gebhart/patrepeval huggingface dataset:
Signalling mechanisms mediated by the phosphoinositide 3‐kinase/Akt cascade in synaptic plasticity and memory in the rat (2006)

The phosphoinositide 3-kinase (PI3K)/Akt signalling cascade has classically been implicated in promoting cell survival but more recently has been shown to regulate a number of other cellular functions. In particular, studies have suggested that PI3K contributes to mechanisms associated with synaptic plasticity and memory processes but the function of this cascade in forms of synaptic plasticity, such as long-term potentiation, remains controversial and the PI3K substrates which mediate these effects are poorly understood. Here we report that the PI3K inhibitor LY294002 infused i.c.v. in vivo blocked maintenance of long-term potentiation induced in the dentate gyrus with a single tetanus to the perforant path but not with repeated tetani. This pattern of stimulation led to rapid and transient phosphorylation of the PI3K substrate Akt at Ser473 but not at Thr308. Functional readout of partial activation of Akt was demonstrated by an increase in phosphorylation of two downstream substrates, Forkhead (FKHR) and mammalian target of rapamycin (mTOR), in a delayed and prolonged manner at Akt-specific phosphorylation sites. LY294002 blocked phosphorylation of Akt and the prolonged phosphorylation of FKHR and mTOR but did not impair long-term potentiation-induced phosphorylation of extracellular receptor kinase. In addition, the same i.c.v. concentration of LY294002 impaired long-term consolidation of recognition memory but not short-term recognition memory or spatial learning and repeated training in the recognition memory task overcame the deficit in consolidation. These results suggest that activation of the PI3K/Akt pathway may contribute to the mechanisms of synaptic plasticity and memory consolidation by promoting cell survival via FKHR and protein synthesis via mTOR. Importantly, only partial activation of Akt at its Ser473 residue was necessary to mediate these effects.
Quantification of Heterogeneity as a Biomarker in Tumor Imaging: A Systematic Review (2014)

In a research setting, heterogeneity quantification methods can differentiate between tumor types, grade tumors, and predict outcome and monitor treatment effects. To translate these methods to clinical practice, more prospective studies are required that use external datasets for validation: these datasets should be made available to the community to facilitate the development of new and improved methods.
Exclusion of RNA strands from a purine motif triple helix (1994)

Research concerning oligonucleotide-directed triple helix formation has mainly focused on the binding of DNA oligonucleotides to duplex DNA. The participation of RNA strands in triple helices is also of interest. For the pyrimidine motif (pyrimidine.purine.pyrimidine triplets), systematic substitution of RNA for DNA in one, two, or all three triplex strands has previously been reported. For the purine motif (purine.purine.pyrimidine triplets), studies have shown only that RNA cannot bind to duplex DNA. To extend this result, we created a DNA triple helix in the purine motif and systematically replaced one, two, or all three strands with RNA. In dramatic contrast to the general accommodation of RNA strands in the pyrimidine triple helix motif, a stable triplex forms in the purine motif only when all three of the substituent strands are DNA. The lack of triplex formation among any of the other seven possible strand combinations involving RNA suggests that: (i) duplex structures containing RNA cannot be targeted by DNA oligonucleotides in the purine motif; (ii) RNA strands cannot be employed to recognize duplex DNA in the purine motif; and (iii) RNA tertiary structures are likely to contain only isolated base triplets in the purine motif.
Training Deep Neural Networks in Situ with Neuromorphic Photonics (2020)

We discuss an optoelectric architecture for executing the direct feedback alignment algorithm for neural network training. Using 1000 microring resonators, we can theoretically obtain speeds of 9.95 tera operations per second.
Chromosomal translocations induced at specified loci in human stem cells (2009)

