gebhart/patrepeval huggingface dataset:
Molecular Analysis of Model Gut Microbiotas by Imaging Mass Spectrometry and Nanodesorption Electrospray Ionization Reveals Dietary Metabolite Transformations (2012)

The communities constituting our microbiotas are emerging as mediators of the health-disease continuum. However, deciphering the functional impact of microbial communities on host pathophysiology represents a formidable challenge, due to the heterogeneous distribution of chemical and microbial species within the gastrointestinal (GI) tract. Herein, we apply imaging mass spectrometry (IMS) to localize metabolites from the interaction between the host and colonizing microbiota. This approach complements other molecular imaging methodologies in that analytes need not be known a priori, offering the possibility of untargeted analysis. Localized molecules within the GI tract were then identified in situ by surface sampling with nanodesorption electrospray ionization Fourier transform ion cyclotron resonance-mass spectrometry (nanoDESI FTICR-MS). Products from diverse structural classes were identified including cholesterol-derived lipids, glycans, and polar metabolites. Specific chemical transformations performed by the microbiota were validated with bacteria in culture. This study illustrates how untargeted spatial characterization of metabolites can be applied to the molecular dissection of complex biology in situ.
Anti-persistence: History Independent Data Structures. (2001)

Many data structures give away much more information than they were intended to. Whenever privacy is important, we need to be concerned that it might be possible to infer information from the memory representation of a data structure that is not available through its &amp;quot;legitimate&amp;quot; interface. Word processors that quietly maintain old versions of a document are merely the most egregious example of a general problem. We deal with data structures whose current memory representation does not reveal their history. We focus on dictionaries, where this means revealing nothing about the order of insertions or deletions. Our first algorithm is a hash table based on open addressing, allowing O(1) insertion and search. We also present a history independent dynamic perfect hash table that uses space linear in the number of elements inserted and has expected amortized insertion and deletion time O(1). To solve the dynamic perfect hashing problem we devise a general scheme for history independent memory allocation. For fixed-size records this is quite efficient, with insertion and deletion both linear in the size of the record. Our variable-size record scheme is efficient enough for dynamic perfect hashing but not for general use. The main open problem we leave is whether it is possible to implement a variable-size record scheme with low overhead.
The Structure of a Stable Serrulatane Diterpenoid Acetal From Eremophila-Rotundifolia (1985)

The serrulatenol (1a), a stable diterpenoid acetal from remophilia rotundifolia, has been shown to be (13S,18R)-5,18:13,18- diepoxyserrulat-14-en-8-ol by chemical and spectroscopic characterization and by single-crystal X-ray analysis of the p- bromobenzoate . This compound crystallizes as clear prisms in the monoclinic space group P21 with a 9.112(1), b 9.743(2), c 13.423(3) ?, ß 102.27(5)° and Z 2. The structural final refinement of a blocked-matrix least-squares calculation converged with R 0.038 and Rw 0.041.
Improved method for predicting linear B-cell epitopes. (2006)

The best single method for predicting linear B-cell epitopes is the hidden Markov model. Combining the hidden Markov model with one of the best propensity scale methods, we obtained the BepiPred method. When tested on the validation data set this method performs significantly better than any of the other methods tested. The server and data sets are publicly available at http://www.cbs.dtu.dk/services/BepiPred.
Engineered bio-nanocapsules, the selective vector for drug delivery system (2006)

The bio-nanocapsule (BNC) is our concept of artificial hollow nanoparticles that have been designed and produced through biotechnological procedures. We proposed an empty virus-like particle, which consists of a recombinant L envelope protein of hepatitis B virus (HBV) and a lipid derived from the host cell, as an engineered BNC. Although this BNC was first developed as an immunogen of hepatitis B vaccine, the pre-S1 region in N-terminus of L envelope protein confers hepatocyte specific infectivity of HBV on the BNC. This recombinant BNC is now being developed as a novel platform of drug delivery system (DDS) vector for selective delivery.
Room-temperature fluorescence characteristics of single dye molecules adsorbed on a glass surface (1998)

