gebhart/patrepeval huggingface dataset:
Population‐based threshold models describe weed germination and emergence patterns across varying temperature, moisture and oxygen conditions (2012)

Summary Opportunities for diversifying the management of weedy populations may be enhanced through accurate predictions of seedling emergence, because the timing and success of control measures often hinges on the timing of weed emergence. We used population‐based threshold models to establish the temperature, moisture and oxygen conditions for optimum germination of herbicide‐resistant and ‐susceptible E chinochloa phyllopogon , a weed of temperate paddy rice, and applied them to predict emergence from field soil. We combined hydrothermal time for germination, accounting for within‐population variation in base water potentials (Ψ b ), with thermal time for early seedling growth to predict the quantity and proportional size of the emergence flushes that constitute final recruitment. Emergence in field soils was reduced by moisture stress and flooding, especially for the resistant population. In all populations, germination rates increased between 9·5 and 31 °C, Ψ b was &lt;−1·0 MPa, and there was no sensitivity to oxygen supply. Synthesis and applications . Population‐based threshold models produced physiologically meaningful germination parameters, which are useful in defining the environmental constraints to germination, and predicting E chinochloa phyllopogon germination and emergence in field soils. By exploring the effects of temperature, water stress and flooding on germination and emergence, we predict irrigation regimes for optimising recruitment and the timing of weed control.
Development and Validation of a High-Throughput Screening Assay for the Hepatitis C Virus p7 Viroporin (2011)

The HCV p7 protein is not involved in viral RNA replication but is essential for production of infectious virus. Based on its putative ion channel activity, p7 belongs to a family of viral proteins known as viroporins that oligomerize after insertion into a lipid membrane. To screen for compounds capable of interfering with p7 channel function, a low-throughput liposome-based fluorescent dye permeability assay was modified and converted to a robust high-throughput screening assay. Escherichia coli expressing recombinant p7 were grown in high-density fed-batch fermentation followed by a detergent-free purification using a combination of affinity and reversed-phase chromatography. The phospholipid composition of the liposomes was optimized for both p7 recognition and long-term stability. A counterscreen was developed using the melittin channel-forming peptide to eliminate nonspecific screening hits. The p7 liposome-based assay displayed robust statistics (Z' > 0.75), and sensitivity to inhibition was confirmed using known inhibitors.
Predictive value of MRP2, p53, bcl2 and topoisomerase II immunostainings for the efficacy of anthracyclines-based adjuvant chemotherapy in breast cancer: Results from two randomized trials (2008)

616 Background: The identification of predictive biomarkers for the efficacy of adjuvant treatments could allow to better tailor adjuvant treatments. We evaluated the predictive value of MRP2, bcl2, topoisomerase IIα (Topo IIα) expression and p53 status for the efficacy of adjuvant anthracyclines (A)-based chemotherapy. Methods: Tumor samples from 823 patients included at Institut Gustave Roussy (IGR) in two randomized trials comparing an A-based chemotherapy with no treatment were used to perform a tissue-array. Chemotherapy consisted of 5FU (500mg/m2), farmorubicine (90% of patients) or doxorubicin (50 mg/m2) and cyclophosphamide (500 mg/m2) (D1=D28) for 6 cycles. Immunostainings (cut-off: >10% stained cells) were performed for MRP2 (M2III-6; 1:300; Alexis), p53 ( DO-7; 1:50; Dako), bcl2 (124; 1:50; Dako), and Topo IIα (KI-S1; 1:5000; Chemicon). We previously reported predictive values of ER, HER2 expression and molecular subclassification using the same tissue-array (Conforti, Annals of Oncology, 2007). Results: After a median follow-up of 10 years, 174 patients (22%) have presented a relapse and 186 patients (24%) died. Chemotherapy improved DFS (HR = 0.77, 95% CI: 0.63- 0.9), but not OS (HR = 0.88, 95% CI: 0.66–1.1). A positive staining for MRP2, p53, Topo IIα and bcl2 was observed in 122 (16%), 157 (20%), 267 (35%) and 251 (34%) assessable samples respectively. P53 and Topo IIα were more frequently expressed in patients with basal-like (51% and 53%) or HER2-overexpressing tumors (44% and 57%), as compared to other groups (HER2- and nonbasal BC) (11% and 28%). Bcl2 was more frequently positive in patients with luminal-like breast cancer (47% versus 16%, p<0.01). No significant interaction was observed between the four biomarkers expression and treatment efficacy for both DFS and OS (adjusted p values for interaction ranged between 0.30 and 0.85). Conclusions: In this study, we did not detect significant interaction between MRP2, p53, bcl2 and Topo Iia expressions and treatment efficacy. Nevertheless, such study cannot exclude a possible interaction with a higher number of events or different methods (DNA sequencing for p53 mutations and lower dilution [1:200] for S1 Ab). No significant financial relationships to disclose.
A search for new MRI criteria for dissemination in space in subjects with a clinically isolated syndrome (2009)

