gebhart/patrepeval huggingface dataset:
IP-QAT (2011)

We present IP-QAT, a new community-based question and answer system for software users. Unlike most community forums, IP-QAT is integrated into the actual software application, allowing users to easily post questions, answers and tips without having to leave the application. Our in-product implementation is context-aware and shows relevant posts based on a user's recent activity. It is also designed with minimal transaction costs to encourage users to easily post, include annotated images and file attachments, as well as tag their posts with relevant UI components. We describe a robust cloud-based system implementation, which allowed us to release IP-QAT to 37 users for a 2 week field study. Our study showed that IP-QAT increased user contributions, and subjectively, users found our system more useful and easier to use, in comparison to the existing commercial discussion board.
Expanded Newborn Screening in Italy Using Tandem Mass Spectrometry: Two Years of National Experience (2022)

Newborn screening (NBS) for inborn errors of metabolism is one of the most advanced tools for secondary prevention in medicine, as it allows early diagnosis and prompt treatment initiation. The expanded newborn screening was introduced in Italy between 2016 and 2017 (Law 167/2016; DM 13 October 2016; DPCM 12-1-2017). A total of 1,586,578 infants born in Italy were screened between January 2017 and December 2020. For this survey, we collected data from 15 Italian screening laboratories, focusing on the metabolic disorders identified by tandem mass spectrometry (MS/MS) based analysis between January 2019 and December 2020. Aminoacidemias were the most common inborn errors in Italy, and an equal percentage was observed in detecting organic acidemias and mitochondrial fatty acids beta-oxidation defects. Second-tier tests are widely used in most laboratories to reduce false positives. For example, second-tier tests for methylmalonic acid and homocysteine considerably improved the screening of CblC without increasing unnecessary recalls. Finally, the newborn screening allowed us to identify conditions that are mainly secondary to a maternal deficiency. We describe the goals reached since the introduction of the screening in Italy by exchanging knowledge and experiences among the laboratories.
Supplementary Figure 5 from Stearoyl-CoA Desaturase 1 Is a Novel Molecular Therapeutic Target for Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure 5: mono and combo effects of temsirolimus - PDF file 350K, Monotherapeutic Dose out of the mTOR inhibitor temsirolimus in ccRCC cell lines&lt;/p&gt;
A Prospective Study of Pain Control by a 2-Step Irradiance Schedule During Topical Photodynamic Therapy of Nonmelanoma Skin Cancer (2014)

Topical PDT can be effectively delivered to sBCC with minimal treatment-related pain by a 2-step irradiance protocol.
ChemInform Abstract: Terpiodiene: A Novel Tricyclic Alcohol from the Okinawan Sponge Terpios hoshinota (2002)

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.
Smart Storytelling: Video and Text Risk Communication to Increase MFA Acceptability (2020)

Exposure of passwords for authentication and access management is a ubiquitous and constant threat. Yet, reliable solutions, including multi-factor authentication (MFA), face issues with wide-spread adoption. Prior research shows that making MFA mandatory helps with tool adoption but is detrimental to users' mental models and leads to security-avoidance behavior. To explore feasible solutions, we implemented text- and video-based risk communication strategies to evaluate if either mode of risk communication was useful. We sought to explore users' technical biases to further examine the mental models that are associated with safer security habits. Our study of N=620 participants found that users are aware of frequent security attacks, including phishing. We found that text- and video-based communication is often useful when information is aligned with individual actions and their consequences, which can range from benign to catastrophic. Shorter mental-model-aligned video snippets piqued user interest in MFA. On the other hand, detailed risk communication videos or textual descriptions improved users' understanding of MFA and the potential risks of non-usage. Our study indicates that, beyond usability and comprehensive education, risk communication offers the potential to increase MFA adoption.
Multi-Layer Lambda Grid With Exact Bandwidth Provisioning Over Converged IP and Optical Networks (2009)