Measurements of the total fluorescence and fluorescence spectra from single carbocyanine dye molecules (DiIC12) as a function of time reveal a wide range of phenomena. Discrete jumps in the fluorescence intensity from single molecules on a glass surface have been observed with correlation times spanning several orders of magnitude (1 ms–10 s). We propose a model for these fluctuations in which two or more ground state potential minima are accessed by twists of the chromophore backbone that alter the quantum efficiency of emission as well as the emission spectrum. Monte Carlo simulations based on this model are shown which qualitatively match experimental data. In addition, we observed emission spectra which range in shape from narrow, well-separated vibronic bands to a broad, featureless band. The distribution of emission parameters from different molecules, not obtained from ensemble measurements, indicates an abundance of distinct nanoenvironments of the glass surface sampled by the adsorbed molecules.
Library analysis of SCHEMA‐guided protein recombination (2003)

The computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three-dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly-related beta-lactamases PSE-4 and TEM-1 at 13 sites to create a library of 2(14) (16,384) chimeras and examined which ones retain lactamase function. Sequencing the genes from ampicillin-selected clones revealed that the percentage of functional clones decreased exponentially with increasing calculated disruption (E = the number of residue-residue contacts that are broken upon recombination). We also found that chimeras with low E have a higher probability of maintaining lactamase function than chimeras with the same effective level of mutation but chosen at random from the library. Thus, the simple distance metric used by SCHEMA to identify interactions and compute E allows one to predict which chimera sequences are most likely to retain their function. This approach can be used to evaluate crossover sites for recombination and to create highly mosaic, folded chimeras.
Extracellular Enzyme System Utilized by the Fungus Sporotrichum pulverulentum (Chrysosporium lignorum) for the Breakdown of Cellulose (1975)

An exo-1,4-beta-glucanase from culture solution of the rot fungus Sporotrichum pulverulentum (formerly called Chrysosporium lignorum) grown on powder cellulose as the sole carbon source has been extensively purified and characterized with respect to some physico-chemical properties. The purification has been carried out in a five-step procedure comprising chromatography on DEAE-Sephadex, gel filtration on polyacrylamide P-150, activation on a Dowex 2-X8 anion exchanger, chromatography on Concanavalin A-Sepharose and chromatography on SP-Sephadex. The purified enzyme was found to be pure and homogeneous by analytical polyacrylamide electrophoresis, by electrophoresis on dodecylsulphate gels and by analytical polyacrylamide electrophoresis, by electrophoresis on dodecylsulphate gels and by analytical isoelectric focusing. A single symmetrical peak was obtained with the free zone electrophoresis method. The purification factor is about 15 and the yield of exo-1,4-beta-glucanase activity 7%. After purification, the enzyme showed no viscosity-decreasing activity towards carboxymethyl-cellulose solutions. The exo-1,4-beta-glucanase was isoelectric at pH 4.3 (4 degrees C). A molecular weight of 48600 was calculated on the basis of a knowledge of the partial specific volume, ultracentrifugation data and the amino acid composition. The enzyme contained no carbohydrate.
Artificial intelligence in emergency department triage (1990)

Assistant Professor Administrative Resident U.S. Army-Baylor University Graduate Program in Health Care Administration Academy of Health Sciences Fort Sam Houston, Texas
PCR protocols: current methods and applications. (1993)