The International Panel on the Diagnosis of Multiple Sclerosis (MS) incorporated the Barkhof/Tintoré (B/T) magnetic resonance criteria into their diagnostic scheme to provide evidence of dissemination in space of central nervous system lesions, a prerequisite for diagnosing MS in patients who present with clinically isolated syndromes (CIS). Although specific for MS, the B/T criteria were criticised for their low sensitivity and relative complexity in clinical use. We used lesion characteristics at onset from 349 CIS patients in logistic regression and recursive partitioning modelling in a search for simpler and more sensitive criteria, while maintaining current specificity. The resulting models, all based on the presence of periventricular and deep white matter lesions, performed roughly in agreement with the B/T criteria, but were unable to provide higher diagnostic accuracy based on information from a single scan. Apparently, findings from contrast-enhanced and follow-up magnetic resonance scans are needed to improve the diagnostic algorithm.
Monitoring 3-D Temperature Distributions and Device Losses in Power Electronic Modules (2018)

This paper presents a methodology for real-time monitoring of 3-D temperature distributions and device losses within power electronic modules. It allows precise thermal management, empirical lifetime prognosis, and detection of critical degradation of the power module. By effective combination of thermal 3-D finite difference modeling, parametric loss models, and model truncation techniques, a compact thermal real-time model is derived. It enables the computation of device losses and temperatures at critical locations within a power module, e.g., at the devices, solder interfaces or the base plate, on a conventional digital signal processor. The real-time model as well as real-time junction temperature information are combined in a new Luenberger-style observer structure. Applying bandwidth partitioning, the observer estimates the temperatures throughout the power module every switching period and averaged over one excitation period with nearly zero lag, even if the junction temperature measurement exhibits delays and has noisy signals. Furthermore, it estimates errors in the loss prediction process that can be tracked over the lifetime of the power module to detect degradation of the devices or the power module. The observer and its features are experimentally evaluated under realistic operating conditions on a load emulator using a state-of-the-art automotive power module.
Egg allergen specific IgE diversity predicts resolution of egg allergy in the population cohort HealthNuts (2018)

Sensitization to multiple egg allergens Gal d 1, 2, 3 or 5 may be a prognostic marker that could be useful for patient management and identifying individuals at risk of developing persistent egg allergy.
Revisión sistemática y evaluación de revisiones sistemáticas que examinan el efecto del tratamiento periodontal sobre el control glucémico en pacientes con diabetes (2017)