This paper proposes for the first time a multi-layer Lambda Grid, which is a platform to establish dynamically a computing environment with a guaranteed level of throughput and bandwidth over converged IP and optical networks according to each client reservation request. It enables client-side visualization of a computing environment comprising converged IP and optical networks and geographically distributed computing domains. In addition, it dynamically reserves a packet switched path/tunnel (sub-lambda) with the exact requested bandwidth and computer resources according to each client reservation request. Moreover, it links the reserved path to the reserved computers, controls the reserved sub-lambda and the relevant lambda as needed, and routes only the reserved packet flow between the reserved computers to the reserved sub-lambda. In terms of cost performance and bandwidth flexibility, it can use network resources more effectively than existing Lambda Grids. Through the multi-layer Lambda Grid, clients can execute applications in an established computing environment as if the environment was a virtual private computing environment for clients. To achieve the multi-layer Lambda Grid, this paper also proposes a novel technology. This technology dynamically reserves a sub-lambda with the exact requested bandwidth according to each client reservation request. Moreover, it links the reserved sub-lambda to the reserved computers, and controls the reserved sub-lambda and the relevant lambda as needed. In addition, it routes only the reserved packet flow between reserved computers to the reserved sub-lambda. To evaluate the feasibility of the technology, a common computing environment with the multi-layer Lambda Grid for scientific calculation, file transfer, and high-definition video streaming services is presented in an actual field environment. Through this experiment, the total feasibility of the multi-layer Lambda Grid is shown.
Electrochemical ‘Lab on a chip’ for Toxicity Detection in Water (2019)

An electrochemical 'Lab-on-a-chip' for water toxicity detection is presented. This miniaturized device containing an array of nano liter electrochemical cells, which integrates bacteria and can emulate physiological reactions in response to different chemicals. Bacteria, which have been genetically engineered to respond to environmental stress, act as a sensor element and trigger a sequence of processes, which leads to generation of electrical current. The silicon chip contains an array of nano-volume electrochemical cells that house the bacteria, connected to a sensing and data analysis unit. Each of the electrochemical cells in the array can be monitored independently and simultaneously with the others. A measurable current signal, well above the noise level, was produced within less than 10 minutes of exposure to representative toxicants. This miniature device provides high throughput rapid and sensitive real-time detection of acute toxicity in water.
Fluorescence Fluctuation Analysis for the Study of Interactions between Oligonucleotides and Polycationic Polymers (2001)

The interactions between a cationic polymer, poly(2-dimethylamino)ethyl methacrylate (pDMAEMA), and negatively charged rhodamine-labeled 25-mer phosphodiester oligonucleotides (Rh-ONs) were studied by fluorescence fluctuation spectroscopy and other techniques. The composition of the pDMAEMA/Rh-ON complexes was investigated as a function of the charge ratio (+/-) by increasing the pDMAEMA concentration and keeping the Rh-ON concentration constant. We applied two different methods for analyzing the fluorescence fluctuation profiles of the pDMAEMA/Rh-ON complexes, which depended on their composition. First, we analyzed the data with the photon counting histogram (PCH) technique, which determines the molecular brightness and the concentration of fluorophores (Chen et al, 1999). A particular challenge for the data analysis is the occurrence of sudden fluorescence bursts in the fluorescence fluctuation profiles, which are linked to the appearance of multimolecular complexes (i. e. when several Rh-ONs were present in one complex). A quantitative interpretation of the analysis for the complexes remains challenging and is connected to the rarity of the fluorescent bursts, which do not provide sufficient data statistics. To specifically address the problem of the fluorescent bursts we employed a method described by Van Craenenbroeck et al. (1999). This method, applicable only when data were integrated over much longer time bins, allowed us to estimate the number of fluorescence bursts which could be considered as a relative measure of the amount of multimolecular complexes present. When monomolecular complexes were formed, i. e. at high values of the charge ratio, highly intense fluorescence peaks were not present and the interpretation of the PCH analysis was more straightforward. The molecular brightness of the species (epsilon), as revealed from PCH analysis, was greater than epsilon for the free Rh-ONs, indicating that the Rh-ONs were attached to pDMAEMA chains.
Modification of Cellular Membrane Functions by Pendolmycin (1989)

