gebhart/patrepeval huggingface dataset:
Susceptibility of mitogen-activated protein kinase kinase family members to proteolysis by anthrax lethal factor (2000)

The lethal factor (LF) produced by toxigenic strains of Bacillus anthracis is a Zn(2+)-endopeptidase that cleaves the mitogen-activated protein kinase kinases (MAPKKs) MEK1, MEK2 and MKK3. Using genetic and biochemical approaches, we have extended the study of LF proteolytic specificity to all known MAPKK family members and found that LF also cleaves MKK4, MKK6 and MKK7, but not MEK5. The peptide bonds hydrolysed by LF within all MAPKKs were identified. Cleavage invariably occurs within the N-terminal proline-rich region preceding the kinase domain, thus disrupting a sequence involved in directing specific protein-protein interactions necessary for the assembly of signalling complexes. Alignment of the sequences flanking the site of cleavage reveals the occurrence of some consensus motifs: position P2 and P1' are occupied by hydrophobic residues and at least one basic residue is present between P4 and P7. The implications of these findings for the biochemical activity and functional specificity of LF are discussed.
Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn (2010)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Circulating cell-free fetal DNA in maternal serum appears to originate from cyto- and syncytio-trophoblastic cells. Case report (2004)

Circulating cell-free fetal DNA in maternal serum offers an early and non-invasive method for prenatal diagnosis, but the origin of this DNA is still unknown. We report the absence of the SRY gene in maternal serum of a pregnant woman despite male genitalia at ultrasound. The karyotype was 45,X after direct trophoblast analysis and 45,X/46,Xidic(Yp) after culture and in all fetal tissues studied. Due to the absence of the SRY sequence in maternal blood and in the cytotrophoblast, we presume that free fetal DNA in this case originates from trophoblastic cells. As the case presented here is exceptional, it only has a minor impact on the accuracy of fetal sex determination by maternal serum analysis, but highlights the importance of and the necessity for the complementary ultrasonographic control.
Epidermal Growth Factor Receptor Down-Regulation Triggers Human Myoblast Differentiation (2013)

Initiation of human myoblast differentiation requires a negative shift (hyperpolarization) of the resting potential of myoblasts that depends on the activation of Kir2.1 potassium channels. These channels are regulated by a tyrosine phosphorylation. Using human primary myoblast culture, we investigated a possible role of various receptor tyrosine kinases in the induction of the differentiation process. We found that Epidermal Growth Factor Receptor (EGFR) is a key regulator of myoblast differentiation. EGFR activity is down-regulated during early human myoblast differentiation, and this event is required for normal differentiation to take place. Furthermore, EGFR silencing in proliferation conditions was able to trigger the differentiation program. This occurs through an increase of Kir2.1 channel activity that, via a rise of store-operated Ca(2+) entry, leads to the expression of myogenic transcription factors and muscle specific proteins (Myogenin, Myocyte Enhancer Factor 2 (MEF2), Myosin Heavy Chain (MyHC)). Finally, blocking myoblast cell cycle in proliferation conditions using a cdk4 inhibitor greatly decreased myoblast proliferation but was not able, on its own, to promote myoblast differentiation. Taken together, these results show that EGFR down-regulation is an early event that is required for the induction of myoblast differentiation.
Monocyte-conditioned medium, interleukin-1, and tumor necrosis factor stimulate the acute phase response in human hepatoma cells in vitro. (1986)

Human hepatoma cells mimic the acute phase response after treatment with monocyte-conditioned medium. Levels of secreted fibrinogen, alpha-1 acid glycoprotein, C-reactive protein, haptoglobin, and the third component of complement were elevated compared with control levels after 48 h of incubation with conditioned supernatant medium from an enriched fraction of normal peripheral monocytes. Albumin levels declined and alpha-1 antitrypsin remained unchanged. Levels of specific mRNA were measured by hybridization to slot blots and Northern blots and changed in correspondence with protein alterations. Interleukin-1 and tumor necrosis factor stimulated the third component of complement, but did not elevate any other member of the acute phase group and were therefore only partially active in this system. The identification of an in vitro model of the human acute phase response will permit analysis of the molecular basis for coordinate regulation of this group of facultative genes.
Stability of High-Density One-Dimensional Excitons in Carbon Nanotubes under High Laser Excitation (2005)

Through ultrafast pump-probe spectroscopy with intense pump pulses and a wide continuum probe, we show that interband exciton peaks in single-walled carbon nanotubes (SWNTs) are extremely stable under high laser excitations. Estimates of the initial densities of excitons from the excitation conditions, combined with recent theoretical calculations of exciton Bohr radii for SWNTs, suggest that their positions do not change at all even near the Mott density. In addition, we found that the presence of lowest-subband excitons broadens all absorption peaks, including those in the second-subband range, which provides a consistent explanation for the complex spectral dependence of pump-probe signals reported for SWNTs.
uPAR isoform 2 forms a dimer and induces severe kidney disease in mice (2019)