Objetivos: Se han realizado varias revisiones sistematicas (RS) acerca de si el tratamiento periodontal en un individuo 
con enfermedad periodontal y diabetes puede mejorar los resultados de la diabetes. El proposito de esta investigacion fue 
realizar una revision sistematica (RS) de metaanalisis previos y evaluar la calidad metodologica de las RSs que examinaban 
los efectos del tratamiento periodontales y la diabetes (Registro PROSPERO # CRD 42015023470).
Diseno del estudio: Se realizaron busquedas en cinco bases de datos electronicas y se identificaron metaanalisis previos 
de ensayos controlados aleatorios publicados hasta Julio 2015. En los casos en los que el metaanalisis no cumplia con 
nuestros criterios, los metaanalisis fueron recalculados. Las caracteristicas generales de cada ensayo incluido fueron resumidas, analizadas y comparadas. La diferencia de medias, los intervalos de confianza del 95% (IC) y del estadistico I2 se 
recogieron o se recalcularon. Se utilizo el Instrumento de Evaluacion de las Revisiones Sistemicas Multiples (AMSTAR) 
para evaluar la calidad metodologica. 
Resultados: De las 475 citas examinadas, se incluyeron nueve revisiones sistematicas. En total, se examinaron 13 metaanalisis incluidos en nueve RS. En los analisis de comparabilidad, los metaanalisis en cuatro RS no cumplieron con nuestros 
criterios, y se recalcularon. De estos 13 metaanalisis, 10 sugirieron efectos significativos del tratamiento periodontal sobre 
la mejora de la HbA1c. Las diferencias medias encontradas en los 13 metaanalisis variaron de -0,93 a 0,13. La evaluacion 
con AMSTAR revelo seis RS con moderada calidad general y tres con alta. 
Conclusiones: Podemos concluir que existe un efecto significativo del tratamiento periodontal sobre la mejoria de la HbA1c 
en pacientes diabeticos, aunque la magnitud del efecto es extremadamente pequena. Ademas de la pequena magnitud del 
efecto, no todos las RS podrian considerarse de alta calidad.
Variation-Tolerant and Low-Power Source-Synchronous Multicycle On-Chip Interconnect Scheme (2007)

A variation-tolerant low-power source-synchronous multicycle (SSMC ) interconnect scheme is proposed. This scheme is scalable and suitable for transferring data across different clock domains such as those in “many-core” SoCs and in 3D-ICs. SSMC replaces intermediate flip-flops by a source-synchronous synchronization scheme. Removing the intermediate flip-flops in the SSMC scheme enables better averaging of delay variations across the whole interconnect, which reduces bit-rate degradation due to within-die WID process variations. Monte Carlo circuit simulations show that SSMC eliminates <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>90</mml:mn><mml:mi>%</mml:mi></mml:mrow></mml:math> of the variation-induced performance degradation in a 6-cycle 9 mm-long 16-bit conventional bus. The proposed multicycle bus scheme also leads to significant energy savings due to eliminating the power-hungry flip-flops and efficiently designing the source synchronization overhead. Moreover, eliminating intermediate flip-flops avoids the timing overhead of the setup time, the flip-flop delay, and the single-cycle clock jitter. This delay slack can then be translated into further energy savings by downsizing the repeaters. The significant delay jitter due to capacitive coupling has been addressed and solutions are put forward to alleviate it. Circuit simulations in a 65-nm process environment indicate that energy savings up to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>20</mml:mn><mml:mi>%</mml:mi></mml:mrow></mml:math> are achievable for a 6-cycle 9 mm long 16-bit bus.
Supplementary Tables 1 - 3, Figures 1 - 4 from Phase II Study of Cetuximab in Combination with Cisplatin and Radiation in Unresectable, Locally Advanced Head and Neck Squamous Cell Carcinoma: Eastern Cooperative Oncology Group Trial E3303 (2023)

&lt;p&gt;Supplemental Table 1. Criteria for Unresectable Disease Supplemental Table 2. Modified RECIST Criteria for Head and Neck Cancer. Supplemental Table 3. Summary of Serum Analyte Levels. Supplemental Figure 1. Study Schematic Supplemental Figure 2. Time to locoregional failure for all eligible and treated patients (a) and by tumor HPV status (b). Log rank test comparing time to failure for HPV+ versus HPV- p value provided. Supplemental Figure 3. Representative tissue cores with high or low expression levels of XPF or ERCC1 as assessed by AQUA. Tumors were stained for cytokeratin (CK) to create a tumor mask and with DAPI to define the nuclear compartment. Supplemental Figure 4. Representative tumor IHC molecular correlates ERCC1, XPF and MET.&lt;/p&gt;
Si bipolar 3.3 V transmitter/receiver IC chip set for 1 Gb/s 12-channel parallel optical interconnects (2003)

In view of the recent progress of data communication and multimedia technology, high-throughput I/O interfaces are required to realize systems that have higher performance. Many types of optical interconnects have been proposed, as alternatives to electrical ones, to solve certain problems respecting electromagnetic interference (EMI) and/or extension of connection distance. An optical parallel interconnect has an advantage of simple structure and short latency time compared with a serial one. This paper presents an IC chip set operating with a 3.3 V single power supply for 12-channel parallel optical transmitter/receiver modules as a universal interface device between inter- and/or intracabinet circuits.
Dimensionality Reduction Using Automatic Supervision for Vision-Based Terrain Learning (2007)