Pendolmycin is a new indole alkaloid isolated from Nocardiopsis as an inhibitor of phosphatidylinositol turnover. Structurally, pendolmycin is similar to teleocidin B and lyngbyatoxin A. Pendolmycin, teleocidin B and 12-O-tetradecanoylphorbol-13-acetate all inhibited phosphatidylinositol turnover in A431 cells. Pendolmycin inhibited binding of epidermal growth factor, activated arachidonic acid release and hexose transport, and inhibited binding of phorbol-12,13-dibutylate in C3H10T1/2 cells. Thus, pendolmycin was as potent as teleocidin B and phorbol ester tumor promoters in modification of cell membrane functions, while having the simplest structure among them.
ChemInform Abstract: An Asymmetric Synthesis of Differentially Protected meso‐2,6‐ Diaminopimelic Acid. (1995)

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.
Flux Melting of Metal-Organic Frameworks (2018)

&lt;div&gt;Recent demonstrations of melting in the metal-organic framework (MOF) family have created&lt;/div&gt;&lt;div&gt;interest in the interfacial domain between inorganic glasses and amorphous organic polymers. The&lt;/div&gt;&lt;div&gt;chemical and physical behaviour of porous hybrid liquids and glasses is of particular interest,&lt;/div&gt;&lt;div&gt;though opportunities are limited by the inaccessible melting temperatures of many MOFs. Here,&lt;/div&gt;&lt;div&gt;we show that the synthetic processing technique of flux melting, ‘borrowed’ from the inorganic&lt;/div&gt;&lt;div&gt;domain, may be applied to MOFs in order to melt materials which do not possess an accessible&lt;/div&gt;&lt;div&gt;liquid state in their pure form. We employ the high-temperature liquid state of one MOF as a solvent&lt;/div&gt;&lt;div&gt;for a secondary, non-melting MOF component. Differential scanning calorimetry, small- and wideangle&lt;/div&gt;&lt;div&gt;X-ray scattering, electron microscopy and X-ray total scattering techniques are used to show&lt;/div&gt;&lt;div&gt;the flux melting of the crystalline component within the liquid. Gas adsorption and positron&lt;/div&gt;&lt;div&gt;annihilation lifetime spectroscopy measurements show that this results in enhanced, accessible&lt;/div&gt;&lt;div&gt;porosity to a range of guest molecules, in the resultant flux melted MOF glass.&lt;/div&gt;
Human Perception Measures for Product Design and Development—A Tutorial to Measurement Methods and Analysis (2017)

This tutorial describes the necessary steps for designing and conducting a perception experiment in order to obtain design parameters for human–machine interactions. It is intended for engineers and product designers, which require design parameters not included in the current state of the art. Topics addressed are the preposition of hypotheses, the selection of parameters, psychophysical measurement procedures and the calculation of sample sizes. Relevant steps for data analysis from psychology and social sciences are applied to the engineering and design context and guidelines for reporting results are given. The required steps are illustrated with an example experiment assessing detection thresholds of damping parameters of haptic automotive rotary controls with regard to parameters like knob diameter and distraction. Results imply significant effects of knob diameter on both absolute and differential thresholds, but no effect of distraction, implying a good transferability of laboratory results to real-world applications.
An Eph receptor regulates integrin activity through R-Ras (1999)

