gebhart/patrepeval huggingface dataset:
Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight (2017)

Genetically encoded calcium indicators (GECIs) produce unprecedentedly large signals that have enabled routine optical recording of single neuron activity in vivo in rodent brain. Genetically encoded voltage indicators (GEVIs) offer a more direct measure of neuronal electrical status, however the signal-to-noise characteristics and signal polarity of the probes developed to date have precluded routine use in vivo. We applied directed evolution to target modulable areas of the fluorescent protein in GEVI ArcLight to create the first GFP-based GEVI (Marina) that exhibits a ΔF/ΔV with a positive slope relationship. We found that only three rounds of site-directed mutagenesis produced a family of "brightening" GEVIs with voltage sensitivities comparable to that seen in the parent probe ArcLight. This shift in signal polarity is an essential first step to producing voltage indicators with signal-to-noise characteristics comparable to GECIs to support widespread use in vivo.
In vitro -generated neural precursors participate in mammalian brain development (1997)

During embryogenesis, pluripotent stem cells segregate into daughter lineages of progressively restricted developmental potential. In vitro, this process has been mimicked by the controlled differentiation of embryonic stem cells into neural precursors. To explore the developmental potential of these cell-culture-derived precursors in vivo, we have implanted them into the ventricles of embryonic rats. The transplanted cells formed intraventricular neuroepithelial structures and migrated in large numbers into the brain tissue. Embryonic-stem-cell-derived neurons, astrocytes, and oligodendrocytes incorporated into telencephalic, diencephalic, and mesencephalic regions and assumed phenotypes indistinguishable from neighboring host cells. These observations indicate that entirely in vitro-generated neural precursors are able to respond to environmental signals guiding cell migration and differentiation and have the potential to reconstitute neuronal and glial lineages in the central nervous system.
Peripheral melatonin mediates neural stimulation of duodenal mucosal bicarbonate secretion (2001)

Melatonin is released from intestinal enterochromaffin cells and from the pineal gland, but its role in gastrointestinal function is largely unknown. Our aim was to study the involvement of intestinal and central nervous melatonin in the neurohumoral control of the duodenal mucosa-protective bicarbonate secretion. Working in anesthetized rats, we cannulated a 12-mm segment of duodenum with an intact blood supply and titrated the local bicarbonate secretion with pH-stat. Melatonin and receptor ligands were supplied to the duodenum by close intra-arterial infusion. Even at low doses, melatonin and the full agonist 2-iodo-N-butanoyl-5-methoxytryptamine increased duodenal bicarbonate secretion. Responses were inhibited by the predominantly MT2-selective antagonist luzindole but not by prazosin, acting at MT3 receptors. Also, luzindole almost abolished the marked rise in secretion induced by intracerebroventricular infusion of the adrenoceptor agonist phenylephrine. This response was also abolished by sublaryngeal ligation of all nerves around the carotid arteries. However, it was insensitive to truncal vagotomy alone or sympathectomy alone and was unaffected by removal of either the pineal gland or pituitary gland. Thus, melatonin stimulates duodenal bicarbonate secretion via action at enterocyte MT2-receptors and mediates neural stimulation of the secretion.
Antibody mapping of tissue factor implicates two different exon-encoded regions in function (1991)

Tissue Factor (TF), a small transmembrane glycoprotein, is the cellular receptor for the zymogen Factor VII and the serine protease Factor VIIa (VIIa). TF provides cofactor function for VIIa in the catalytically active (TF: VIIa) binary complex. To explore the structural loci of TF that are responsible for binding of VII and VIIa, monoclonal antibodies (MAbs) and sequence-specific polyclonal antibodies to the native TF protein were analysed for inhibition of VII binding. Two independent epitopes of MAbs were localized by reciprocal competition and by binding of the MAbs to different proteolytic fragments of TF. The epitopes were also characterized in part by progressive C-terminal deletional mutation of the TF protein. Reactivity of the anti-(locus II) MAb TF9-6G4 is consistent with epitope localization in residues Thr40-Val83, encoded by exon 3. In contrast, the anti-(locus I) MAb TF9-5G9 was reactive with fragments encompassing exon 4 (Thr106-Lys165). Antibodies to linear sequences encoded by the same two exons also inhibited VII binding. These data suggest a minimum requirement for two of the four exon-encoded regions of TF for the functional integrity of this receptor cofactor with respect to ligand recognition and high-affinity binding.
The effect of mild hyperthermia and hypothermia on brain damage following 5, 10, and 15 minutes of forebrain ischemia (1990)