This paper considers the problem of learning to recognize different terrains from color imagery in a fully automatic fashion, using the robot's mechanical sensors as supervision. We present a probabilistic framework in which the visual information and the mechanical supervision interact to learn the available terrain types. Within this framework, a novel supervised dimensionality reduction method is proposed, in which the automatic supervision provided by the robot helps select better lower dimensional representations, more suitable for the discrimination task at hand. Incorporating supervision into the dimensionality reduction process is important, as some terrains might be visually similar but induce very different robot mobility. Therefore, choosing a lower dimensional visual representation adequately is expected to improve the vision-based terrain learning and the final classification performance. This is the first work that proposes automatically supervised dimensionality reduction in a probabilistic framework using the supervision coming from the robot's sensors. The proposed method stands in between methods for reasoning under uncertainty using probabilistic models and methods for learning the underlying structure of the data.
Developmental Control of Crassulacean Acid Metabolism Inducibility by Salt Stress in the Common Ice Plant (1990)

Ice plant (Mesembryanthemum crystallinum) is a facultative halophyte that responds to water stress in the form of drought or high salinity by switching from C(3) photosynthesis to Crassulacean acid metabolism (CAM), a physiological adaptation that increases water conservation. Although CAM is clearly environmentally controlled, and reversible upon removal of water stress, the competence to switch is developmentally determined. We have demonstrated this by measuring three parameters in the expression of a gene encoding a stress-specific isoform of a key enzyme of CAM, phosphoenolpyruvate carboxylase (PEPCase, Ppc1): (a) protein accumulation; (b) steady-state amounts of mRNA; and (3) transcriptional activity in isolated nuclei. Young plants (3 weeks of age) show little induction of PEPCase protein, mRNA, or transcription when stressed. In contrast, salt stress elicits a strong induction at all three levels of expression at 6 weeks of age. By 9 weeks of age, plants have already accumulated PEPCase protein and mRNA without being stressed. More importantly, transcriptional activation of Ppc1 by salt stress in 9-week-old plants is no longer observed despite an increase of both Ppc1 mRNA and protein. From these results we suggest that a developmental program exists that regulates PEPCase transcription and mRNA stability. This program appears to be synchronized with the climatic conditions in the plant's native environment.
Reaction Kinetics and Grain Growth Behavior In BaTiO3-SrTiO3-CaTiO3 Ceramics. (1994)

Kinetics of solid state reaction and grain growth behavior of BaTiO3-CaTiO3-SrTiO3 system ceramics has been studied. It is shown that the formations of both BaTiO3 and SrTiO3 are due to the phase boundary controlled reaction. On the other hand, that of CaTiO3 is diffusion controlled. Grain growth of this system could be expressed by the equation Gn=kt, where n=8.0 and Q=690kJ/mol (activation energy) were obtained under Po2=10-10Pa. It is possible to control the microstructure of this system by oxygen partial pressure(Po2) during firing. When Po2≤10-8Pa, the microstructure of this system becomes fine and uniform.
Aerodynamic and Electrostatic Properties of Model Dry Powder Aerosols: a Comprehensive Study of Formulation Factors (2021)

The impact of formulation variables on aerodynamic and electrostatic properties of dry powder aerosol particles is of great importance to the development of efficient and reproducible inhaler products. Systematic evaluation requires a well-designed series of experiments using appropriate methods. A factorial experimental design was employed. In broad terms, the conditions considered were two drugs, albuterol and budesonide, in combination with different excipients, drug concentrations, delivered doses, and metering system (capsule composition) and sampled under different flow conditions using standard entrainment tubes. Samples were collected in an electrical low-pressure impactor, to evaluate distribution of electrostatic properties, and an Andersen eight-stage nonviable cascade impactor, to estimate aerodynamic particle size distribution, concurrently. The deposition studies allowed calculation of approximate per particle charge levels for drug. The results showed very high particle charge levels, often in the 1,000-10,000 of elementary charges per particle range, orders of magnitude higher than charge levels predicted by the Boltzmann charge distribution. The charge levels are considerably higher than had previously been estimated (200e per particle).
ONE-YEAR RESULTS OF A PILOT STUDY USING ORAL 13-CIS RETINOIC ACID AS A TREATMENT FOR SUBFOVEAL PREDOMINANTLY OCCULT CHOROIDAL NEOVASCULARIZATION IN PATIENTS WITH AGE-RELATED MACULAR DEGENERATION (2006)

