gebhart/patrepeval huggingface dataset:
Bisindolylmaleimide VIII Enhances DR5-mediated Apoptosis through the MKK4/JNK/p38 Kinase and the Mitochondrial Pathways (2002)

Bisindolylmaleimide VIII (Bis VIII) has been previously shown to enhance Fas-mediated apoptosis through a protein kinase C-independent mechanism. In the present study, we examined the effect of Bis VIII on apoptosis induced by DR5 (TRAIL-R2), using an agonistic anti-human DR5 monoclonal antibody, TRA-8. Our results demonstrated that Bis VIII was able to enhance the apoptosis-inducing activity of TRA-8 both in vitro and in vivo. The combination of TRA-8 and Bis VIII led to a synergistic and sustained activation of the c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase, which was mediated by MAPK kinase 4 and was caspase-8-dependent. The mitochondrial pathway is involved in the synergistic induction of apoptosis by Bis VIII and TRA-8. Bis VIII alone induced the loss of mitochondrial membrane potential in a caspase-independent fashion without subsequent release of cytochrome c. However, in the presence of Bis VIII, TRA-8 induced more profound loss of mitochondrial membrane potential and release of cytochrome c. These results suggest that the enhanced and persistent activation of the JNK/p38 and the decreased mitochondrial membrane potential play a crucial role in synergistic induction of the death receptor-mediated apoptosis by Bis VIII. The unique ability of Bis VIII to enhance DR5-mediated apoptosis signal transduction discloses a potential utility of this compound in combination with anti-DR5 antibody in cancer therapy.
Abstract 5651: A LAG-3/PD-L1 bispecific antibody inhibits tumor growth in two syngeneic colon carcinoma models (2017)

Abstract Combining immunotherapeutic antibodies in cancer treatment has shown benefits over single agents. An alternative to combining two antibodies is the development of bispecific antibodies that not only bring two biologies together but may result in novel mechanisms of action that are impossible to attain with combinations. Lymphocyte Activation Gene-3 (LAG-3) is a member of the Ig superfamily expressed on activated T cells, NK cells, pDCs, B cells, γδ T cells and participates in immune suppression. Programmed Cell Death receptor (PD-1) binds to its ligand PD-L1, expressed not only on activated immune cells to inhibit cellular immune responses but also on tumor cells. Expression of both these surface molecules therefore leads to T cell exhaustion allowing the tumor to escape immune surveillance. A mAb² TM (bispecific antibody) was engineered which binds murine LAG-3 and PD-L1 simultaneously and with nanomolar affinities. The anti-LAG-3/PD-L1 mAb² inhibits LAG-3 binding to MHCII and PD-L1 binding to PD-1 and CD80, resulting in T cell activation in vitro. This translates into in vivo efficacy, where the mAb² decreased tumor burden in the MC38 colon carcinoma tumor model. At the end of the study tumor-free animals were more numerous in the LAG-3/PD-L1 bispecific group than in the group given a combination of individual anti-LAG-3 and PD-L1 antibodies. The results were recapitulated in the CT26 murine colon cancer model, where the mAb² showed an increase of antitumor activity as compared to the antibodies given in combination. Thus, the preclinical data supports developing an anti-human LAG-3/PD-L1 mAb² for the treatment of cancer patients. Citation Format: Matthew Kraman, Katarzyna Kmiecik, Carlo Zimarino, Katy Everett, Mustapha Faroudi, Mateusz Wydro, Jacqueline Doody. A LAG-3/PD-L1 bispecific antibody inhibits tumor growth in two syngeneic colon carcinoma models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5651. doi:10.1158/1538-7445.AM2017-5651
Nucleotide sequence of the large double-stranded RNA segment of bacteriophage phi 6: genes specifying the viral replicase and transcriptase (1988)

The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We determined the nucleotide sequence of cDNA derived from the largest RNA segment (L). This segment specifies the procapsid proteins necessary for transcription and replication of the phi 6 genome. The coding sequences of the four proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through analysis of isolated proteins. This report completes the sequence analysis of phi 6. This constitutes the first complete sequence of a double-stranded RNA genome virus.
Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system (2016)

