. The strain relaxation changes discontinuously between pyramids and domes, indicating that the underlying shape transition is first order.
Characterization and overproduction of the <i>Escherichia coli</i> <i>appA</i> encoded bifunctional enzyme that exhibits both phytase and acid phosphatase activities (2000)

The appA gene that was previously shown to code for an acid phosphatase instead codes for a bifunctional enzyme exhibiting both acid phosphatase and phytase activities. The purified enzyme with a molecular mass of 44,708 Da was further separated by chromatofocusing into two isoforms of identical size with isoelectric points of 6.5 and 6.3. The isoforms had identical pH optima of 4.5 and were stable at pH values from 2 to 10. The temperature optimum for both phytase isoforms was 60 degrees C. When heated at different pH values the enzyme showed the greatest thermal resistance at pH 3. The pH 6.5 isoform exhibited K(m) and Vmax values of 0.79 mM and 3165 U.mg-1 of protein for phytase activity and 5.5 mM and 712 U.mg-1 of protein for acid phosphatase, respectively. The pH 6.3 isoform exhibited slightly lower K(m) and Vmax values. The enzyme exhibited similar properties to the phytase purified by Greiner et al. (1993), except the specific activity of the enzyme was at least 3.5-fold less than that previously reported, and the N-terminal amino acid sequence was different. The Bradford assay, which was used by Greiner et al. (1993) for determination of enzyme concentration was, in our hands, underestimating protein concentration by a factor of 14. Phytase production using the T7 polymerase expression system was enhanced by selection of a mutant able to grow in a chemically defined medium with lactose as the carbon source and inducer. Using this strain in fed-batch fermentation, phytase production was increased to over 600 U.mL-1. The properties of the phytase including the low pH optimum, protease resistance, and high activity, demonstrates that the enzyme is a good candidate for industrial production as a feed enzyme.
Culture of vascular cells in tridimensional (3-D) collagen: a methodological review. (2000)

Experimental models based on the culture of cells within tridimensional (3-D) gels add a 3-D organization to the classical 2-D culture of vascular cells. They allow the study of cell structure in an environment which is more representative of the in vivo situation and the investigation of cellular functions which cannot be studied using the basic 2-D models. This review shows examples of the use of cultures of vascular cells (endothelial cells, smooth muscle cells as well as fibroblasts) in 3-D collagen matrices for the study of cellular functions as diverse as angiogenesis, extracellular matrix reorganization, migration through 3-D collagen gels or phenotype modulation. It also describes recent advances in the in vitro reconstruction of biological blood vessels by bioengineering. A method for the preparation of 3-D collagen gels is described.
Performance of Uplink Multiuser Massive MIMO Systems (2013)

We study the performance of uplink transmission in a large-scale (massive) MIMO system, where all the transmitters have single antennas and the receiver (base station) has a large number of antennas. Specifically, we analyze achievable degrees of freedom of the system without assuming channel state information at the receiver. Also, we quantify the amount of power saving that is possible with increasing number of receive antennas.
Performance Evaluation in All-Wireless Wi-Fi Networks (2008)

This study establishes a set of basic requirements for the network architecture of an all-wireless Internet, implemented using mesh network concepts. An implementation model to evaluate network performance at single hop level is defined, and a detailed analysis of the results obtained from several simulation runs with OPNET modeler reveals that: the standard for backbone network with better performance is 802.11a; the number of clients associated to each mesh access point must be lower than 30; the distance between mesh access points must be lower than 140 m; and that the minimum nominal data rate at the backbone is 5.5 Mbps. Using these requirements, the maximum throughput obtained at the backbone network is 5.35 Mbps. This value can be used as a figure of merit of the network in order to measure the relative gain of future network architectures and protocol enhancements.
Role of a positive regulator of root hair development, CAPRICE ,in Arabidopsis root epidermal cell differentiation (2002)

