gebhart/patrepeval huggingface dataset:
Modeling the spatio-temporal dynamics of malaria parasite population genetics (2014)

A model of malaria transmission dynamics is presented that tracks the genetic barcodes of individual Plasmodium falciparum infections using seasonally-driven effective reproduction rates for clonal propagation, external importation, and the outcrossing of strains both within and between infections. We explore quantitatively the relationship between transmission intensity and genetic observations, for example the repeated observation of identical strains and their persistence across successive transmission seasons. Extending to a spatially connected network of human and parasite populations, we model the sensitivity of genetic sequencing to identify the relative contributions of local hotspots versus re-importation in sustaining transmission in pre-elimination settings. Finally, we model the effects of local transmission intensity and anti-malarial drug pressure on the population-level genetic signatures of emerging drug resistance.
Mac-1 (CD11b/CD18) is crucial for effective Fc receptor–mediated immunity to melanoma (2002)

Antibody-reliant destruction of tumor cells by immune effector cells is mediated by antibody-dependent cellular cytotoxicity, in which Fc receptor (FcR) engagement is crucial. This study documents an important role for the beta(2) integrin Mac-1 (CD11b/CD18) in FcR-mediated protection against melanoma. CD11b-deficient mice, those that lack Mac-1, were less protected by melanoma-specific monoclonal antibody TA99 than wild-type (WT) mice. Significantly more lung metastases and higher tumor loads were observed in Mac-1(-/-) mice. Histologic analyses revealed no differences in neutrophil infiltration of lung tumors between Mac-1(-/-) and WT mice. Importantly, Mac-1(-/-) phagocytes retained the capacity to bind tumor cells, implying that Mac-1 is essential during actual FcR-mediated cytotoxicity. In summary, this study documents Mac-1 to be required for FcR-mediated antimelanoma immunity in vivo and, furthermore, supports a role for neutrophils in melanoma rejection.
Design and development of nanostructure based antireflection coatings for EO/IR sensor applications (2009)

EO/IR Nanosensors are being developed for a variety of Defense and Commercial Systems Applications. These include UV, Visible, NIR, MWIR and LWIR Nanotechnology based Sensors. The conventional SWIR Sensors use InGaAs based IR Focal Plane Array (FPA) that operate in 1.0-1.8 micron region. Similarly, MWIR Sensors use InSb or HgCdTe based FPA that is sensitive in 3-5 micron region. More recently, there is effort underway to evaluate low cost SiGe visible and near infrared band that covers performance up to 1.6 micron. The use of Nanowires for developing high quality antireflection coatings that allows minimizing the reflection loss is discussed. We have explored the possibility of using nanostructures grown by oblique angle deposition technique. A graded-index coating with different index profiles has been investigated for broadband antireflection properties, particularly with air as the ambient medium. In this paper, we present, modeling and experimental results for nanostructure AR coatings for UV, Visible and calculations for NIR sensors and also their utility for longer wavelength application.
Activation of a Cryptic TACTAAC Box in the Saccharomyces cerevisiae Actin Intron (1986)

We constructed a translational fusion between the Saccharomyces cerevisiae actin gene and the Escherichia coli beta-galactosidase structural gene such that expression of beta-galactosidase activity required accurate splicing of the actin intron. Using this chimeric gene, we generated a series of internal deletions which removed the TACTAAC box or, in addition, TACTAAC-like sequences within the intron. Analysis of the fusion transcripts produced in these deletions allowed us to conclude that the TACTAAC-like sequence TACTAAG can substitute, albeit inefficiently, for the authentic TACTAAC box in the splicing process. These results indicate that the yeast splicing machinery can utilize a cryptic TACTAAC box, but there are requirements for primary sequence and proper position.
ChemInform Abstract: Synthesis and Activity of Sulfonamide‐Substituted 4,5‐Diaryl Thiazoles as Selective Cyclooxygenase‐2 Inhibitors. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Impact of Tungsten Capping Layer on Yttrium Silicide for Low-Resistance n+-Source/Drain Contacts (2009)