PCR has been successfully utilized in every facet of basic, cli- cal, and applied studies of the life sciences, and the impact that PCR has had on life science research is already staggering. C- comitant with the essentially universal use of PCR has been the creative and explosive development of a wide range of PCR-based techniques and applications. These increasingly numerous pro- cols have each had the general effect of facilitating and acceler- ing research. Because PCR technology is relatively easy and inexpensive, PCR applications are well within the reach of every research lab. In this sense, PCR has become the "equalizer" between "small" and "big" labs, since its use makes certain projects, especially those related to molecular cloning, now far more feasible for the small lab with a modest budget. This new volume on PCR Protocols does not attempt the impossible task of representing all PCR-based protocols. Rather, it presents a range of protocols, both analytical and preparative, that provide a solid base of knowledge on the use of PCR in many c- mon research problems. The first six chapters provide some basic information on how to get started. Chapters 7-19 represent primarily analytical uses of PCR, both for simple DNA and RNA detection, as well as for more complex analyses of nucleic acid (e. g. , DNA footprin ting, RNA splice site localization). The remaining chapters represent "synthetic," or preparative, uses of PCR.
THz interconnect with low-loss and low-group velocity dispersion (2001)

We report the demonstration of a physically flexible, practicable THz interconnect with minimal pulse distortion and loss. The interconnect is a parallel-plate waveguide, with the TEM mode excited, constructed of two thin copper strips. The incoming 0.22 ps THz pulse broadens to 0.39 ps after propagating 250 mm in the waveguide and is also attenuated by a factor of ten. We show that this attenuation is mainly due to the finite conductivity of copper with some additional loss caused by the beam spread in the unguided dimension. The pulse broadening is due to the frequency-dependent loss since the group velocity dispersion is negligible.
ITRS commodity memory roadmap (2004)

The ITRS (International Technology Roadmap for Semiconductors) roadmap is updated on a yearly basis to forecast industry silicon trends. The ITRS Test Working Group (TWG) identifies the key trends that will have an impact on device test and summarizes them to provide direction to test suppliers. The commodity memory roadmap is a key part of that forecast and covers discrete and embedded DRAM and Flash. The material in this paper represents a very early look at the potential commodity memory roadmap due for release in November of 2003 and is based upon the 2002 roadmap.
Smart sender: a practical rate adaptation algorithm for multirate IEEE 802.11 WLANs (2008)

Wireless local area networks (WLANs) have become Increasingly popular due to the availability of affordable devices providing multirate capabilities. Under time- varying wireless channels, a device needs to tune its transmission rate dynamically for more efficient utilization of the physical link. Hence, rate adaptation mechanism, which is intentionally unspecified by the IEEE 802.11 standards, is critical to the system performance. In this paper, we propose a practical rate adaptation algorithm, Smart Sender, which utilizes both statistics and the received signal strength indicator (RSSI) of ACK packets to determine the transmission rate that maximizes the throughput. We implement our algorithm in commercial WLAN products and carry out extensive experiments for performance evaluation. The results demonstrate that using both statistics and RSSI of ACKs greatly improves system throughput and responsiveness under various wireless environments.
Examination of the Therapeutic Potential of Delta-24-RGD in Brain Tumor Stem Cells: Role of Autophagic Cell Death (2007)

The eradication of brain tumor stem cells is essential for long-term brain tumor remission after treatment. In this study, we examined the therapeutic potential of an oncolytic adenovirus, Delta-24-RGD, targeted to the abnormal p16INK4/Rb pathway in brain tumor stem cells. Four brain tumor stem cell lines from surgical glioblastoma specimens expressed high levels of adenoviral receptors and allowed for efficient viral infection, replication, and oncolysis in an Rb-dependent manner. Delta-24-RGD induced autophagic cell death, as indicated by accumulation of Atg5 and LC3-II protein and autophagic vacuoles. Treatment of xenografts derived from brain tumor stem cells with Delta-24-RGD statistically significantly improved the survival of glioma-bearing mice (means: 38.5 versus 66.3 days, difference = 27.8 days, 95% confidence interval = 19.5 to 35.9 days, P <.001). Analyses of treated tumors showed that Atg5 expression colocalized with viral fiber protein and delineated a wave front of autophagic cells that circumscribed areas of virally induced necrosis. Our results show for the first time that brain tumor stem cells are susceptible to adenovirus-mediated cell death via autophagy in vitro and in vivo.
Inner mitochondrial membrane potential ( m), cytoplasmic ATP content and free Ca2+ levels in metaphase II mouse oocytes (2003)

