gebhart/patrepeval huggingface dataset:
Cell Death Induced in a Murine Mastocytoma by 42–47°C Heatingin Vitro: Evidence that the Form of Death Changes from Apoptosis to Necrosis Above a Critical Heat Load (1990)

The pathogenesis of heat-induced cell death is controversial. Categorizing the death occurring after various heat loads as either apoptosis or necrosis might help to elucidate this problem, since it has been shown that these two processes differ in their mode of initiation as well as in their morphological and biochemical features. Log-phase cultures of mastocytoma P-815 x 2.1 were heated at temperatures ranging from 42 to 47 degrees C for 30 min. After 42 degrees C heating a slight increase in apoptosis was observed morphologically. However, after heating at 43, 43.5 and 44 degrees C, there was marked enhancement of apoptosis, and electrophoresis of DNA showed characteristic internucleosomal cleavage. With heating at 45 degrees C both apoptosis and necrosis were enhanced, whereas at 46 and 47 degrees C only necrosis was produced. DNA extracted from the 46 and 47 degrees C cultures showed virtually no degradation, which contrasts with the random DNA breakdown observed in necrosis produced by other types of injury; lysosomal enzymes released during heat-induced necrosis may be inactivated at the higher temperatures. It is suggested that apoptosis following heating may be triggered either by a limited increase in cytosolic calcium levels resulting from mild membrane changes or by DNA damage. Necrosis, on the other hand, is likely to be a consequence of severe membrane disruption.
Polymorphisms in the large subunit of human RNA polymerase II as target for allele-specific inhibition (2000)

The lack of specificity of cancer treatment causes damage to normal cells as well, which limits the therapeutic range. To circumvent this problem one would need to use an absolute difference between normal cells and cancer cells as therapeutic target. Such a difference exists in the genome of all individuals suffering from a tumor that is characterized by loss of genetic material [loss of heterozygosity (LOH)]. Due to LOH, the tumor is hemizygous for a number of genes, whereas the normal cells of the individual are heterozygous for these genes. Theoretically, polymorphic sites in these genes can be utilized to selectively target the cancer cells with an antisense oligonucleotide, provided that it can discriminate the alleles and inhibit gene expression. Furthermore, the targeted gene should be essential for cell survival, and 50% gene expression sufficient for the cell to survive. This will allow selective killing of cancer cells without concomitant toxicity to normal cells. As an initial step in the experimental test of this putative selective cancer cell therapy, we have developed a set of antisense phosphorothioate oligonucleotides which can discriminate the two alleles of a polymorphic site in the gene encoding the large subunit of RNA polymerase II. Our data show that the exact position of the antisense oligonucleotide on the mRNA is of essential importance for the oligo-nucleotide to be an effective inhibitor of gene expression. Shifting the oligonucleotide position only a few bases along the mRNA sequence will completely abolish the inhibitory activity of the antisense oligonucleotide. Reducing the length of the oligonucleotides to 16 bases increases the allele specificity. This study shows that it is possible to design oligonucleotides that selectively target the matched allele, whereas the expression level of the mismatched allele, that differs by one nucleotide, is only slightly affected.
Progressive Mining of Transition Dynamics for Autonomous Control (2012)

Autonomous agents are emerging in diverse areas and many rely on reinforcement learning (RL) to learn optimal control policies by acting in the environment. This form of learning generates large amounts of transition dynamics data, which can be mined to improve the agent's understanding of the environment. There could be many uses for this data, here we focus on mining it to identify a relevant feature subspace. This is vital since RL performs poorly in high-dimensional spaces, such as those that autonomous agents would commonly face in real-world problems. This paper demonstrates the necessity and feasibility of integrating data mining into the learning process while an agent is learning, enabling it to learn to act by both acting and understanding. Doing so requires overcoming challenges regarding data quantity and quality, and difficulty measuring feature relevance with respect to the control policy. We propose the progressive mining framework to address these challenges by relying on cyclic interaction between data mining and RL. We show that a feature selection algorithm developed under this framework, PROFESS, can improve RL scalability better than a competing approach.
Blockade of Tim-3 binding to phosphatidylserine and CEACAM1 is a shared feature of anti-Tim-3 antibodies that have functional efficacy (2017)

