gebhart/patrepeval huggingface dataset:
Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device (2018)

We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.
A Primer On Internet and TCP/IP Tools (1994)

This memo is an introductory guide to some of the TCP/IP and Internet
tools and utilities that allow users to access the wide variety of
information on the network, from determining if a particular host is
up to viewing a multimedia thesis on foreign policy. It also describes
discussion lists accessible from the Internet, ways to obtain Internet
documents, and resources that help users weave their way through the
Internet. This memo provides information for the Internet community.
This memo does not specify an Internet standard of any kind.
Unlocking Short Read Sequencing for Metagenomics (2010)

This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.
Effect of Margin Status on Local Recurrence After Breast Conservation and Radiation Therapy for Ductal Carcinoma In Situ (2009)

Surgical margins negative for DCIS should be obtained after BCS for DCIS. A margin threshold of 2 mm seems to be as good as a larger margin when BCS for DCIS is combined with RT.
Reoxygenation‐specific activation of the antioxidant transcription factor Nrf2 mediates cytoprotective gene expression in ischemia‐reperfusion injury (2006)

Tissue reoxygenation following hypoxia is associated with ischemia-reperfusion injury (IRI) and may signal the development of ischemic preconditioning, an adaptive state that is protective against subsequent IRI. Here we used microarray RNA analysis of in vivo and in vitro models of IRI to delineate the underlying molecular mechanisms. Microarray analysis of renal tissue after ischemia-reperfusion revealed a number of highly up-regulated antioxidant genes including aldehyde dehydrogenases (ALDH1A1 and ALDH1A7), glutathione S-transferases (GSTM5, GSTA2 and GSTP1), and NAD(P)H quinone oxidoreductase (NQO1). The transcription factor NF-E2-related factor-2 (Nrf2), a master regulator of this antioxidant response, is also elevated in IRI. Furthermore, microarray analysis of renal epithelial cells exposed to hypoxia/reoxygenation identified Nrf2 to be up-regulated on reoxygenation. We also reveal a reoxygenation-specific nuclear accumulation of Nrf2 protein and subsequent activation of a NQO1 promoter reporter construct. Attenuating reactive oxygen species (ROS) in reoxygenation using the antioxidant N-acetyl cysteine results in inhibition of Nrf-2 activation. mRNA levels for Nrf2-dependent genes were detected in human liver biopsy 1 h after transplantation. These results indicate that reoxygenation-dependent Nrf-2 activity facilitates ischemic preconditioning through the induction of antioxidant gene expression and that ROS may be critical in signaling this event.
Sex difference in the near-24-hour intrinsic period of the human circadian timing system (2011)

The circadian rhythms of melatonin and body temperature are set to an earlier hour in women than in men, even when the women and men maintain nearly identical and consistent bedtimes and wake times. Moreover, women tend to wake up earlier than men and exhibit a greater preference for morning activities than men. Although the neurobiological mechanism underlying this sex difference in circadian alignment is unknown, multiple studies in nonhuman animals have demonstrated a sex difference in circadian period that could account for such a difference in circadian alignment between women and men. Whether a sex difference in intrinsic circadian period in humans underlies the difference in circadian alignment between men and women is unknown. We analyzed precise estimates of intrinsic circadian period collected from 157 individuals (52 women, 105 men; aged 18-74 y) studied in a month-long inpatient protocol designed to minimize confounding influences on circadian period estimation. Overall, the average intrinsic period of the melatonin and temperature rhythms in this population was very close to 24 h [24.15 ± 0.2 h (24 h 9 min ± 12 min)]. We further found that the intrinsic circadian period was significantly shorter in women [24.09 ± 0.2 h (24 h 5 min ± 12 min)] than in men [24.19 ± 0.2 h (24 h 11 min ± 12 min); P < 0.01] and that a significantly greater proportion of women have intrinsic circadian periods shorter than 24.0 h (35% vs. 14%; P < 0.01). The shorter average intrinsic circadian period observed in women may have implications for understanding sex differences in habitual sleep duration and insomnia prevalence.
Photoacoustic detection of metastatic melanoma cells in the human circulatory system (2006)

Detection of disseminating tumor cells among patients suffering from various types and stages of cancer can function as an early warning system, alerting the physician of the metastatic spread or recurrence of the disease. Early detection of such cells can result in preventative treatment of the disease, while late stage detection can serve as an indicator of the effectiveness of chemotherapeutics. The prognostic value of exposing disseminating tumor cells poses an urgent need for an efficient, accurate screening method for metastatic cells. We propose a system for the detection of metastatic circulating tumor cells based on the thermoelastic properties of melanoma. The method employs photoacoustic excitation coupled with a detection system capable of determining the presence of disseminating cells within the circulatory system in vitro. Detection trials consisting of tissue phantoms and a human melanoma cell line resulted in a detection threshold of the order of ten individual cells, thus validating the effectiveness of the proposed mechanism. Results imply the potential to assay simple blood draws, from healthy and metastatic patients, for the presence of cancerous melanoma providing an unprecedented method for routine cancer screening.
Raman studies of bovine serum albumin (1976)