The precise genetic manipulation of stem and precursor cells offers extraordinary potential for the analysis, prevention, and treatment of human malignancies. Chromosomal translocations are hallmarks of several tumor types where they are thought to have arisen in stem or precursor cells. Although approaches exist to study factors involved in translocation formation in mouse cells, approaches in human cells have been lacking, especially in relevant cell types. The technology of zinc finger nucleases (ZFNs) allows DNA double-strand breaks (DSBs) to be introduced into specified chromosomal loci. We harnessed this technology to induce chromosomal translocations in human cells by generating concurrent DSBs at 2 endogenous loci, the PPP1R12C/p84 gene on chromosome 19 and the IL2Rgamma gene on the X chromosome. Translocation breakpoint junctions for t(19;X) were detected with nested quantitative PCR in a high throughput 96-well format using denaturation curves and DNA sequencing in a variety of human cell types, including embryonic stem (hES) cells and hES cell-derived mesenchymal precursor cells. Although readily detected, translocations were less frequent than repair of a single DSB by gene targeting or nonhomologous end-joining, neither of which leads to gross chromosomal rearrangements. While previous studies have relied on laborious genetic modification of cells and extensive growth in culture, the approach described in this report is readily applicable to primary human cells, including multipotent and pluripotent cells, to uncover both the underlying mechanisms and phenotypic consequences of targeted translocations and other genomic rearrangements.
A novel calcitonin carboxyl-terminal peptide produced in medullary thyroid carcinoma by alternative RNA processing of the calcitonin/calcitonin gene-related peptide gene. (1991)

The calcitonin/calcitonin gene-related peptide gene expresses two different mRNAs by tissue-specific alternative processing. The calcitonin mRNA is produced in thyroid C cells by splicing of the first three exons to the fourth polyadenylated exon. It encodes a protein precursor containing an amino-terminal peptide, calcitonin, and a carboxyl-terminal peptide (CCP I). Calcitonin gene-related peptide (CGRP) mRNA is produced in neuronal cells by splicing of the three common exons to the fifth exon and the polyadenylated sixth exon, leading to the production of a CGRP precursor. Our studies concerning the expression of the calcitonin/CGRP gene in human medullary thyroid carcinoma revealed the presence of a new RNA transcript. Amplification by polymerase chain reaction and direct sequencing showed that the novel transcript is composed of exons 1, 2, and 3, part of exon 4, exon 5, and a polyadenylated exon 6. This transcript contains an open reading frame coding for the known amino-terminal and calcitonin peptides, as well as for a novel calcitonin carboxyl-terminal peptide, CCP II. This third alternative pathway utilizes an internal donor site within the exon coding for calcitonin. The presence of CCP II was demonstrated in plasma and thyroidal tissues of medullary thyroid carcinoma patients, implying that this novel mRNA is actively translated in medullary thyroid carcinoma.
Voltage gating is a fundamental feature of porin and toxin β‐barrel membrane channels (1998)

Beta-barrel pores are found in outer membrane porins of gram-negative bacteria, bacterial toxins and mitochondrial channels. Apart from the beta-barrel the three groups show no close sequence or structural homology but these pores exhibit symmetrical voltage gating when reconstituted into planar lipid bilayers. The structures of several of these are known and many site-directed mutants have been examined. As a result it seems evident that the gating is a common characteristic of these unrelated large pores and is not generated by specialised structures in the pore lumen.
Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes (2003)

The function of the ATR (ataxia-telangiectasia mutated- and Rad3-related)-ATRIP (ATR-interacting protein) protein kinase complex is crucial for the cellular response to replication stress and DNA damage. Here, we show that replication protein A (RPA), a protein complex that associates with single-stranded DNA (ssDNA), is required for the recruitment of ATR to sites of DNA damage and for ATR-mediated Chk1 activation in human cells. In vitro, RPA stimulates the binding of ATRIP to ssDNA. The binding of ATRIP to RPA-coated ssDNA enables the ATR-ATRIP complex to associate with DNA and stimulates phosphorylation of the Rad17 protein that is bound to DNA. Furthermore, Ddc2, the budding yeast homolog of ATRIP, is specifically recruited to double-strand DNA breaks in an RPA-dependent manner. A checkpoint-deficient mutant of RPA, rfa1-t11, is defective for recruiting Ddc2 to ssDNA both in vivo and in vitro. Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling.
The NKB1 and HP-3E4 NK cells receptors are structurally distinct glycoproteins and independently recognize polymorphic HLA-B and HLA-C molecules. (1995)