Oligodendrocytes have been considered as a functionally homogeneous population in the central nervous system (CNS). We performed single-cell RNA sequencing on 5072 cells of the oligodendrocyte lineage from 10 regions of the mouse juvenile and adult CNS. Thirteen distinct populations were identified, 12 of which represent a continuum from Pdgfra(+) oligodendrocyte precursor cells (OPCs) to distinct mature oligodendrocytes. Initial stages of differentiation were similar across the juvenile CNS, whereas subsets of mature oligodendrocytes were enriched in specific regions in the adult brain. Newly formed oligodendrocytes were detected in the adult CNS and were responsive to complex motor learning. A second Pdgfra(+) population, distinct from OPCs, was found along vessels. Our study reveals the dynamics of oligodendrocyte differentiation and maturation, uncoupling them at a transcriptional level and highlighting oligodendrocyte heterogeneity in the CNS.
AMoRe: an automated package for molecular replacement (1994)

A new molecular-replacement package is presented. It is an improvement on conventional methods, based on more powerful algorithms and a new conception that enables automation and rapid solution.
High Rate of Durable Remissions After Treatment of Newly Diagnosed Aggressive Mantle-Cell Lymphoma With Rituximab Plus Hyper-CVAD Alternating With Rituximab Plus High-Dose Methotrexate and Cytarabine (2005)

Rituximab plus hyper-CVAD alternating with rituximab plus high-dose methotrexate and cytarabine is effective in untreated aggressive MCL. Toxicity is significant but expected. Because of the shorter FFS concurrent with significant toxicity in patients more than 65 years of age, this regimen is not recommended as standard therapy for this age subgroup. Larger prospective randomized studies are needed to define the role of this regimen in the treatment of MCL patients compared with existing and new treatment modalities.
Interferon beta in multiple sclerosis: experience in a British specialist multiple sclerosis centre (2003)

IFN beta is effective in reducing the relapse rate in patients with relapsing-remitting MS in routine clinical practice. However, after a median treatment duration of 26 months, 40% of initially relapsing-remitting MS patients seem to have ongoing disease activity, presenting as disabling relapses or insidious progression.
Self-Organizing 3D Human Neural Tissue Derived from Induced Pluripotent Stem Cells Recapitulate Alzheimer’s Disease Phenotypes (2016)

The dismal success rate of clinical trials for Alzheimer's disease (AD) motivates us to develop model systems of AD pathology that have higher predictive validity. The advent of induced pluripotent stem cells (iPSCs) allows us to model pathology and study disease mechanisms directly in human neural cells from healthy individual as well as AD patients. However, two-dimensional culture systems do not recapitulate the complexity of neural tissue, and phenotypes such as extracellular protein aggregation are difficult to observe. We report brain organoids that use pluripotent stem cells derived from AD patients and recapitulate AD-like pathologies such as amyloid aggregation, hyperphosphorylated tau protein, and endosome abnormalities. These pathologies are observed in an age-dependent manner in organoids derived from multiple familial AD (fAD) patients harboring amyloid precursor protein (APP) duplication or presenilin1 (PSEN1) mutation, compared to controls. The incidence of AD pathology was consistent amongst several fAD lines, which carried different mutations. Although these are complex assemblies of neural tissue, they are also highly amenable to experimental manipulation. We find that treatment of patient-derived organoids with β- and γ-secretase inhibitors significantly reduces amyloid and tau pathology. Moreover, these results show the potential of this model system to greatly increase the translatability of pre-clinical drug discovery in AD.
Fundamental investigation of the Bosch reaction (1971)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1971.
Use of serotonergic agents in the clinical assessment of central serotonin function. (1986)

To assess the status of the brain serotonergic system in relation to ongoing behavior, agents with predominant actions on serotonin synthesis, release, uptake, and receptor mechanisms are being evaluated. Abnormalities in the neuroendocrine responses to tryptophan, 5-hydroxytryptophan, fenfluramine, and m-chlorophenylpiperazine are under exploration in depressed patients. These agents are also being used to assess postulated changes in serotonin metabolism and serotonin receptor adaptation during longer term treatment with antidepressant drugs, lithium, and other psychoactive agents. Concurrent studies in rodent and nonhuman primate models are helping to validate these approaches to the exploration of the role of serotonin in psychiatric and neurologic disorders.
Molecular cloning of mRNA from 3T3 adipocytes. Regulation of mRNA content for glycerophosphate dehydrogenase and other differentiation-dependent proteins during adipocyte development. (1983)

