gebhart/patrepeval huggingface dataset:
Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative breast cancers and a biomarker predicting aggressive biology (2009)

Breast carcinogenesis is a multistep process involving both genetic and epigenetic changes. Since epigenetic changes like histone modifications are potentially reversible processes, much effort has been directed toward understanding this mechanism with the goal of finding novel therapies as well as more refined diagnostic and prognostic tools in breast cancer. Lysine-specific demethylase 1 (LSD1) plays a key role in the regulation of gene expression by removing the methyl groups from methylated lysine 4 of histone H3 and lysine 9 of histone H3. LSD1 is essential for mammalian development and involved in many biological processes. Considering recent evidence that LSD1 is involved in carcinogenesis, we investigated the role of LSD1 in breast cancer. Therefore, we developed an enzyme-linked immunosorbent assay to determine LSD1 protein levels in tissue specimens of breast cancer and measured very high LSD1 levels in estrogen receptor (ER)-negative tumors. Pharmacological LSD1 inhibition resulted in growth inhibition of breast cancer cells. Knockdown of LSD1 using small interfering RNA approach induced regulation of several proliferation-associated genes like p21, ERBB2 and CCNA2. Additionally, we found that LSD1 is recruited to the promoters of these genes. In summary, our data indicate that LSD1 may provide a predictive marker for aggressive biology and a novel attractive therapeutic target for treatment of ER-negative breast cancers.
Expression of Nodal, Lefty-A, and Lefty-B in Undifferentiated Human Embryonic Stem Cells Requires Activation of Smad2/3 (2004)

Human embryonic stem cells will remain undifferentiated or undergo differentiation when grown in conditioned or non-conditioned medium, respectively. The factors and signaling events that control the maintenance of the undifferentiated state are not well characterized and their identification is of major importance. Based on the data from global expression analyses, we set out to identify genes and the signaling pathways controlling them that are regulated in the early phase of the differentiation process. This study shows that nodal and the inhibitors of Nodal signaling, lefty-A and lefty-B, are down-regulated very early upon differentiation. High expression of these genes in undifferentiated cells is maintained by activation of the transcription factor Smad2/3, downstream of the activin-linked kinases (ALK) 4/5/7. Treatment of differentiating cells with Activin A leads to activation of Smad2/3 and expression of nodal, lefty-A and lefty-B, while inhibition of ALK4/5/7 by the kinase inhibitor SB-431542 blocks activation of Smad2/3 and expression of these genes in the undifferentiated state. In addition, when cells are maintained undifferentiated by treatment with the GSK3-inhibitor, BIO, high expression of nodal, lefty-A, and lefty-B also requires activation of ALK4/5/7. Conversely, BMP signaling leading to Smad1/5/8 activation via ALK2/3/6 is blocked in undifferentiated cells and becomes activated upon differentiation. Taken together, these observations establish that Smad2/3 is activated in undifferentiated hESCs and required for the expression of genes controlling Nodal signaling. Moreover, there appears to be cross-talk between inhibition of GSK3, a hallmark of Wnt signaling and the Activin/Nodal pathway.
Serum marker KL-6/MUC1 for the diagnosis and management of interstitial pneumonitis. (1999)

Interstitial pneumonitis includes more than a hundred diseases in which alveolitis is the main manifestation of the affected lung. Symptoms such as dry cough and exertional dyspnea, fine crackles on chest auscultation, interstitial infiltrates on chest X-ray films and CT scans, respiratory function tests, and Ga-67 scintigraphy have been used for the diagnosis and the evaluation of disease activity. However, the poor prognosis of some types of interstitial pneumonitis has not been improved. We discovered a high molecular weight mucin-like antigen, designated KL-6, which is also known as MUC1. The serum level of KL-6/MUC1 was elevated in 70-100% of patients with interstitial pneumonitis, such as pulmonary fibrosis (either idiopathic or related to collagen-vascular disorders), hypersensitivity pneumonitis, sarcoidosis, and radiation pneumonitis. The levels were significantly higher in patients with active disease than in those with inactive disease. In contrast, patients with noninterstitial lung disease did not show a significant elevation of KL-6/MUC1. Furthermore, the serum KL-6/MUC1 level was found to be an early predictive marker of the therapeutic effect of high-dose corticosteroids in patients with rapidly progressing idiopathic pulmonary fibrosis. These results indicate that KL-6/MUC1 may be a useful serum marker for the diagnosis and monitoring of patients with interstitial pneumonitis.
Interictal heart rate patterns in partial seizure disorders (1993)

