gebhart/patrepeval huggingface dataset:
A multidisciplinary approach to optimizing care of patients treated with alpelisib (2021)

Overall, alpelisib-associated AEs are generally manageable with prompt recognition, regular monitoring, and appropriate intervention, preferably with a multidisciplinary approach.
Changes in phytic acid and acid‐soluble phosphorus in maturing pinto beans (1969)

Abstract Changes in the content of phytic acid and total acid‐soluble phosphorus were measured in Pinto beans at several levels of seed maturity. Phytic acid content in bean seeds increased rapidly with advancing maturity, while total acid‐soluble phosphorus decreased. Mature dry beans contained about 1% phytic acid which accounted for half the total acid‐soluble seed phosphorus. the most immature beans studied contained about 0.13% phytic acid which represents only 4% of the total acid‐soluble phosphorus in these ovules. Little phytic acid was found in pods at any level of maturity.
Calpain I Activation Causes GLUT3 Proteolysis and Downregulation of O-GlcNAcylation in Alzheimer’s Disease Brain (2018)

Impairment of cerebral glucose uptake/metabolism in individuals with Alzheimer's disease (AD) is believed to lead to downregulation of protein O-GlcNAcylation, which contributes to tau pathogenesis through tau hyperphosphorylation. Level of glucose transporter 3 (GLUT3), a neuronal specific glucose transporter, is decreased in AD brain, which may contribute to impaired brain glucose uptake/metabolism. However, what causes the reduction of GLUT3 in AD brain is not fully understood. Here, we report 1) that decrease of GLUT3 is associated with the reduction of protein O-GlcNAcylation in AD brain, 2) that GLUT3 level is negatively correlated with calpain I activation in human brain, 3) that calpain I proteolyzes GLUT3 at the N-terminus in vitro, and 4) that activation of calpain I is negatively correlated with protein O-GlcNAcylation in AD brain. Furthermore, we found that overexpression of GLUT3 enhances protein O-GlcNAcylation in N2a cells. Overexpression of calpain I suppresses protein O-GlcNAcylation in these cells. These findings suggest a novel mechanism by which calpain I overactivation leads to GLUT3 degradation and the consequent down-regulation of protein O-GlcNAcylation in AD brain.
Prediction of pore facies using GMDH-type neural networks: a case study from the South Pars gas field, Persian Gulf basin (2018)

The current study proposes a two-step approach for pore facies characterization in the carbonate reservoirs with an example from the Kangan and Dalanformations in the South Pars gas field. In the first step, pore facies were determined based on Mercury Injection Capillary Pressure (MICP) data incorporation with the Hierarchical Clustering Analysis (HCA) method. In the next step, polynomial meta-models were established based on the evolved Group Method of Data Handling (GMDH) neural networks for the purpose of pore facies identification from well log responses. In this way, the input data table used for training GMDH-type neural network consists of CALI, GR , CGR , SGR, DT, NPHI, RHOB, PEF, PHIE and VDL logs. The MICP-HCA derived pore facies were considered as the desired outputs. Moreover, multi-objective genetic algorithms (GAs) are used to the evolutionary design of GMDH-type neural networks. Training error and prediction error of neural network have been considered as conflicting objectives for Pareto multi-objective optimization. The results of this study indicate the successful implementation of GMDH neural networks for classification of pore facies in the heterogeneous gas bearing carbonate rocks of South Pars gas field.
Digit-length ratios (2D:4D) as a phenotypic indicator of in utero androgen exposure is not prognostic for androgenic alopecia: a descriptive-analytic study of 1200 Iranian men (2016)

The etiology of androgenic alopecia (AGA) involves several factors, including genetics, androgens, age and nutrition. Digit-length ratio of the index and ring finger (2D:4D) is an indicator of prenatal exposure to sex hormones. There is a paucity of studies that systemically review the possible positive predictive value of 2D:4D in the development of AGA. We performed a single-site, descriptive-analytical study among a racially homogeneous population. Our results revealed that no significant association was determined between right 2D:4D and AGA severity within our entire population (P=0.384, r=0.025), however a positive correlation coefficient was identified in subjects above the age of 40. Based on the receiver operating characteristic curve analysis, 2D:4D does not predict the development of AGA. AGA is truly a multifactorial disease. Further, our findings suggest that increased <i>in utero</i> exposure to androgens as a fetus does not predispose men to develop AGA.
Estimation of blood perfusion using phase shift in temperature response to sinusoidal heating at the skin surface (1999)