NK cells lyse hematopoietic cells that lack expression of MHC class I molecules on the cell surface. Transfection of certain MHC class I negative cell lines with MHC class I genes renders these cells resistant to NK cell-mediated cytotoxicity. Recently, we described an NK cell receptor, NKB1, that inhibits NK cells from killing target cells expressing Bw4-reactive HLA-B molecules (-B*2705, -B*5101, -B*5801). In this study, we have demonstrated that another structurally distinct NK cell membrane glycoprotein, HP-3E4, is involved in the recognition of certain polymorphic HLA-C molecules (-Cw*0401 and -Cw*1503). NK cell clones co-expressing both the NKB1 and HP-3E4 receptors fail to lyse targets expressing HLA-Cw*0401 and -B*5801, but are able to kill the transfectants in the presence of mAbs against both receptors. These studies demonstrate that a single NK cell clone may possess multiple structurally distinct receptors for different polymorphic HLA class I molecules that function independently.
An introduction to electrochemical DNA biosensors (2007)

Electrochemical DNA biosensors exploit the affinity of single-stranded DNA for complementary strands of DNA and are used in the detection of specific sequences of DNA with a view towards developing portable analytical devices. Great progress has been made in this field but there are still numerous challenges to overcome. This review for researchers new to the field describes the components of electrochemical DNA biosensors and the important issues in their design. Methods of transducing DNA binding events are discussed along with future directions for DNA biosensors.
The use of porcine small intestinal submucosa to enhance the healing of the medial collateral ligament—a functional tissue engineering study in rabbits (2003)

Healing of a gap MCL injury was significantly enhanced with SIS. The improved mechanical properties and histological appearance of the MCL suggest that SIS treatment improves the quality of tissue and renders the possibility for future studies investigating functional tissue engineering of healing ligaments.
Improved internal antenna forhand-held terminals (1994)

An analysis is made of the performance of a radiation-coupled dual-L antenna (RCDLA). In the simulation the antenna is mounted on the back side of the hand-held terminal, making use of the metallic housing as a shielding structure. The simulations show that this structure has a similar performance to that of the recently proposed full short circuit planar inverted-F antenna (FS-PIFA) in terms of shielding and radiation characteristics. In terms of bandwidth, size, and matching capabilities the RCDLA outperforms the FS-PIFA. Placement of the antenna on the back side of the housing instead of the top of the terminal results in a radiation pattern that points away from the user&apos;s head regardless of the antenna type.
Persistent eNOS activation secondary to caveolin-1 deficiency induces pulmonary hypertension in mice and humans through PKG nitration (2009)

Pulmonary hypertension (PH) is an unremitting disease defined by a progressive increase in pulmonary vascular resistance leading to right-sided heart failure. Using mice with genetic deletions of caveolin 1 (Cav1) and eNOS (Nos3), we demonstrate here that chronic eNOS activation secondary to loss of caveolin-1 can lead to PH. Consistent with a role for eNOS in the pathogenesis of PH, the pulmonary vascular remodeling and PH phenotype of Cav1-/- mice were absent in Cav1-/-Nos3-/- mice. Further, treatment of Cav1-/- mice with either MnTMPyP (a superoxide scavenger) or l-NAME (a NOS inhibitor) reversed their pulmonary vascular pathology and PH phenotype. Activation of eNOS in Cav1-/- lungs led to the impairment of PKG activity through tyrosine nitration. Moreover, the PH phenotype in Cav1-/- lungs could be rescued by overexpression of PKG-1. The clinical relevance of the data was indicated by the observation that lung tissue from patients with idiopathic pulmonary arterial hypertension demonstrated increased eNOS activation and PKG nitration and reduced caveolin-1 expression. Together, these data show that loss of caveolin-1 leads to hyperactive eNOS and subsequent tyrosine nitration-dependent impairment of PKG activity, which results in PH. Thus, targeting of PKG nitration represents a potential novel therapeutic strategy for the treatment of PH.
Emerging Pharmacologic Therapies for Wet Age-Related Macular Degeneration (2009)

