gebhart/patrepeval huggingface dataset:
Ferric Enterobactin Binding and Utilization by Neisseria gonorrhoeae (1999)

FetA, formerly designated FrpB, an iron-regulated, 76-kDa neisserial outer membrane protein, shows sequence homology to the TonB-dependent family of receptors that transport iron into gram-negative bacteria. Although FetA is commonly expressed by most neisserial strains and is a potential vaccine candidate for both Neisseria gonorrhoeae and Neisseria meningitidis, its function in cell physiology was previously undefined. We now report that FetA functions as an enterobactin receptor. N. gonorrhoeae FA1090 utilized ferric enterobactin as the sole iron source when supplied with ferric enterobactin at approximately 10 microM, but growth stimulation was abolished when an omega (Omega) cassette was inserted within fetA or when tonB was insertionally interrupted. FA1090 FetA specifically bound 59Fe-enterobactin, with a Kd of approximately 5 microM. Monoclonal antibodies raised against the Escherichia coli enterobactin receptor, FepA, recognized FetA in Western blots, and amino acid sequence comparisons revealed that residues previously implicated in ferric enterobactin binding by FepA were partially conserved in FetA. An open reading frame downstream of fetA, designated fetB, predicted a protein with sequence similarity to the family of periplasmic binding proteins necessary for transporting siderophores through the periplasmic space of gram-negative bacteria. An Omega insertion within fetB abolished ferric enterobactin utilization without causing a loss of ferric enterobactin binding. These data show that FetA is a functional homolog of FepA that binds ferric enterobactin and may be part of a system responsible for transporting the siderophore into the cell.
The Importance of the Statement in Addition and Subtraction Word Problems (2004)

The intricate nature of these data can be overwhelming and exceed the capabilities of current statistical software. Machine learning (ML), a branch of artificial intelligence (AI), can help health care providers navigate through this complex labyrinth of information and unravel hidden discoveries. Furthermore, ML algorithms can help automate several tasks in echocardiography and clinical care. ML can serve as a valuable diagnostic tool for physicians in the field of echocardiography. In addition, it can help expand the capabilities of research and discover alternative pathways in medical management. In this review article, we describe the role of AI and ML in echocardiography.
Analyzing Social Media Networks with NodeXL: Insights from a Connected World (2010)

Businesses, entrepreneurs, individuals, and government agencies alike are looking to social network analysis (SNA) tools for insight into trends, connections, and fluctuations in social media. Microsoft's NodeXL is a free, open-source SNA plug-in for use with Excel. It provides instant graphical representation of relationships of complex networked data. But it goes further than other SNA tools -- NodeXL was developed by a multidisciplinary team of experts that bring together information studies, computer science, sociology, human-computer interaction, and over 20 years of visual analytic theory and information visualization into a simple tool anyone can use. This makes NodeXL of interest not only to end-users but also to researchers and students studying visual and network analytics and their application in the real world. In Analyzing Social Media Networks with NodeXL, members of the NodeXL development team up provide readers with a thorough and practical guide for using the tool while also explaining the development behind each feature. Blending the theoretical with the practical, this book applies specific SNA instructions directly to NodeXL, but the theory behind the implementation can be applied to any SNA. *Walks readers through using NodeXL while explaining the theory and development behind each step, providing takeaways that can apply any SNA *Demonstrates how visual analytics research can be applied to SNA tools for the mass market *Presents readers with case studies using NodeXL on popular networks like email, Facebook, Twitter, and wikis
Comparison of the basal ganglia in rats, marmosets, macaques, baboons, and humans: Volume and neuronal number for the output, internal relay, and striatal modulating nuclei (2002)