A closed form analytical solution of the Pennes' bio-heat equation was obtained for temperature distributions in the skin tissue subject to the sinusoidal heat flux. Phase shifts in the surface temperature response were revealed to be related to local blood perfusion rate and heating frequency. The influence of the thermal contact resistance on the perfusion estimation was investigated. It has been proved that this influence is relatively small because of the phase shift based estimation and can be effectively eliminated by application of highly conductive grease. This analysis provides the theoretical foundation for a new noninvasive modality of blood perfusion estimation based on the surface temperature measurement which can have significant applications in future clinical practices.
Relationships between the material properties of silicone hydrogels: Desiccation, wettability and lubricity (2020)

Silicone hydrogels (SiHy), represent composite matrices composed of hydrophobic gas permeable silicone (Si) rich core and a surface enriched with hydrophilic polymer moieties. Their utilization in contact lens design requires number of SiHy properties (hydration, wettability, lubricity) to be optimized for the challenging conditions at the ocular surface. Typical limitations in literature are that (i) these properties are studied in isolation, monitoring only one parameter but not the rest of them, and (ii) measurements are performed with hydrated samples immediately after removal from storage solutions. Here we study the simultaneous evolution of critical material properties (evaporative loss of water, water contact angle, coefficient of friction) of different SiHy subjected to continuous blink-like desiccation/rehydration cycling. SiHy with wetting agents incorporated in their core (narafilcon A, senofilcon A) were particularly susceptible to extended desiccation. Stenfilcon A, a material with only 3% bulk Si content maintained its performance for 4 h of cycling, and delefilcon A (80% surface water content) resisted extended 8 h of desiccation/rehydration runs. Strong correlation exists between the evolution of SiHy wettability and lubricity at ≥4 h of blink-like cycling. Understanding the interplay between SiHy properties bears insights for knowledge based design of novel ophthalmic materials.
Solid‐Phase Synthesis of Peptidomimetics with Peptide Backbone Modifications (2021)

Abstract Peptidomimetics are a class of compounds with promising pharmacological properties. Peptidomimetics reduce limitations of peptides including low bioavailability, poor stability, and poor cell‐permeability. Peptide backbone modifications are a frequently used manipulation to reach desirable properties of the peptide molecules. The development of accessible synthetic methodologies plays an important role in peptidomimetic progress. Synthesis of peptidomimetics proceeds via solution and solid‐phase synthesis strategies. Solid‐phase organic synthesis serves as a powerful tool for the preparation of peptidomimetic molecules, thus, numerous strategies have been developed over the years. In this review, we discuss solid‐phase synthetic approaches for peptide backbone modifications that were presented in the last two decades.
Perceptual Decision Making “Through the Eyes” of a Large-Scale Neural Model of V1 (2013)

Sparse coding has been posited as an efficient information processing strategy employed by sensory systems, particularly visual cortex. Substantial theoretical and experimental work has focused on the issue of sparse encoding, namely how the early visual system maps the scene into a sparse representation. In this paper we investigate the complementary issue of sparse decoding, for example given activity generated by a realistic mapping of the visual scene to neuronal spike trains, how do downstream neurons best utilize this representation to generate a "decision." Specifically we consider both sparse (L1-regularized) and non-sparse (L2 regularized) linear decoding for mapping the neural dynamics of a large-scale spiking neuron model of primary visual cortex (V1) to a two alternative forced choice (2-AFC) perceptual decision. We show that while both sparse and non-sparse linear decoding yield discrimination results quantitatively consistent with human psychophysics, sparse linear decoding is more efficient in terms of the number of selected informative dimension.
A Real Time System For Dynamic Hand Gesture Recognition With A Depth Sensor (2016)

Publication in the conference proceedings of EUSIPCO, Bucharest, Romania, 2012
A survey on the reactive ion etching of silicon in microtechnology (1996)

