gebhart/patrepeval huggingface dataset:
Flow cytometry as an improved method for the titration of Chlamydiaceae and other intracellular bacteria (2016)

Chlamydiaceae is a family of intracellular bacteria causing a range of diverse pathological outcomes. The most devastating human diseases are ocular infections with C. trachomatis leading to blindness and genital infections causing pelvic inflammatory disease with long-term sequelae including infertility and chronic pelvic pain. In order to enable the comparison of experiments between laboratories investigating host-chlamydia interactions, the infectious titer has to be determined. Titer determination of chlamydia is most commonly performed via microscopy of host cells infected with a serial dilution of chlamydia. However, other methods including fluorescent ELISpot (Fluorospot) and DNA Chip Scanning Technology have also been proposed to enumerate chlamydia-infected cells. For viruses, flow cytometry has been suggested as a superior alternative to standard titration methods. In this study we compared the use of flow cytometry with microscopy and Fluorospot for the titration of C. suis as a representative of other intracellular bacteria. Titer determination via Fluorospot was unreliable, while titration via microscopy led to a linear read-out range of 16 - 64 dilutions and moderate reproducibility with acceptable standard deviations within and between investigators. In contrast, flow cytometry had a vast linear read-out range of 1,024 dilutions and the lowest standard deviations given a basic training in these methods. In addition, flow cytometry was faster and material costs were lower compared to microscopy. Flow cytometry offers a fast, cheap, precise, and reproducible alternative for the titration of intracellular bacteria like C. suis. © 2016 International Society for Advancement of Cytometry.
Electrically Tunable Valley Dynamics in Twisted WSe2/WSe2 Bilayers (2020)

The twist degree of freedom provides a powerful new tool for engineering the electrical and optical properties of van der Waals heterostructures. Here, we show that the twist angle can be used to control the spin-valley properties of transition metal dichalcogenide bilayers by changing the momentum alignment of the valleys in the two layers. Specifically, we observe that the interlayer excitons in twisted WSe_{2}/WSe_{2} bilayers exhibit a high (>60%) degree of circular polarization (DOCP) and long valley lifetimes (>40 ns) at zero electric and magnetic fields. The valley lifetime can be tuned by more than 3 orders of magnitude via electrostatic doping, enabling switching of the DOCP from ∼80% in the n-doped regime to <5% in the p-doped regime. These results open up new avenues for tunable chiral light-matter interactions, enabling novel device schemes that exploit the valley degree of freedom.
Experimental verification of a zero-index near-infrared metamaterial (2011)

In this paper, we present a free-standing optical zero-index metamaterial (ZIM) with a symmetric structure in the direction of wave propagation. The metamaterial consists of a gold-polyimide-gold tri-layer stack perforated by air holes to form a fishnet geometry. With the aid of a genetic algorithm (GA), this structure is optimized to exhibit a near-zero refractive index with low absorption loss and a good impedance match to free space. The ZIM was fabricated and characterized. The measured results are found to be in strong agreement with the simulation predictions.
Magnetron-type radio-frequency plasma control yielding vertically well-aligned carbon nanotube growth (2003)

In order to understand the effects of plasma parameters on the nanotube formation and further controlled growth, we have investigated the optimal growth condition using a rf plasma-enhanced chemical vapor deposition method. The magnetic field introduced for a magnetron discharge enhances the nanotube growth as a result of the plasma-density increment and the self-bias reduction of a rf electrode. It is also found that the optimum ion flux and ion bombardment energy is a key parameter for the uniform, well-aligned, and density-controlled nanotube growth.
Basin-Scale Ocean Monitoring with Acoustic Thermometers (1992)

Aliasing: mapping errors at long space or time scales originating from oscillations whose wavelengths or periods are less than twice the sampling interval
“A neural prosthesis for restoring lost cognitive function: Brain-implantable biomimetic micro-electronic models of hippocampal input-output activity” (2009)