As researchers and clinicians are beginning to understand that wet age-related macular degeneration (AMD) is more than simply a vascular disease that includes angiogenic, vascular and inflammatory components, they are exploring new agents with different mechanisms of action addressing multiple targets in this complex pathophysiology. Some of them are already available in human trials or even approved vascular epithelial growth factor (VEGF) blockers such as Macugen, Lucentis, Avastin, VEGF Trap-Eye and Cand5; VEGF receptor blockers such as TG100801, vatalanib, pazopanib, Sirna-027 and a vaccine approach; inflammation inhibitors and immunosuppressants such as Retaane, Kenalog, ARC1905, POT-4, OT-551. The last group is mixed, containing agents such as Zybrestat, AdPEGF, Sirolimus, JSM6427, ATG003, E10030. This article reviews these currently emerging agents and briefly discusses the next step for the treatment of wet AMD.
ChemInform Abstract: ISOCOUMARINS PART 14, SYNTHESIS OF 3‐BENZYLISOCOUMARINS AND 3‐BENZYL‐1(2H)‐ISOQUINOLONES (1975)

Abstract Homophthalsäureanhydrid (I) setzt sich.mit Phenylessigsäureanhydrid (II) zu dem Isocumarin (IIIa) um, das, ebenso wie sein Decarboxylierungsprodukt (IIIb), von heißer wäßriger Natronlauge zu der Säure (IV) aufgespalten wird.
High-Performance, Stable Organic Thin-Film Field-Effect Transistors Based on Bis-5‘-alkylthiophen-2‘-yl-2,6-anthracene Semiconductors (2005)

The development of new organic semiconductors with improved electrical performance and enhanced environmental stability is the focus of considerable research activity. This communication presents the design, synthesis, and device stability data for novel bis-5'-alkylthiophen-2'yl-2,6-anthracene organic semiconductors. When incorporated into thin-film field-effect transistors, mobilities as high as 0.5 cm2/Vs and on/off current ratios greater than 107 are observed. We have investigated device stability in terms of both shelf life and operating lifetime. Devices incorporating the reported semiconductors display an average field-effect mobility of 0.4 cm2/Vs for DHTAnt and an on/off current ratio of 106 even after 15 months of storage. Furthermore, there is no decrease in performance during continuous operation of the devices over several thousand cycles.
Increased Prevalence of Significant Recurrent Headache in Preclinical Familial Alzheimer’s Disease Mutation Carriers (2008)

In this population, headache was more common in nondemented FAD MCs than NCs. Possible mechanisms for this include cerebral inflammation, aberrant processing of Notch3, or disrupted intracellular calcium regulation.
A randomized, double-blind, placebo-controlled study of vortioxetine on cognitive function in depressed adults (2014)

The efficacy of vortioxetine 10 and 20 mg/d vs. placebo on cognitive function and depression in adults with recurrent moderate-to-severe major depressive disorder (MDD) was evaluated. Patients (18-65 yr, N = 602) were randomized (1:1:1) to vortioxetine 10 or 20 mg/d or placebo for 8 wk in a double-blind multi-national study. Cognitive function was assessed with objective neuropsychological tests of executive function, processing speed, attention and learning and memory, and a subjective cognitive measure. The primary outcome measure was change from baseline to week 8 in a composite z-score comprising the Digit Symbol Substitution Test (DSST) and Rey Auditory Verbal Learning Test (RAVLT) scores. Depressive symptoms were assessed using the Montgomery-Åsberg Depression Rating Scale (MADRS). In the pre-defined primary efficacy analysis, both doses of vortioxetine were significantly better than placebo, with mean treatment differences vs. placebo of 0.36 (vortioxetine 10 mg, p < 0.0001) and 0.33 (vortioxetine 20 mg, p < 0.0001) on the composite cognition score. Significant improvement vs. placebo was observed for vortioxetine on most of the secondary objectives and subjective patient-reported cognitive measures. The differences to placebo in the MADRS total score at week 8 were -4.7 (10 mg: p < 0.0001) and -6.7 (20 mg: p < 0.0001). Path and subgroup analyses indicate that the beneficial effect of vortioxetine on cognition is largely a direct treatment effect. No safety concern emerged with vortioxetine. Vortioxetine significantly improved objective and subjective measures of cognitive function in adults with recurrent MDD and these effects were largely independent of its effect on improving depressive symptoms.
Thyroid Hormone Negatively Regulates the Transcriptional Activity of the β-Amyloid Precursor Protein Gene (1998)