Both <i>in vivo</i> data in preclinical cancer models and <i>in vitro</i> data with T cells from patients with advanced cancer support a role for Tim-3 blockade in promoting effective anti-tumor immunity. Consequently, there is considerable interest in the clinical development of antibody-based therapeutics that target Tim-3 for cancer immunotherapy. A challenge to this clinical development is the fact that several ligands for Tim-3 have been identified: galectin-9, phosphatidylserine, HMGB1, and most recently, CEACAM1. These observations raise the important question of which of these multiple receptor:ligand relationships must be blocked by an anti-Tim-3 antibody in order to achieve therapeutic efficacy. Here, we have examined the properties of anti-murine and anti-human Tim-3 antibodies that have shown functional efficacy and find that all antibodies bind to Tim-3 in a manner that interferes with Tim-3 binding to both phosphatidylserine and CEACAM1. Our data have implications for the understanding of Tim-3 biology and for the screening of anti-Tim-3 antibody candidates that will have functional properties <i>in vivo</i>.
Reversible chromosome condensation induced in Drosophila embryos by anoxia: visualization of interphase nuclear organization. (1985)

We have studied the morphology of nuclei in Drosophila embryos during the syncytial blastoderm stages. Nuclei in living embryos were viewed with differential interference-contrast optics; in addition, both isolated nuclei and fixed preparations of whole embryos were examined after staining with a DNA-specific fluorescent dye. We find that: (a) The nuclear volumes increase dramatically during interphase and then decrease during prophase of each nuclear cycle, with the magnitude of the nuclear volume increase being greatest for those cycles with the shortest interphase. (b) Oxygen deprivation of embryos produces a rapid developmental arrest that is reversible upon reaeration. During this arrest, interphase chromosomes condense against the nuclear envelope and the nuclear volumes increase dramatically. In these nuclei, individual chromosomes are clearly visible, and each condensed chromosome can be seen to adhere along its entire length to the inner surface of the swollen nuclear envelope, leaving the lumen of the nucleus devoid of DNA. (c) In each interphase nucleus the chromosomes are oriented in the "telophase configuration," with all centromeres and all telomeres at opposite poles of the nucleus; all nuclei at the embryo periphery (with the exception of the pole cell nuclei) are oriented with their centromeric poles pointing to the embryo exterior.
Polymerization of 1,3‐dienes with neodymium catalysts (1998)

Abstract Neodymium catalysts are typical for the cis polymerization of 1,3‐dienes. The systems prepared from a neodymium‐carboxylate, a chlorine donor and A1( i ‐C 4 H 9 ) 3 are characterized by a low efficiency, only ca. 6% of the neodymium being active in the catalysis. Much more active systems are obtained using allyl derivatives of neodymium in combination with aluminoxanes, in particular with methylaluminoxane (MAO). These systems have the characteristics of a single site catalyst. Evidence suggesting an ionic structure for the catalytic species is reported. Terminally substituted butadienes give polymers with a cis‐1,4 isotactic structure, with the exception of (E, E)‐2,4‐hexadiene, which gives trans‐1,4 polymers. An interpretation is reported.
Cellular mechanisms of redox cell signalling: role of cysteine modification in controlling antioxidant defences in response to electrophilic lipid oxidation products (2004)