The present study examines the effects of mild hypothermia and hyperthermia on the density and distribution of ischemic brain damage, and compares these effects to those induced by variations in the duration of ischemia. Body temperatures were maintained at 35 degrees C, 37 degrees C, and 39 degrees C, before, during, and after ischemia, and brain temperatures were held at similar values with a technique that in preliminary experiments proved to avoid intracerebral temperature gradients or overheating of surface structures. In all animals, brain damage was assessed by histopathological analysis of perfusion-fixed brains after six to seven days of recovery. Our results confirm previous findings showing that a decrease in temperature of only 2 degrees C significantly reduces damage to several selectively vulnerable neuronal populations. The results also showed that an increase in temperature of 2 degrees C significantly enhances brain damage. In general, a rise in temperature had effects similar to an increased duration of the ischemia. In some areas, such as the CA1-subiculum sectors of the hippocampus, temperature and ischemic duration altered damage in a gradual manner, but in others, such as the caudoputamen, there was a steplike change from virtually no to virtually complete damage. In some areas, the effects of hypothermia and hyperthermia appeared symmetrical around the normal temperature of 37 degrees C. Hyperthermia had some seemingly "specific" effects, however, notably the tendency to induce pannecrosis ("infarction") in the neocortex and caudoputamen, and to cause damage to the substantia nigra pars reticulata. The results underscore the potentially devastating effects of fever in patients with cerebrovascular disease.
The Role of Internal Models in Motion Planning and Control: Evidence from Grip Force Adjustments during Movements of Hand-Held Loads (1997)

We investigated the issue of whether or not the CNS makes use of an internal model of the motor apparatus in planning and controlling arm movements. In particular, we tested the ability of subjects to predict different hand-held loads by examining grip force adjustments used to stabilize the load in the hand during arm movements. Subjects grasped a manipulandum using a precision grip with the tips of the thumb and index finger on either side. The grip force (normal to the contact surfaces) and the load force (tangential to the surfaces) were measured, along with the trajectory of the hand. The manipulandum was attached to two servo-controlled linear motors used to create inertial and viscous loads as well as a composite load, including inertial, viscous, and elastic components. The form of the hand trajectory was independent of load for some subjects but varied systematically across load conditions in others. Nevertheless, under all load conditions and in all subjects, grip force was modulated in parallel with, and thus anticipated, fluctuations in load force despite the marked variation in the form of the load function. This indicates that the CNS is able to predict the load force and the kinematics of hand movement on which the load depends. We suggest this prediction is based on an internal model of the motor apparatus and external load and is used to determine the grip forces required to stabilize the load.
Bacteriocins of Lactic Acid Bacteria: Microbiology, Genetics and Applications (2012)

Bacteriocins of lactic acid bacteria: microbiology, genetics, and applications , Bacteriocins of lactic acid bacteria: microbiology, genetics, and applications , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Penetration loss in BSCCO tape without transport current (1999)

A penetration loss formula for superconducting tapes has been derived in our previous work. In this paper, the orientation of the magnetic field is considered in the formula. This formula includes the E-j characteristics represented with a power law and the magnetic field dependence of the critical current density. The analytical estimations with the formula are compared with experimental results on the magnetization loss for a BSCCO tape with no transport current for several field orientations. The losses estimated by this formula agree well with the experimental results, when the magnetic field is applied parallel or perpendicular to the tape face. For the magnetic field with another field orientation, the experimental results are smaller than the analytical predications, because of the demagnetizing effect.
Casper the Friendly Finality Gadget (2017)

