gebhart/patrepeval huggingface dataset:
Observations of distribution, abundance and production related aspects of aquatic macro-invertebrates in natural thermal gradients (2015)

The aquatic macroinvertebrate communities of the thermal gradients produced by the Ringling-Drumheller, Norris and Potosi hot springs were investigated in 1974 and 1975.The three thermal gradients differed in chemical composition, size and age.Macroinvertebrate samples were collected with Surber and Hester-Dendy samplers and an Ekman grab.Macroinvertebrate life was excluded by temperatures in excess of 40C.The communities typical of high thermal regimes appeared to be formed by an exclusion, rather than addition, of genera or species as temperature increased.Macroinvertebrate numbers, taxa and biomass were found to be negatively correlated with temperature.Despite the observed depression of standing crop at elevated temperatures, higher substrate colonization rates and larger sizes of selected taxa at higher temperatures suggested that production rate may increase with temperature.Data compiled at the genus-species level indicated that most forms were eurythermal.Cold, hot and intermediate stenothermal forms were also observed.The eurythermal group was further analyzed to yield patterns of cold preference, warm preference, preference for intermediate temperatures or a lack of preference within broader ranges of tolerance.Abundance at the total, ordinal and genus-species levels was affected by an interaction between temperature and season.Patterns of abundance did not respond the same for all levels of temperature when taken over all seasonal levels.Data suggest community avoidance of, rather than adaptation to, high temperatures at a relatively small thermal plume.It was speculated that longer adaptation time resulted in a higher thermal tolerance for invertebrate communities at Potosi than at Ringling although this higher tolerance may have been influenced by differences in water chemistry or stability of thermal regime.Data further suggest a higher thermal tolerance for communities of pools or slower flows than for riffle communities.vii Table Page 14. Annual and seasonal correlation coefficients and coefficients of determination3 for the mean number of invertebrates per sample collected in bottom samples at Ringling, Norris and Potosi as correlated with temperature...............
The eye photoreceptor protein rhodopsin. Structural implications for retinal disease1 (2002)

Rhodopsin is the membrane receptor responsible for photoreception in the vertebrate retina. Its characteristic seven-transmembrane helical structural motif is today widely recognised as a paradigm in signal transduction. Rhodopsin and the phototransduction system are frequently used as structural and mechanistic models for the G-protein coupled receptor superfamily. Recent advances in the activation mechanism (as derived from the structural available data) and the implications for normal and pathological - in retinal disorders - visual function will be reviewed.
Recrystallization Texture Formation of Cold Rolled 3%Si-Fe &lang;100&rang;\varparallelND Single Crystal Related to Active Slip Systems (1999)

A 3%Si-Fe (100)[011] single crystal was investigated to analyze its texture evolution during rolling and recrystallization. Cold rolled (100)[011] could be fully recrystallized by utilizing dynamic strain aging, and a sharp recrystallized texture was obtained.Rolled texture maintained the initial orientation (100)[011] with TD rotational dispersion. The recrystallized texture was composed of eight orientations rotated about 30 degrees around eight 〈112〉 axes from the initial orientation (100)[011], which is the central orientation of cold rolled matrix. On the assumption that single slip operates locally, recrystallized texture formation is explained by eight kinds of {110}〈111〉 slip cause crystal rotations around eight kinds of 〈112〉, which are perpendicular to both slip plane normal and slip direction. The sense of the crystal rotation is always towards the direction which makes the angles between slip plane and rolling plane increase, which is consistent with Furubayashi’s Hard Model.It was found, furthermore, that the intensity of each component of recrystallized texture corresponds to the Schmid factor of the slip system to which recrystallized orientation is attributable. Such correspondence between the intensity of each recrystallized orientation and Schmid factor was clearly verified by an experiment using single crystal whose initial orientation deviates ten degrees deviated from (100)[011] around ND axis.
INTERACTION BETWEEN PHENYLMETHANEPHOSPHONIC ACID DIETHYL ESTER AND ISOTHIOCYANATES (1990)