The molecular mechanisms through which oxidized lipids and their electrophilic decomposition products mediate redox cell signalling is not well understood and may involve direct modification of signal-transduction proteins or the secondary production of reactive oxygen or nitrogen species in the cell. Critical in the adaptation of cells to oxidative stress, including exposure to subtoxic concentrations of oxidized lipids, is the transcriptional regulation of antioxidant enzymes, many of which are controlled by antioxidant-responsive elements (AREs), also known as electrophile-responsive elements. The central regulator of the ARE response is the transcription factor Nrf2 (NF-E2-related factor 2), which on stimulation dissociates from its cytoplasmic inhibitor Keap1, translocates to the nucleus and transactivates ARE-dependent genes. We hypothesized that electrophilic lipids are capable of activating ARE through thiol modification of Keap1 and we have tested this concept in an intact cell system using induction of glutathione synthesis by the cyclopentenone prostaglandin, 15-deoxy-Delta12,14-prostaglandin J2. On exposure to 15-deoxy-Delta12,14-prostaglandin J2, the dissociation of Nrf2 from Keap1 occurred and this was dependent on the modification of thiols in Keap1. This mechanism appears to encompass other electrophilic lipids, since 15-A(2t)-isoprostane and the lipid aldehyde 4-hydroxynonenal were also shown to modify Keap1 and activate ARE. We propose that activation of ARE through this mechanism will have a major impact on inflammatory situations such as atherosclerosis, in which both enzymic as well as non-enzymic formation of electrophilic lipid oxidation products are increased.
Bromodomain-Containing Protein 4: A Dynamic Regulator of Breast Cancer Metastasis through Modulation of the Extracellular Matrix (2011)

Metastasis is an extremely complex process that accounts for most cancer-related deaths. Malignant primary tumors can be removed surgically, but the cells that migrate, invade, and proliferate at distant organs are often the cells that prove most difficult to target therapeutically. There is growing evidence that host factors outside of the primary tumors are of major importance in the development of metastasis. Recently, we have shown that the bromodomain-containing protein 4 or bromodomain 4 (Brd4) functions as an inherited susceptibility gene for breast cancer progression and metastasis. In this paper, we will discuss that host genetic background on which a tumor arises can significantly alter the biology of the subsequent metastatic disease, and we will focus on the role of Brd4 in regulating metastasis susceptibility.
Organization of RNA transcripts from a vaccinia virus early gene cluster (1984)

The detailed organization of the RNAs transcribed from an early gene cluster encoded by vaccinia virus has been determined from the information derived from several complementary techniques. These include hybrid selection coupled with cell-free translation to locate DNA sequences complementary to mRNAs encoding specific polypeptides; RNA filter hybridization to size and locate on the DNA mature RNAs as well as higher-molecular-weight RNAs; S1 nuclease mapping to precisely locate the 5' and 3' ends of the RNAs; S1 nuclease mapping to precisely locate the 5' and 3' ends of the RNAs; and fractionation of hybrid-selected mRNAs in an agarose gel containing methyl mercury hydroxide followed by the cell-free translation of these mRNAs to definitively ascertain the size of the mRNA encoding each polypeptide. The early gene cluster is located between 21 and 26 kilobases from the left end of the vaccinia virus genome and is encoded by a 5.0-kilobase EcoRI fragment which spans the HindIII-N, -M, and -K fragments. Transcribed towards the left terminus are four mature mRNAs, 1,450, 950, 780, and 400 nucleotides in size, encoding polypeptides of 55, 30, 20, and 10 kilodaltons, respectively. These mRNAs are colinear with the DNA template and are closely spaced such that the 5' terminus of one mRNA is within 50 base pairs of the 3' terminus of the adjacent RNA. In addition to the mature size mRNAs, there are higher-molecular-weight RNAs, 5,000, 3,300, 2,350, 2,300, 1,800, 1,700, and 1,350 nucleotides in size. The 5' and 3' termini of the high-molecular-weight RNAs are coterminal with the 5' and 3' termini of the mature size mRNA. The implications of this arrangement and the biogenesis of these early mRNAs are discussed.
Pilot Contamination and Precoding in Multi-Cell TDD Systems (2011)

This paper considers a multi-cell multiple antenna system with precoding used at the base stations for downlink transmission. Channel state information (CSI) is essential for precoding at the base stations. An effective technique for obtaining this CSI is time-division duplex (TDD) operation where uplink training in conjunction with reciprocity simultaneously provides the base stations with downlink as well as uplink channel estimates. This paper mathematically characterizes the impact that uplink training has on the performance of such multi-cell multiple antenna systems. When non-orthogonal training sequences are used for uplink training, the paper shows that the precoding matrix used by the base station in one cell becomes corrupted by the channel between that base station and the users in other cells in an undesirable manner. This paper analyzes this fundamental problem of pilot contamination in multi-cell systems. Furthermore, it develops a new multi-cell MMSE-based precoding method that mitigates this problem. In addition to being linear, this precoding method has a simple closed-form expression that results from an intuitive optimization. Numerical results show significant performance gains compared to certain popular single-cell precoding methods.
Dynamic application composition: customizing the behavior of an active space (2004)