This study compares the basal ganglia of rats, marmosets, macaques, baboons, and humans. It uses established protocols to estimate the volume and number of neurons within the output nuclei (internal globus pallidus, IGP; and nondopaminergic substantia nigra, SNND), two internal relay and modulating nuclei (subthalamic nucleus, STh; and external globus pallidus, EGP), and a modulator of the striatum (dopaminergic substantia nigra, SND). Nuclear boundaries were defined by using immunohistochemistry for striatal afferents. Total numbers of Nissl-stained and parvalbumin-immunoreactive neurons were calculated by using the fractionator technique. Comparisons between species were standardized relative to brain mass (rats < marmosets < macaques < baboons < humans). The EGP consistently had more neurons relative to the IGP, STh, and SND, which had similar neuronal numbers within each species. The SNND had proportionally more neurons in rats than in primates (especially humans). The distribution of SND neurons varied substantially between rats and primates (very few ventrally located neurons in rats) with humans containing fewer SND neurons than other primates. The reduction in SND neurons in humans suggests less dopaminergic regulation of the basal ganglia system compared with other species. The consistency in the number of IGP neurons across all species, combined with the reduction in SNND neurons in humans, suggests a greater emphasis on output pathways through the IGP and that there are proportionally more STh and EGP neurons in humans.
Ultrafast switching in a synthetic antiferromagnetic magnetic random-access memory device (2011)

The dynamics of a synthetic antiferromagnet (a metallic trilayer) have been explored and are shown to exhibit ultrafast switching on a time scale of tens of ps. This conclusion is based on first-principles, atomistic spin dynamics simulations. The simulations are performed at finite temperature, as well as at $T=0$ K (the macrospin limit), and we observe a marked temperature dependence of the switching phenomenon. It is shown that, to reach very high switching speeds, it is important that the two ferromagnetic components of the synthetic antiferromagnet have oppositely directed external fields to one another. Then a complex collaboration between precession switching of an internal exchange field and the damping switching of the external field occurs, which considerably accelerates the magnetization dynamics. We discuss a possible application of this fast switching as a magnetic random access memory device, which has as a key component intrinsic antiferromagnetic couplings and an applied Oersted field.
Alternating phase-shifting mask with reduced aberration sensitivity: lithography considerations (2001)

Aberration sensitivity of alternating phase-shifting masks (PSMs) can be reduced by taking advantage of the trim exposure. Rather than a single phase region bordering each edge of a line, the enhanced alternating PSM technique uses multiple phase regions. The number of phase regions and their widths can be optimized for overall process tolerance including aberration sensitivity and exposure latitude. For exposure with a wavelength of 248 nm and a numerical aperture of 0.68, the optimal number of phase regions is two, with widths between 100 nm and 200 nm. These auxiliary phase regions do not affect the final pattern if a light-field trim mask is used. No extra processing step is necessary. With the enhanced alternating PSM technique, isolated lines of average dimension as small as 36 nm can be delineated using 248 nm lithography with a 3(sigma) linewidth control of 13.4 nm. The mean critical dimension of 36 nm corresponds to k<SUB>1</SUB> equals 0.1.
Antiestrogens and Selective Estrogen Receptor Modulators as Multifunctional Medicines. 2. Clinical Considerations and New Agents (2003)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTAntiestrogens and Selective Estrogen Receptor Modulators as Multifunctional Medicines. 2. Clinical Considerations and New AgentsV. Craig JordanView Author Information Robert H. Lurie Comprehensive Cancer Center, The Feinberg School of Medicine of Northwestern University, 303 East Chicago Avenue, MS N505, Chicago, Illinois 60611 Cite this: J. Med. Chem. 2003, 46, 7, 1081–1111Publication Date (Web):February 27, 2003Publication History Received9 October 2002Published online27 February 2003Published inissue 1 March 2003https://pubs.acs.org/doi/10.1021/jm020450xhttps://doi.org/10.1021/jm020450xreview-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views2158Altmetric-Citations335LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cancer,Cancer therapy,Cells,Receptors,Rodent models Get e-Alerts
Epstein‐Barr virus (EBV)‐associated antibody patterns in malignant lymphoma and leukemia. I. Hodgkin's disease (1970)