In order to form a stable silicide having a low Schottky barrier height (SBH) for electrons, we employed a tungsten (W) capping layer on yttrium (Y) and investigated its physical and electrical properties. Our experimental results show that W can effectively protect against Y oxidation during silicidation. The Schottky barrier diode fabricated on p-type Si shows excellent properties, such as a near-ideal n-value of 1.02 and a very low reverse-biased current of 3.87×10-7 A/cm2, corresponding to a high SBH for holes of 0.767 eV. Also, the Schotky barrier diode fabricated on n-type Si shows a SBH for electrons of as low as 0.311 eV. We also confirm that the W capping layer can be applied to other rare-earth metals. The technology developed in this work is applied to silicide formation with no oxygen contamination to realize low-resistance source/drain contacts, which will improve the performance of metal–insulator–semiconductor field-effect transistors (MISFETs).
A Multi Agent Framework for Pervasive Computing: Mobeet Framework (2003)

Pervasive computing is becoming a more important issue for open distributed systems. It is, however, hard to design such distributed systems when the user uses many kinds of terminals and migrates with these. This paper has proposed a new framework for pervasive computing. The framework includes three kinds of agents: User Interface Agents, Programmable Agents and Service Mediation Agents. We can easily design a flexible distributed system by collaborating these agents. We also evaluate the framework from flexibility point of view.
How to prioritize patients and redesign care to safely resume planned surgery during the COVID-19 pandemic (2021)

Our widely generalizable model enabled the restart of planned surgery during the COVID-19 pandemic, without compromising patient safety or excluding high-risk or complex cases. Patients classified as Urgent or P<sub>2</sub> were most likely to undergo surgery, including those deemed high-risk. This model, which includes assessment of biopsychosocial factors alongside disease severity, can assist in equitably prioritizing the substantial list of patients now awaiting planned orthopaedic surgery worldwide. Cite this article: <i>Bone Jt Open</i> 2021;2(2):134-140.
Supplementary Table 1 from Monitoring of Natural Killer Cell Immunotherapy Using Noninvasive Imaging Modalities (2023)

Supplementary Table 1 from Monitoring of Natural Killer Cell Immunotherapy Using Noninvasive Imaging Modalities
EGFR and MET Amplifications Determine Response to HER2 Inhibition in ERBB2 -Amplified Esophagogastric Cancer (2018)

The anti-HER2 antibody trastuzumab is standard care for advanced esophagogastric (EG) cancer with <i>ERBB2</i> (HER2) amplification or overexpression, but intrinsic and acquired resistance are common. We conducted a phase II study of afatinib, an irreversible pan-HER kinase inhibitor, in trastuzumab-resistant EG cancer. We analyzed pretreatment tumor biopsies and, in select cases, performed comprehensive characterization of postmortem metastatic specimens following acquisition of drug resistance. Afatinib response was associated with coamplification of <i>EGFR</i> and <i>ERBB2</i>. Heterogeneous <sup>89</sup>Zr-trastuzumab PET uptake was associated with genomic heterogeneity and mixed clinical response to afatinib. Resistance to afatinib was associated with selection for tumor cells lacking <i>EGFR</i> amplification or with acquisition of <i>MET</i> amplification, which could be detected in plasma cell-free DNA. The combination of afatinib and a MET inhibitor induced complete tumor regression in <i>ERBB2</i> and <i>MET</i> coamplified patient-derived xenograft models established from a metastatic lesion progressing on afatinib. Collectively, differential intrapatient and interpatient expression of HER2, EGFR, and MET may determine clinical response to HER kinase inhibitors in <i>ERBB2</i>-amplified EG cancer. SIGNIFICANCE: Analysis of patients with <i>ERBB2</i>-amplified, trastuzumab-resistant EG cancer who were treated with the HER kinase inhibitor afatinib revealed that sensitivity and resistance to therapy were associated with <i>EGFR</i>/<i>ERBB2</i> coamplification and <i>MET</i> amplification, respectively. HER2-directed PET imaging and cell-free DNA sequencing could help guide strategies to overcome the emergence of resistant clones.<i>See related commentary by Klempner and Catenacci, p. 166</i>.<i>This article is highlighted in the In This Issue feature, p. 151</i>.
Using the “One Shot” Concept for Immediate Loading Implant Protocol in Edentulous Patient Rehabilitation with a Fixed Prosthesis: A 6‐Year Follow‐Up (2021)