Abstract Diethyl esters of 1-N-substituted thioamido-phenylmethanephosphonic acids are obtained from 0,0-diethyl phenylmethanephosphonate, sodium amide as a metallation agent and alkyl- or arylisothiocyanates. It is established that parallel reactions also occur, resulting in the formation of the respective 1,3-disubstituted thioureas and 0-ethylthiocarbamates. These represent the main reaction products in the cases when ethanephosphonic acid diethyl ester is used as a starting reagent.
A distributed system improves inter-observer and AI concordance in annotating interstitial fibrosis and tubular atrophy (2021)

Histologic examination of interstitial fibrosis and tubular atrophy (IFTA) is critical to determine the extent of irreversible kidney injury in renal disease. The current clinical standard involves pathologist's visual assessment of IFTA, which is prone to inter-observer variability. To address this diagnostic variability, we designed two case studies (CSs), including seven pathologists, using HistomicsTK- a distributed system developed by Kitware Inc. (Clifton Park, NY). Twenty-five whole slide images (WSIs) were classified into a training set of 21 and a validation set of four. The training set was composed of seven unique subsets, each provided to an individual pathologist along with four common WSIs from the validation set. In CS 1, all pathologists individually annotated IFTA in their respective slides. These annotations were then used to train a deep learning algorithm to computationally segment IFTA. In CS 2, manual and computational annotations from CS 1 were first reviewed by the annotators to improve concordance of IFTA annotation. Both the manual and computational annotation processes were then repeated as in CS1. The inter-observer concordance in the validation set was measured by Krippendorff's alpha (KA). The KA for the seven pathologists in CS1 was 0.62 with CI [0.57, 0.67], and after reviewing each other's annotations in CS2, 0.66 with CI [0.60, 0.72]. The respective CS1 and CS2 KA were 0.58 with CI [0.52, 0.64] and 0.63 with CI [0.56, 0.69] when including the deep learner as an eighth annotator. These results suggest that our designed annotation framework refines agreement of spatial annotation of IFTA and demonstrates a human-AI approach to significantly improve the development of computational models.
Nitric oxide in fracture repair (1999)

Our aim was to investigate whether nitric oxide synthase (NOS) isoforms, responsible for the generation of NO, are expressed during the healing of fractures. To localise the sites of expression compared with those in normal bone we made standardised, stabilised, unilateral tibial fractures in male Wistar rats. Immunostaining was used to determine the precise tissue localisation of the different NOS isoforms. Western blotting was used to assess expression of NOS isoform protein and L-citrulline assays for studies on NOS activity. Control tissue was obtained from both the contralateral uninjured limb and limbs of normal rats. Immunohistochemistry showed increased expression of endothelial NOS (eNOS) to be strongest in the cortical blood vessels and in osteocytes in the early phase of fracture repair. Western blot and image analysis confirmed this initial increase. Significantly elevated calcium-dependent NOS activity was observed at day 1 after fracture. Inducible NOS (iNOS) was localised principally in endosteal osteoblasts and was also seen in chondroblasts especially in the second week of fracture healing. Western blotting showed a reduction in iNOS during the early healing period. Significantly reduced calcium-independent NOS activity was also seen. No neuronal NOS was seen in either fracture or normal tissue. Increased eNOS in bone blood vessels is likely to mediate the increased blood flow recognised during fracture healing. eNOS expression in osteocytes may occur in response to changes in either mechanical or local fluid shear stress. The finding that eNOS is increased and iNOS reduced in early healing of fractures may be important in their successful repair.
Report of the Korean Society of Infectious Diseases Roundtable Discussion on Responses to the Measles Outbreaks in Korea in 2019 (2021)

During the 2019 domestic measles outbreak in Korea, measles occurred in healthcare workers with two doses of the measles, mumps and rubella vaccine, and the strict application of the Occupational Safety and Health Act required medical institutions to identify healthcare workers' immunity to measles and vaccinate the susceptible pockets. In response to the frontline medical institutions' request to review the measles recommendations and guidelines, the Korean Society of Infectious Diseases held a roundtable discussion on the causes of measles outbreak, timing of vaccinations, antibody tests, and booster vaccinations for healthcare workers, and financial support from the government and municipality as well as response strategies against the outbreak in healthcare settings. In Korea, the seroprevalence of measles is decreasing in the vaccine-induced immunity group during the maintenance of measles elimination over several years. The susceptible group against measles is in their 20s and 30s, and this may be because of waning immunity rather than non-response considering Korea's vaccine policy. The risk of measles nosocomial infection from community increases as these susceptible pockets actively engage in medical institutions. Thus, data on the immunity of low seroprevalence group in Korea are needed, further discussion is needed on the booster vaccination based on the data. Especially, antibody testing and vaccination in healthcare workers may be necessary to prevent the spread of measles in medical insutitutions, and further discussion is needed regarding specific testing methods, and the timing and frequency of test and vaccination.
Degenerate neckpinches in Ricci flow (2013)