We have constructed a recombinant bacterial library containing cDNA prepared from mRNA of adipose 3T3 cells. We have screened this library by several methods and isolated colonies containing sequences complementary to mRNAs for glycerophosphate dehydrogenase, two other major differentiation-dependent proteins of Mr = 28,000 and 13,000, and actin. These recombinants were identified by hybrid selection of total adipocyte mRNA, translation in vitro and subsequent immunoprecipitation, and two-dimensional electrophoresis of translated proteins. Three of the four cloned cDNAs hybridized to single adipocyte mRNA species of size close to that expected from the size of the polypeptide it specifies, but the mRNA for glycerophosphate dehydrogenase contained 3,550 bases, far larger than necessary to code for its polypeptide (Mr = 34,000). The increase in amount of mRNA during differentiation was 150-fold for the protein of Mr = 13,000 and considerably greater for glycerophosphate dehydrogenase and the protein of Mr = 28,000. The time course of mRNA accumulation was different for each of these mRNAs, indicating they do not respond synchronously during differentiation.
End-To-End Memory Networks (2015)

We introduce a neural network with a recurrent attention model over a possibly large external memory. The architecture is a form of Memory Network (Weston et al., 2015) but unlike the model in that work, it is trained end-to-end, and hence requires significantly less supervision during training, making it more generally applicable in realistic settings. It can also be seen as an extension of RNNsearch to the case where multiple computational steps (hops) are performed per output symbol. The flexibility of the model allows us to apply it to tasks as diverse as (synthetic) question answering and to language modeling. For the former our approach is competitive with Memory Networks, but with less supervision. For the latter, on the Penn TreeBank and Text8 datasets our approach demonstrates comparable performance to RNNs and LSTMs. In both cases we show that the key concept of multiple computational hops yields improved results.
Increased Brain Injury and Worsened Neurological Outcome in Interleukin-4 Knockout Mice After Transient Focal Cerebral Ischemia (2011)

Loss of IL-4 signaling in KO mice was associated with worse outcome, and this was reversed by giving exogenous IL-4. Worsened outcome was associated with increased inflammation in the core, which was reversed in IL-4 KO but not significantly changed in wild-type mice by exogenous IL-4. This is consistent with IL-4 signaling leading to reduced inflammation in the core and a possible beneficial role for activated astrocytes in the penumbra.
Dual-energy X-ray absorptiometry: fat estimation errors due to variation in soft tissue hydration (1998)

Dual-energy X-ray absorptiometry (DXA) is rapidly gaining acceptance as a reference method for analyzing body composition. An important and unresolved concern is whether and to what extent variation in soft tissue hydration causes errors in DXA fat estimates. The present study aim was to develop and validate a DXA physical hydration model and then to apply this model by simulating errors arising from hypothetical overhydration states. The DXA physical hydration model was developed by first linking biological substance elemental content with photon attenuation. The validated physical model was next extended to describe photon attenuation changes anticipated when predefined amounts of two known composition components are mixed, as would occur when overhydration develops. Two overhydration models were developed in the last phase of study, formulated on validated physical models, and error was simulated for fluid surfeit states. Results indicate that systematic errors in DXA percent fat arise with added fluids when fractional masses are varied as a percentage of combined fluid + soft tissue mass. Three independent determinants of error magnitude were established: elemental content of overhydration fluid, fraction of combined fluid + soft tissue as overhydration fluid, and initial soft tissue composition. Small but systematic and predictable errors in DXA soft tissue composition analysis thus can arise with fluid balance changes.
Follicular expression of a human ß-cell leukaemia/lymphoma-2 (Bcl-2) transgene does not decrease atresia or increase ovulation rate in swine* (2005)