Abstract Sera from Swedish patients with Hodgkin's disease as well as control sera from donors without known disease were titrated for antibodies to the Epstein‐Barr virus (EBV) by the indirect immunofluorescence technique. In the same sera antibodies capable of blocking the direct membrane immunofluorescence reaction obtained between Epstein‐Barr virus carrying lymphoblastoid cell lines and a fluorescein‐conjugated reference serum from a patient with Burkitt's lymphoma (F‐Mutua conjugate) were tested. The serological reactivity of the control sera was very similar to that described in previous reports. In contrast, sera from Hodgkin's disease patients showed an increased reactivity in both tests. When the donors were grouped in relation to clinical and histological data of prognostic importance, an inverse relationship was found between the frequency of lymphoid cells and EBV‐associated serological reactivity. Whereas paragranuloma cases did not exceed the reactivity level of the controls, patients with Hodgkin's sarcoma were highly reactive in both tests, reaching levels comparable to those seen in Burkitt's lymphoma and nasopharyngeal carcinoma. The granuloma group was intermediate with regard to serological reactivity.
Neutrino signals from ultracompact minihalos and constraints on the primordial curvature perturbation (2013)

Compared with that of standard dark matter halos, the density profile of the recently proposed new kind of dark matter structure named ultracompact minihalos (UCMHs) is steeper and its formation time is earlier. If the dark matter is composed of weakly interactive massive particles, the potential signals, e.g., neutrinos, from UCMHs due to dark matter annihilation would be detected by IceCube/DeepCore or other detectors and such signals would have a very useful complementarity of $\ensuremath{\gamma}$-ray observations. On the other hand, the formation of UCMHs is related to primordial curvature perturbations on the smaller scales. So constraints on the abundance of UCMHs can be used to give a limit on the perturbations on these scales. In previous works in the literature, the authors focused on the $\ensuremath{\gamma}$-ray signals from UCMHs due to dark matter annihilation. In this work, we investigate the neutrino signals from nearby UCMHs. Although no excess of neutrino signals from dark matter annihilation has been observed, the constraints on the abundance of UCMHs can be obtained and these constraints can be translated into the limit on the primordial curvature perturbations on small scales.
Trehalases: A neglected carbon metabolism regulator? (2013)

Trehalases are enzymes that carry out the degradation of the non-reducing disaccharide trehalose. Trehalase phylogeny unveiled three major branches comprising those from bacteria; plant and animals; and those from fungal origin. Comparative analysis between several deduced trehalase structures and the crystallographic structure of bacterial trehalase indicated that these enzyme's structures are highly conserved in spite of the marked differences found at the sequence level. These results suggest a bacterial origin for the trehalases in contrast to an eukaryotic origin, as previously proposed. Trehalases structural analysis showed that they contain six discrete motifs which are characteristic of each phylogenetic group, suggesting a positive evolutionary selection pressure for the structural conservation. Interestingly, trehalases are involved in multiple regulatory functions: In the response against pathogens (plant-pathogen interactions); the regulation of bacterial viability in symbiotic interactions (legume-Rhizobium); carbon partitioning in plants; regulating chitin biosynthesis, as well as energy supply in the hemolymph for flight, in insects. In summary, trehalases seem to have a prokaryotic origin and play an active role in carbon metabolism and other diverse regulatory effects on cell physiology.
Comparison of the Antimicrobial Effect of Chlorhexidine and Saline for Irrigating a Contaminated Open Fracture Model (2012)

This study does not support the use of CHG as an irrigant. This may be due to the antibacterial effect of CHG being offset by the associated host tissue toxicity. Host tissue damage from high irrigation pressures and cytotoxic solutions has been shown to allow bacteria to thrive. We believe this is due to a "rebound" of bacteria growth in a wound bed containing small quantities of necrotic tissue damaged by CHG exposure.
Conservative Treatment of Scald Burns Is Superior to Early Excision (1991)