In 1985, Dolev and Reischuk proved a fundamental communication lower bounds on protocols achieving fault tolerant synchronous broadcast and consensus: any deterministic protocol solving those tasks (even against omission faults) requires at least a quadratic number of messages to be sent by nonfaulty parties. In contrast, many blockchain systems achieve consensus with seemingly linear communication per instance against Byzantine faults. We explore this dissonance in three main ways. First, we extend the Dolev-Reischuk family of lower bounds and prove a new lower bound for Crusader Broadcast protocols. Our lower bound for crusader broadcast requires non-trivial extensions and a much stronger Byzantine adversary with the ability to simulate honest parties. Secondly, we extend our lower bounds to all-but-m Crusader Broadcast, in which up to m parties are allowed to output a different value. Finally, we discuss the ways in which these lower bounds relate to the security of blockchain systems. We show how Eclipse-style attacks in such systems can be viewed as specific instances of the attacks used in our lower bound for Crusader Broadcast. This connection suggests a more systematic way of analyzing and reasoning about Eclipse-style attacks through the lens of the Dolev-Reischuk family of attacks.
Problem characterization and abstraction for visual analytics in behavior-based malware pattern analysis (2014)

Behavior-based analysis of emerging malware families involves finding suspicious patterns in large collections of execution traces. This activity cannot be automated for previously unknown malware families and thus malware analysts would benefit greatly from integrating visual analytics methods in their process. However existing approaches are limited to fairly static representations of data and there is no systematic characterization and abstraction of this problem domain. Therefore we performed a systematic literature study, conducted a focus group as well as semi-structured interviews with 10 malware analysts to elicit a problem abstraction along the lines of data, users, and tasks. The requirements emerging from this work can serve as basis for future design proposals to visual analytics-supported malware pattern analysis.
Tissue-specific expression and alternative mRNA processing of the mammalian acetylcholinesterase gene. (1993)

This study examines the tissue specificity and the gene products arising from alternative mRNA processing of the mammalian acetylcholinesterase gene. By splicing either alternative exons 5 or 6 in the mouse and human genes directly to the invariant exons (exons 2, 3, and 4), we show that the acetylcholinesterase species expressed by transfected recombinant DNA have the properties expected for the respective enzyme forms found in tissue. Antisense mRNA derived from these cDNAs has been employed to examine differential splicing in various tissues. In most cells, the hydrophilic form of AChE encoded by the exon 4 to exon 6 splice to form the mRNA is the predominant species. However, splicing of exon 4 to exon 5, yielding a mRNA encoding the glycophospholipid-linked form of acetylcholinesterase, is seen primarily in erythroid and to a lesser extent in AtT-20 cells. Only small amounts of this mRNA species appear in some other cells in culture. A novel third mRNA species, which arises from an extension of exon 4 without splicing to a downstream exon, is seen in mouse erythroid but not in human erythroid cells. A cDNA encoding this species when expressed in COS cells gives rise to a unique hydrophilic, secreted form of acetylcholinesterase. Transfection of a human genomic clone into mouse erythroleukemia cells does not result in the appearance of a mRNA species with an extension of exon 4 as seen with the endogenous mouse gene. Hence, differential splicing between the mouse and human genes appears intrinsic to the coding sequence and is not dependent solely on specific factors in the mouse erythroleukemia cell.
The t(4;14) Translocation in Myeloma Dysregulates Both FGFR3and a Novel Gene, MMSET, Resulting in IgH/MMSET Hybrid Transcripts (1998)