Damage to the hippocampus is frequently associated with epilepsy, stroke, and dementia (Alzheimer's disease), and is considered to underlie the memory deficits characteristic of these neurological conditions. The essential goals of this multi-laboratory effort include: (1) experimental study of hippocampal neuron and neural network function - how does the hippocampus encode information?, (2) formulation of biologically realistic models of neural system dynamics - can that encoding process be described mathematically to realize a predictive model of how the hippocampus responds to events that need to be remembered?, (3) microchip implementation of neural system models - can the mathematical model be realized as a set of electronic circuits to achieve parallel processing, rapid computational speed, and miniaturization?, and (4) creation of hybrid neuron-silicon interfaces - can structural and functional connections between electronic devices and neural tissue be achieved for long-term, bi-directional communication with the brain? By integrating solutions to these component problems, the team is realizing a microchip-based model of hippocampal nonlinear dynamics that can perform the same memory function as part of the hippocampus.
Effect of rotation on the translational and vibrational energy dependence of the dissociative adsorption of D2 on Cu(111) (1993)

We have investigated the dependence on the rotational and vibrational states of the translational energy of D2(v,J) formed in recombinative desorption from Cu(111). These results provide information about the effect of rotational energy relative to that of vibrational and translational energy on the dissociative chemisorption of D2 on Cu(111). The range of rovibrational states measured includes rotational states J=0–14 for vibrational state v=0, J=0–12 for v=1, and J=0–8 for v=2. D2 molecules were detected in a quantum-state-specific manner using three-photon resonance-enhanced multiphoton ionization (2+1 REMPI). Kinetic energies of desorbed molecules were obtained by measuring the flight time of D2+ ions in a field-free region. The mean kinetic energies determined from these measurements depend strongly on the rotational and vibrational states. Analyzing these results using the principle of detailed balance confirms previous observations that vibrational energy is effective, though not as effective as translational energy, in promoting adsorption. Rotational motion is found to hinder adsorption for low rotational states (J≤5) and enhance adsorption for high rotational states (J≥5). Even for high J states, however, rotational energy is less effective than either vibrational energy, which is 30%–70% more effective than rotational energy, or translational energy, which is 2.5–3 times more effective than rotational energy in promoting adsorption. The measured internal state distributions for the rovibrational states listed above are consistent with the observed dependence of the kinetic energy of the de- sorbed molecules with the rotational state. In addition, the analysis performed yields the dependence of the adsorption probability on kinetic energy separately for each rovibrational state. These functions have very similar sigmoidal shapes for all states examined. Changing the quantum state is primarily associated with a shift in the position, or threshold energy, for the curves. The level at which these functions saturate or level off at high energy is independent of rotational state but varies nonmonotonically with the vibrational state.
Design of a Haptic Device for Weight Sensation in Virtual Environments (2002)

The research presented in this paper is the design and implementation of a force feedback hand master called AirGlove. The device uses six ports arranged in a Cartesian coordinate frame setting to apply a point force to the user’s hand. Compressed air is exhausted through the ports, creating thrust forces. The magnitude and direction of the resultant force are controlled by changing the flow rate of the air jets and by activating different ports. The AirGlove can apply an arbitrary point force to the user’s hand. However, the main goal of this research is to reflect gravitational forces to the user so that sensation of weight of a virtual object can be created. After introduction of the main concept of the AirGlove, the paper presents design and implementation details of the device. Integration of the AirGlove with a virtual assembly system called VADE is explained next. Finally, details of experiments with the device are presented and discussed. Results indicate that users wearing the AirGlove can feel a minimum weight of about 100 grams and the device can create a fairly realistic weight sensation.
ChemInform Abstract: Cylindradines A (I) and B (II): Novel Bromopyrrole Alkaloids from the Marine Sponge Axinella cylindratus. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
A framework to orchestrate security SLA lifecycle in cloud computing (2016)