In Arabidopsis, root hairs are formed only from a set of epidermal cells named trichoblasts or hair-forming cells. Previous studies showed CAPRICE (CPC) promotes differentiation of hair-forming cells by controlling a negative regulator, GLABRA2 (GL2), which is preferentially expressed in hairless cells. Here, we show that CPC is also predominantly expressed in the hairless cells, but not in the neighboring hair-forming cells, and that CPC protein moves to the hair-forming cells and represses the GL2 expression. We also show that the N terminus of bHLH protein interacts with CPC and is responsible for the GL2 expression. We propose a model in which CPC plays a key role in the fate-determination of hair-forming cells.
A Versatile Linkage Strategy for Solid-Phase Synthesis of N,N-Dimethyltryptamines and β-Carbolines (2002)

Various tryptamines are captured by a vinylsulfonylmethyl polystyrene resin, generating a safety-catch linkage. Beta-carbolines can be formed from 4 by a Pictet-Spengler reaction with the introduction of R(1). Tryptamine 4 can also be derivatized by acylation or copper-mediated coupling to introduce R(2). If X = Br, Suzuki coupling can be used to introduce R(3). After derivatization, the indole derivatives are activated with methyl iodide and released under mild basic condition. [reaction: see text]
Deregulated signal transduction by the K1 gene product of Kaposi’s sarcoma-associated herpesvirus (1999)

The Kaposi's sarcoma (KS)-associated herpesvirus is a lymphotropic virus strongly implicated in the pathogenesis of KS and several lymphoproliferative disorders. The KS-associated herpesvirus K1 gene encodes a transmembrane protein bearing a functional immunoreceptor tyrosine-based activation motif (ITAM)-like sequence; it previously has been proposed to be important in viral tumorigenesis because its expression can trigger cell proliferation in vitro and in vivo. Here we show that expression of the full-length K1 protein can initiate calcium-dependent signal transduction in B cells; however, unlike other ITAM-based signal transduction events, K1 signaling occurs constitutively, in the absence of exogenous crosslinking ligands. This property is caused by its cysteine-rich ectodomain, which when transferred to other consensus ITAMs induces constitutive signaling. Although ITAM-based signaling by K1 involves classical syk and phospholipase C gamma2 activation, both ITAM- and syk-independent signaling pathways are activated by K1 expression. These studies indicate that K1 is a deregulated signaling molecule with pleitropic effects that may explain its known growth deregulatory properties.
Interplay of Chemical Microenvironment and Redox Environment on Thiol–Disulfide Exchange Kinetics (2011)

The interplay between the chemical microenvironment surrounding disulfides and the redox environment of the media on thiol-disulfide exchange kinetics was examined by using a peptide platform. Exchange kinetics of up to 34 cysteine-containing peptides were measured in several redox buffers. The electrostatic attraction/repulsion between charged peptides and reducing agents such as glutathione was found to have a very pronounced effect on thiol-disulfide exchange kinetics (differences of ca. three orders of magnitude). Exchange kinetics could be directly correlated to peptide charge over the entire range examined. This study highlights the possibility of finely and predictably tuning thiol-disulfide exchange, and demonstrates the importance of considering both the local environment surrounding the disulfide and the nature of the major reducing species present in the environment for which their use is intended (e.g., in drug delivery systems, sensors, etc).
Umbrella catheter for nonoperative closure of atrial septal defects. (1978)

Since a 1974 report of nonoperative closure of atrial septal defects (ASDs) using an umbrella catheter device, an additional 25 dogs have undergone creation of atrial septal defects, 12 of which have subsequently had successful transvenous closure. An improved model of the closure device has been developed, still using a pair of interlocking umbrella-like components made of stainless steel and Dacron. The umbrellas are smaller, lighter, and have an automatic opening ring. They are loaded simultaneously into a single capsule on the distal end of the outer catheter and are passed into the heart on a single passage, thus eliminating several steps of the original technique. Closure time has diminished from an average of 30 minutes to 5-10 minutes. The completeness of closure was documented in 12 animals by repeat cardiac catheterization which included hydrogen electrode studies. Autopsies on 10 sacrificed dogs revealed no adverse effects or migration of the device; two dogs are living and healthy. In the one clinical application, the patient has done well, remaining afebrile with an increased activity tolerance and resumption of normal activities. The umbrella has remained in position and appears to be functioning well.
Targeting the adenosine 2A receptor enhances chimeric antigen receptor T cell efficacy (2017)