The expression of the beta-amyloid precursor protein (APP), which plays a key role in the development of Alzheimer's disease, is regulated by a variety of cellular mediators in a cell-dependent manner. In the present study, we present evidence that thyroid hormones negatively regulate the expression of the APP gene in neuroblastoma cells. Transient transfection studies using plasmids that contain progressive deletions of the 5' region of the gene demonstrate that triiodothyronine (T3), the more active form of the thyroid hormones, represses APP promoter activity by a mechanism that requires binding of the nuclear T3 receptor (TR) to a specific sequence located in the first exon. The unliganded receptor increases promoter activity, and T3 reverses that activity to basal levels. The repressive effect of T3 does not exhibit TR isoform specificity, and it is equally mediated by TRalpha and TRbeta. Gel mobility shift assays using in vitro synthesized nuclear receptors and nuclear extracts led to the identification of a negative thyroid hormone response element, at nucleotide position +80/+96, that preferentially binds heterodimers of TR with the retinoid X receptor. Insertion of sequences containing this element confers negative regulation by T3 to a heterologous TK promoter, thus indicating the functionality of the element.
In Vitro Affinity Maturation of Human IgM Antibodies Reactive with Tumor-Associated Antigens (2001)

Human lymphocytes secreting tumor cell-specific IgM antibodies were enriched in vitro following the stimulation of allogeneic human splenocytes from nontumor-bearing donors with cytostatic tumor cells or tumor cell plasma membrane fractions. The antibodies were generally of the IgM class and displayed low intrinsic affinity (K(d) > 100 nM). Nonetheless, the avidity arising from multivalent binding sites permitted the identification of multiple monoclonal antibodies (MAbs) displaying specificity for cultured tumor cells. Five antibodies were cloned from the B cells and two of these were expressed as human Fabs with IgG(1) constant regions. Although the avidity of the human IgM antibodies was sufficient to permit detection in the original screening, the monovalent Fabs displayed low binding activities, consistent with their low intrinsic affinity. Thus, in vitro affinity maturation was used to rapidly generate multiple variants of both antibodies displaying greater than 100-fold higher affinity. Two of the antibodies were characterized further and shown to have distinct specificities. One of the targets, LH11238, is associated both with the plasma membrane and with lysosomes and is rapidly internalized following incubation of the antibody with intact live cell monolayers. The second antigen, designated LH13, is a secreted antigen that has been enriched 200-fold from conditioned media and consists of two reactive bands at 42 and 45 kDa on denaturing Western blots. The stimulation and enrichment of human lymphocytes in culture coupled with rapid in vitro affinity maturation of low affinity antibodies potentially enables the discovery of human antibodies to a broader range of epitopes, including those that might be of greater therapeutic relevance.
The M184V Mutation in the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 Impairs Rescue of Chain-Terminated DNA Synthesis (2000)

Nucleoside analog chain terminators such as 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxy-3'-thiacytidine (3TC) represent an important class of drugs that are used in the clinic to inhibit the reverse transcriptase (RT) of human immunodeficiency virus type 1. Recent data have suggested that mutant enzymes associated with AZT resistance are capable of removing the chain-terminating residue with much greater efficiency than wild-type RT and this may, in turn, facilitate rescue of DNA synthesis; these experiments were performed using physiological concentrations of pyrophosphate or nucleoside triphosphates, respectively. The present study demonstrates that the M184V mutation, which confers high-level resistance to 3TC, can severely compromise the removal of chain-terminating nucleotides. Pyrophosphorolysis on 3TC-terminated primer strands was not detectable with M184V-containing, as opposed to wild-type, RT, and rescue of AZT-terminated DNA synthesis was significantly decreased with the former enzyme. Thus, mutated RTs associated with resistance to AZT and 3TC possess opposing, and therefore incompatible, phenotypes in this regard. These results are consistent with tissue culture and clinical data showing sustained antiviral effects of AZT in the context of viruses that contain the M184V mutation in the RT-encoding gene.