The ability of integrins to mediate cell attachment to extracellular matrices and to blood proteins is regulated from inside the cell. Increased ligand-binding activity of integrins is critical for platelet aggregation upon blood clotting and for leukocyte extravasation to inflamed tissues. Decreased adhesion is thought to promote tumor cell invasion. R-Ras, a small intracellular GTPase, regulates the binding of integrins to their ligands outside the cell. Here we show that the Eph receptor tyrosine kinase, EphB2, can control integrin activity through R-Ras. Cells in which EphB2 is activated become poorly adherent to substrates coated with integrin ligands, and a tyrosine residue in the R-Ras effector domain is phosphorylated. The R-Ras phosphorylation and loss of cell adhesion are causally related, because forced expression of an R-Ras variant resistant to phosphorylation at the critical site made cells unresponsive to the anti-adhesive effect of EphB2. This is an unusual regulatory pathway among the small GTPases. Reduced adhesiveness induced through the Eph/R-Ras pathway may explain the repulsive effect of the Eph receptors in axonal pathfinding and may facilitate tumor cell invasion and angiogenesis.
Accommodation of physostigmine and its analogues by acetylcholinesterase is dominated by hydrophobic interactions (2008)

The role of the functional architecture of the HuAChE (human acetylcholinesterase) in reactivity toward the carbamates pyridostigmine, rivastigmine and several analogues of physostigmine, that are currently used or considered for use as drugs for Alzheimer's disease, was analysed using over 20 mutants of residues that constitute the interaction subsites in the active centre. Both steps of the HuAChE carbamylation reaction, formation of the Michaelis complex as well as the nucleophilic process, are sensitive to accommodation of the ligand by the enzyme. For certain carbamate/HuAChE combinations, the mode of inhibition shifted from a covalent to a noncovalent type, according to the balance between dissociation and covalent reaction rates. Whereas the charged moieties of pyridostigmine and rivastigmine contribute significantly to the stability of the corresponding HuAChE complexes, no such effect was observed for physostigmine and its analogues, phenserine and cymserine. Moreover, physostigmine-like ligands carrying oxygen instead of nitrogen at position -1 of the tricyclic moiety (physovenine and tetrahydrofurobenzofuran analogues) displayed comparable structure-function characteristics toward the various HuAChE enzymes. The essential role of the HuAChE hydrophobic pocket, comprising mostly residues Trp(86) and Tyr(337), in accommodating (-)-physostigmine and in conferring approximately 300-fold stereoselectivity toward physostigmines, was elucidated through examination of the reactivity of selected HuAChE mutations toward enantiomeric pairs of different physostigmine analogues. The present study demonstrates that certain charged and uncharged ligands, like analogues of physostigmine and physovenine, seem to be accommodated by the enzyme mostly through hydrophobic interactions.
Fecal Microbiota Transplantation (FMT) for Treatment of Clostridium difficile Infection (CDI) in Immunocompromised Patients: ACG Governors Award for Excellence in Clinical Research (2013)

Purpose: Patients who are immunocompromised (IC) are at increased risk of CDI, which has increased to epidemic proportions over the past decade. FMT appears effective for the treatment of CDI, though there is concern that IC patients may be at increased risk of having adverse events (AE) related to FMT. In this multicenter study, we aimed to describe rates of CDI cure after FMT as well as AE experienced by IC patients after FMT. Methods: A multicenter retrospective series was performed of the use of FMT in IC patients with CDI that was recurrent, refractory, or severe. A 32-item questionnaire soliciting demographic and pre- and post-FMT data was completed at 16 centers for 83 patients, of which 66 were eligible based on at least 12 weeks of post-FMT follow up. Outcomes included: (1) rates of CDI cure after FMT, (2) serious adverse events (SAE) such as death or hospitalization within 12 weeks of FMT, (3) infection within 12 weeks of FMT, and (4) AE related and unrelated to FMT. Results: Cases included adult (61) and pediatric (5) patients treated with FMT for refractory (12%), recurrent (54%), and overlap of recurrent/refractory and severe CDI (34%). Seventy eight percent were outpatients at time of FMT. The mean follow-up period between FMT and data collection was 12 months (range: 3-51 months). Reasons for IC included: HIV/AIDS (2), solid organ transplant (14), oncologic conditions (6), immunosuppressive therapy for IBD (32), and other IC due to medical condition/medication (12). The CDI cure rate after a single FMT was 78%, with 52 patients experiencing no recurrence at least 12 weeks post-FMT. Nine patients underwent repeat FMT, of which seven had no further CDI. Thus, the overall cure rate was 89%. Ten (15%) patients had a SAE within 12 weeks post-FMT, of which eight were hospitalizations. Two deaths occurred within 12 weeks of FMT, one of which was the result of aspiration during sedation for FMT administered via colonoscopy; the other was unrelated to FMT. None suffered infections definitely related to FMT, but one patient developed unrelated infection and two had self-limited diarrheal illness, which were probably unrelated, and for which no causal organism was identified. Three IBD patients (9%) experienced disease flare post-FMT. Two ulcerative colitis (UC) patients underwent colectomy related to course of UC >100 days after FMT. One patient had a superficial mucosal tear caused by the FMT colonoscopy and four patients reported mild, self limited abdominal discomfort post-FMT. Conclusion: This series demonstrates effective use of FMT for CDI in IC patients with few SAE or related AE. Importantly, there were no infectious complications in these high-risk patients. Further prospective studies of FMT in IC patients are needed to confirm safety and efficacy in this population. Disclosure - Dr. Khoruts-Research Support: CIPAC, Ltd Dr. Brandt-Speaker's Bureau/Research Support: Optimer Pharmaceuticals, Inc. Dr. Gordon-Speaker: Cubist.
Nominal Scaling of Print Substrates (2009)