The findings support a mitochondrial basis for pericortical J-aggregate fluorescence but not for a direct association between high DeltaPsim and metabolism. The results extend previous findings indicating that high-polarized (high DeltaPsim, JC-1 J-aggregate-forming) mitochondria occur in pericortical domains in mouse and human oocytes and early preimplantation stage embryos and support the notion that this spatial distribution may be related to localized ionic and metabolic regulation.
The immunological profile of B-cell disorders and proposal of a scoring system for the diagnosis of CLL. (1994)

We have investigated the role of immunophenotyping in distinguishing between leukemic B-cell lymphoproliferative disorders. Circulating cells from 666 cases were analyzed with a panel of markers by flow cytometry. The diseases included: chronic lymphocytic leukemia (CLL), 400; prolymphocytic leukemia, 22; hairy cell leukemia (HCL), 40; HCL variant, 15; splenic lymphoma with villous lymphocytes, 100; follicular lymphoma, 26; lymphoplasmacytic lymphoma, 25; mantle-cell lymphoma, 20; and large cell lymphoma, 18. On the basis of the most common marker profile in CLL, CD5+, CD23+, FMC7- and weak expression (+/-) of surface immunoglobulin (SmIg) and CD22, we devised a scoring system that gives for each of these five markers a value of 1 or 0 according to whether it is typical or atypical for CLL. Scores range from 5 (typical of CLL) to 0 (atypical for CLL). Application of the scoring system to all the cases showed that 87% of CLL scored 5 and 4 and only 0.4% scored 0 or 1, whereas 89% of other B-cell leukemias and 72% of lymphomas scored 0 or 1; only one case (0.3%) scored 4 and none scored 5 (p < 0.0001). There were no differences between CLL with high and low scores but higher scores were found in cases with more typical morphology (p < 0.0015). Considering each individual marker, there was no single one that distinguished CLL from other diseases, although the most reliable were SmIg intensity and FMC7. The proposed score will facilitate the diagnosis of B-lymphoproliferative disorders and improve their classification.
Synthetic CD4 Peptide Derivatives That Inhibit HIV Infection and Cytopathicity (1988)

Synthetic peptide segments of the CD4 molecule were tested for their ability to inhibit infection of CD4+ cells by the human immunodeficiency virus (HIV) and to inhibit HIV-induced cell fusion. A peptide mixture composed of CD4(76-94), and synthesis side products, blocked HIV-induced cell fusion at a nominal concentration of 125 micromolar. Upon high-performance liquid chromatography, the antisyncytial activity of the peptide mixture was found not in the fraction containing the peptide CD4(76-94) itself, but in a side fraction containing derivatized peptide products generated in the automated synthesis. Derivatized deletion and substitution peptides in the region CD4(76-94) were used to demonstrate sequence specificity, a requirement for benzyl derivatization, and a core seven-residue fragment required for antisyncytial activity. A partially purified S-benzyl-CD4(83-94) peptide mixture inhibited HIV-induced cell fusion at a nominal concentration of less than or equal to 32 micromolar. Derivatized CD4 peptides blocked cell fusion induced by several HIV isolates and by the simian immunodeficiency virus, SIV, and blocked infection in vitro by four HIV-1 isolates with widely variant envelope gene sequences. Purified CD4(83-94) dibenzylated at cysteine 86 and glutamate 87 possessed antisyncytial activity at 125 micromolar. Derivatization may specifically alter the conformation of CD4 holoreceptor peptide fragments, increasing their antiviral efficacy.
Psychopharmacology in Autism (1999)