This article is a brief review of dry etching as applied to pattern transfer, primarily in silicon technology. It focuses on concepts and topics for etching materials of interest in micromechanics. The basis of plasma-assisted etching, the main dry etching technique, is explained and plasma system configurations are described such as reactive ion etching (RIE). An important feature of RIE is its ability to achieve etch directionality. The mechanism behind this directionality and various plasma chemistries to fulfil this task will be explained. Multi-step plasma chemistries are found to be useful to etch, release and passivate micromechanical structures in one run successfully. Plasma etching is extremely sensitive to many variables, making etch results inconsistent and irreproducible. Therefore, important plasma parameters, mask materials and their influences will be treated. Moreover, RIE has its own specific problems, and solutions will be formulated. The result of an RIE process depends in a non-linear way on a great number of parameters. Therefore, a careful data acquisition is necessary. Also, plasma monitoring is needed for the determination of the etch end point for a given process. This review is ended with some promising current trends in plasma etching.
Acoustic Scenery Recognition Using CWT and Deep Neural Network (2021)

The development of acoustic scenes recognition systems has been a topic of extensive research due to its applications in several fields of science and engineering. This paper proposes an environmental system in which firstly a time-frequency representation is obtained using the Continuous Wavelet Transform (CWT). The time frequency representation is then represented as a color image using the Viridis color map, which is then inserted into a Deep Neural Network (DNN) to carry out the classification task. Evaluation results using several public data bases show that proposed scheme provides a classification performance better than the performance provided by other previously proposed schemes.
Mouse cerebellar granule cell differentiation: electrical activity regulates the GABAA receptor alpha 6 subunit gene. (1998)

GABAA receptor alpha6 subunit gene expression marks cerebellar granule cell maturation. To study this process, we used the Deltaalpha6lacZ mouse line, which has a lacZ reporter inserted into the alpha6 gene. At early stages of postnatal cerebellar development, alpha6-lacZ expression is mosaic; expression starts at postnatal day 5 in lobules 9 and 10, and alpha6-lacZ is switched on inside-out, appearing first in the deepest postmigratory granule cells. We looked for factors regulating this expression in cell culture. Membrane depolarization correlates inversely with alpha6-lacZ expression: granule cells grown in 25 mM [K+]o for 11-15 d do not express the alpha6 gene, whereas cultures grown for the same period in 5 mM [K+]o do. This is influenced by a critical early period: culturing for >/=3 d in 25 mM [K+]o curtails the ability to induce the alpha6 gene on transfer to 5 mM [K+]o. If the cells start in 5 mM [K+]o, however, they still express the alpha6-lacZ gene in 25 mM [K+]o. In contrast to granule cells grown in 5 mM [K+]o, cells cultured in 25 mM [K+]o exhibit no action potentials, mEPSCs, or mIPSCs. In chronic 5 mM [K+]o, factors may therefore be released that induce alpha6. Blockade of ionotropic and metabotropic GABA and glutamate receptors or L-, N-, and P/Q-type Ca2+ channels did not prevent alpha6-lacZ expression, but inhibition of action potentials with tetrodotoxin blocked expression in a subpopulation of cells.
Matrix loading: Assembly of extracellular matrix collagen fibrils during embryogenesis (2004)

Nothing in biology stimulates the imagination like the development of a single fertilized egg into a newborn child. Consequently, a major focus of biomedical research is aimed at understanding cell differentiation, proliferation, and specialization during child health and human development. However, the fact that the increase in size and shape of the growing embryo has as much to do with the extracellular matrix (ECM) as with the cells themselves, is largely overlooked. Cells in developing tissues are surrounded by a fiber-composite ECM that transmits mechanical stimuli, maintains the shape of developing tissues, and functions as a scaffold for cell migration and attachment. The major structural element of the ECM is the collagen fibril. The fibrils, which are indeterminate in length, are arranged in different tissues in exquisite supramolecular architectures, including parallel bundles, orthogonal lamellae, and concentric weaves. This article reviews our current understanding of the synthesis and assembly of collagen fibrils, and discusses challenging questions about how cells assemble an organized ECM during embryogenesis.
Practical Aspects of Proactive TDM for Anti-TNF Agents in IBD: Defining Time Points and Thresholds to Target (2019)