Transgenic (TG) gilts carrying a human Bcl-2 cDNA transgene driven by mouse inhibin-alpha subunit promoter were produced and evaluated to determine if ectopic expression of Bcl-2 in the ovaries would decrease the frequency of atresia in antral follicles and increase ovulation rate. Immunohistochemical analysis showed that the Bcl-2 transgene protein was expressed in granulosa and theca cells, in 86% of healthy and 54% of atretic follicles analysed in TG prepubertal and Day 50 pregnant gilts combined (n = 24). In contrast, Bcl-2 transgene protein was expressed in only 1.4% of healthy and 0% of atretic follicles in non-TG littermates (n = 13). Real-time reverse transcription-polymerase chain reaction analysis confirmed that human Bcl-2 was expressed in follicles of TG gilts. The atresia rate for the TG and non-TG groups did not differ (P > 0.05) for prepubertal (45 v. 59%) and Day 50 pregnant gilts (53 v. 52%) respectively. The mean +/- s.e.m. ovulation rate did not differ (P > 0.5) between TG (15.9 +/- 0.8, n = 12) and non-TG (16.4 +/- 0.6, n = 7) Day 50 pregnant gilts. The molecular basis of the failure of ectopic Bcl-2 expression to increase the ratio of healthy to atretic follicles is unknown, but it is possible that the activity of the mitochondrial-dependent cell death pathway was not neutralized by ectopic expression of human Bcl-2 or that other cell death pathways compensated for the decreased mitochondrial-dependent cell death.
Synthesis of 3‐ or 4‐Phenyl‐1,8‐naphthyridine Derivatives and Evaluation of Antimycobacterial and Antimicrobial Activity. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Molecular Mechanisms Involved in CD43-mediated Apoptosis of TF-1 Cells (2002)

CD43 (leukosialin, sialophorin), an abundant leukocyte surface sialoglycoprotein, regulates leukocyte adhesion and transmits activating signals in T cells and dendritic cells. Immobilized anti-CD43 monoclonal antibody (mAb) MEM-59 has been previously shown to induce apoptosis of hematopoietic progenitors. In this study we show that it also triggers apoptosis of the myeloid progenitor-derived cell line TF-1. The kinetics of the MEM-59-induced apoptosis were unusually slow, with the first apoptotic cells appearing 36-48 h after their contact with the immobilized antibody; in 5 days, 90% of the cells were dead. CD43-mediated apoptosis was enhanced by coimmobilized anti-CD45 mAb and partly suppressed by coimmobilized anti-CD50 (ICAM-3) or anti-CD99 mAb. The MEM-59-triggered apoptosis of TF-1 cells was also inhibited by the overexpression of an apoptotic regulator, Daxx. CD43-mediated apoptosis was preceded by the repression of the DNA binding activity of the transcription factor AP-1. DNA array screening revealed that the expression of several genes encoding apoptosis-regulating proteins, including 14-3-3 proteins and the granulocyte macrophage colony-stimulating factor (GM-CSF) receptor beta-subunit, was repressed in TF-1 cells bound to immobilized MEM-59. The down-regulation of 14-3-3 proteins and GM-CSF receptor beta was accompanied by translocation of the proapoptotic protein Bad to the mitochondria. These results suggest that engagement of CD43 may, presumably through the repressing transcription, initiate a Bad-dependent apoptotic pathway.
OCD Dolores - Recovering Logical Structures for Dummies (2012)

This paper presents OCD Dolores, an environment that aims at recovering the logical structures from documents by interactively inferring their models. Dolores is based on OCD, an XML canonical document format used to represent structured electronic content efficiently. The relevance of our restructuring system is assessed through a deep evaluation of Dolores' logical labeling capacities.
Akt inhibitors induce apoptosis in chronic lymphocytic leukemia cells (2009)

These results demonstrate that Akt inhibitors induce apoptosis of chronic lymphocytic leukemia cells and might be a new therapeutic option for the treatment of chronic lymphocytic leukemia.
Sergeants‐and‐Soldiers Principle in Chiral Columnar Stacks of Disc‐Shaped Molecules with C3 Symmetry (1997)