Early excision of deep burns has been advocated; however, it is difficult to clinically determine the depth of scald burns during the early postburn period. This prospective, randomized study was designed to determine whether early excision was superior to conservative treatment of scald injuries. Patients with scald injuries (which were not caused by grease) of clinically indeterminant depth were randomized to early (n = 12) or late (n = 12) excision; all patients with obvious superficial and full-thickness injuries were excluded. In the early excision group, all deep wounds were tangentially excised and grafted within 72 hours of admission, whereas in the late treatment group wounds were excised and grafted after 2 weeks had passed since injury. Area excised, postburn day of excision, percent graft take, operating-room time, blood replacement, incidence of infection, and length of hospital stay were compared. No patient experienced a significant wound infection or systemic sepsis. A significantly smaller area of excision was necessary for those patients who were treated with delayed surgery, and concomitant decreases in operating-room time and blood loss were observed. Notably, only one half of the patients who were randomized to the delayed excision group ultimately required surgical intervention to achieve wound closure. Graft take was comparable for both groups, as was length of hospital stay. Early clinical evaluation of scald injuries appears to be equivocal, and later evaluations reveal a less severe injury. Financial gains can be made when surgical excision of scald injuries is delayed until 2 weeks after injury because of a related reduction in hospital expenditures.
Ulcerative colitis and Crohn's disease: distinctive gene expression profiles and novel susceptibility candidate genes (2001)

To elucidate the biological dysregulation underlying two forms of inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD), we examined global gene expression profiles of inflamed colonic tissue using DNA microarrays. Our results identified several genes with altered expression not previously linked to IBD. In addition to the expected upregulation of various cytokine and chemokine genes, novel immune function-related genes such as IGHG3, IGLL2 and CD74, inflammation-related lipocalins HNL and NGAL, and proliferation-related GRO genes were over-expressed in UC. Certain cancer-related genes such as DD96, DRAL and MXI1 were differentially expressed only in UC. Other genes over-expressed in both UC and CD included the REG gene family and the calcium-binding S100 protein genes S100A9 and S100P. The natural antimicrobial defensin DEFA5 and DEFA6 genes were particularly over-expressed in CD. Overall, significant differences in the expression profiles of 170 genes identified UC and CD as distinct molecular entities. The genomic map locations of the dysregulated genes may identify novel candidates for UC and CD genetic susceptibility.
Paclitaxel Through the Ages of Anticancer Therapy: Exploring Its Role in Chemoresistance and Radiation Therapy (2015)

Paclitaxel (Taxol(®)) is a member of the taxane class of anticancer drugs and one of the most common chemotherapeutic agents used against many forms of cancer. Paclitaxel is a microtubule-stabilizer that selectively arrests cells in the G2/M phase of the cell cycle, and found to induce cytotoxicity in a time and concentration-dependent manner. Paclitaxel has been embedded in novel drug formulations, including albumin and polymeric micelle nanoparticles, and applied to many anticancer treatment regimens due to its mechanism of action and radiation sensitizing effects. Though paclitaxel is a major anticancer drug which has been used for many years in clinical treatments, its therapeutic efficacy can be limited by common encumbrances faced by anticancer drugs. These encumbrances include toxicities, de novo refraction, and acquired multidrug resistance (MDR). This article will give a current and comprehensive review of paclitaxel, beginning with its unique history and pharmacology, explore its mechanisms of drug resistance and influence in combination with radiation therapy, while highlighting current treatment regimens, formulations, and new discoveries.
A Persistent Hindlimb Ischemia Model in the Rabbit (1994)