Abstract In earlier work [Nonlinearity 24 (2011), 2265–2280], we derived formal matched asymptotic profiles for families of Ricci flow solutions developing Type-II degenerate neckpinches. In the present work, we prove that there do exist Ricci flow solutions that develop singularities modeled on each such profile. In particular, we show that for each positive integer k ≥ 3, there exist compact solutions in all dimensions m ≥ 3 that become singular at the rate <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msup> <m:mrow> <m:mo>(</m:mo> <m:mi>T</m:mi> <m:mo>-</m:mo> <m:mi>t</m:mi> <m:mo>)</m:mo> </m:mrow> <m:mrow> <m:mo>-</m:mo> <m:mn>2</m:mn> <m:mo>+</m:mo> <m:mn>2</m:mn> <m:mo>/</m:mo> <m:mi>k</m:mi> </m:mrow> </m:msup> </m:math> $(T-t)^{-2+2/k}$ .
Accelerometer based Active Snore Detection for Behavioral Modification (2018)

Habitual snoring has been known to increase the risk for serious health problems in addition to affecting the quality of others' sleep. Several recent consumer products aim to automatically detect snoring events and wake the snorer to elicit a posture change. In this paper, we present a study comparing two of the methods, electromyography vs. accelerometry, proposed for automated snoring detection and incorporation of these into a wearable system. The study includes (a) the testing of various sensor configurations and placements to obtain optimal electromyography and accelerometry signals, (b) a review of the accuracy of a variety of snore detection algorithms from previously attained biological signals, and (3) design of an embedded device with integrated sensors and haptic feedback capability. Our preliminary results indicate superiority of accelerometry over electromyography. Further research opportunities to prove the concept and improve the design are then detailed for future work.
7-fluoroindole as an antivirulence compound against Pseudomonas aeruginosa (2012)

The emergence of antibiotic resistance has necessitated new therapeutic approaches for combating persistent bacterial infection. An alternative approach is regulation of bacterial virulence instead of growth suppression, which can readily lead to drug resistance. The virulence of the opportunistic human pathogen Pseudomonas aeruginosa depends on a large number of extracellular factors and biofilm formation. Thirty-one natural and synthetic indole derivatives were screened. 7-fluoroindole (7FI) was identified as a compound that inhibits biofilm formation and blood hemolysis without inhibiting the growth of planktonic P. aeruginosa cells. Moreover, 7FI markedly reduced the production of quorum-sensing (QS)-regulated virulence factors 2-heptyl-3-hydroxy-4(1H)-quinolone, pyocyanin, rhamnolipid, two siderophores, pyoverdine and pyochelin. 7FI clearly suppressed swarming motility, protease activity and the production of a polymeric matrix in P. aeruginosa. However, unlike natural indole compounds, synthetic 7FI did not increase antibiotic resistance. Therefore, 7FI is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection.
Phase-unwrapping algorithm for noisy phase-map processing (1994)

Automated fringe-pattern processing is important in a great number of industrial applications, such as optical data testing and quality control. One of the main problems that arises with these processes is the automated phase unwrapping of the phase map associated with the fringe pattern. Usually the phase map presents problems such as noise, and low-modulation areas. A new phase-unwrapping algorithm with high noise immunity is presented. The algorithm is easily implemented and can process arbitrary shapes. The main features of this algorithm are the use of a queue for the processing of arbitrary shapes and a selection criterion that determines which pixels are going to be processed.
Generation of Aza-ortho-xylylenes via Ring Opening of 2-(2-Acylaminophenyl)aziridines:  Application in the Construction of the Communesin Ring System (2006)