Security issues of cloud computing environments are considered a major challenge for its full adoption. A Service Level Agreement (SLA) corroborates the shared management vision provided by the cloud computing paradigm, which can assist with related security issues. The necessity to address security requirements in cloud computing SLAs is considered important for both providers and consumers, along with the tools and mechanisms necessary to deal with these requirements. These issues are current research challenges; therefore, this paper aims at proposing a framework to orchestrate the management of cloud services based on security requirements defined by the SLA in an automated manner during its entire lifecycle. In addition, mechanisms to support the phases of the SLA lifecycle are proposed as a part of the framework. also the preliminary validation of the proposed framework. Finally, it is presented the integration of the framework with a cloud solution and in what manner the SLA lifecycle is supported by the framework.
Receiver Hardware Considerations (2000)

This chapter discusses the hardware of the receiver. Since the basic design of GPS receiver in this book is software oriented, the hardware presented here is rather simple. The only information needed for a software receiver is the sampled data. These sampled or digitized data will be stored in memory to be processed. For postprocessing the memory size dictates the length of data record. A minimum of 30 seconds of data is needed to find the user position as mentioned earlier. In real-time processing the memory serves as a buffer between the hardware and the software signal processing. The hardware includes the radio frequency (RF) chain and analog-to-digital converter (ADC). Thus, the signal processing software must be capable of processing the digitized data in the memory at a real-time rate. Under this condition, the size of the memory determines the latency allowable for the signal processing software. This chapter includes the discussion of the antenna, the RF chain, and the digitizers. Two types of designs are discussed. One is a single channel to collect real data and the other is an in-phase and quadrature phase (I-Q) channel to collect complex data. In both approaches, the input signals can be either down-converted to a lower intermediate frequency (IF) before digitization or directly digitized at the transmitted frequency. The relation between the sampling frequency and the input frequency is presented. Some suggestions on the sampling frequency selection are included. Two hardware setups to collect real data will be discussed in detail as examples. The impact of the number of digitized bits will also be discussed. A digital band folding technique is discussed that can alias two or more narrow frequency bands into the baseband. Other uses for this technique are discussed.
CpG Combined with Chemotherapy in the Immunotherapy of Large Tumor. (2004)

Abstract Unmethylated cytosine-phosphorothioate-guanine nucleotides (CpG) are immuostimulators that can activate both innate and adaptive immunity. By binding to its receptor, TLR9, CpG can activate dendritic cells and B cells by inducing the secretion of cytokines, and increasing the expression of costimulatory molecules, such as CD80 and CD86. In this study, a B type CpG, CpG1826, was given intratumorally in an A20 lymphoma animal model. CpG alone can delay the growth of tumor in this model, however, the majority of the treated tumor-bearing mice still die, and it has very little effect on systemic tumor cells. Here we propose a new therapeutic strategy, a combination of cyclophosphomide (CTX), followed by subsequent intratumoral injection of CpG. BALB/c mice were inoculated s.c. with 107 A20 cells in the lower back, and treatment started on day 17 when tumor reached approximately 1.0 cm in diameter. CTX (100mg/Kg) was given i.p. on day 17 and 18, and for the groups that received CpG, CpG was injected intratumorally on day 19,20,21,24, and 26 with 100μg/dose. As shown in Fig.1, the combination of CTX with CpG could cure well-established large size (&gt;1.2cm in diameter) tumor, and mice remained tumor-free 5–6 months after the initial treatment. Conversely, the majority of mice that received CTX or CpG alone died of lymphoma. Tumor-free mice from this combined maneuver are protected from a lethal dose of A20 challenge even 5 months after the initial treatment. Our studies also showed that this combination is site dependent, as CTX combined with intratumoral injection of CpG had a much better therapeutic effect (100% survival), as compared to injection of CpG into a distant normal site (20% survival). Our studies also indicated that this combined maneuver is CD8+T cell dependent, as no therapeutic effect was observed when we repeated this experiment in a CD8+ T cell knockout model. We also demonstrated the systemic effect of this combination strategy in mice bearing tumors at two different sites. In combination with CTX, injection of one site with CpG controlled the growth of the second site tumor as opposed to a transient effect from chemotherapy or CpG alone. This led to significant prolongation of overall survival (Fig.2). In summary, we have shown that this combined chemoimmunotherapy strategy can cure both local and systemic tumor, which may provide a powerful antitumor therapy in the clinic. Figure Figure
Assessment of medical professionalism: A Delphi study (2020)

