gebhart/patrepeval huggingface dataset:
Disc-Like Mesogens: A Classification (1981)

Abstract Five mesomorphic phases are described in several disc-like liquid-crystals. They are hexalkanoyloxy benzenes, triphenylenes or truxenes, hexa-alkoxy triphenylenes, hexa-benzoates of triphenylene. Several of these compounds exhibit a complex polymorphism. Informations on the structures of these phases have been obtained by means of X-Ray diffraction; except a Nd namatic phase all the others one are columnar phases. At the same time a systematic study has been performed by the well known method of isomorphy. All these results allow us to propose a general classification of these phases.
Real-time focus range sensor (2002)

Structures of dynamic scenes can only be recovered using a real-time range sensor. Depth-from-defocus offers a direct solution to fast and dense range estimation. It is computationally efficient as it circumvents the correspondence problem faced by stereo and feature tracking in structure-from-motion. However, accurate depth estimation requires theoretical and practical solutions to a variety of problems including the recovery of textureless surfaces, precise blur estimation, and magnification variations caused by defocusing. Both textured and textureless surfaces are recovered using an illumination pattern that is projected via the same optical path used to acquire images. The illumination pattern is optimized to ensure maximum accuracy and spatial resolution in the computed depth. The relative blurring in two images is computed using a narrow-band linear operator that is designed by considering all the optical, sensing and computational elements of the depth-from-defocus system. Defocus-invariant magnification is achieved by the use of an additional aperture in the imaging optics. A prototype focus range sensor has been developed that produces up to 512/spl times/480 depth estimates at 30 Hz with an accuracy better than 0.3%. Several experimental results are included to demonstrate the performance of the sensor.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anti-PD-1/PD-L1 therapy for infectious diseases: learning from the cancer paradigm (2017)

Anti-PD-1/PD-L1 therapy holds promise as adjunctive therapy for chronic infectious diseases such as tuberculosis and HIV, and must therefore be tested in randomized clinical trials.
THEORETICAL MODEL OF THE HIPPOCAMPAL-CORTICAL MEMORY SYSTEM MOTIVATED BY PHYSIOLOGICAL FUNCTIONS IN THE HIPPOCAMPUS (1994)

Electrical stimulation in the hippocampus leads to an increase in synaptic efficacy that lasts for many hours. This long-term potentiation (LTP) of synaptic transmission is presumed to play a crucial role in learning and memory in the brain. Our experimental data on the hippocampus show that the homosynaptic LTP and the associative LTP are highly sensitive to temporal pattern stimuli given by different correlations between successive interstimulus events, even when the mean rate of the stimuli is held constant; negatively correlated stimuli have relatively little LTP, whereas positively correlated stimuli have greater LTP. This suggests that the detailed temporal properties of the stimulus are an important factor in inducing LTP and supports the possibility that temporal codes are used as indexes in associating/dissociating memory events in the hippocampus. Based on the physiological evidence, we propose a hypothesis on how association and dissociation of event memories are done in the hippocampal-cortical memory system. It is postulated that the association/dissociation memory is carried out by indexing the representations of events (memory contents) with temporal codes. The memory contents are supplied from the sensory association cortices, while the temporal codes are supplied from the decision-making/motivation area. The two inputs are mixed (indexing) in the ento-perirhinal area. Indexed signals are fed to hippocampus, where connection or disconnection of memory contents occurs, depending on the kind of index. Finally, association/dissociation of event memories is done in the association cortex according to a covariance rule: two events memories are associated when direct cortico-cortical inputs and indirect inputs from the hippocampus are positively correlated through the consolidation in hippocampus, and they are dissociated when two inputs are negatively correlated as a consequence of the disconnection in the hippocampus.
The eae gene of Citrobacter freundii biotype 4280 is necessary for colonization in transmissible murine colonic hyperplasia (1993)