The proliferation of wireless networks, hand-held PCs, touch panels, large flat displays, sensors, and embedded devices is transforming traditional habitats and living spaces into ubiquitous computing environments, or active spaces. We envision a middleware software infrastructure that abstracts the heterogeneity of these environments and transforms them into programmable environments. This middleware infrastructure provides support to manage the resources contained in an active space (low-level functionality), support to develop applications (application-level functionality), and support to define interaction rules among applications (active space-level functionality). In this paper, we present a mechanism called "application bridge" that implements active space-level functionality. Application bridges provide a simple, yet effective, mechanism to define dynamic application composition interaction rules that confer the active space a specific behavior based on a number of parameters, including context, application status, and user actions.
Reverse water-filling in predictive encoding of speech (2003)

Reverse water-filling suggests that, at low bit rates, the synthesis filter for predictive encoding should differ from the model filter of the signal to be encoded. However, reverse water-filling follows from optimum encoding and stationary Gaussian assumptions. By means of simple experiments, we show that reverse water-filling applies to predictive encoding of speech. For a vector analysis-by-synthesis encoding based on a first order autoregressive signal model, the use of a synthesis filter derived from reverse water-filling resulted in consistently improved segmental SNR measures.
Environmental and occupational disorders Lipopolysaccharide augments IgG and IgE responses of mice to the latex allergen Hev b 5 (1998)

Background: LPS is a common contaminant in the health care environment and in latex examination gloves. Objective: We sought to investigate the role of LPS in enhancing the immune responses of mice to inhaled latex allergen. Methods: As our model allergen, we used a fusion protein containing the potent latex allergen Hev b 5. BALB/c mice were lightly anesthetized and given repeated intranasal doses of saline, LPS, and/or Hev b 5. The doses were given in 2 courses separated by a 6-week period, with the first course consisting of 6 doses and the second consisting of 3 doses. Results: After the first set of immunizations, mice given Hev b 5 alone had no detectable IgG1 or IgE responses to Hev b 5, whereas mice given the antigen along with LPS had significant responses (IgG1, 0.73 U ± 0.05; IgE, 0.88 U ± 0.2). No enhancement of specific IgG2a was observed. A stimulatory effect of LPS on all 3 immunoglobulin types was apparent after the second course. Lymphocytes from mice immunized with LPS and Hev b 5 had increased proliferation to Hev b 5 and its fusion partner. Conclusions: LPS may be an important immunoadjuvant for the development of allergic reactions to latex protein allergens. (J Allergy Clin Immunol 199;102:977-83.)
Apoptosis and Cancer Therapy (2006)

Apoptosis and cancer therapy , Apoptosis and cancer therapy , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
The Clinical Management of Neuropathic Pain (2006)

Chronic neuropathic pain as a result of injury to the central or peripheral nervous system is common in clinical practice, and is especially predominant in the elderly. The present review summarizes the epidemiology, clinical features, pathophysiology, differential diagnosis and management of neuropathic pain and specifically details an evidence‐based approach to the pharmacological treatment of this disabling condition. Preventive strategies and novel treatment approaches are required to improve the management of neuropathic pain.
Immunization with synthetic peptides containing epitopes of the class 1 outer-membrane protein of Neisseria meningitidis: production of bactericidal antibodies on immunization with a cyclic peptide (1993)

