gebhart/patrepeval huggingface dataset:
Confronting theCOVID‐19 Pandemic: December 2019–May 2020 (2021)

Abstract The SARS‐CoV‐2 (COVID‐19) pandemic was officially declared by the World Health Organization on 11 March, 2020. From the initial public reports from China in December 2019, the contagion blazed its way from ground zero in Wuhan, China into 165 countries. The health disaster caught the planet by surprise. At the time of this writing, 6.6 million COVID‐19 cases were confirmed worldwide. Central and South America are the latest hotspots. Utilizing state‐of‐the‐art science and technology, industry, government, and academic enterprises internationally are engaged in a monumental campaign to combat and eliminate the viral threat. Small‐molecule therapeutics discovery largely by way of drug repurposing and accelerated vaccine development are at the forefront of this campaign. Within five months time, 500 unique therapeutic agents have advanced into development, &gt;150 clinical trials initiated, and seven agents authorized for emergency use. This article presents a snapshot of these activities as of 29 May 2020.
ChemInform Abstract: Electrophilic Chemistry of Dodecahedrane. Direct Entry to Epoxydodecahedrane and the First Tethered Derivative. (1992)

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.
Accuracy of Protein Synthesis and <i>in vitro</i> Aging (1977)

The authors have looked for altered proteins in senescent cultured cells from adult liver. Four enzymes (phosphoglycerate kinase, M2 type pyruvate kinase, glucose phosphate isomerase and glucose-6-phosphate dehydrogenase) have been studied by immunological and enzymatic titration and electrofocusing. In addition, heat stability of glucose-6-phosphate dehydrogenase (G6PD) was appraised in cell crude extracts and in partially purified preparations. Enzymatic aactivity as well as immunological reactivity of the four enzymes studied were identical 16 lines in phase II and in 13 lines in phase III. Electrofocusing pattern of the enzymes from 'young cells' was identical to the ones from 'old cells'. Finally, G6PD from old cells seemed to be more unstable than G6PD from young cells when studied in crude extracts. These differences, however, disappeared as G6PD was partially purified from old or young cultured cells. Consequently, no evidence of altered protein, either missynthesized or posttranslationally modified, was found in the senescent cultured cells studied. Moreover, this work indicated that the modification of heat stability of G6PD from old cells was not due to the enzyme molecule itself but rather to the cell medium.
Real-time Error Monitoring System Considering Endurance and Data-retention Characteristics of TaOX-based ReRAM Storage with Workloads at Data Centers (2020)

Approximate Computing attracts attention due to reducing power consumption and improving performance by tolerating errors. However, to use Approximate Computing, systems should control amounts of errors occurred in storage. This paper proposes real-time error monitoring system using ReRAM storage in order to understand how many errors occur in storage. To evaluate this system, measured ReRAM data and one-week long workload logs at data centers are input to the proposed system. The proposed system outputs Total bit error rate (BER) calculated from Set/Reset cycles and write interval time. In addition, the proposed system reveals that Total BER of some sectors exceeds the error correction limit set to 0.9 code rate of BCH ECC for a week.
LScanner (2007)

This note describes the prototype named "LScanner", a "peephole" type graphical user interface to control sound sources localization in an augmented reality environment. We put here the focus on technical aspects of the implementation. The corresponding demo will illustrate its use while controlling a wave fiel synthesis spatialization system.
Interactions of gaseous nitric acid with surfaces of environmental interest (2004)