Transmissible murine colonic hyperplasia is characterized by proliferation of anchored stem cells in the mucosa of the descending colon of laboratory mice and is caused by Citrobacter freundii biotype 4280. This bacterium produces attaching and effacing lesions in the descending colon prior to the onset of gross hyperplasia. By mutational analysis, the chromosomal eae gene of C. freundii biotype 4280 was shown to be necessary for colonic colonization. Conversely, bacteria cured of a 65-kb plasmid, which was identified in C. freundii biotype 4280, were not attenuated for colonic colonization or for the induction of colonic hyperplasia.
Deformation mechanisms in silicon nanoparticles (2011)

We report here on the observation of dislocation nucleation and glide in silicon nanoparticles, after phase transformation from diamond cubic to β-tin crystal structure, within the formed β-tin metallic phase region in atomistic simulations of indentation. The simulation results provide an explanation of the super-high hardness of silicon nanoparticles measured in experiments. By comparing the simulation results with experimental measurement of hardness, we are able to evaluate the performance of two widely used interatomic potential functions: Stillinger–Weber and Tersoff potentials. Through simulations, we have found a critical size of silicon nanoparticles where there is a change in deformation mechanisms, strength, and hardness. The effect of the applied strain rate on simulation results is also investigated.
Ancymidol blocks trichothecene biosynthesis and leads to accumulation of trichodiene in Fusarium sporotrichioides and Gibberella pulicaris (1987)

Ancymidol, a plant growth regulator, inhibited biosynthesis of diacetoxyscirpenol by Gibberella pulicaris (Fusarium sambucinum) in a defined liquid medium. Ancymidol also inhibited biosynthesis of T-2 toxin by a wild-type strain of Fusarium sporotrichioides and biosynthesis of diacetoxyscirpenol, deacetylated calonectrin, and dideacetylated calonectrin by mutant strains of this species. Ancymidol-treated cultures accumulated the hydrocarbon trichodiene, a biosynthetic precursor of the trichothecenes. Ancymidol did not block trichodiene accumulation by a trichodiene-producing mutant strain of F. sporotrichioides. Ancymidol appears to block the trichothecene biosynthetic pathway after formation of trichodiene and before formation of trichothecenes containing four or more oxygen atoms.
Phase 2 Trial of Single Agent Ipilimumab (Anti-CTLA-4) for Locally Advanced or Metastatic Pancreatic Adenocarcinoma (2010)

New, effective therapies are needed for pancreatic ductal adenocarcinoma. Ipilimumab can mediate an immunologic tumor regression in other histologies. This phase II trial evaluated the efficacy of Ipilimumab for advanced pancreatic cancer. Subjects were adults with locally advanced or metastatic pancreas adenocarcinoma with measurable disease, good performance status, and minimal comorbidities. Ipilimumab was administered intravenously (3.0 mg/kg every 3 wk; 4 doses/course) for a maximum of 2 courses. Response rate by response evaluation criteria in solid tumors criteria and toxicity were measured. Twenty-seven subjects were enrolled (metastatic disease: 20 and locally advanced: 7) with median age of 55 years (27 to 68 y) and good performance status (26 with Eastern Cooperative Oncology Group performance status =0 to 1). Three subjects experienced ≥ grade 3 immune-mediated adverse events (colitis:1, encephalitis:1, hypohysitis:1). There were no responders by response evaluation criteria in solid tumors criteria but a subject experienced a delayed response after initial progressive disease. In this subject, new metastases after 2 doses of Ipilimumab established progressive disease. But continued administration of the agent per protocol resulted in significant delayed regression of the primary lesion and 20 hepatic metastases. This was reflected in tumor markers normalization, and clinically significant improvement of performance status. Single agent Ipilimumab at 3.0 mg/kg/dose is ineffective for the treatment of advanced pancreas cancer. However, a significant delayed response in one subject of this trial suggests that immunotherapeutic approaches to pancreas cancer deserve further exploration.
DNA probes for the detection of mycoplasmas in genital specimens. (1987)