Print substrates are often measured or characterized using optical measurements, such as spectra or colorimetric measurements. Specialized devices or techniques exist to measure other properties, such as thickness, surface roughness, fluorescence, opacity or gloss. However, these measurements are often disjoint and, with respect to color imaging requirements, they are often a secondary consideration. We present specific measurement data for a collection of digital commercial print substrates and explore the correlations of these measures and their general distributions. We then present the results of a nominal scaling experiment in which both the visual and tactile properties of 72 print substrates was evaluated by 21 subjects. These evaluations were based on unconstrained text descriptions of the samples. The analysis made use of techniques from corpus linguistics to determine multivariate clustering by keywords and by samples. This allows both a global view of the visual and tactile categorization schemes of the subjects, as well as specific pairing of print substrates deemed to be most similar by subjects. We conclude with a discussion of nominal scaling and it's relevance to perceptual categorization.
Spinal progenitor cell differentiation in collagen-based hydrogels: Directing oligodendrocyte differentiation using ECM signals (2014)

Over 11,000 people sustain spinal cord injury (SCI) each year in the United States [1]. Researchers have examined spinal progenitor cell implantation into the injury area to encourage axonal regeneration and found functional improvement with this treatment [2]. However, transplanted cell viability was low and there was no scaffold for axonal growth within the injured area. By providing a scaffold, cell viability should increase and axonal growth through the injury area should be supported. Further, the implanted spinal progenitor cells differentiated into astrocytes, neurons, and oligodendrocytes. Oligodendrocyte progenitors are promising in promoting functional recovery [3]. Oligodendrocytes mature during neonatal development; therefore, cells are expected to respond favorably to mechanical properties similar to the neonatal environment. The mechanical and extracellular matrix properties of the scaffolds described here have been tuned to direct spinal progenitor cell differentiation toward oligodendrocytes. Thermally gelling systems were developed in 4 combinations: collagen alone, collagen and laminin, collagen and high molecular weight hyaluronic acid (hHA), and collagen, hHA, and laminin. All of these gel types have the same concentration of collagen (1.5 mg/mL), and compressive moduli below 2 kPa, which is within range of neural tissue (between 0.5–8 kPa) [4]. Multi-component hydrogels mimic mechanical properties of neonatal neural tissue most closely. After 5 days in culture, hydrogels provided an environment that allowed for spinal progenitor differentiation into astrocytes, neurons, and oligodendrocytes. Collagen-based hydrogels are viable thermally gelling systems to direct progenitor differentiation. These gels may promote regeneration after SCI in vivo by directing cell differentiation toward oligodendrocytes.