Oral 13-cis retinoic acid is too toxic to be useful in patients with ARMD. Oral 13-cis retinoic acid did not improve vision although it may have slowed visual acuity loss in patients with ARMD with occult subfoveal CNV.
Abstract 1823: Imipridones show pre-clinical efficacy in MYCN-amplified and MYCN non-amplified neuroblastoma cell lines (2022)

Abstract Neuroblastoma is the most common extracranial solid tumor of childhood, accounting for 15% of all pediatric cancer-related deaths, with around 63% survival for high-risk patients. Treatment remains limited for advanced disease, calling for the development of novel therapies. We investigated the anti-tumor effect of three imipridones (ONC201, ONC206, and ONC212), a promising new class of small molecules, in the treatment of neuroblastoma. Imipridones are potent anticancer drugs that have previously shown efficacy for a variety of adult and pediatric malignancies. ONC201 and ONC206 are antagonists of dopamine receptor D2 (DRD2), while ONC212 is an agonist of GPR132, both of which are overexpressed in many cancers. We performed drug treatment with ONC201, ONC206, and ONC212 on established MYCN-amplified SK-N-BE(2) and MYCN non-amplified SH-SY5Y pediatric neuroblastoma cell lines in vitro. Cell viability assays were performed 72 hours post-treatment to generate dose responses curves. The IC50s for ONC201, ONC206, and ONC212 were 17.82 uM, 547 nM, and 70 nM for SK-N-BE(2), and 997 nM, 314 nM, and 6 nM for SH-SY5Y. Imipridones demonstrated greater efficacy for the non-MYCN-amplified cell line. Using protein quantification studies and downstream target analysis on drug-treated cells, we investigated the mechanisms of how these therapies caused cell death. We showed that imipridones inactivate cell proliferation kinases Akt/ERK and induce cell death through the pro-apoptotic tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). They also induce tumor cell apoptosis by modifying the mitochondrial Clp protease complex, decreasing expression of chaperone subunit ClpX and activating mitochondrial proteolysis. Histone deacetylases (HDACs) play a role in controlling MYCN function, which is amplified in more aggressive neuroblastoma; HDAC activity and MYCN are also upregulated in chemotherapy-resistant neuroblastoma. Cell viability assays with HDAC inhibitors Vorinostat and Panobinostat demonstrated single-agent efficacy in vitro. The IC50s for Vorinostat and Panobinostat were 609 nM and 5.51 nM for SK-N-BE(2), and 884 nM and 6.13 nM for SH-SY5Y. However, further investigation is needed to determine synergy and mechanisms of synergy when histone deacetylase (HDAC) inhibitors are used in novel combinations with imipridones. Overall, our data reveals promise in imipridone therapy for neuroblastoma, and future studies are proposed to explore potential novel therapeutic combinations in this difficult-to-treat pediatric cancer. Citation Format: Claire Lin, Wen-I Chang, Joshua N. Honeyman, Lanlan Zhou, Varun V. Prabhu, Joshua Allen, Wafik El-Deiry. Imipridones show pre-clinical efficacy in MYCN-amplified and MYCN non-amplified neuroblastoma cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1823.
Analyzing protocol implementations for interoperability (2015)

Abstract — We propose PIC, a tool that helps devel-opers search for non-interoperabilities in protocol imple-mentations. We formulate this problem using intersec-tion of the sets of messages that one protocol partici-pant can send but another will reject as non-compliant. PIC leverages symbolic execution to characterize these sets and uses two novel techniques to scale to real-world implementations. First, it uses joint symbolic execution, in which receiver-side program analysis is constrained based on sender-side constraints, dramatically reducing the number of execution paths to consider. Second, it in-corporates a search strategy that steers symbolic execu-tion toward likely non-interoperabilities. We show that PIC is able to find multiple previously unknown non-interoperabilities in large and mature implementations of the SIP and SPDY (v2 through v3.1) protocols, some of which have since been fixed by the respective developers. 1