Epileptogenic mesial temporal damage may alter interictal autonomic patterning. Analysis of heart rate variability in 19 patients with complex partial seizures revealed cases of persistent, high-amplitude, 4 to 9 per minute fluctuations in heart rate during alert waking. This pattern was most pronounced in poor candidates for anterior temporal lobe resection (2/19). The 4 to 9 per minute heart-rate variability pattern may emerge following diffuse, extratemporal, or bilateral mesial temporal damage, which interferes with descending forebrain influences on cardiovascular regulation.
Solution of an integral equation encountered in rotation therapy (1982)

An integral equation relating the lateral absorbed dose profile of a photon beam to the resultant absorbed dose distribution during single-turn rotating-beam therapy has been set up and solved for the case of a cylindrical phantom with the axis of rotation coinciding with the axis of symmetry of the cylinder. In the first approximation the results obtained are also valid when the axis of rotation is somewhat off-centred, even in a phantom that deviates from circular symmetry, provided the rotation is performed in both clockwise and counter clockwise directions. The calculated dose profiles indicate that improved dose uniformity can be achieved using a new type of non-linear wedge-shaped filter, which can easily be designed using the derived general analytic solution to the integral equation.
Genomic clone for sandbar shark lambda light chain: generation of diversity in the absence of gene rearrangement. (1993)

While the general structure of immunoglobulin chains has remained relatively unchanged throughout evolution, the organization of the genes encoding these molecules differs substantially. To understand how the rearranging immunoglobulin system arose, it is necessary to examine living representatives of the most early vertebrate phyla. Elasmo-branches, which include the sharks, skates, and rays, are the most primitive phylogenetic class of vertebrates from which immunoglobulin DNA sequences have been obtained. In the sandbar shark (Carcharhinus plumbeus), the genes are arranged in individual clusters in which a single variable (V), joining (J), and constant (C) region gene, along with upstream regulatory elements, span a distance of approximately 4.4 kb or approximately 5.8 kb. We report the complete sequence of a genomic clone encoding sandbar shark lambda light chain. A unique finding of our study is that the V and J genes are fused in the germ line. Three additional clones have been shown by DNA sequencing to also have fused V and J genes. The four clones have complementarity-determining regions 3 of various lengths and amino acid sequence variability similar to the products of rearranged genes. Furthermore, analysis by polymerase chain reaction technology revealed an additional 26 genomic clones demonstrating fusion of the V and J segments. Therefore, VJ fusion is the prominent organizational feature of sandbar shark immunoglobulin light chain genes. This finding raises questions concerning the necessity of recombination to produce an antibody repertoire capable of reacting against a diverse array of antigens.
Performance of transport protocols over a multicasting-based architecture for Internet host mobility (2002)

IP multicasting provides a mechanism for location independent addressing and packet delivery to a group of hosts that belong to a multicast group. It also provides efficient mechanisms for hosts to join and leave multicast groups. The problem of supporting macro and micro level host mobility in the Internet involves similar issues of location independent addressing, address translation, packet forwarding and location management of mobile hosts. We have developed a new approach called MSM-IP for supporting host mobility using IP multicasting as the sole mechanism for addressing and routing packets to mobile hosts. In this paper, we present the performance of UDP and TCP over MSM-IP, and compare it with their performance over Mobile-IP. Our analysis shows that our approach is very effective in supporting seamless mobility for both handoffs and interface changes within and across networks. The performance of both UDP and TCP are better when used with MSM-IP than with Mobile-IP. We briefly explain our approach, and present performance results, and explain the results.
Gated Conditional Displacement Readout of Superconducting Qubits (2019)