Extremely effective cooperative effects operate during the formation of chiral stacks of C3-symmetrical molecules in alkane solvents (a molecule is depicted on the right). The sergeants-and-soldiers principles as well as chiral solvation lead to a preferred helical sense in the columnar aggregates. The amplification of chirality in dynamic systems shows the precision in aggregation.
Example-Based Color Transformation of Image and Video Using Basic Color Categories (2007)

Color transformation is the most effective method to improve the mood of an image, because color has a large influence in forming the mood. However, conventional color transformation tools have a tradeoff between the quality of the resultant image and the amount of manual operation. To achieve a more detailed and natural result with less labor, we previously suggested a method that performs an example-based color stylization of images using perceptual color categories. In this paper, we extend this method to make the algorithm more robust and to stylize the colors of video frame sequences. We present a variety of results, arguing that these images and videos convey a different, but coherent mood.
Interaction of Escherichia coli RecA Protein with LexA Repressor (1996)

Essential to the two distinct cellular events of genetic recombination and SOS induction in Escherichia coli, RecA protein promotes the homologous pairing and exchange of DNA strands and the proteolytic cleavage of the LexA repressor, respectively. Since both of these activities require single-stranded DNA (ssDNA) and ATP, the inter-relationship between these reactions was investigated and found to display many parallels. The extent of active complex formed between RecA protein and M13 ssDNA, as measured by both ATP hydrolysis and LexA proteolysis, is stimulated in a similar manner by either a reduction in magnesium ion concentration or the presence of single-stranded DNA binding (SSB) protein. However, unexpectedly, SSB protein inhibits both LexA proteolysis and ATP hydrolysis (in assays containing repressor) at concentrations of RecA protein that are substoichiometric to the ssDNA, arguing that LexA repressor affects the competition between RecA and SSB proteins for limited ssDNA binding sites. Additionally, attenuation of LexA repressor cleavage in the presence of double-stranded DNA or by an excess of ssDNA suggests that interaction of the RecA nucleoprotein filament with either LexA repressor or a secondary DNA molecule is mutually exclusive. The significance of these results is discussed in the context of both the regulation of inducible responses to DNA damage, and the competitive relationship between the processes of SOS induction and genetic recombination.
The Chemical Form of Mercury in Fish (2003)

The primary dietary source of neurotoxic mercury compounds is via the ingestion of methylmercury species accumulated in fish. Methylmercury from fish has been linked to neurological damage (Minamata disease) ([ 1 ][1]) and increased risk of myocardial infarction ([ 2 ][2]). Despite its importance,
The contribution of wood to the flavor of alcoholic beverages (1989)

Abstract Wood can play a significant role in contributing flavor to alcoholic beverages. Specific aspects covered in this review include wood composition in general; the various types of wood used in aging alcoholic products; oak composition and flavor properties; cork composition and its desirable and undesirable flavors; the effect of wood on wine flavor; the effect of wood on distilled spirit flavor; and the practice of accelerated wood aging of alcoholic beverages.
Resiliencia, territorios y empleo: El caso de las comarcas catalanas (2011)

La resiliencia es un concepto que ayuda a explicar el diferencial de los territorios para responder, reaccionar y enfrentarse a diferentes shocks con impacto económico. Los debates sobre desarrollo regional han dejado de centrarse exclusivamente en el crecimiento, para abarcar la resiliencia relativa de los territorios en responder a las crisis. Este artículo busca determinar el impacto de diferentes factores en el grado de resiliencia de las comarcas de Cataluña. Los resultados indican que la densidad empresarial, la especialización sectorial, el porcentaje de población extranjera, y el carácter de ruralidad impactan sobre el nivel de resiliencia de estos territorios.
Biocatalytic deuterium- and hydrogen-transfer using over-expressed ADH-‘A’: enhanced stereoselectivity and2H-labeled chiral alcohols (2006)

Employing the over-expressed highly organic solvent tolerant alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541, versatile building blocks, which were not accessible by the wild type catalyst, were obtained in > 99% e.e.; furthermore, employing d8-2-propanol as deuterium source, stereoselective biocatalytic deuterium transfer was made feasible to furnish enantiopure deuterium labeled sec-alcohols on a preparative scale employing a single enzyme.