The class 1 outer-membrane protein of Neisseria meningitidis is the target for subtype-specific, bactericidal monoclonal antibodies (mAbs). The epitopes recognized by these antibodies have been mapped previously to linear peptides corresponding to the sequences thought to be exposed at the apices of surface-exposed loops of the protein. In this work several synthetic peptides containing the subtype Pl.16b epitope have been synthetized with the aim of inducing a polyclonal immune response resembling the reactivity of the mAbs. Initially, peptides of 9 and 15 amino acid residues were synthesized and used for immunization after coupling to a carrier protein. The reactivity of the resulting antisera, with synthetic linear decapeptides, resembled that seen in previous epitope mapping experiments with the protective mAbs. However, despite the induction of antibodies having the desired specificity, the antisera reacted poorly with the native protein in outer membranes, and were non-bactericidal. A 36mer peptide, consisting of the entire surface-exposed loop 4 of the class 1 protein was then synthesized and used for immunization as (i) free peptide, (ii) peptide coupled to carrier and (iii) peptide subjected to cyclization, in an attempt to restrict it to conformations that might more closely resemble the native loop structure. In contrast to antisera raised against linear peptides, antibodies raised by immunization with the 36mer cyclic peptide, did not react with linear peptides recognized by the mAbs, but instead appeared to recognize conformational determinants. This antiserum promoted complement-mediated bactericidal killing of the homologous meningococcal strain, demonstrating the potential of synthetic peptide immunogens for inducing a protective immune response against group B meningococci.
Power-gated spectral holeburning in MgS:Eu2+, Eu3+: A case for high-density persistent spectral holeburning (1998)

We present the case of photoionization-induced holeburning in rare-earth-doped II–VI compounds for high-density persistent holeburning. In this case, the photoproduct of holeburning is distributed across the entire zero-phonon line. This maximizes the total number of possible spectral holes that can be burned into an inhomogeneous line as well as produces holes that are photoerasable. Experimental data on photon-gated holeburning in MgS:Eu2+, Eu3+ are presented. With the proper choice of the host electronic band structure, the optically active rare-earth ion and its electronic transitions involved in the holeburning process, to the best of our knowledge we have observed the highest number of photon-gated holes ever burned in a single electronic transition. The features of these holes are that they suffer no detectable erasure after several thousands of read cycles, they survive thermal cycling to ∼150 K, and they are completely photoerasable. A special case of photon-gated holeburning, power-gated holeburning, was employed to demonstrate that, in such systems, a single laser can be used for burning, reading, and erasing of the spectral holes.
Site specific mutagenesis: insertion of single noncomplementary nucleotides at specified sites by error-directed DNA polymerization (1984)

We have utilized infidelity of DNA synthesis as a basis for site-directed mutagenesis. Both an endonuclease restriction fragment and a synthetic oligonucleotide were used as primers. DNA polymerase from bacteriophage T4 was used to elongate primer termini to a position immediately adjacent to two different preselected positions on phiX174 DNA templates. Then, the error-prone DNA polymerase from avian myeloblastosis virus was used to insert single non-complementary nucleotides at the designated positions at high efficiency. DNA sequence analysis confirmed that the mutant phage produced as a result of each site-specific mutagenesis reaction contained the nucleotide that was complementary to the one provided during the DNA copying reaction. The general applicability of this methodology to cloned DNAs will be discussed.
Interleukin‐21 is a T‐helper cytokine that regulates humoral immunity and cell‐mediated anti‐tumour responses (2004)

Cytokines and their receptors represent key targets for therapeutic intervention. Ligands are being used to supplement cell numbers that become depleted as a result of disease (organ failure, infection) or subsequent disease treatments (i.e. chemotherapy). Conversely, the inhibition of target cell binding by cytokines is an established strategy for abrogating pathologic cellular activities common to many immunological diseases. Considerable effort in biomedical research is being focused on the cytokine families that play a dominant role in regulating immunity and then prioritizing each member for its therapeutic potential. Currently, the interleukin-2 (IL-2) family of cytokines is widely recognized for its central involvement in controlling lymphocyte function and is the most explored for medical utility. Collectively, these proteins (or their antagonists) are either marketed drugs or have received advanced testing for an impressive array of indications including cancer, infectious disease, transplantation, inflammation and allergic asthma. Here we review the current understanding of IL-21, the most recent member of this cytokine family to be discovered. As will be discussed, IL-21 shares many of the same attributes as its relatives in that it has broad immunoregulatory activity and can modulate both humoral and cell-mediated responses. Its ability to stimulate durable anti-tumour responses in mice defines one therapeutic indication that merits clinical development.