Gaseous nitric acid removal by surfaces in experimental systems and in the atmospheric boundary layer is rapid. However, neither the form of HNO3 on surfaces nor its impact on the properties of the thin surface film are known. We report here studies of surfaces that have been exposed at room temperature (295 ± 2 K) to gaseous mixtures of water vapor with HNO3 at concentrations from 46 ppb to 4 × 103 ppm. The surfaces were probed using a combination of Fourier transform infrared spectrometry (FTIR), non-contact atomic force microscopy (AFM), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and X-ray photoelectron spectroscopy (XPS). Exposure of borosilicate glass, quartz, and thin Teflon films to mixtures of gaseous HNO3 and water vapor leads to the subsequent uptake of much larger amounts of water than occurs on the corresponding unexposed surfaces. Infrared spectra show evidence for the formation of nitric acid–water complexes on the surface that leads to this enhanced water uptake. On borosilicate glass, exposure to the nitric acid–water vapor mixture results in surface segregation of the trace metal oxides and their nitrates formed from reaction with HNO3. The majority of these oxides can be removed by rinsing with water; however, smaller, segregated regions of ZnO remain on the surface. The implications for heterogeneous reactions in thin films on surfaces in laboratory systems and in the atmosphere are discussed.
The Mystery of Chemotherapy Brain: Kynurenines, Tubulin and Biophoton Release (2020)

The majority of patients receiving chemotherapy experience post-chemotherapy cognitive impairment, sometimes referred to as "chemo brain" or "chemo fog." The cognitive impairment associated with this syndrome can be severe, and can sometimes last for many years after therapy discontinuation. Despite extensive investigations, its etiology is unknown. We argue that chemo brain results from damage to tubulin within microtubules. This damage can occur directly from tubulin inhibitors such as taxanes, epothilones or vinca alkaloids. Other chemotherapies stimulate increased mitochondrial activity and biophoton release. This results in abnormal tryptophan metabolism and excess production of neurotoxic kynurenines, which, in turn, damage microtubules.
A study of the relationship between remote thermocouple temperatures and tool wear in machining (1977)

Experimental data are presented which demonstrate a strong correlation between tool wear and the signal of a thermocouple located at a position on the cutting tool remote from the cutting edge. A mathematical model is proposed for explaining this relationship between tool wear and- temperature. The model is supported by good statistical agreement between the data and the form of the proposed equation. For a total of nine different machining conditions with replications for several of the conditions, the correlation coefficient ranged in value between 0·837 and 0·978.
New Developments in OCT Imaging Technology (2007)

We review recent advances in the use of low-coherence spectral interferometry to obtain nanometer to micron-scale measurements of structure, motion, and molecular composition in living cells, tissues, and organisms.
Evolution of carbon nanotubes and their metallurgical reactions in Al-based composites in response to laser irradiation during selective laser melting (2019)

Aluminium-based composites reinforced with carbon nanotubes are widely sought for their outstanding metallurgical and structural properties that largely depend on the manufacturing route. In this work, the process-structure-property relationship for a composite made from high-energy-ball-milled pure Al and multi-walled carbon nanotubes (MWCNT) processed by laser powder-bed-fusion additive manufacturing was investigated. The strong good bond between MWCNT (high laser absorptivity) and Al (low laser absorptivity) allowed the energy transfer from the former to the latter and maintained the heat for longer allowing for better melt efficiency hence improved processability. The response of MWCNT to laser irradiation and their interfacial reactions with Al were probed in a holistic investigation. X-ray diffraction confirmed the partial transformation of C into Al-carbides in addition to the presence of some nano-crystalline graphitic materials. Microscopy revealed evidence of carbides segregation at the melt pool boundaries as well as migration along the build direction. Raman spectroscopy showed that laser irradiation promoted re-graphitisation in MWCNT, reducing the amount of defects introduced by milling. Two types of Al4C3 formed as a result of the metallurgical reaction between Al and MWCNT. These were needle-like and hexagonal Al4C3 and their mechanisms of formation, direct precipitation and dissolution-precipitation, respectively, were explained in light of the thermal profile experienced by the material during melting and solidification. Large scale electron backscatter diffraction showed that there is no distinctive texture developing during melting and solidification. Micro- and nano-indentation testing showed uniform mechanical properties.
Functional skewing of the global CD8 T cell population in chronic hepatitis B virus infection (2008)