The utility of whole-genomic DNA probes for the detection of infections by genital mycoplasmas was investigated in 220 men attending a sexually transmitted diseases clinic. In 144 patients, probe results were compared with quantitative culture results. The prevalence of Mycoplasma hominis was 11% by culture, whereas the prevalence of ureaplasmas was 38%. The M. hominis DNA probe detected 9 of 16 M. hominis culture-positive specimens and 2 of 128 culture-negative specimens. The Ureaplasma urealyticum DNA probe detected 36 of 57 U. urealyticum culture-positive specimens and 18 of 87 culture-negative specimens. Most of the probe-negative culture-positive specimens had colony counts of less than 10(3) organisms/ml of specimen. The DNA probe does not require viable organisms, and the probe-positive, culture-negative specimens suggest that false-negative cultures occurred, perhaps due to specimen handling or insensitivity of culture methods for some strains of mycoplasmas.
A Methodology &#x00026; Tool for Determining Inter-component Dependencies Dynamically in J2EE Environments (2007)

The emergence of server side component models such as J2EE has considerably simplified the construction of enterprise applications. However the dependence of the enterprise on these applications and their proliferation has shifted the complexity in managing the environment in which these applications operate. The difficulty in management is cheifly due to the inter-dependencies that exist between the components that make up these applications. Changing one component can have unpredictable side effects in the performance and functional behavior of other components because of this coupling. Self management or autonomic computing looks into techniques of self for self-configuration, self-healing and self protection. We believe that in order for a middleware to be self-managing, it is first necessary to obtain and maintain its topology which characterizes the components and their inter-dependencies making up this complex distributed environment. We present here a methodology and a tool to non-intrusively and dynamically extract and store the component topology from a distributed execution environment. The techniques presented in this paper have been evolved primarily for a J2EE environment although they can be applied without loss of generality to any distributed object system.
Isolation, Solution Structure, and Insecticidal Activity of Kalata B2, a Circular Protein with a Twist:  Do Möbius Strips Exist in Nature?, (2004)

A large number of macrocyclic miniproteins with diverse biological activities have been isolated from the Rubiaceae, Violaceae, and Cucurbitaceae plant families in recent years. Here we report the three-dimensional structure determined using (1)H NMR spectroscopy and demonstrate potent insecticidal activity for one of these peptides, kalata B2. This peptide is one of the major components of an extract from the leaves of the plant Oldenlandia affinis. The structure consists of a distorted triple-stranded beta-sheet and a cystine knot arrangement of the disulfide bonds and is similar to those described for other members of the cyclotide family. The unique cyclic and knotted nature of these molecules makes them a fascinating example of topologically complex proteins. Examination of the sequences reveals that they can be separated into two subfamilies, one of which contains a larger number of positively charged residues and has a bracelet-like circularization of the backbone. The second subfamily contains a backbone twist due to a cis-peptidyl-proline bond and may conceptually be regarded as a molecular Mobius strip. Kalata B2 is the second putative member of the Mobius cyclotide family to be structurally characterized and has a cis-peptidyl-proline bond, thus validating the suggested name for this subfamily of cyclotides. The observation that kalata B2 inhibits the growth and development of Helicoverpa armigera larvae suggests a role for the cyclotides in plant defense. A comparison of the sequences and structures of kalata B1 and B2 provides insight into the biological activity of these peptides.
Toward functional magnetic stimulation (FMS) theory and experiment (1994)

This paper examines the use of magnetic fields to functionally stimulate peripheral nerves. All electric fields are induced via a changing magnetic field whose flux is entirely confined within a closed magnetic circuit. Induced electric fields are simulated using a nonlinear boundary element solver. The induced fields are solved using duality theory. The accuracy of these predictions is verified by saline bath experiments. Next, the theory is applied to the stimulation of nerves using small, partially occluded ferrite and laminated vanadium permendur cores. Experiments demonstrate the successful stimulation of peripheral nerves in the African bullfrog with 11 mA, 153 mV excitations. These results offer a new vista of possibilities in the area of functional nerve stimulation. Unlike functional electric stimulation (FES), FMS does not involve any half cell reactions, and thus would not have the commensurate FES restrictions regarding balanced biphasic stimulation, strength duration balances, and oxidation issues, always exercising care that the electrodes remain in the reversible operating regime.
Concordant and Discordant Regulation of Target Genes by miR-31 and Its Isoforms (2013)