Chimeric antigen receptor (CAR) T cells have been highly successful in treating hematological malignancies, including acute and chronic lymphoblastic leukemia. However, treatment of solid tumors using CAR T cells has been largely unsuccessful to date, partly because of tumor-induced immunosuppressive mechanisms, including adenosine production. Previous studies have shown that adenosine generated by tumor cells potently inhibits endogenous antitumor T cell responses through activation of adenosine 2A receptors (A2ARs). Herein, we have observed that CAR activation resulted in increased A2AR expression and suppression of both murine and human CAR T cells. This was reversible using either A2AR antagonists or genetic targeting of A2AR using shRNA. In 2 syngeneic HER2+ self-antigen tumor models, we found that either genetic or pharmacological targeting of the A2AR profoundly increased CAR T cell efficacy, particularly when combined with PD-1 blockade. Mechanistically, this was associated with increased cytokine production of CD8+ CAR T cells and increased activation of both CD8+ and CD4+ CAR T cells. Given the known clinical relevance of the CD73/adenosine pathway in several solid tumor types, and the initiation of phase I trials for A2AR antagonists in oncology, this approach has high translational potential to enhance CAR T cell efficacy in several cancer types.
A Quantitative Model for the Effect of Wettability on the Conductivity of Porous Rocks (2007)

Abstract Reservoir rock wettability is an important parameter to consider for oil recovery optimization. The great majority of sandstone formations is known to be strongly water-wet. In contrast, most carbonate reservoir rocks are believed to be mixed-wet or oil-wet to some degree with a non-uniform distribution of the wettability in the reservoir. Despite the importance of this parameter there is currently no proven quantitative logging technique that can provide a continuous wettability log. A detailed analysis of a new model for the conductivity of reservoir rock called the ‘connectivity equation’ is provided in the paper. Similar to Archie's law this simple model has only two parameters: An exponent called the conductivity exponent μ, and the water connectivity parameter Cw. Under some conditions Cw can be equal to zero and the equation becomes identical to Archie's law in its simplest form (n = m = μ). However, in the general case the model is fundamentally different from Archie's law because in the connectivity equation resistivity is only a function of the water volume fraction. Cw is shown to account for water connectivity effects in the pore network. These effects are encoded in the expression of Cw with three terms linked respectively to 1- the ‘super-connectivity’ of micro pores in micritic grains for carbonate rocks, or the super-connectivity created by shale in shaly sandstones, 2- wettability effects in meso/macro pores, and 3- the low connectivity of vuggy porosity. This model is compared with published data and is shown to correctly account for most situations, including ‘non-Archie’ rocks such as low resistivity pay in carbonates, strongly oil-wet rocks, and the dual water model for shaly sands. A good correlation between Cw – obtained from a combination of wireline logs – and wettability measured on cores is found on data from a Middle East carbonate reservoir.
Dengue Fever Seroprevalence and Risk Factors, Texas–Mexico Border, 2004 (2007)

Reported autochthonous dengue fever transmission in the United States has been limited to 5 south Texas border counties since 1980. We conducted a cross-sectional serosurvey in Brownsville, Texas, and Matamoros, Tamaulipas, Mexico (n = 600), in 2004 to assess dengue seroprevalence. Recent dengue infection was detected in 2% (95% confidence interval [CI] 0.5%-3.5%) and 7.3% (95% CI 4.3%-10.3%) of residents in Brownsville and Matamoros, respectively. Past infection was detected in 40% (95% CI 34%-45%) of Brownsville residents and 78% (95% CI 74%-83%) of Matamoros residents. For recent infection, only weekly family income <or=$100 was a significant predictor (adjusted odds ratio 3.2, 95% CI 1.3-8.0). Risk factors that predicted past dengue infection were presence of larval habitat, absence of air-conditioning and street drainage, and weekly family income <or=$100. Mosquito larvae were present in 30% of households in both cities. Our results show that dengue fever is endemic in this area of the southern Texas-Mexico border.
Research on high way construction and non-governmental capital utilization (2012)