Immediate-loaded implants with a fixed prosthesis are a viable option for the restoration of edentulous ridges. Several procedures now allow for the fabrication of immediate-loading provisional and definitive prostheses. However, this complex treatment is not accessible to all patients with budget restrictions. By using a unique master model with a single titanium framework prosthesis can simplify and shorten the treatment, as well as reduce costs. After surgical placement of implant fixtures, an interim prosthesis was fabricated using a laser-welded definitive titanium framework. The prosthesis was fitted intraorally following the immediate loading protocols. The master cast model used to fabricate interim prosthesis was conserved and subsequently used in modifying the final prosthesis. After the healing process and complete soft tissue stability, an impression was made to register the clearance between the gingiva and resin. The light silicone material was directly injected under the prosthesis screwed in the mouth. In the master cast model, the stone was eliminated between the implants and a new plaster was poured to modify the crest profile with the posthealing new shape. With this modified model, it is possible to rehabilitate the denture to the new gingival anatomy in 3 to 4 hours and, if necessary, the tooth rearrangement. This "one shot" concept combines the single definitive titanium welded framework and limited laboratory work with a unique master model thereby decreasing the cost and the time of treatment.
Effect of annealing on charging properties of electret fibers (2016)

In the present work, effect of annealing on charging and surface morphology of isotactic polypropylene (PP) filaments was reported. To enhance the surface crystallinity of the filaments, samples were annealed at 70 and 110 °C for 12 h. As expected, fiber surface crystallinity increased upon annealing which led more stable electret fibers. However, the change in the initial surface potential was not so remarkable. The same trend was also observed in filaments containing a commercial nucleating agent, NA11 (sodium 2,2′-methylene-bis(4,6-di-tertbutylphenyl)-phosphate). Surface crystallinity was analyzed using the intensity of specific peaks obtained from attenuated total reflection infrared spectroscopy analysis. The surface charge characteristics of fibers were determined using a modified surface potential decay test.
Motion estimation via dynamic vision (2002)

Estimating the 3D motion of an object from a sequence of projections is of paramount importance in a variety of applications in control and robotics. Although "visual motion estimation" is an old problem, only recently tools from control and estimation theory have hinted at acceptable solutions. Moreover, the problem raises a number of issues of system theoretic interest, such as nonlinear estimation and identification on topological manifolds and observability in a projective geometric framework. In this paper we analyze a formulation of the visual motion estimation problem in terms of identification of nonlinear implicit systems with parameters on the so-called "essential manifold"; the estimation is performed either in the local coordinates or in the embedding space of the parameter manifold.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid Prototyping of an Open-Surface Microfluidic Platform Using Wettability-Patterned Surfaces Prepared by an Atmospheric-Pressure Plasma Jet (2019)

Open-surface microfluidics is promising in terms of enabling economical and rapid biochemical analysis for addressing challenges associated with medical diagnosis and food safety. To this end, we present a simple and economical approach to develop an open-surface microfluidic platform suitable for facile liquid transport and mixing. Customizable patterns with tailored wettability are deposited using a plasma-assisted deposition technique under atmospheric pressure. The flow of the dispensed liquid is driven by gravity, and the tilting angle of the device determines the extent of mixing. First, a hexamethyldisiloxane film was deposited to create hydrophobic patterns on glass, and then, hydrophilic acrylic acid was deposited by a patterned cardboard mask to construct a channel suitable for forming channels to transport aqueous liquids without the need of an external energy input; the liquid can be confined to designated pathways. Several designs including Y-junctions, serpentine-shaped patterns, splitting channels, and concentration gradient generation patterns are presented. The proposed method can spatially pattern a surface with a hydrophobic/hydrophilic area, which can function as a microfluidic channel, and the surface can be applied in microfluidic devices with other types of substrates.
Reduction of mutual coupling by near-field coupled resonators (2009)