Abstract Serum biologic drug concentrations have been associated with favorable therapeutic outcomes in inflammatory bowel diseases, while low or undetectable drug levels have been linked to immunogenicity and treatment failure. Therapeutic drug monitoring (TDM) in the context of clinical relapse can guide decision making and is supported by professional groups. Proactive TDM consists of measurement of trough concentration with the goal of optimizing drug concentration in patients with clinical response/remission. Recent findings suggest that this approach can improve the efficacy of antitumor necrosis factor agents (anti-TNF). In this article, we summarize the rationale for proactive TDM for anti-TNF agents in practice, identify limitations in this evidence base, and provide practical advice for use in the clinic.
What is unknown in using microbiota as a therapeutic? (2021)

Abstract Fecal microbiota transplantation (FMT) has been used extensively in the treatment of various gastrointestinal and extraintestinal conditions, despite that there are still a lot of missing gaps in our knowledge in the gut microbiota and its behavior. This article describes the unknowns in microbiota biology (undetected microbes, uncertain colonization, unclear mechanisms of action, uncertain indications, unsure long‐term efficacy, or side effects). We discuss how these unknowns may affect the therapeutic uses of FMT, and the potentials and caveats of other related microbiota‐based therapies. When used as an experimental therapy or last resort in difficult conditions, caution should be taken against inadvertent complications. Clear documentations of post‐treatment events should be made mandatory, classified, and graded as in clinical trials. Further robust scientific experiments and properly designed clinical studies are needed.
ChemInform Abstract: Atom Transfer Cyclization Reactions of Hex‐5‐ynyl Iodides: Synthetic and Mechanistic Studies. (1989)

Abstract Three useful sets of reaction conditions (portionwise or syringe pump addition of catalytic Bu 3 SnH and photolysis with catalytic hexabutyltin) are given for the cyclization of hex‐5‐ynyl iodides such as (I) to (iodomethylene)cyclopentanes such as (II).
Use of surface‐immobilized Trichoderma in batch and fed‐batch fermentations (1988)

Needle-punch polyester was shown to be an effective support material for the immobilization of Trichoderma reesei Rut C30. When used as a resident inoculum for a batch process, the immobilized Trichoderma was very stable and resulted in a reduced rate of biomass generation in the bulk liquid phase as compared to cultures inoculated with free mycelium. Fed-batch fermentations with the immobilized Trichoderma produced ca. 80% of the activity of those using free cells; however, the activity was more stable and the crude enzyme broth produced had a greatly reduced biomass concentration.
Systems of Uniform Recurrence Equations (2000)

This chapter is very technical. It can be skipped on first reading if the reader wants only a description of the parallelism detection algorithms presented in the next chapter and does not care about optimality proofs. However, this chapter may be of interest for the reader who is curious to see the link between the seminal paper of Karp, Miller, and Winograd entitled “The Organization of Computations for Uniform Recurrence Equations” [65] and affine loop transformations.
Magnetic Susceptibilities of Single Crystal NiCl2·6H2O and CoCl2·6H2O at Low Temperatures (1960)

The magnetic susceptibilities of single crystal NiCl2·6H2O and CoCl2·6H2O have been measured down to 1.3°K for various orientations. The occurrence of antiferromagnetism in CoCl2·6H2O below ∼2.3°K is confirmed as is the anisotropy of the g-factor of the Co++ ion over the whole range. It is concluded that NiCl2·6H2O is antiferromagnetic in the helium region and that the temperature-independence of the powder susceptibility here is caused by the fact that χ⊥ rises as T falls below TN.
Mystery Case: Metronidazole-induced encephalopathy (2016)

An 84-year-old woman who received 2-month oral metronidazole therapy (500 mg 3 times daily) for Clostridium difficile –associated diarrhea was hospitalized for falls. Clinical examination revealed moderate dysarthria and cerebellar ataxia. MRI performed at admission showed bilateral fluid-attenuated inversion recovery (FLAIR) symmetric hyperintense lesions in cerebellar dentate nuclei, superior colliculi, and periaqueductal gray matter (figure). Biological investigations showed no vitamin B1, B9, or B12 deficiency. Dysarthria and gait disturbance resolved within days after interruption of the metronidazole treatment. Metronidazole-induced encephalopathy must be considered whenever a patient on metronidazole experiences a subacute cerebellar syndrome.1
Fabrication of 3D microbatteries using solid polymer electrolytes (2015)