The study of new approaches for the treatment of limb-threatening ischemia has been hampered by the lack of a suitable animal model of persistent limb ischemia. We describe the development and evaluation of an animal model of persistent hindlimb ischemia, in which ischemia was induced in the left hindlimb of 28 rabbits by ligation of the distal external iliac artery and excision of the common and superficial femoral arteries. The severity of the ischemia and its relief in each animal were evaluated every 10 days postoperatively until day 40 (all animals) or day 90 (five animals). Nine animals developed superficial tissue necrosis in the foot, but no deaths were attributable to the ischemia-inducing procedure. Angiography demonstrated minimal collateralization and sluggish filling of distal vessels up to postoperative day 90. This was accompanied by a decrease at rest in the calf blood flow ratio (p < 0.005 vs day 0), an increase in lactic acid in the femoral venous blood (left vs right side, p < 0.002) up to postoperative day 40, and a decrease in the calf blood pressure ratio (p < 0.0001 vs day 0) up to day 90. Histologic study of the gastrocnemius muscle demonstrated evidence of atrophy and fibrosis in the left hindlimb. This model can be used to evaluate direct and indirect approaches to the treatment of chronic limb ischemia.
Parasites in Social Insects (1999)

Preface and Acknowledgments1The Biology of Social Insects32The Parasites and Their Biology243Breaking into the Fortress774Parasites and the Organization of the Colony1195Breeding Strategies and Parasites1636Host-Parasite Dynamics2047Virulence and Resistance2378Social Evolution273App. 1: Glossary287App. 2The Parasites of Social Insects291References325Subject Index381Host Taxonomic Index386Parasite Taxonomic Index393Author Index399
HIV-1 Drug Resistance Profiles in Children and Adults With Viral Load of &lt;50 Copies/mL Receiving Combination Therapy (2001)

Based on the samples that could be amplified, low-level viremia in children and adults receiving HAART with prolonged suppression of viremia to less than 50 copies/mL of HIV-1 RNA may result primarily from archival, pre-HAART virus, reflecting earlier treatment conditions, and does not appear to require development of new, HAART-selected mutations reflecting partial resistance to therapy. Low-level viremia below 50 copies/mL may represent less of a concern regarding impending drug failure of current HAART regimens. However, the archival drug-resistant virus may be relevant regarding future treatment strategies.
Locadio: inferring motion and location fron Wi-Fi signal strengths (2004)

Context is a critical ingredient of ubiquitous computing. While it is possible to use specialized sensors and beacons to measure certain aspects of a user's context, we are interested in what we can infer from using the existing 802.11 wireless network infrastructure that already exists in many places. The context parameters we infer are the location of a client (with a median error of 1.5 meters) and an indicator of whether or not the client is in motion (with a classification accuracy of 87%). Our system, called LOCADIO, uses Wi-Fi signal strengths from existing access points measured on the client to infer both pieces of context. For motion, we measure the variance of the signal strength of the strongest access point as input to a simple two-state hidden Markov model (HMM) for smoothing transitions between the inferred states of "still" and "moving". For location, we exploit the fact that Wi-Fi signal strengths vary with location, and we use another HMM on a graph of location nodes whose transition probabilities are a function of the building's floor plan, expected pedestrian speeds, and our still/moving inference. Our probabilistic approach to inferring context gives a convenient way of balancing noisy measured data such as signal strengths against our a priori assumptions about a user's behavior.
Numerical investigation of Fluidic Injection as a means of Thrust Modulation (2009)

Interest in fluidic thrust vectoring has promoted many numerical and experimental investigations to explore its validity in real world applications. The benefits of such technology are numerous making investigations into their effectiveness a valid and worthwhile exercise. A comprehensive literature review of previous work was conducted from which an appropriate numerical simulation criterion was devised. This was carried out to replicate experimental results and in-turn validate two dimensional computational fluid dynamic simulations using FLUENT® as an appropriate method of investigation. Specifically the method of fluidic thrust vectoring using the technique of shock vector control will be used. Numerical simulations conducted aim to replicate previous experimental work by Stagg (2008), using the Australian Defence Force Academy fluidic thrust vectoring experimental apparatus, and Neely et al (2007). Following initial CFD validations a numerical exploration of fluidic thrust spoiling as a means of thrust magnitude control in solid fuel rocket motors will be conducted. Results obtained from computational fluid dynamics simulations will be then used to develop a suitable control system for both thrust magnitude and direction will be carried out.