We have realized a new interaction between superconducting qubits and a readout cavity that results in the displacement of a coherent state in the cavity, conditioned on the state of the qubit. This conditional state, when it reaches the cavity-following, phase-sensitive amplifier, matches its measured observable, namely, the in phase quadrature. In a setup where several qubits are coupled to the same readout resonator, we show it is possible to measure the state of a target qubit with minimal dephasing of the other qubits. Our results suggest novel directions for faster readout of superconducting qubits and implementations of bosonic quantum error-correcting codes.
Clinical significance of different serum tumor markers in gynecological malignancies. (1985)

The purpose of this study was to compare the diagnostic significance of serum tumor markers in patients with gynecological malignancies and to evaluate the usefulness of the markers in the follow-up after primary treatment. Determined were tissue polypeptide antigen (TPA), carcinoembryonic antigen (CEA), and phosphohexose isomerase (PHI). Serum samples from 200 patients with cervical cancer, 206 patients with endometrial cancer, and 254 patients with ovarian cancer were analyzed. With regard to specificity, CEA and PHI exhibited false positive rates below 10% in normal controls (N = 96). For TPA, the same result was obtained only by using 120 U/l as a cut-off level. As for sensitivity, positive rates above 50% prior to therapy were demonstrated by PHI and TPA in ovarian cancer as well as CEA in cervical cancer. All three tumor markers showed some decline in positiveness after primary therapy. In ovarian cancer the decline of PHI and TPA strongly correlates with the achievable tumor resection. During the follow-up, all markers demonstrated some discriminatory power by comparing patients with recurrent disease versus recurrence free. Especially PHI and TPA in ovarian cancer, CEA in cervical cancer, and PHI in endometrial cancer seem to be the most suitable markers.
In vivo application of RNA leads to induction of specific cytotoxic T lymphocytes and antibodies (2000)

To study the efficiency of RNA-based vaccines, RNA coding for the model antigen beta-galactosidase (beta-gal) was transcribed in vitro from a lacZ gene flanked by stabilizing Xenopus laevis beta-globin 5' and 3' sequences and was protected from RNase degradation by condensation with the polycationic peptide protamine. The liposome-encapsulated condensed RNA-peptide complex, the condensed RNA-peptide complex without liposome or naked, unprotected RNA, was injected into BALB/c (H-2(d)) mice. All preparations led to protein expression in the local tissue, activation of L(d)-restricted specific cytotoxic T lymphocytes (CTL) and production of IgG antibodies reactive against beta-gal. RNA-triggered CTL were as efficient in the lysis of lacZ-transfected target cells as CTL triggered by a lacZ-DNA eukaryotic expression vector. Immunization with RNA transcribed from a cDNA library from the beta-gal-expressing cell line P13.1 again led to beta-gal-specific CTL and IgG induction. Thus, both naked and protected RNA can be used to elicit a specific immune response in vivo, whereby the protected RNA is stable in vitro for a longer period of time. RNA vaccines can be produced in high amounts and have the same major advantages as DNA vaccines but lack the potentially harmful effect of DNA integration into the genome.
Classification And Regression Trees (2017)

The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.
Lamellar Structures in Aqueous Solutions of a Dimeric Surfactant (2000)

The effect of salt (KBr) additions on the behavior of the dimeric surfactant 12-2-12 (ethanediyl-1,2-bis(dodecyldimethylammonium bromide)) has been investigated using small-angle neutron scattering and electron microscopy. In the range of surfactant volume fraction 0.08−0.25 only wormlike micelles or lamellar structures are obtained depending on the temperature and the salt content. Two different bilayer structures are observed: one, metastable, which obeys the dilution law up to a maximum swelling corresponding to an intermicellar distance of ∼220 Å; the other at equilibrium with a constant swelling corresponding to an interlamellar distance of ∼70 Å. These results confirm the propensity of the gemini surfactants with a short spacer between the polar heads to form collapsed bilayers structured in stacks.
Reverse Curriculum Generation for Reinforcement Learning (2017)