Abstract The Raman Spectra of bovine serum albumin have been obtained in the solute state, in alkaline and acidic solutions, and in the gel. The reversible denaturations of bovine serum albumin solutions by heat, acid's, and alkali were studied and a new mechanism for heat denaturation has been proposed based on a continuous unfolding of the α‐helices.
Interferon-α Induces TRAIL Expression and Cell Death Via an IRF-1-Dependent Mechanism in Human Bladder Cancer Cells (2007)

Apoptosis induced by interferon-alpha (IFNalpha) is associated with induction of TRAIL in a number of different cell types. Here we examined whether or not TRAIL was required for apoptosis in a model human bladder cancer cell line (UM-UC-12) and defined the molecular mechanisms involved in IFNalpha-induced TRAIL expression. Exposure to IFNalpha resulted in concentration-dependent induction of TRAIL and apoptosis. Inhibition of TRAIL or downstream components of the TRAIL cell death pathway (FADD, caspase-8) via siRNA-mediated knockdown attenuated IFNalpha-induced cell death, thereby implicating TRAIL in the response. IFNalpha induced rapid STAT-1 phosphorylation and DNA binding activity and subsequent accumulation of IRF-1. Transfection with siRNAs directed against STAT-1 or IRF-1 inhibited IFNalpha-induced TRAIL production and cell death, and chromatin immunprecipitation (ChIP) analyses demonstrated that IFNalpha induced direct, time-dependent binding of both transcription factors to the TRAIL promoter. Together, our results demonstrate that IFNalpha induces TRAIL expression via a STAT-1/IRF-1-dependent mechanism in human bladder cancer cells, and this induction of TRAIL plays an important role in IFNalpha-induced cell killing.
Bacterial Biofilms: A Common Cause of Persistent Infections (1999)

Bacteria that attach to surfaces aggregate in a hydrated polymeric matrix of their own synthesis to form biofilms. Formation of these sessile communities and their inherent resistance to antimicrobial agents are at the root of many persistent and chronic bacterial infections. Studies of biofilms have revealed differentiated, structured groups of cells with community properties. Recent advances in our understanding of the genetic and molecular basis of bacterial community behavior point to therapeutic targets that may provide a means for the control of biofilm infections.
Current balloon‐expandable transcatheter heart valve and delivery systems (2009)

Transcatheter valves and delivery systems continue to improve in terms of profile and ease of use.
The human Ah receptor: hints from dioxin toxicities to deregulated target genes and physiological functions (2013)

Marked species differences of dioxin toxicity prompted the review of three well-studied human dioxin toxicities (chloracne, inflammation and cancer) and deregulated Ah receptor (AhR) target genes to obtain hints as to the physiological functions of this receptor. Dioxin here stands for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Microarray analysis of dermal cysts from a dioxin-poisoned patient revealed, in addition to induced CYP1A1, increased expression of gremlin, an antagonist of bone morphogenetic proteins. Dioxin-mediated skin and intestinal inflammation is associated with deregulated T cell differentiation. In the supernatant of CD4+ T cells obtained from the dioxin-poisoned patient, increased interleukin-22 was detected, a cytokine that may be controlled in part by AhR-regulated Notch. Cancer is one of the long-term consequences of chronic inflammation. In line with dioxin-sensitive lymphoid tissue, enhanced death of lymphoid cancer was observed in the dioxin-exposed Seveso population 25 years after poisoning. Accumulating evidence suggests that endogenous AhR ligands, notably the tryptophan photoproduct 6-formylindolo[3,2-b]carbazole, in contrast to TCDD, is rapidly metabolized by AhR-induced CYP1A1. The feedback loop between 6-formylindolo[3,2-b]carbazole, AhR and CYP1A1 guarantees transient activation that, in contrast to sustained activation by TCDD, may be essential for a putative role of the AhR in stem/progenitor cell homeostasis.
A Harpin Binding Site in Tobacco Plasma Membranes Mediates Activation of the Pathogenesis-Related Gene HIN1 Independent of Extracellular Calcium but Dependent on Mitogen-Activated Protein Kinase Activity (2001)