With the rapid development of our super high way construction, the conflict between the capital shortage and swift development existing in super high way construction becomes increasingly obvious, which results in the emergency of introducing the non-governmental capital. In this paper, it is proposed that a fair developing space should be created and our policies should be innovated based on the analysis of the dilemma and problems the non-governmental capital face, aiming to lead the non-governmental capital enter the field of the super high way construction positively and efficiently. All these are supposed to promote the development of our road construction.
Population-based, real-world prognostic factors related to survival among patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). (2021)

389 Background: Pancreatic cancer is expected to be the third deadliest cancer in the US in 2020. Many real-world studies of pts with mPDAC are restricted to single centers, limiting the generalizability of the insights they generate. There is a need to understand prognostic factors of survival in a broader setting to aid in tailoring treatment strategies for pts. This study aimed to identify important population-based predictors related to survival among pts diagnosed with mPDAC. Methods: Data were extracted for pts diagnosed with mPDAC between Jan 2017 and Dec 2019 from the Flatiron Health database. Predictive models for overall survival from the start of each treatment were developed using multivariable Cox proportional hazards regression. Treatment specific predictive models were generated for pts treated with first line (1L) gemcitabine + nab-paclitaxel (GNP), 1L FOLFIRINOX, 1L gemcitabine monotherapy (gem-mono), and 2L liposomal irinotecan-based regimens. The holdout method was used for cross-validation, splitting the data into 70% training / 30% validation. Age at diagnosis, sex, body mass index, smoking status, and ECOG performance score (PS) were included in all models due to clinical importance. Demographic, clinical characteristics, hematological labs, liver function tests (LFTs), and serum bilirubin levels were assessed for inclusion into the models. Uno’s concordance statistic (c-statistic) was used to assess the predictive accuracy of the models. Results: Of the 3,572 pts included in the study, 44% (n = 1,557) received 1L GNP, 27% (n = 954) received 1L FOLFIRINOX, 7% (n = 265) received gem-mono, and 22% (n = 796) received other regimens. 38% (n = 1,345) pts received 2L and of those, 17% (n = 222) received liposomal irinotecan-based regimens. Among all 1L pts, the following were included in the final model: prior surgery, white blood cell (WBC) counts, serum albumin, LFTs (ALP and ALT), serum bilirubin, and ascites (c-statistic: 0.65). The model for pts treated with GNP differed from the overall model via the addition of neutrophil counts and removal of serum bilirubin and ascites (c-statistic: 0.67). Stage at initial diagnosis was included in the model only for pts treated with 1L FOLFIRINOX (c-statistic: 0.68). Among pts treated with gem-mono the LFTs were not included in the model (c-statistic: 0.78). ALP, serum albumin, and WBC counts were important predictors of survival among pts treated with 2L liposomal irinotecan-based regimens (c-statistic: 0.70). Across all regimens the strongest predictors of survival were ECOG PS, serum albumin, and ALP. Conclusions: In one of the largest contemporary real-world studies of patients with mPDAC to date, important population predictors of survival in pts receiving systemic treatment were identified. Further validation studies are needed to understand the generalizability of these results.
Monovalent cation metabolism and cytopathic effects of poliovirus-infected HeLa cells (1981)

To better understand the significance of 22Na+ accumulation by poliovirus-infected HeLa cells (C. N. Nair, J. W. Stowers, and B. Singfield, J. Virol. 31:184, 1979), measurements of cellular Na+, K+, and Cl- contents, volume, and density were carried out at intervals after infection. In addition, the rates of 22Na+ washout from infected and control cells were determined. Starting at around 3 h postinfection, the Na+ content of infected cells increased, whereas the K+ content decreased progressively, resulting in a net loss in the monovalent cation content decreased progressively, resulting in a net loss in the monovalent cation content per cell. The loss in cellular chloride content exceeded that in monovalent cation content. The kinetics of 22Na+ washout from infected and control cells revealed the presence of an extra Na+ compartment in infected cells. A net loss in the monovalent cation activity of infected cells was indicated by the loss of cell water as reflected in a decrease in cell volume and an increase in cell density. In spite of a net loss in monovalent cation content per cell, Na+ accumulation coupled with cell shrinkage resulted in substantial increases in the concentrations of not only Na+ but also K+. The results suggested a possible role for tonicity change in the morphological lesions of poliovirus cytotoxicity.