A new protocol for generating aza-ortho-xylylenes via acid-catalyzed or fluoride-promoted ring opening of 2-(2-acylaminophenyl)aziridines is described. This methodology has been exploited in the rapid construction of a hexacyclic substructure of communesin B.
Factors Affecting Steady State Locus in Triaxial Tests (2016)

Abstract Models based on critical state soil mechanics (“CSSM”) require careful calibration of laboratory parameters in order to ensure accurate prediction of the behavior of soil under in situ conditions. This paper presented research on the testing of two distinct materials, a silt and a silty sand. Several triaxial tests were conducted under drained and undrained conditions, with low to very high confining pressures. Distinct mechanical responses were observed: some samples liquefied, some softened, and others hardened when loaded under undrained conditions. The degree of saturation, the induced anisotropy and the induced stress-path were found to influence the state limits between these distinct behaviors. This affected the steady state line (“SSL”) position defined by specimens showing strain softening in the experiment. Furthermore, the “critical state line” was only achieved when the specimens experienced strain hardening despite the stress-path during shear and the initial state conditions. Therefore, as these factors can impact the steady state line (SSL) position, it is essential when assessing the geomechanical behavior of the soil that these factors are monitored and controlled under laboratory conditions according to the in situ state condition and stress-path during shear. In the future, constitutive models have therefore to be adapted in order to determine the influence of these conditioning factors in the ultimate CSSM reference lines positions.
Water Hydrogen Bonds Study by Opto-Magnetic Fingerprint Technique (2010)

Hydrogen bond has dual property, classical (electrostatic interaction based on Coulomb's law) and quantum (wave function based on Schrdinger equation). Since Planck's constant is one of the main criteria for decision which process is quantum, or how much is close to be quantum, we use electrical and magnetic forces of valence electrons, as point of departure, to develop method for opto-magnetic fingerprint of matter. During the study of different type of matter we observed phenomena from spectral convolution data of digital images which characterize matter from both covalent and non-covalent bonding. Since water is matter that is most abundant with hydrogen bonds, we present results of 18.2 M water investigation on different temperature and under influence of constant and variable magnetic fields by opto-magnetic method. Bearing in mind that Linus Pauling, in his book Nature of the Chemical Bond (Cornel University Press, 1939), for the first time presented the systematic concept of the hydrogen bond to the molecular world and its machinery, this paper is written in honor to him and 70th anniversary of one of the most important scientific paradigm.
Biodiversidade de sirfídeos em olivais da região de Mirandela (Nordeste de Portugal) (2012)

As larvas de sirfídeo têm potencial como agentes de luta biológica e no olival podem ser particularmente importantes como predadores naturais de algodão-daoliveira, Euphyllura olivina Costa (Hemiptera: Psyllidae) e de larvas da geração filófaga da traça-da-oliveira, Prays oleae Bernard (Lepidoptera: Yponomeutidae). Com o presente trabalho pretendeu-se conhecer a diversidade da sirfideofauna em olivais na zona de Mirandela (Trás-os-Montes). O trabalho de campo foi realizado em duas parcelas de um olival conduzido em Modo de Produção Biológico (Valbom-dos-Figos) e em três olivais conduzidos em Modo de Produção Integrada (Cedães, Paradela e Suçães). A amostragem decorreu de agosto a outubro de 2009, de abril a novembro de 2010 e de maio a novembro de 2011. Os sirfídeos foram recolhidos com recurso a: (1) garrafas Olipe, (2) rede entomológica e (3) armadilhas cromotrópicas amarelas. Todos os sirfídeos recolhidos foram levados para o laboratório, separados, conservados em álcool e identificados até à espécie. A riqueza específica para os sirfídeos capturados nas garrafas Olipe variou entre uma a três espécies em 2011, três e cinco em 2010 e quatro em 2009. A espécie mais abundante para os três anos de amostragem e neste tipo de armadilha foi Episyrphus balteatus (De Geer), com uma abundância relativa que variou entre 36,4 e 64,62%. Através da rede entomológica foi possível capturar quatro espécies, sendo Sphaerophoria scripta (L.) a espécie dominante com 72,7% de abundância relativa. As armadilhas cromotrópicas capturaram um número muito baixo de sirfídeos, mas uma das espécies capturadas foi única neste estudo, Myathropa florea (L.). Neste estudo foi possível registar um total de nove espécies pertencentes à sirfideofauna no olival transmontano.
Production of Element Correction Factors for Thermoluminescent Dosimeters (1985)