It has been shown that imprecise cleavage of a primary or precursor RNA by Drosha or Dicer, respectively, may yield a group of microRNA (miRNA) variants designated as "isomiR". Variations in the relative abundance of isoforms for a given miRNA among different species and different cell types beg the question whether these isomiRs might regulate target genes differentially. We compared the capacity of three miR-31 isoforms (miR-31-H, miR-31-P, and miR-31-M), which differ only slightly in their 5'- and/or 3'-end sequences, to regulate several known targets and a predicted target, Dicer. Notably, we found isomiR-31s displayed concordant and discordant regulation of 6 known target genes. Furthermore, we validated a predicted target gene, Dicer, to be a novel target of miR-31 but only miR-31-P could directly repress Dicer expression in both MCF-7 breast cancer cells and A549 lung cancer cells, resulting in their enhanced sensitivity to cisplatin, a known attribute of Dicer knockdown. This was further supported by reporter assay using full length 3'-untranslated region (UTR) of Dicer. Our findings not only revealed Dicer to be a direct target of miR-31, but also demonstrated that isomiRs displayed similar and disparate regulation of target genes in cell-based systems. Coupled with the variations in the distribution of isomiRs among different cells or conditions, our findings support the possibility of fine-tuning gene expression by miRNAs.
Vascular endothelial growth factor causally contributes to the angiogenic response upon ultraviolet B irradiation in vivo (2002)

Summary Background Ultraviolet (UV)‐B irradiation has been shown to be an inducer of vascular endothelial growth factor (VEGF) in primary keratinocytes and epidermal cell lines in vitro. Objectives To determine the expression pattern and the causal role of VEGF in the UVB‐mediated angiogenic response in vivo in human skin and in a mouse model. Methods Skin biopsies or epidermal lysates thereof were studied for VEGF expression following UVB irradiation at a dose of 50 or 60 mJ cm−2, respectively, using immunostaining and a VEGF‐specific highly sensitive sandwich enzyme‐linked immunosorbent assay. The VEGF‐dependent increase in vessels upon repetitive UVB irradiation was studied in skh‐1 hairless mice using immunostaining for factor VIII‐related antigen (FVIII RAG) in the presence and absence of intraperitoneally injected neutralizing VEGF antibodies. Results VEGF was found to be induced in the epidermis following UVB irradiation of human and mouse skin. Repetitive UVB irradiation of skh‐1 hairless mice resulted in an increase in FVIII RAG positive vessels in the skin. UVB‐induced angiogenic response could be partly abrogated by neutralizing antibodies against VEGF, while isotype‐matched IgG control antibodies did not reveal any suppressive effect. Conclusions Our results support previous in vitro data and show the in vivo relevance of VEGF as a paracrine inducer of cutaneous vessels after UVB irradiation.
Functional analysis of human T cell subsets defined by monoclonal antibodies. V. Suppressor cells within the activated OKT4+ population belong to a distinct subset. (1982)

In the present report, we characterize a monoclonal antibody directed at a surface differentiation antigen on human T cells. The monoclonal antibody, OKT17, recognizes a cell surface antigen present on the majority of resting normal peripheral T cells. In contrast, OKT17 is unreactive with normal B cells, B cell lines, T cell lines, or SIg+ CLL. Interestingly, after activation, the antigen recognized by OKT17 is lost from a subset of OKT4+ cells. We took advantage of this finding to explore further the functional heterogeneity within activated OKT4+ cells. Evidence was obtained that the PWM-activated OKT4+ subset remaining after depletion of OKT17-reactive T cells (OKT4+ 17-) contains radiosensitive helperr cells but is devoid of suppressor cells. In contrast, the activated OKT4+ 17+ population contains potent radiosensitive suppressor cells as well as radioresistant helpe cells. Taken together, these studies suggest that the OKT17 monoclonal antibody can differentiate two functionally mature, activated OKT4+ human T cells: OKT4+ OKT17+ radiosensitive suppressor cells and OKT4+ 17- radiosensitive helper cells.
Signal processing handbook (1988)