Previously we reported that a karyotypically silent t(4;14)(p16. 3;q32.3) translocation is present in about 25% of multiple myeloma (MM) tumors, and causes overexpression of FGFR3, which is 50 to 100 kb telomeric to the 4p16 breakpoints. Frequent FGFR3 kinase activating mutations in MM with t(4;14) translocations substantiate an oncogenic role for FGFR3. We now report that the 4p16 breakpoints occur telomeric to and within the 5' introns of a novel gene, MMSET (Multiple Myeloma SET domain). In normal tissues, MMSET has a complex pattern of expression with a short form (647 amino acids [aa]) containing an HMG box and hath region, and an alternatively spliced long form (1365 aa) containing the HMG box and hath region plus 4 PHD fingers and a SET domain. Although t(4;14) translocation results in IgH/MMSET hybrid transcripts, overexpression of MMSET also occurs from endogenous promoters on 4p16. Given the homology to HRX/MLL1/ALL1 at 11q23 that is dysregulated by translocations in acute leukemia, we hypothesize that dysregulation of MMSET contributes to neoplastic transformation in MM with t(4;14) translocation. This is the first example of an IgH translocation that simultaneously dysregulates two genes with oncogenic potential: FGFR3 on der(14) and MMSET on der(4).
Face Recognition Using Pseudo-2D Ergodic HMM (2006)

The work presented in this paper describes a novel pseudo-2D ergodic hidden Markov model (EHMM) based architecture for automatic face recognition. The primary HMM of this model being ergodic in nature, gives the flexibility to switch between the states, contrary to conventional pseudo-2D HMM, which follows a top-to-bottom approach. The new approach helps in better modeling the different variations of a human face. We present a segmental K-means algorithm for training the pseudo-2D EHMM, thereby jointly optimizing the observation densities and the state transitions corresponding to different variations of the face. The performance of the proposed method is presented with discrete cosine transform (DCT) and the DCT-mod2 feature sets for the Olivetti Research Laboratory (ORL) database. The better modeling capability of the proposed architecture along with the robustness of DCT-mod2 feature set to illumination direction changes, proves to be an excellent combination for automatic face recognition
Antigenic lipopolysaccharide components of Legionella pneumophila recognized by monoclonal antibodies: possibilities and limitations for division of the species into serogroups (1997)

Legionella pneumophila accounts for the majority of cases of Legionnaires' disease. By using rabbit antisera, the species has been divided into 14 numbered and 1 unnumbered serogroups. To recognize the antigenic diversity of the lipopolysaccharide (LPS) responsible for this classification, the Dresden Legionella LPS MAb panel, containing 98 monoclonal antibodies (MAbs), was created. Each serogroup reference strain possesses at least one specific epitope not found on any other reference strain and therefore designated the serogroup-specific epitope. When the appropriate MAbs were used for serotyping of 1,064 human and environmental isolates, 1,045 (98%) could be placed into the known serogroups. In most cases (97%), this was in agreement with the polyclonal typing. Of the 29 isolates that showed strong cross-reactivities with the rabbit antiserum panel, 11 could be typed easily by MAbs; for the remaining 18, however, only serogroup-cross-reactive epitopes could be determined. Below the serogroup level, monoclonal subtypes were found for 11 serogroups. Altogether, the Dresden Legionella LPS MAb panel was able to divide the 1,064 isolates tested into 64 phenons, indicating its usefulness for both serogrouping and subgrouping of L. pneumophila strains. In order to compare the identities of patient and environmental isolates, testing their reactivity with MAbs should be the first step, especially if large numbers of colonies are to be typed. Only in cases of identical patterns are the more time consuming and expensive genetic fingerprints necessary. Moreover, the MAbs can also be used for specific antigen detection in respiratory specimens on the serogroup or subgroup level.
Identification of isoaspartyl-containing sequences in peptides and proteins that are usually poor substrates for the class II protein carboxyl methyltransferase. (1990)