The inflamed liver in chronic hepatitis B virus (HBV) infection (CHB) is characterized by a large influx of non-virus-specific CD8 T cells. Little is known about the functional capacity of these lymphocytes, which could provide insights into mechanisms of failure of viral control and liver damage in this setting. We compared the effector function of total circulating and intrahepatic CD8 T cells in CHB patients and healthy donors. We demonstrated that CD8 T cells from CHB patients, regardless of their antigen specificity, were impaired in their ability to produce interleukin-2 and proliferate upon TCR-dependent stimulation. In contrast, these CD8 T cells had preserved production of the proinflammatory cytokines interferon-gamma and tumor necrosis factor-alpha. This aberrant functional profile was partially attributable to down-regulation of the proximal T cell receptor signaling molecule CD3zeta, and could be corrected in vitro by transfection of CD3zeta or replenishment of the amino acid arginine required for its expression. We provide evidence for depletion of arginine in the inflamed hepatic microenvironment as a potential mechanism for these defects in global CD8 T cell signaling and function. These data imply that polarized CD8 T cells within the HBV-infected liver may impede proliferative antiviral effector function, while contributing to the proinflammatory cytokine environment.
Observation of Quantum Coherence in the Nonlinear Emission of Semiconductor Microcavity Polaritons (2002)

The fascination of macroscopic quantum coherence formed in a degenerate Bose gas drives the worldwide work on atomic Bose-Einstein condensates. Semiconductor polaritons1 are another promising system to explore the physics of degenerate Bose gases in a stronger interaction regime. It is also a system easily produced and probed through optical methods. In this work we present the first observation of the onset of a quantum coherence formed out of an initially thermal population of polaritons in a microcavity quantum well system. The quantum coherence is measured by a time domain second order coherence g(2)(0) of the light emitted from the polaritons. Second and higher order coherence functions are crucial in quantum optics to distinguish among various pure states of light, such as coherent state or squeezed state, from classical thermal light2. They have been measured indirectly in the spatial domain for atomic BECs3,4. In our system, with supporting evidence from measurements of the input-output, dispersion, and time evolution of the emission, the phase transition was identified by a decrease of g(2)(0) ≈2, the value for a thermal state, toward g(2)(0) ≈1 for a coherent state. This is a direct evidence of the formation of a macroscopic quantum coherence in the lower polariton ground state.
SQuINTing at VQA Models: Introspecting VQA Models With Sub-Questions (2020)

Existing VQA datasets contain questions with varying levels of complexity. While the majority of questions in these datasets require perception for recognizing existence, properties, and spatial relationships of entities, a significant portion of questions pose challenges that correspond to reasoning tasks - tasks that can only be answered through a synthesis of perception and knowledge about the world, logic and / or reasoning. Analyzing performance across this distinction allows us to notice when existing VQA models have consistency issues - they answer the reasoning questions correctly but fail on associated low-level perception questions. For example, in Figure 1, models answer the complex reasoning question “Is the banana ripe enough to eat?” correctly, but fail on the associated perception question “Are the bananas mostly green or yellow?” indicating that the model likely answered the reasoning question correctly but for the wrong reason. We quantify the extent to which this phenomenon occurs by creating a new Reasoning split of the VQA dataset and collecting VQAintrospect, a new dataset1 which currently consists of 200K new perception questions which serve as sub questions corresponding to the set of perceptual tasks needed to effectively answer the complex reasoning questions in the Reasoning split. Our evaluation shows that state-of-the-art VQA models have comparable performance in answering perception and reasoning questions, but suffer from consistency problems. To address this shortcoming, we propose an approach called Sub-Question Importance-aware Network Tuning (SQuINT), which encourages the model to attend to the same parts of the image when answering the reasoning question and the perception sub question. We show that SQuINT improves model consistency by ~7%, also marginally improving performance on the Reasoning questions in VQA, while also displaying better attention maps.
Significance of Periprocedural Myonecrosis on Outcomes After Percutaneous Coronary Intervention (2008)