A method for reduction of undesirable coupling between two antennas by means of a small resonant element is proposed. The parasitic resonant element is strongly excited by the aggressor antenna radiation and produces a cancellation effect at the victim antenna. This effect is achieved mainly due to the near field of the resonant circuit. Being electrically small the resonant element is an inefficient radiator, which only slightly affects the radiation patterns of the antennas. The proposed technique is demonstrated by reduction of coupling between two monopole antennas using a small capacitively loaded loop.
ChemInform Abstract: SYNTHESIS OF 1‐(P‐CARBOMETHOXYPHENYL)‐3‐PYRROLIDINONE BY A DIELS‐ALDER ROUTE (1984)

Abstract p‐Amino‐benzoesäureester (I) liefert mit Dimethylsulfid und NCS das Sulfilimin (II), das bei der weiteren Oxidation mit Persäure zur Nitrosoverbindung (III) führt.
Faculty Opinions recommendation of Down-regulation of pili and capsule of Neisseria meningitidis upon contact with epithelial cells is mediated by CrgA regulatory protein. (2002)

Read the full review for this Faculty Opinions recommended article: Down-regulation of pili and capsule of Neisseria meningitidis upon contact with epithelial cells is mediated by CrgA regulatory protein.
Application of three-dimensional rendering in joint-related ganglion cysts (2006)

The origin of para-articular cysts is poorly understood and controversial. The relatively common, simple (extraneural) cysts are presumed to be derived from joints, although joint connections are not always established. Rarer complex cysts are thought by many to form de novo within nerves (intraneural ganglion cysts) or within vessels (adventitial cysts) (degenerative theory). We believe that these simple and complex ganglion cysts are joint-related (articular theory). Joint connections are often not readily appreciated with routine imaging or at surgery. Not identifying and/or treating joint connections frequently leads to cyst recurrence. More sophisticated imaging may enhance visualization of these joint connections. We created a 3D rendering technique to assess potential joint connections of simple and complex cysts localized to the knee and superior tibiofibular joints in patients with fibular (peroneal) neuropathy. Two- and three-dimensional data sets from MRI examinations were segmented semiautomatically by signal intensity with further refinement based on interaction with the user to identify specific anatomic structures, such as small nerves and vessels on serial images. The bone, cysts, nerves, and vessels were each assigned different color representations, and 3D renderings were created in ANALYZE using the data sets closest to isotropic (voxel with equal length in all dimensions) resolution as the primary background rendering. We selected four cases to illustrate the spectrum of pathology. In all of these cases, we demonstrated joint connections and correlated imaging and operative findings. Surgery addressing the cyst and the joint connection resulted in excellent outcomes; postoperative MRIs done more than 6 months later confirmed that there was no recurrence. In addition to highlighting the important relationship of these cysts to neighboring anatomic structures, this 3D technique allows visualization of "occult" connections not readily appreciated with standard MR imaging. We believe that these joint-related cysts have a common pathogenesis; they dissect through a capsular rent and follow the path of least resistance; they may form simple cysts by dissecting out into the soft tissue, or more complex cysts by dissecting within the epineurium of nerves or adventitia of vessels (along an articular branch), or various combinations of all of these types of cysts. Understanding the pathogenesis for cyst formation will improve surgical management and outcomes. We have adapted this 3D technique to enhance the visualization of cysts occurring at other joints.
Frequency Spectrum for New Aviation Data Links: Initial Study Results (2004)