We have found that a chicken egg lysozyme derivative (beta-101-lysozyme) containing an L-isoaspartyl residue at position 101 has a Km for methylation by the human erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase (EC 2.1.1.77) of 183 microM, about 30 times higher than that expected from previous studies with isoaspartyl-containing peptides. In the course of investigating the reasons for this poor enzyme recognition, we found that charged residues on the carboxyl side of isoaspartyl residues had a large effect on the affinity of the enzyme for synthetic peptides. This is best illustrated by the lysozyme-related peptide YVSisoDGDG, which has a Km for methylation of 469 microM. When the penultimate aspartyl residue is replaced by a cysteinyl residue, the Km drops to 4.6 microM, comparable to other peptides of similar size. Furthermore, replacing it with a cysteic acid residue results in a Km of 104 microM, suggesting that a negative charge at this position may lead to a weaker affinity of the peptide substrate for the methyltransferase. Assays with additional synthetic peptides indicate that moving the negative charge to the first or third residue on the carboxyl side of the isoaspartyl residue has a similar but less severe effect in reducing its affinity for the methyltransferase. Enzymatic methylation has recently been proposed to be the first step in the conversion of abnormal isoaspartyl residues to aspartyl residues. The results reported here, however, along with previous evidence that protein tertiary structure can inhibit isoaspartyl methylation, suggest that only a subclass of damaged sites are capable of efficiently entering a putative repair pathway; the sites not recognized by the methyltransferase may accumulate in vivo.
Celecoxib for the Prevention of Colorectal Adenomatous Polyps (2006)

The use of 400 mg of celecoxib once daily significantly reduced the occurrence of colorectal adenomas within three years after polypectomy. (ClinicalTrials.gov number, NCT00141193 [ClinicalTrials.gov].).
Plasminogen Activator Inhibitor Type 1 Promotes the Self-association of Vitronectin into Complexes Exhibiting Altered Incorporation into the Extracellular Matrix (2002)

Serine proteinase inhibitors, including plasminogen activator inhibitor type 1 (PAI-1) and antithrombin, are key regulators of hemostatic processes such as thrombosis and wound healing. Much evidence suggests that PAI-1 can influence such processes, as well as pathological events like tumor metastasis, through its ability to directly regulate binding of blood platelets and cells to extracellular substrata. One way that PAI-1 influences these processes may be mediated through its binding to the plasma protein vitronectin. Binding to PAI-1 results in the incorporation of vitronectin into a higher order complex with a potential for multivalent interactions (Podor, T. J., Shaughnessy, S. G., Blackburn, M. N., and Peterson, C. B. (2000) J. Biol. Chem. 275, 25402-25410). In this study, evidence is provided to support this concept from studies on the effects of PAI-1-induced multimerization on the interactions of vitronectin with matrix components and cell surface receptors. By monitoring complex formation and stability over time using size-exclusion high performance liquid chromatography, a correlation is made between PAI-1-induced multimerization and enhanced cell/matrix binding properties of vitronectin. This evidence indicates that PAI-1 alters the adhesive functions of vitronectin by converting the protein via the higher order complex to a self-associated, multivalent species that is functionally distinct from the abundant monomeric form found in the circulation.
Establishment and characterization of three new continuous cell lines derived from human breast carcinomas. (1978)

Three continuous lines of mammary tumor cells (ZR-75-1, ZR-75-27, and ZR-75-30) have been established from malignant effusions of two women with breast cancer. Differentiated properties expressed by each cell line include: (a) epithelial morphology (by light and electron microscopy) resembling that of the parental tumors; (b) presence of receptors for estrogen and other steroid hormones; and (c) growth responsiveness to estrogen and/or progesterone. All three cell lines possess human karyotypes that differ from one another in modal chromosome number as well as in characteristic marker chromosomes. Two of the cultures (ZR-75-27 and ZR-75-30), although derived from the same patient, have stable differences in their karyotypes.
An integrated approach to legacy data for multimedia applications (2002)

We describe our experimental approach to legacy data for multimedia applications in the WWW environment. There have been many proposals for the connection to legacy data and there have been considerable results. Unfortunately these results do not cover some real environmental factors such as the guarantee of persistent results for existing data (for example, payment for a purchase). Our approach allows easy access to legacy data via the Web and our new WWW interface enables users easily to perform common gateway interface (CGI) programming. We also expect that mission critical jobs such as banking and financial operations can be served through the WWW effectively.
Nerve Growth Factor Expression Correlates With Perineural Invasion and Pain in Human Pancreatic Cancer (1999)

Enhanced expression of the NGF/TrkA system may influence perineural invasion and may contribute to the pain syndrome in human pancreatic cancer.