A preprocedural cTnT level >0.01 is a powerful independent predictor of prognosis after PCI and is of greater prognostic significance than the postprocedural biomarker levels. PCI-related myonecrosis occurs frequently and predicts short-term but not long-term risk of death.
Glucose movement into rat uterine fluid (1979)

The uterine horns of anaesthetized rats were cannulated and 2.5 ml 0.9% NaCl at 37 degrees C were recirculated for up to 90 min. Glucose appeared in the medium, reaching a concentration of approximately 1 mM. Various aspects of the transport process were examined, and it is suggested that the glucose is mainly derived from the plasma, and probably enters the uterine lumen by a process involving facilitated diffusion.
A trifluoromethylphenyl diazirine-based SecinH3 photoaffinity probe (2011)

The synthesis of a trifluoromethylphenyl diazirine photoaffinity probe of the cytohesin inhibitor SecinH3 is described. The probe exhibits improved labelling efficiency over a benzophenone-based probe and thus is more suitable for photoaffinity labelling in complex biological samples.
When Outcomes Diverge: Age and Cardiovascular Risk as Determinants of Mortality and ICU Admission in COVID-19 (2022)

Once adjusted for the main determinant of mortality (age) heart failure only remained independently associated with mortality. Admission to the ICU was less likely for elderly patients. This may reflect the catastrophic impact of the first wave of COVID-19 pandemic in terms of ICU bed availability in Lombardy, leading to a selection process for ICU admission.
Atomic force sensors constructed from carbon and quartz fibers (1990)

A simple design of force sensors constructed from carbon and fused quartz fibers is presented. The handmade force sensors exhibit characteristics similar to those of cantilevers produced by micromechanic techniques. Atomically resolved force maps of the c surface of graphite and boron nitride and a topographic image of mica have been obtained using an atomic force microscope equipped with a fiber sensor.
Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review (2021)

The accelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID-19-convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), a few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of the spike protein (e.g., ΔHV69-70, ΔLGVY141-144 and ΔAL243-244). The continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and the fitness of emerging variants.
2D nonlinear finite element modelling of electromagnetic retarders using time-stepping algorithms, and the Petrov-Galerkin method with homogenization techniques (1996)

This paper describes a method for finite element modelling of transient 2D eddy currents in the nonlinear moving conductor of an electromagnetic retarder. The magnetic vector potential A formulation is used, with a general single-step time-marching algorithm, and the fixed and moving coordinate systems are compared. A homogenization technique, inspired by the lamination modelling, is used to make the geometry of a moving region invariant along the speed direction, in order to use a more direct method to compute the steady state eddy currents in the whole rotor. Results are compared to measurements.
Studies on Stability of Protease during Storage and on the Relationship between Temperatures and Washing Ability of the Detergents for Operation Apparatus (2000)

Detergents contained enzymes that claim stronger washing ability and less damages are used widely for washing out blood or minute tissues adhered to various operation apparatus. It is known that enzyme protein shows maximum activity at 40℃ and is more stable when stored at the lower temperature. However, detergents contained enzymes are stored at room temperature in the most of operation theaters, and furthermore they are transported from manufacturers to any of distribution route in nonrefrigerated condition. When we measured Protease activities at 4℃ and 40℃ during 161 days storage period, the activity at 4℃ was stable but at 40℃ decreased 38.0% in average. In comparison of Protease activities at 20℃ and 40℃, the latter showed twice higher activity. When we studied the correlation between temperatures and the washing ability of detergents contained enzymes using Adenosine triphosphate as the marker, the washing ability at 40℃ was stronger than that at 20℃.
A phase 2 basket trial of ulixertinib (BVD-523) in combination with hydroxychloroquine in patients with advanced gastrointestinal malignancies harboring MAPK pathway mutations (BVD-523-HCQ). (2023)