Many relevant tasks require an agent to reach a certain state, or to manipulate objects into a desired configuration. For example, we might want a robot to align and assemble a gear onto an axle or insert and turn a key in a lock. These goal-oriented tasks present a considerable challenge for reinforcement learning, since their natural reward function is sparse and prohibitive amounts of exploration are required to reach the goal and receive some learning signal. Past approaches tackle these problems by exploiting expert demonstrations or by manually designing a task-specific reward shaping function to guide the learning agent. Instead, we propose a method to learn these tasks without requiring any prior knowledge other than obtaining a single state in which the task is achieved. The robot is trained in reverse, gradually learning to reach the goal from a set of start states increasingly far from the goal. Our method automatically generates a curriculum of start states that adapts to the agent's performance, leading to efficient training on goal-oriented tasks. We demonstrate our approach on difficult simulated navigation and fine-grained manipulation problems, not solvable by state-of-the-art reinforcement learning methods.
Look-up table (LUT) method for inverse halftoning (2001)

In this paper we propose look-up table (LUT) based methods for inverse halftoning of images. The LUT for inverse halftoning is obtained from the histogram gathered from a few sample halftone images and corresponding original images. The method is extremely fast (no filtering is required) and the PSNR and visual image quality achieved is comparable to the best methods known for inverse halftoning. The LUT inverse halftoning method does not depend on the specific properties of the halftoning method, and can be applied to any halftoning method. Then, an algorithm for template selection for LUT inverse halftoning is introduced. We demonstrate the performance of the LUT inverse halftoning algorithm on error diffused images and ordered dithered images. We also extend LUT inverse halftoning to color halftones.
Phosphorylation of MafA Is Essential for Its Transcriptional and Biological Properties (2001)

We previously described the identification of quail MafA, a novel transcription factor of the Maf bZIP (basic region leucine zipper) family, expressed in the differentiating neuroretina (NR). In the present study, we provide the first evidence that MafA is phosphorylated and that its biological properties strongly rely upon phosphorylation of serines 14 and 65, two residues located in the transcriptional activating domain within a consensus for phosphorylation by mitogen-activated protein kinases and which are conserved among Maf proteins. These residues are phosphorylated by ERK2 but not by p38, JNK, and ERK5 in vitro. However, the contribution of the MEK/ERK pathway to MafA phosphorylation in vivo appears to be moderate, implicating another kinase. The integrity of serine 14 and serine 65 residues is required for transcriptional activity, since their mutation into alanine severely impairs MafA capacity to activate transcription. Furthermore, we show that the MafA S14A/S65A mutant displays reduced capacity to induce expression of QR1, an NR-specific target of Maf proteins. Likewise, the integrity of serines 14 and 65 is essential for the MafA ability to stimulate expression of crystallin genes in NR cells and to induce NR-to-lens transdifferentiation. Thus, the MafA capacity to induce differentiation programs is dependent on its phosphorylation.
Reach out and touch someone (1993)

This article describes the author's step-by-step reconstruction of a highway accident involving a van and a downed telephone pole. Using mathematical equations and physics the author presents the physical results of the mishap.
Assessing the prediction potential of an in silico computer model of intracranial pressure dynamics* (2009)

The protocol for collecting physiologic data in subjects with severe TBI was feasible. The in silico ICP model with session-specific parameters accurately reproduced observed ICP response to changes in head-of-bed and respiration rate. We demonstrated modest success at predicting future ICP within a session and to a lesser extent between sessions.
Degradation of a Mutant Secretory Protein, α1-Antitrypsin Z, in the Endoplasmic Reticulum Requires Proteasome Activity (1996)