Abstract Background The importance of medical professionalism and its assessment has been well documented in the literature. However, there is currently no culturally-adapted tool to assess medical professionalism in Singapore. This study sets out to find consensus on relevance of the items from the Professional Mini Evaluation Exercise (P-MEX) for assessing medical professionalism in Singapore. Methods A two-round Delphi survey was completed by an expert panel consisting of program directors, associate designated institutional officials, and designated institutional official (n=15) from residency programs in Singapore. Round 1 comprised of 23 items from the P-MEX rated on a 5-point scale (1= Definitely include, 2= Possibly include, 3= Neutral, 4= Possibly exclude, 5= Definitely exclude). In round 2, the experts received feedback from the previous round, and were asked to re-rate the items which did not achieve consensus in the previous round. The threshold for consensus in the study was defined as 70% or greater agreement among experts. Results Completed questionnaires for both rounds were received from all 15 experts. In round 1, 18 items (78%) achieved consensus to be included. In round 2, 1 (4%) item achieved consensus to be included. However, none of the remaining item achieved consensus to be removed. A consensual list of 23 items covering four domains of medical professionalism (Doctor-patient relationship skills, Reflective skills, Time management and Inter-professional relationship skills) was obtained during the two-rounds of Delphi survey. Conclusions This 23-item P-MEX has garnered consensus and is suitable for assessing medical professionalism in Singapore. The findings of this study can provide guidance for faculty and institutions who want to assess medical professionalism of their medical trainees.
Efficacy of Antiviral Agents against the Omicron Subvariant BA.2.75 (2022)

Efficacy of Antiviral Agents against the Omicron Subvariant BA.2.75To the Editor: Five sublineages of the B.1.1.529(omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -BA.1, BA.2, BA.3, BA.4, and BA.5 -are recognized, and BA.5 is currently the predominant variant circulating globally. 1In India and Nepal, however, the prevalence of a subvariant of BA.2 (designated BA.2.75) is increasing rapidly and is now becoming dominant in Nepal. 2 Moreover, BA.2.75 has been detected in at least 25 other countries, including the United States, Singapore, Canada, the United Kingdom, Japan, and Australia; as such, it has spread across multiple continents. 2-4The World Health Organization designated BA.2.75 as a "variant of concern lineage under monitoring."Of additional concern, BA.2.75 may differ antigenically from BA.2.The receptor-binding domain of the spike (S) protein of SARS-CoV-2 is capable of inducing neutralizing antibodies and is the major target for monoclonal antibodybased therapy.BA.2, as compared with the reference strain Wuhan/Hu-1/2019, possesses 16 amino acid substitutions in the receptor-binding domain; BA.2 and BA.2.75 share 14 of these 16 substitutions.However, BA.2.75 possesses 4 amino acid changes in the receptor-binding domain (i.e., G339H, G446S, N460K, and the wild-type amino acid at position 493) that differ from those in BA.2, which suggests that the monoclonal antibodies authorized for emergency use by the Food and Drug Administration (FDA) may be less effective against BA.2.75 than against other SARS-CoV-2 strains and variants.To assess the efficacy of authorized therapeutic monoclonal antibodies against BA.2.75, we examined their neutralizing abilities against the BA.2.75 variant hCoV-19/Japan/TY41-716/2022 (TY41-716), which was isolated from a person traveling from India to Japan.Whole-genome sequencing of TY41-716 revealed that it possesses nine amino acid changes (K147E, W152R, F157L, I210V, G257S, D339H, G446S, N460K, and Q493
Improved Device Performances of Organic Solar Cells with Au Cathode Using a Phosphine Sulfide Type Cathode Modification Layer (2011)