TPS4174 Background: RAS-induced signaling through the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathway plays an important role in the pathogenesis of many solid tumors. Ulixertinib (BVD-523) is a first-in-class and best-in-class small molecule inhibitor of ERK 1/2 that is currently being investigated in multiple cancer clinical trials, both as a single agent and as part of combination therapy. Preclinical studies have demonstrated that inhibition of the RAS/MAPK/ERK signaling cascade leads to upregulation of autophagy, a catabolic pathway that includes the lysosomal degradation of proteins to support cellular metabolism during times of cellular stress. Given cancer cells’ increased reliance on autophagy to enhance their survival in this context, this study seeks to evaluate the combination of ulixertinib with hydroxychloroquine, an antimalarial drug known to suppress autophagy, in patients with advanced gastrointestinal malignancies harboring mutations in genes involved in MAPK signaling. Methods: This is an open-label, multicenter, phase II basket study of ulixertinib in combination with hydroxychloroquine in patients with advanced GI malignancies harboring mutations in one of the following MAPK signaling-associated genes: KRAS, NRAS, HRAS, BRAF (non-V600), MEK1/2, or ERK1/2. The completed Phase 1 dose-escalation trial (NCT04145297) established the recommended Phase 2 dose which will be the doses used in this study; ulixertinib 450mg PO BID combined with hydroxychloroquine 600mg PO BID, both drugs administered daily in 28-day cycles, with tumor assessments after every 2 cycles. The trial has five baskets based on primary disease: cholangiocarcinoma, pancreatic adenocarcinoma, colorectal adenocarcinoma, esophageal adenocarcinoma, and gastric adenocarcinoma. A Simon two-stage design will be employed within each of the 5 disease-specific baskets noted above, with the first stage of enrollment consisting of n=13 patients/ basket. To be considered evaluable, a patient must complete at least one cycle of therapy and receive at least 75% of the prescribed dose during that first cycle. If ≥ 4 patients in a specific basket achieve a response (complete or partial), that basket will then open to Stage 2 with enrollment of an additional 30 patients. Primary study endpoints will include safety/toxicity as well as ORR by RECIST 1.1. The secondary endpoint for efficacy is progression-free survival. Exploratory endpoints include pharmacokinetics of both ulixertinib and hydroxychloroquine, as well as predictive biomarkers from blood and tumor tissue-based samples. At the time of abstract submission, 26 of the planned 65 patients in Stage 1 had been enrolled. Clinical trial information: NCT05221320 .
A Remarkable Difference in Pharmacokinetics of Fluorinated Versus Iodinated Photosensitizers Derived from Chlorophyll-a and a Direct Correlation between the Tumor Uptake and Anti-Cancer Activity (2023)

To investigate and compare the pharmacokinetic profile and anti-cancer activity of fluorinated and iodinated photosensitizers (PSs), the 3-(1'-(<i>o</i>-fluorobenzyloxy)ethyl pyropheophorbide and the corresponding meta-(<i>m</i>-) and para (<i>p</i>-) fluorinated analogs (methyl esters and carboxylic acids) were synthesized. Replacing iodine with fluorine in PSs did not make any significant difference in fluorescence and singlet oxygen (a key cytotoxic agent) production. The nature of the delivery vehicle and tumor types showed a significant difference in uptake and long-term cure by photodynamic therapy (PDT), especially in the iodinated PS. An unexpected difference in the pharmacokinetic profiles of fluorinated vs. iodinated PSs was observed. At the same imaging parameters, the fluorinated PSs showed maximal tumor uptake at 2 h post injection of the PS, whereas the iodinated PS gave the highest uptake at 24 h post injection. Among all isomers, the <i>m</i>-fluoro PS showed the best in vivo anti-cancer activity in mice bearing U87 (brain) or bladder (UMUC3) tumors. A direct correlation between the tumor uptake and PDT efficacy was observed. The higher tumor uptake of <i>m</i>-fluoro PS at two hours post injection provides a solid rationale for developing the corresponding <sup>18</sup>F-agent (half-life 110 min only) for positron imaging tomography (PET) of those cancers (e.g., bladder, prostate, kidney, pancreas, and brain) where <sup>18</sup>F-FDG-PET shows limitations.