Soluble urokinase plasminogen activator receptor (suPAR) is an immune-derived circulating signaling molecule that has been implicated in chronic kidney disease, such as focal segmental glomerulosclerosis (FSGS). Typically, native uPAR (isoform 1) translates to a 3-domain protein capable of binding and activating integrins, yet the function of additional isoforms generated by alternative splicing is unknown. Here, we characterized mouse uPAR isoform 2 (msuPAR2), encoding domain I and nearly one-half of domain II, as a dimer in solution, as revealed by 3D electron microscopy structural analysis. In vivo, msuPAR2 transgenic mice exhibited signs of severe renal disease characteristic of FSGS with proteinuria, loss of kidney function, and glomerulosclerosis. Sequencing of the glomerular RNAs from msuPAR2-Tg mice revealed a differentially expressed gene signature that includes upregulation of the suPAR receptor Itgb3, encoding β3 integrin. Crossing msuPAR2-transgenic mice with 3 different integrin β3 deficiency models rescued msuPAR2-mediated kidney function. Further analyses indicated a central role for β3 integrin and c-Src in msuPAR2 signaling and in human FSGS kidney biopsies. Administration of Src inhibitors reduced proteinuria in msuPAR2-transgenic mice. In conclusion, msuPAR2 may play an important role in certain forms of scarring kidney disease.
Adenosine monophosphate-activated protein kinase mediates the protective effects of ischemic preconditioning on hepatic ischemia-reperfusion injury in the rat (2001)

Hepatic ischemia-reperfusion (I/R) injury associated with liver transplantation and hepatic resections are an unresolved problem in the clinical practice. Preconditioning is known to preserve energy metabolism in liver during sustained ischemia, but the molecular mechanisms underlying this effect are still unclear. Different metabolic signals, including adenosine monophosphate (AMP) and nitric oxide (NO), have been implicated in preconditioning. AMP-activated protein kinase (AMPK) protects cells by acting as a low-fuel warning system, becoming switched on by adenosine triphosphate (ATP) depletion. NO synthesis is induced by AMPK in the heart during ischemia. The aim of this study was to investigate: 1) whether preconditioning induces AMPK activation; and 2) if AMPK activation leads to ATP preservation and reduced lactate accumulation during prolonged ischemia and its relationship with NO. Preconditioning activated AMPK and concomitantly reduced ATP degradation, lactate accumulation, and hepatic injury. The administration of an AMPK activator, AICAR, before ischemia simulated the benefits of preconditioning on energy metabolism and hepatic injury. The inhibition of AMPK abolished the protective effects of preconditioning. The effect of AMPK on energy metabolism was independent of NO because the inhibition of NO synthesis in the preconditioned group and the administration of the NO donor before ischemia, or to the preconditioned group with previous inhibition of AMPK, had no effect on energy metabolism. Both preconditioning and AICAR pretreatment, through AMPK activation, may be useful surgical and pharmacologic strategies aimed at reducing hepatic I/R injury.
Unsupervised Learning of Generative and Discriminative Weights Encoding Elementary Image Components in a Predictive Coding Model of Cortical Function (2011)

A method is presented for learning the reciprocal feedforward and feedback connections required by the predictive coding model of cortical function. When this method is used, feedforward and feedback connections are learned simultaneously and independently in a biologically plausible manner. The performance of the proposed algorithm is evaluated by applying it to learning the elementary components of artificial and natural images. For artificial images, the bars problem is employed, and the proposed algorithm is shown to produce state-of-the-art performance on this task. For natural images, components resembling Gabor functions are learned in the first processing stage, and neurons responsive to corners are learned in the second processing stage. The properties of these learned representations are in good agreement with neurophysiological data from V1 and V2. The proposed algorithm demonstrates for the first time that a single computational theory can explain the formation of cortical RFs and also the response properties of cortical neurons once those RFs have been learned.
Low-Dose Combined Therapy with Fluvastatin and Cholestyramine in Hyperlipidemic Patients (1994)

Low-density lipoprotein cholesterol reductions of about 25% to 30% can be achieved with low-dose combination therapy with fluvastatin and cholestyramine. The addition of low-dose resin appears to produce greater overall cholesterol reduction than does a simple doubling of the fluvastatin dosage. The low-dose combination treatment was highly successful in achieving the goals of the National Cholesterol Education Program guidelines.
Plasma etch removal of poly(methyl methacrylate) in block copolymer lithography (2008)