Organic solar cells (OSCs) with Au as an electron collecting electrode were developed using a phosphine sulfide type cathode modification layer. Spirobifluorene based phosphine sulfide was used as the interlayer between the poly(3-hexylthiophene): [6,6]-phenyl C61-butyric acid methyl ester active layer and Au electrode. The open circuit voltage of the OSC was enhanced from 0.31 to 0.56 V and the efficiency was improved from 1.04 to 2.73% by the phosphine sulfide type cathode modification layer.
A Low-Output-Noise Multistage Shift Register Using Tin Dioxide Nanowire Transistors (2012)

A multistage shift register using the parallel connection technique of n-channel nanowire transistors for low output noise is proposed. The proposed circuit decreases the output noise by eliminating the direct connection of the clock signal to the gate of the pull-down transistor of the output stage. Measured results show that the output noise of the proposed circuit is under 0.16 V when the input voltage is 5.0 V and the operating frequency of the proposed circuit is 900 Hz at the capacitive load of 150 pF. The maximum operating frequency of the proposed circuit at the loading condition of the wide-video-graphic-array resolution can be up to 46 kHz.
Biomechanical analysis of limited intercarpal fusion for the treatment of Kienböck's disease: A three‐dimensional theoretical study (1998)

Although several types of intercarpal fusion have been advocated for the treatment of Kienbock's disease, the clinical outcome of each procedure is still inconclusive. The joint load and ligament tension based on a three-dimensional model were measured to determine which intercarpal fusion procedures unload the lunate and whether they alter the force transmission through the entire wrist joint. Ten theoretical models of wrists were used to simulate three different operative procedures: capitate-hamate fusion, scapho-trapezial-trapezoidal fusion, and scaphocapitate fusion. A discrete element analysis technique was used to perform these investigations. The joint force and ligament tension of normal wrists and of simulated operative procedures were calculated according to the deformation of each spring element, simulating the articular cartilage and the carpal ligaments. Scaphocapitate and scapho-trapezial-trapezoidal fusions significantly decreased the joint force at the radiolunate joint and the lunocapitate joint compared with the intact wrist. In contrast, these fusions significantly increased this value at the radioscaphoid joint in comparison with the intact wrist. In the midcarpal joint, scaphocapitate fusion also increased the joint force at the scapho-trapezial-trapezoidal joints and at the triquetral-hamate joint, whereas scapho-trapezial-trapezoidal fusion increased it at the scapho-capitate joint. Capitate-hamate fusion yielded no significant changes of the joint forces through the entire wrist joint. In the analysis of ligament tension, scaphocapitate and scapho-trapezial-trapezoidal fusions significantly decreased the tension only in the dorsal scapholunate ligament. These findings demonstrate that scaph-ocapitate and scapho-trapezial-trapezoidal fusions are effective in decompressing the lunate. By contrast, capitate-hamate fusion is ineffective in reducing lunate compression. Although scaphocapitate and scapho-trapezial-trapezoidal fusions are recommended for the treatment of Kienbock's disease, clinicians should consider that the increase of force transmission through the radioscaphoid and the midcarpal joints may lead to early degenerative changes after these procedures have been performed.
Engineering nanomedicines using stimuli-responsive biomaterials (2020)

The ability to engineer particles has the potential to shift the paradigm in the creation of new medicines and diagnostics. Complete control over particle characteristics, such as size, shape, mechanical property, and surface chemistry, can enable rapid translation and facilitate the US Food and Drug Administration (FDA) approval of particle technologies for the treatment of cancer, infectious diseases, diabetes, and a host of other major illnesses. The incorporation of natural and artificial external stimuli to trigger the release of drugs enables exquisite control over the release profiles of drugs in a given environment. In this article, we examine several readily scalable top-down methods for the fabrication of shape-specific particles that utilize stimuli-responsive biomaterials for controlled drug delivery. Special attention is given to Particle Replication In Nonwetting Templates (PRINT®) technology and the application of novel triggered-release synthetic and natural polymers.