Harpin from the bean halo-blight pathogen Pseudomonas syringae pv phaseolicola (harpin(Psph)) elicits the hypersensitive response and the accumulation of pathogenesis-related gene transcripts in the nonhost plant tobacco. Here, we report the characterization of a nonproteinaceous binding site for harpin(Psph) in tobacco plasma membranes, which is assumed to mediate the activation of plant defense responses in a receptor-like manner. Binding of 125I-harpin(Psph) to tobacco microsomal membranes (dissociation constant = 425 nM) and protoplasts (dissociation constant = 380 nM) was specific, reversible, and saturable. A close correlation was found between the abilities of harpin(Psph) fragments to elicit the transcript accumulation of the pathogenesis-related tobacco gene HIN1 and to compete for binding of 125I-harpin(Psph) to its binding site. Another elicitor of the hypersensitive response and HIN1 induction in tobacco, the Phytophthora megasperma-derived beta-elicitin beta-megaspermin, failed to bind to the putative harpin(Psph) receptor. In contrast to activation by beta-megaspermin, harpin(Psph)-induced activation of the 48-kD salicylic acid-responsive mitogen-activated protein kinase (MAPK) and HIN1 transcript accumulation were independent of extracellular calcium. Moreover, use of the MAPK kinase inhibitor U0126 revealed that MAPK activity was essential for pathogenesis-related gene expression in harpin(Psph)-treated tobacco cells. Thus, a receptor-mediated MAPK-dependent signaling pathway may mediate the activation of plant defense responses induced by harpin(Psph).
Hardware-software co-design of embedded reconfigurable architectures (2000)

In this paper we describe a new hardware/software partitioning approach for embedded reconfigurable architectures consisting of a general-purpose processor (CPU), a dynamically reconfigurable datapath (e.g. an FPGA), and a memory hierarchy. We have developed a framework called Nimble that automatically compiles system-level applications specified in C to executables on the target platform. A key component of this framework is a hardware/software partitioning algorithm that performs fine-grained partitioning (at loop and basic-block levels) of an application to execute on the combined CPU and datapath. The partitioning algorithm optimizes the global application execution time, including the software and hardware execution times, communication time and datapath reconfiguration time. Experimental results on real applications show that our algorithm is effective in rapidly finding close to optimal solutions.
A large deletion together with a point mutation in the GALC gene is a common mutant allele in patients with infantile Krabbe disease (1995)

Galactocerebrosidase (GALC) activity is deficient in all patients with globoid cell leukodystrophy (GLD). While most patients have the severe infantile form of this autosomal recessive disorder (Krabbe disease), patients up to 50 years of age have been diagnosed in this laboratory. With the cloning of the GALC cDNA and availability of information regarding the gene organization, patients can be evaluated for their disease-causing mutations. We now report that a large deletion, together with a polymorphic C to T transition at position 502 of cDNA (counting from the A of the initiation codon), is responsible for a large number of disease-causing alleles in patients with Krabbe disease. Of 48 patients evaluated, 10 were found to be homozygous for the 502/del allele, five patients were heterozygous for this allele, 21 patients were heterozygous for the 502 mutation (presence of the deletion could not be confirmed), and one infantile patient was homozygous for the 502 mutation but at least one allele was not deleted. No patient was found to have the deletion without the 502 polymorphism. The delineation of mutations causing infantile Krabbe disease will provide new information regarding structure-function relationships in this multi-subunit enzyme and will improve the identification of patients and carriers in some families.
Brain–computer interfaces for communication with nonresponsive patients (2012)

A substantial number of patients who survive severe brain injury progress to a nonresponsive state of wakeful unawareness, referred to as a vegetative state (VS). They appear to be awake, but show no signs of awareness of themselves, or of their environment in repeated clinical examinations. However, recent neuroimaging research demonstrates that some VS patients can respond to commands by willfully modulating their brain activity according to instruction. Brain-computer interfaces (BCIs) may allow such patients to circumvent the barriers imposed by their behavioral limitations and communicate with the outside world. However, although such devices would undoubtedly improve the quality of life for some patients and their families, developing BCI systems for behaviorally nonresponsive patients presents substantial technical and clinical challenges. Here we review the state of the art of BCI research across noninvasive neuroimaging technologies, and propose how such systems should be developed further to provide fully fledged communication systems for behaviorally nonresponsive populations.
Biochemical Methods for Detection and Measurement of Cyclic AMP and Adenylyl Cyclase Activity (2003)

Many drugs and hormones interact with plasma membrane receptors to induce changes in the production of intracellular second messengers. The first such messenger to be identified was adenosine-3′,5′ cyclic monophosphate (cAMP), discovered by Sutherland and Rall in the late 1950s (1). Changes in cellular cAMP levels can occur from increases or decreases in its biosynthesis (which results from the catalytic conversion of ATP to cAMP by the enzyme adenylyl cyclase) or by altering its degradation (which results from hydrolysis of the cyclic phosphodiester bond by cyclic nucleotide or cAMP phosphodiesterases).
A novel thermoregulatory system maintains perioperative normothermia in children undergoing elective surgery (2001)

Perioperative thermoregulation using the Allon system is safe and effective in maintaining body temperature within a narrow range in children undergoing brief surgical procedures.
Norovirus Vaccine against Experimental Human Norwalk Virus Illness (2011)