Polystyrene-block-poly(methyl methacrylate), (PS-b-PMMA) diblock copolymer is a promising lithography alternative for nanometer scale features. The two components segregate into nanoscale domains when the polymer solution is spun on to form a thin film and annealed above the glass transition temperatures of both components. Preferential removal of PMMA domains through plasma etching to leave behind a PS mask for subsequent etching of underlying layers is the focus of this work. The quality of the PS mask is characterized by the thickness and lateral dimension of the PS structures after removal of the PMMA, as well as the smoothness of their surfaces. The effects of different plasma chemistries including O2, Ar/O2, Ar, CF4, and CHF3/O2 on etch selectivity and surface/sidewall roughness for PS and PMMA have been characterized. Ar/O2 produced the overall best results for the range of conditions studied.
Alpha Interferon for Induction of Remission in Hairy-Cell Leukemia (1984)

We treated seven patients who had progressive hairy-cell leukemia with daily doses of 3 million units of partially pure alpha (leukocyte) interferon by the intramuscular route. Three patients had a complete remission, and four had a partial remission, according to strict criteria for a response. After treatment, bone-marrow aspirates showed an absence of leukemia cells in three patients and 5 per cent or fewer in three others. Normalization of subnormal peripheral-blood values occurred in six of six patients with anemia, in seven of seven with granulocytopenia, and in four of four with thrombocytopenia. Remissions have been maintained for over 6 to over 10 months. Alpha interferon appears to be highly effective in patients with hairy-cell leukemia.
The Mediation Formula: A Guide to the Assessment of Causal Pathways in Nonlinear Models (2012)

This chapter contains sections titled: Mediation: Direct and indirect effects The mediation formula: A simple solution to a thorny problem Relation to other methods Conclusions Acknowledgments References
DNA sequencing of maternal plasma to identify Down syndrome and other trisomies in multiple gestations (2012)

Although study size is limited, the underlying biology combined with the present data provide evidence that MPSS testing can be reliably used as a secondary screening test for Down syndrome in women with high-risk twin gestations.
On the optimal solutions of beamformer assisted acoustic echo cancellers (2011)

Acoustic echo cancellation constitutes a major challenge for full-duplex communication and human-machine speech interaction. Beamforming is a well-known technique for suppression of local interferers, including acoustic echoes. Those techniques can be combined to jointly achieve better echo cancellation at an additional computational cost. Experimental results available in the literature show significant increase in echo cancellation performance when assisted by a beamformer. Different implementation schemes have been proposed. Performance comparisons of these solutions have been mostly experimental, which limits the generalization of the results. This work compares the optimal solutions provided by the original cascaded BF-AEC structure and by the alternative scheme that jointly optimizes the beamformer and the acoustic echo canceler coefficients.
Preoperative Chemotherapy: Updates of National Surgical Adjuvant Breast and Bowel Project Protocols B-18 and B-27 (2008)

B-18 and B-27 demonstrate that preoperative therapy is equivalent to adjuvant therapy. B-27 also showed that the addition of preoperative taxanes to AC improves response.
Bacterial Spore Detection and Determination by Use of Terbium Dipicolinate Photoluminescence (1997)

A new method to detect bacterial endospores and determine their concentration was demonstrated by the addition of a solution of terbium chloride to a suspension of bacterial endospores. The terbium chloride reacted with the calcium dipicolinate in the spore case to form terbium(III) dipicolinate anion. Solid particles, including residual bacterial particles, were removed by filtering. The photoluminescence from the solution was measured as a function of excitation wavelength, emission wavelength, and bacterial endospore concentration. The photoluminescence from terbium(III) dipicolinate anion in the solution was easily identified.
S100A11, A Putative Tumor Suppressor Gene, Is Overexpressed in Pancreatic Carcinogenesis (2006)

The present data suggest that expression of S100A11, a putative tumor suppressor gene, is increased in the early stage of pancreatic carcinogenesis and decreased during subsequent progression to cancer. Analysis of the S100A11 level in pancreatic juice may be an effective tool for screening of patients with high-risk lesions that could progress to pancreatic cancer or detecting early-stage pancreatic cancer.
Prognostic significance of NQO1 expression in intrahepatic cholangiocarcinoma. (2011)

This study aimed to evaluate the association between the immunohistochemical expression of NAD(P) H:quinone oxidoreductase-1 (NQO1) and nuclear factor erythroid 2-related factor 2 (Nrf2) in resected specimens of intrahepatic cholangiocarcinoma (ICC) and to elucidate the prognostic value of NQO1 and Nrf2 expression. A retrospective analysis was conducted of 34 consecutive patients who underwent surgical resection for ICC. Immunohistochemistry of the resected specimens was conducted using each of the following primary monoclonal antibodies against NQO1 and Nrf2. Of the 34 patients, 23 were classified as having tumors with NQO1-positive expression and 11 had tumors with loss of NQO1 expression, whereas 22 patients had tumors with Nrf2-positive expression and 12 had tumors with loss of Nrf2 expression. NQO1 expression showed a positive association with Nrf2 expression (p=0.005). Loss of NQO1 expression was more frequent in tumor specimens that were moderately or poorly differentiated (11/26; 42%) than in well-differentiated tumors (0/8; 0%; p=0.034). Post-resection survival was significantly worse in patients with tumors with loss of NQO1 expression than in patients with NQO1-positive tumors (cumulative 5 -year survival rate of 0% and 51%, respectively; p=0.005). Nrf2 expression was not associated with survival after resection (p=0.287). The Cox proportional hazards regression analysis revealed that lymph node involvement (p<0.001) and loss of NQO1 expression (p<0.001) had an independent adverse effect on survival. Loss of NQO1 expression reflects dedifferentiation and thus indicates a poor prognosis for patients undergoing resection for ICC.
Robust radial basis function neural networks (1999)