This book contains introductory, systematic treatment of the many interrelated aspects. Twenty-three contributions address the fundamentals, spectral estimation algorithms, image processing, land and ocean seismic data, telecommunications, 3-D object reconstructions.
Ontologies: principles, methods and applications (1996)

Abstract This paper is intended to serve as a comprehensive introduction to the emerging field concerned with the design and use of ontologies. We observe that disparate backgrounds, languages, tools and techniques are a major barrier to effective communication among people, organisations and/or software understanding (i.e. an “ontology”) in a given subject area, can improve such communication, which in turn, can give rise to greater reuse and sharing, inter-operability, and more reliable software. After motivating their need, we clarify just what ontologies are and what purpose they serve. We outline a methodology for developing and evaluating ontologies, first discussing informal techniques, concerning such issues as scoping, handling ambiguity, reaching agreement and producing definitions. We then consider the benefits and describe, a more formal approach. We re-visit the scoping phase, and discuss the role of formal languages and techniques in the specification, implementation and evalution of ontologies. Finally, we review the state of the art and practice in this emerging field, considering various case studies, software tools for ontology development, key research issues and future prospects.
Managing Hematologic Toxicities in the Oncology Patient (2007)

Myelosuppression associated with antineoplastic therapy may lead to neutropenia, anemia, or both, resulting in an increased risk for infection, fatigue, diminished quality of life, and reduced survival. Neutropenia can result in dose reductions and treatment delays. Hematopoietic growth factors have been used effectively as supportive therapy to reduce antineoplastic therapy-associated neutropenia and anemia. This article discusses management of neutropenia and anemia secondary to antineoplastic therapy, new medications, and nursing considerations.
Total Internal Reflection Fluorescence Microscopy in Cell Biology (2001)

Key events in cellular trafficking occur at the cell surface, and it is desirable to visualize these events without interference from other regions deeper within. This review describes a microscopy technique based on total internal reflection fluorescence which is well suited for optical sectioning at cell-substrate regions with an unusually thin region of fluorescence excitation. The technique has many other applications as well, most notably for studying biochemical kinetics and single biomolecule dynamics at surfaces. A brief summary of these applications is provided, followed by presentations of the physical basis for the technique and the various ways to implement total internal reflection fluorescence in a standard fluorescence microscope.
Isolation and expression of a cDNA clone encoding a bovine UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (1993)

NH2-terminal amino acid sequence obtained from a UDP-GalNAc:polypeptide N-acetylgalactosaminyl-transferase (GalNAc-transferase) isolated from bovine colostrum was used for the construction of synthetic oligonucleotide primers. Subsequent polymerase chain reaction and library screenings of a bovine intestine cDNA library produced seven positive clones. The largest clone had a 2294-base pair insert that contained an open reading frame coding for a protein composed of 559 amino acids with a predicted polypeptide molecular mass of 64,173 Da. The cloned molecule has no significant sequence homology to previously reported cloned glycosyltransferases, but appears to have a similar domain structure. It is a type II membrane protein with a 23-amino acid putative transmembrane region starting 8 amino acids from the NH2 terminus. The transmembrane segment of the molecule is immediately followed by a sequence rich in proline residues. The molecule contains three consensus sequences for N-linked glycosylation and five predicted sites for O-glycosylation. Northern blot analysis of poly(A+) mRNA isolated from Madin-Darby bovine kidney cells, bovine mammary tissue, and eight human tissues demonstrated the expression of two transcripts differing in size by approximately 1 kilobase. The cloned DNA was expressed in insect cells using a baculovirus vector. This resulted in an almost 100-fold increase in GalNAc-transferase activity in lysates prepared from cells infected with virus containing the GalNAc-transferase gene compared to cells infected with virus containing DNA coding for an unrelated molecule or uninfected cells. Immunoprecipitation from lysates prepared from infected cells labeled in vivo with [35S] methionine showed a large increase in the recovery of an approximately 67-kDa protein.