This norovirus VLP vaccine provides protection against illness and infection after challenge with a homologous virus. (Funded by LigoCyte Pharmaceuticals and the National Institutes of Health; ClinicalTrials.gov number, NCT00973284.).
The applicability of the visual programming language LabVIEW to large real-world applications (2002)

Graphical programming languages allow a natural, intuitive man-machine interaction. As a result, graphical programming has gained much popularity over the past several years, primarily because many scientists and engineers have experienced improvements in programming efficiency due to the natural understandability of graphical programming tools. In general, however, there is a perception that the graphical paradigm does not lend itself well to large-scale applications. The paper examines the suitability of graphical programming languages to real-world applications. The specific graphical programming language evaluated in this paper is LabVIEW, though some of the concepts discussed apply to other visual programming languages as well. A relatively large case study involving simulation as well as real-time acquisition programmed in LabVIEW is investigated. Advantages and limitations of LabVIEW for such applications are discussed.
Human cardiac troponin I: precise identification of antigenic epitopes and prediction of secondary structure (1998)

The presence of human cardiac troponin I (hcTnI) in serum is considered to be a highly specific biochemical marker of acute myocardial infarction. To better understand the antigenic properties of hcTnI, a set of 68 overlapping peptides covering the complete amino acid sequence of hcTnI was prepared and used in epitope mapping experiments. All 16 anti-hcTnI monoclonal antibodies tested were found to recognize a peptide epitope, indicating that recognition by anti-hcTnI monoclonal antibodies was not dependent on the tertiary structure of the protein. Furthermore, the peptide reactivity with anti-hcTnI polyclonal antibodies indicated that most of the sequence of the protein was antigenic; in particular, the N- and C-terminal extremities were found to be the strongest antigenic regions. By using accurate secondary structure prediction methods, hcTnI was found to be an all-alpha type protein, with five regions predicted as helices. Matching the results of the epitope analysis with the structural prediction led us to the view that hcTnI is not a globular protein but probably adopts an extended conformation, allowing a large part of the amino acid sequence of this molecule to be recognized by the immune system. This improved knowledge of the antigenic and structural properties of hcTnI may help in developing new antibodies and immunoassays for use in diagnosing myocardial infarction.
Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes (2007)

Parallel tetramolecular quadruplexes may be formed with short oligodeoxynucleotides bearing a block of three or more guanines. We analyze the properties of sequence variants of parallel quadruplexes in which each guanine of the central block was systematically substituted with a different base. Twelve types of substitutions were assessed in more than 100 different sequences. We conducted a comparative kinetic analysis of all tetramers. Electrospray mass spectrometry was used to count the number of inner cations, which is an indicator of the number of effective tetrads. In general, the presence of a single substitution has a strong deleterious impact on quadruplex stability, resulting in reduced quadruplex lifetime/thermal stability and in decreased association rate constants. We demonstrate extremely large differences in the association rate constants of these quadruplexes depending on modification position and type. These results demonstrate that most guanine substitutions are deleterious to tetramolecular quadruplex structure. Despite the presence of well-defined non-guanine base quartets in a number of NMR and X-ray structures, our data suggest that most non-guanine quartets do not participate favorably in structural stability, and that these quartets are formed only by virtue of the docking platform provided by neighboring G-quartets. Two notable exceptions were found with 8-bromo-guanine (X) and 6-methyl-isoxanthopterin (P) substitutions, which accelerate quadruplex formation by a factor of 10 when present at the 5' end. The thermodynamic and kinetic data compiled here are highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties.
CEACAM6 Cross-linking Induces Caveolin-1-dependent, Src-mediated Focal Adhesion Kinase Phosphorylation in BxPC3 Pancreatic Adenocarcinoma Cells (2004)

Despite lacking transmembrane or intracellular domains, glycosylphosphatidylinositol-anchored proteins can modulate intracellular signaling events, in many cases through aggregation within membrane "lipid raft" microdomains. CEACAM6 is a glycosylphosphatidylinositol-linked cell surface protein of importance in the anchorage-independent survival and metastasis of pancreatic adenocarcinoma cells. We examined the effects of antibody-mediated cross-linking of CEACAM6 on intracellular signaling events and anchorage-independent survival of the CEACAM6-overexpressing pancreatic ductal adenocarcinoma cell line, BxPC3. CEACAM6 cross-linking increased c-Src activation and induced tyrosine phosphorylation of p125(FAK) focal adhesion kinase. Focal adhesion kinase phosphorylation was dependent on c-Src kinase activation, for which caveolin-1 was required. CEACAM6 cross-linking induced a significant increase in cellular resistance to anoikis. These observations represent the first characterization of the mechanism through which this important cell surface oncoprotein influences intracellular signaling events and hence malignant cellular behavior.