Degradation of proteins that are retained in the quality control apparatus of the endoplasmic reticulum (ER) has been attributed to a third proteolytic system, distinct from the lysosomal and the cytoplasmic ubiquitin-dependent proteosomal proteolytic pathways. However, several recent studies have shown that ER degradation of a mutant membrane protein, CFTRdeltaF508, is at least in part mediated from the cytoplasmic side by the 26 S proteasome. In this study, we examined the possibility that ER degradation of mutant secretory protein alpha1-antitrypsin (alpha1-AT) Z, the mutant protein associated with infantile liver disease and adult-onset emphysema of alpha1-AT deficiency, is mediated by the proteasome. The results show that a specific proteasome inhibitor, lactacystin, inhibits ER degradation of alpha1-ATZ in transfected human fibroblast cell lines and in a cell-free microsomal translocation system. Although it is relatively easy to conceptualize how a transmembrane protein like CFTRDeltaF508 might be accessible on the cytoplasmic aspect of the ER membrane for ubiquitination and degradation by the proteasome, it is more difficult to conceptualize how this might occur for a luminal polypeptide. The results show that, once within the lumen of the ER, alpha1-ATZ interacts with the transmembrane molecular chaperone calnexin and specifically induces the polyubiquitination of calnexin. The results, therefore, provide evidence that the proteasome, from its cytoplasmic localization, induces the degradation of the luminal alpha1-ATZ molecule by first attacking the cytoplasmic tail of calnexin molecules that are associated with alpha1-ATZ.
Very small oxide-confined vertical-cavity surface-emitting lasers with a bulk active region (1997)

Data are presented characterizing very small oxide aperture vertical-cavity surface-emitting lasers with a 0.5-μm-thick bulk GaAs active region. The transverse far field is independent of the aperture size for diameters ⩽3 μm, although threshold reduction occurs with reducing aperture size down to ∼0.5 μm diam. Threshold reduction is attributed to improved overlap between the optical mode and gain profile. The large signal temporal response is characterized using optical gain switching.
Room‐Temperature, Hydrochloride‐Assisted, One‐Step Deposition for Highly Efficient and Air‐Stable Perovskite Solar Cells (2016)

Uniform perovskite films are achieved by HCl-assisted one-step spin-coating at room temperature. By this method, a highest power conversion efficiency of 17.9% is obtained for perovskite solar cells (PSCs). The devices retain ≈95% of their original efficiency after storage in air for two months. The highest efficiency obtained for large-area PSCs (0.86 cm<sup>2</sup> ) is 15.7%.
Fluorodeoxyglucose uptake in human cancer cell lines is increased by hypoxia. (1995)

Hypoxia increases cellular uptake of FDG in two different malignant human cell lines. Increased glucose transport, in part due to increased membrane expression of the Glut-1 glucose transporter, contributes to this phenomenon. Increased FDG uptake in tumors visualized during PET imaging may be partly reflective of tumor hypoxia.
Thermal Pathways for the Transfer of Amines, Including Nicotine, to the Gas Phase and Aerosols (2001)

Two pathways are proposed to explain the thermal transfer and/or pyrolysis of amines, a major class of plant constituents, to smoke.A crucial distinction is made based on the relative ease of evaporation of the amines compared to the ease of their pyrolytic decomposition.The temperatures required to transfer nicotine to the gas phase from nicotine and nicotine carboxylic acid salts, such as are found in tobacco, are lower than the decomposition temperatures of the nicotine ring system.Thermal gradient studies may better mimic the balance between evaporation and pyrolytic destruction of tobacco volatiles and semi-volatiles during smoking, as such thermolyses are performed by heating the substrate from ambient temperature to a higher temperature under a flow of gas.
A Simple Subthreshold CMOS Voltage Reference Circuit With Channel- Length Modulation Compensation (2006)

This brief presents a simple reference circuit with channel-length modulation compensation to generate a reference voltage of 221 mV using subthreshold of MOSFETs at supply voltage of 0.85 V with power consumption of 3.3 muW at room temperature using TSMC 0.18-mum technology. The proposed circuit occupied in less than 0.0238 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sup> achieves the reference voltage variation of 2 mV/V for supply voltage from 0.9 to 2.5V and about 6 mV of temperature variation in the range from -20degC to 120 degC. The agreement of simulation and measurement data is demonstrated