Function approximation has been found in many applications. The radial basis function (RBF) network is one approach which has shown a great promise in this sort of problems because of its faster learning capacity. A traditional RBF network takes Gaussian functions as its basis functions and adopts the least-squares criterion as the objective function, However, it still suffers from two major problems. First, it is difficult to use Gaussian functions to approximate constant values. If a function has nearly constant values in some intervals, the RBF network will be found inefficient in approximating these values. Second, when the training patterns incur a large error, the network will interpolate these training patterns incorrectly. In order to cope with these problems, an RBF network is proposed in this paper which is based on sequences of sigmoidal functions and a robust objective function. The former replaces the Gaussian functions as the basis function of the network so that constant-valued functions can be approximated accurately by an RBF network, while the latter is used to restrain the influence of large errors. Compared with traditional RBF networks, the proposed network demonstrates the following advantages: (1) better capability of approximation to underlying functions; (2) faster learning speed; (3) better size of network; (4) high robustness to outliers.
High-resolution optical coherence tomographic imaging using a mode-locked Ti:Al_2O_3 laser source (1995)

A Kerr-lens mode-locked Ti:Al(2)O(3) oscillator, optimized for minimal coherence length, is demonstrated as a high-power source for high-resolution optical coherence tomographic imaging. Dispersion compensation and heterodyne noise rejection are demonstrated to yield in situ images of biological tissues with 3.7-mum resolution and 93-dB dynamic range.
Template-directed synthesis of donor/acceptor [2]catenanes and [2]rotaxanes (2008)

Abstract The synthesis of mechanically interlocked molecular compounds has advanced by leaps and bounds since the early days of statistical methods and covalent-directing strategies. Template-directed synthesis has emerged as the method of choice for the construction of increasingly complex and functional [2]catenanes and [2]rotaxanes. In particular, mechanically interlocked molecules employing π-donating and π-accepting recognition units have been produced with remarkable efficiencies and show great promise in technologies as diverse as molecular electronics and drug delivery.
Digital image forensics (2009)

The article explains how photo-response nonuniformity (PRNU) of imaging sensors can be used for a variety of important digital forensic tasks, such as device identification, device linking, recovery of processing history, and detection of digital forgeries. The PRNU is an intrinsic property of all digital imaging sensors due to slight variations among individual pixels in their ability to convert photons to electrons. Consequently, every sensor casts a weak noise-like pattern onto every image it takes. This pattern, which plays the role of a sensor fingerprint, is essentially an unintentional stochastic spread-spectrum watermark that survives processing, such as lossy compression or filtering. This tutorial explains how this fingerprint can be estimated from images taken by the camera and later detected in a given image to establish image origin and integrity. Various forensic tasks are formulated as a two-channel hypothesis testing problem approached using the generalized likelihood ratio test. The performance of the introduced forensic methods is briefly illustrated on examples to give the reader a sense of the performance.
Selective blockade of B7‐H3 enhances antitumour immune activity by reducing immature myeloid cells in head and neck squamous cell carcinoma (2017)

Immature myeloid cells including myeloid-derived suppressor cells (MDSCs) and tumour-associated macrophages (TAMs) promote tumour growth and metastasis by facilitating tumour transformation and angiogenesis, as well as by suppressing antitumour effector immune responses. Therefore, strategies designed to reduce MDSCs and TAMs accumulation and their activities are potentially valuable therapeutic goals. In this study, we show that negative immune checkpoint molecule B7-H3 is significantly overexpressed in human head and neck squamous cell carcinoma (HNSCC) specimen as compared with normal oral mucosa. Using immunocompetent transgenic HNSCC models, we observed that targeting inhibition of B7-H3 reduced tumour size. Flow cytometry analysis revealed that targeting inhibition of B7-H3 increases antitumour immune response by decreasing immunosuppressive cells and promoting cytotoxic T cell activation in both tumour microenvironment and macroenvironment. Our study provides direct in vivo evidence for a rationale for B7-H3 blockade as a future therapeutic strategy to treat patients with HNSCC.