Pressing demands for high power and high energy densities in novel electrical energy storage units have caused reconsiderations regarding both the choice of battery chemistry and design. Practical concerns originating in the conventional use of flammable liquid electrolytes have renewed the interests of using solvent-free polymer electrolytes (SPEs) as solid ionic conductors for safer batteries.In this thesis work, SPEs developed from two polymer host structures, polyethers and polycarbonates, have been investigated for all-solid-state Li- and Li-ion battery applications. In the first part, functional polyether-based polymer electrolytes, such as poly(propylene glycol) triamine based oligomer and poly(propylene oxide)-based acrylates, were investigated for 3D-microbattery applications. The amine end-groups were favorable for forming conformal electrolyte coatings onto 3D electrodes via self-assembly. In-situ polymerization methods such as UV-initiated and electro-initiated polymerization techniques also showed potential to deposit uniform and conformal polymer coatings with thicknesses down to nano-dimensions.Moreover, poly(trimethylene carbonate) (PTMC), an alternative to the commonly investigated polyether host materials, was synthesized for SPE applications and showed promising functionality as battery electrolyte. High-molecular-weight PTMC was first applied in LiFePO4-based batteries. By incorporating an oligomeric PTMC as an interfacial mediator, enhanced surface contacts at the electrode/SPE interfaces and obvious improvements in initial capacities were realized. In addition, room-temperature functionality of PTMC-based SPEs was explored through copolymerization of e-caprolactone (CL) with TMC. Stable cycling performance at ambient temperatures was confirmed in P(TMC/CL)-based LiFePO4 half cells (e.g., around 80 and 150 mAh g-1 at 22 °C and 40 °C under C/20 rate, respectively). Through functionalization, hydroxyl-capped PTMC demonstrated good surface adhesion to metal oxides and was applied on non-planar electrodes. Ionic transport behavior in polycarbonate-SPEs was examined by both experimental and computational approaches. A coupling of Li ion transport with the polymer chain motions was demonstrated.The final part of this work has been focused on exploring the key characteristics of the electrode/SPE interfacial chemistry using PEO and PTMC host materials, respectively. X-ray photoelectron spectroscopy (XPS) was used to get insights on the compositions of the interphase layers in both graphite and LiFePO4 half cells.
Simulering av tvåfasflöde och neutronbrus i en kokvattenreaktor (2016)

I detta kandidatarbete vidareutvecklas en redan befintlig modell för simulering\nav tvåfasflöde i en kokvattenreaktor. Simuleringen av systemet sker genom\nproduktion av bubblor som sedan tillåts färdas genom reaktorkanalen. Utöver\nimplementation av ytterligare fysikaliska aspekter i genereringen av bubblorna\nutvärderas modellen utifrån exempelvis längd på dess transienta förlopp, karaktär\npå hastighetsprofilanpassning samt giltigt parameterområde. Det kan\nkonstateras att modellen är ett bra nästa steg för att inkludera mer fysik och\nsåledes bättre efterlikna verkligheten. Beräkningstiden som implementationen\nmedför är dock ett stort problem och något som begränsat möjligheten till\nanalys av större parameterintervall.\nKorrelation mellan fluktuationer i ånghalten och neutronbruset gör det\nmöjligt att ta fram neutronbruset för systemet. Detta används sedan för att\nta fram transittiderna; tiderna det tar för en fluktuation att färdas mellan\ntvå neutrondetektorer. Dessa används som indata till ett artificiellt neuralt\nnätverk för att rekonstruera systemets hastighetsprofil, och i förlängingen även\nåterskapa dess ånghaltsprofil. Det kan konstateras att detta tillvägagångssätt\nger förhoppningar om att en mer generell och exakt modell går att uppnå, men\natt resultaten av de aspekter som undersökts i denna studie inte nått fram dit.