We describe results from an initial study to assess the suitability of various spectral bands for supporting the deployment of new aviation data links (ADL). The study focused on systems and spectral bands that can deliver VHF data link (VDL)-or-higher data rates in a two-way communication setting, including air-ground, ground-air, and air-air modes of operation. In the first part of our paper, we briefly discuss the current situation regarding communications, navigation, and surveillance (CNS) links and existing spectrum, and the well-known need for new aviation data links. We next provide an overview of related systems, and discuss key factors involved in the use of spectrum in various bands for any future integrated CNS data link, addressing primarily the lower few layers of the communications protocol stack. Desired attributes of a new ADL system are discussed, and the beneficial aspects of a particular transmission technique spread spectrum are summarized. We also provide a short list of several example potential spectral regions, and note that while none of the existing systems will likely meet the full range of desired features of a new ADL, several systems and spectral regions offer promise in terms of one or more characteristics. A detailed discussion and evaluation of these spectral regions is proposed as future work. We include a few brief examples to illustrate initial technical results regarding spread spectrum overlay, also a subject for future work.
The complex-formation behaviour of His residues in the fifth Cu2+ binding site of human prion protein: a close look (2009)

Human Prion Protein (hPrPC) is able to bind up to six Cu2+ ions. Four of them can be allocated in the “octarepeat domain”, a region of the unstructured N-terminal domain containing four tandem-repetitions of the sequence PHGGGWGQ. It is widely accepted that the additional binding sites correspond to His-96 and His-111 residues. However, recent literature does not agree on the role and the behavior of these sites in Cu2+ complexation to hPrPC. In order to shed more light on this topic, some peptidic analogues of the PrP92–113 fragment were synthesized: (H96A)PrP92–113, (H111A)PrP92–113, (H96Nτ-Me-His)PrP92–113, (H111Nτ-Me-His)PrP92–113, (H96Nτ-Me-His)PrP92–100, (H111Nτ-Me-His)PrP106–113, where an alanine or a histidine methylated at the τ nitrogen atom of its imidazole ring have been substituted to His-96 or His-111. The first two ligands allowed to confirm that His-111 binding site is stronger than His-96 one: they act as independent sites even at Cu2+-ion substoichiometric levels. Neither multi-histidine binding nor bis-complex formation has been detected at neutral pH. Nτ methylation gave evidence that τ nitrogens of imidazole residues can participate in complex-formation only at acidic pH, where displacement of amidic protons by Cu2+ ions is not allowed. Finally, the length of the fragment does not appear to have any significant influence on the behavior of the two His-96 and His-111 binding sites, from the point of view of either the coordination geometry or their relative strength.
A Hall thruster performance model incorporating the effects of a multiply-charged plasma (2001)

A Hall thruster performance model that predicts anode specific impulse, anode efficiency, and thrust is discussed. The model is derived as a function of a voltage loss parameter, an electron loss parameter, and the charge state of the plasma. Experimental data from SPT and TAL type thrusters up to discharge powers of 21.6 kW are used to determine the best fit for model parameters. General values for the model parameters are found, applicable to high power thrusters and irrespective of thruster type. Performance of a 50 kW thruster is calculated for an anode specific impulse of 2500 seconds or a discharge current of 100 A.
Rhythmic reference of a human while a rope turning task (2011)

This paper addresses the rhythmic reference in physical human-robot interaction. Human refers to a rhythm from multiple sensing modalities when turning a rope with another human synchronously. This study verifies a hypothesis that some humans mix several rhythms of the modalities into a rhythm (rhythmic reference). Six participants, four males and two females, 21-23 years old, took part in eight experiments which examined the hypothesis. In each experiment, we masked the perception of each participant using eight combination of three kinds of masks, an eye-mask, headphones, and a force mask. Each participant interacted with an operator that turned a rope with a constant frequency. As a result of the experiments, a participant increased the controlling error as the number of masks was increased regardless the types of masked modalities. The result strongly supported our hypothesis.