Autism is a neurobiological disorder. The core clinical features of autism include impairment in social interaction, impairments in verbal and nonverbal communication, and restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. Autism often has coexisting neuropsychiatric disorders, including seizure disorders, attention deficit hyperactivity disorder, affective disorders, anxiety disorder, obsessive-compulsive disorder, and Tourette disorder. No etiology-based treatment modality has been developed to cure individuals with autism. However, comprehensive intervention, including parental counseling, behavior modification, special education in a highly structured environment, sensory integration training, speech therapy, social skill training, and medication, has demonstrated significant treatment effects in many individuals with autism. Findings from preliminary studies of major neurotransmitters and other neurochemical agents strongly suggest that neurochemical factors play a major role in autism. The findings also provide the rationale for psychopharmacotherapy in individuals with autism. This article reviews studies of neurochemical systems and related psychopharmacological research in autism and related neuropsychiatric disorders. Clinical indications for pharmacotherapy are described, and uses of various medications are suggested. This article also discusses new avenues of investigation that may lead to the development of more effective medication treatments in persons with autism.
The CRISPR-Cas immune system: Biology, mechanisms and applications (2015)

Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus-host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues.
Efficient Mixing and Reactions within Microfluidic Channels Using Microbead-Supported Catalysts (2002)

A strategy for efficiently mixing solutions and carrying out multistep catalytic reactions in microfluidic systems is described. The approach involves immobilizing catalysts on microbeads, placing the beads into well-defined microreactor zones, and then passing reactants through one or more of the reactor zones to yield products. The catalyst-modified beads effectively mix reactants and increase the effective surface area of the channel interior, both of which improve reaction velocities compared to open channels. This approach is demonstrated using two sequential reactions catalyzed by glucose oxidase and horseradish peroxidase. In addition to providing a general route to chemical synthesis within microfluidic systems, this design strategy may also be applicable to modeling reaction pathways within cells and to bio/chemical sensing applications.
Hageman Factor (Factor XII) Deficiency in Marine Mammals (1969)

Hematologic and coagulation studies were conducted on Atlantic bottlenose dolphins and killer whales. Hematologic values were similar to those in man. These animals differed from other mammals in that the Hageman factor (factor XII) was absent and this absence caused marked prolongation of coagulation. Levels of factors VIII and V were high and those of VII and X were low compared with levels in man.
Integrin-dependent phosphorylation and activation of the protein tyrosine kinase pp125FAK in platelets. (1992)

We have investigated mechanisms involved in integrin-mediated signal transduction in platelets by examining integrin-dependent phosphorylation and activation of a newly identified protein tyrosine kinase, pp125FAK (FAK, focal adhesion kinase). This kinase was previously shown to be localized in focal adhesions in fibroblasts, and to be phosphorylated on tyrosine in normal and Src-transformed fibroblasts. We show that thrombin and collagen activation of platelets causes an induction of tyrosine phosphorylation of pp125FAK and that pp125FAK molecules isolated from activated platelets display enhanced levels of phosphorylation in immune-complex kinase assays. pp125FAK was not phosphorylated on tyrosine after thrombin or collagen treatment of Glanzmann's thrombasthenic platelets deficient in the fibrinogen receptor GPIIb-IIIa, or of platelets pretreated with an inhibitory monoclonal antibody to GP IIb-IIIa. Fibrinogen binding to GP IIb-IIIa was not sufficient to induce pp125FAK phosphorylation because pp125FAK was not phosphorylated on tyrosine in thrombin-treated platelets that were not allowed to aggregate. These results indicate that tyrosine phosphorylation of pp125FAK is dependent on platelet aggregation mediated by fibrinogen binding to the integrin receptor GP IIb-IIIa. The induction of tyrosine phosphorylation of pp125FAK was inhibited in thrombin- and collagen-treated platelets preincubated with cytochalasin D, which prevents actin polymerization following activation. Under all of these conditions, there was a strong correlation between the induction of tyrosine phosphorylation of pp125FAK in vivo and stimulation of the phosphorylation of pp125FAK in vitro in immune-complex kinase assays. This study provides the first genetic evidence that tyrosine phosphorylation of pp125FAK is dependent on integrin-mediated events, and demonstrates that there is a strong correlation between tyrosine phosphorylation of pp125FAK in platelets, and the activation of pp125FAK-associated phosphorylating activity in vitro.