Approximately 80 processors of personal dosimetry in the United States use thermoluminescent dosimeters (TLDs). Recent demands that dosimetry processors be able to measure radiation doses to within +/- 50% of the correct value have focused attention on the reproducibility of the TL elements within each TLD. The phosphors for these TLDs are manufactured by three companies. A dosimetry processor faces three options concerning the quality of the TL elements purchased; trust the supplier's quality control program, screen new TL elements and discard those that are extremely bad, or use element correction factors (ECFs). The first option results in dosimetry processors failing the +/- 50% accuracy requirement due to excessive variability among the TL elements. The second option still permits large precision errors that come close to the +/- 50% accuracy requirement. This paper advocates the third option and presents a 10-step procedure to produce ECFs. The procedure ensures that the ECFs represent only variations among the TL elements and not variations caused by stability problems with the TLD reader. Following is an example of ECF production for 3000 TLDs.
NADPH debt drives redox bankruptcy: SLC7A11/xCT-mediated cystine uptake as a double-edged sword in cellular redox regulation (2020)

Cystine/glutamate antiporter solute carrier family 7 member 11 (SLC7A11; also known as xCT) plays a key role in antioxidant defense by mediating cystine uptake, promoting glutathione synthesis, and maintaining cell survival under oxidative stress conditions. Recent studies showed that, to prevent toxic buildup of highly insoluble cystine inside cells, cancer cells with high expression of SLC7A11 (SLC7A11<sup>high</sup>) are forced to quickly reduce cystine to more soluble cysteine, which requires substantial NADPH supply from the glucose-pentose phosphate pathway (PPP) route, thereby inducing glucose- and PPP-dependency in SLC7A11<sup>high</sup> cancer cells. Limiting glucose supply to SLC7A11<sup>high</sup> cancer cells results in significant NADPH "debt", redox "bankruptcy", and subsequent cell death. This review summarizes our current understanding of NADPH-generating and -consuming pathways, discusses the opposing role of SLC7A11 in protecting cells from oxidative stress-induced cell death such as ferroptosis but promoting glucose starvation-induced cell death, and proposes the concept that SLC7A11-mediated cystine uptake acts as a double-edged sword in cellular redox regulation. A detailed understanding of SLC7A11 in redox biology may identify metabolic vulnerabilities in SLC7A11<sup>high</sup> cancer for therapeutic targeting.
Artifact Removal in Histopathology Images (2022)

In the clinical setting of histopathology, whole-slide image (WSI) artifacts frequently arise, distorting regions of interest, and having a pernicious impact on WSI analysis. Image-to-image translation networks such as CycleGANs are in principle capable of learning an artifact removal function from unpaired data. However, we identify a surjection problem with artifact removal, and propose an weakly-supervised extension to CycleGAN to address this. We assemble a pan-cancer dataset comprising artifact and clean tiles from the TCGA database. Promising results highlight the soundness of our method.
A New Approach to High Speed Digital Signal Processing Based on Microprogramming (1983)

On presente un processeur de signal a grande vitesse microprogramme. Les unites de logique arithmetique combinees avec des multiplicateurs en parallele permettent d'executer les programmes de traitement tels que les filtres numeriques et les simulations de reverberation necessitant beaucoup d'additions et de multiplications
HMGB1 and its membrane receptors as therapeutic targets in an intravesical substance P-induced bladder pain syndrome mouse model (2020)

HMGB1, a nuclear protein, once released to the extracellular space, promotes somatic and visceral pain signals. We thus analyzed the role of HMGB1 in an intravesical substance P-induced bladder pain syndrome (BPS) mouse model. Intravesical administration of substance P caused referred hyperalgesia/allodynia in the lower abdomen and hindpaw without producing severe urothelial damage, which was prevented by an anti-HMGB1-neutralizing antibody, thrombomodulin α capable of inactivating HMGB1 and antagonists of RAGE or CXCR4. The HMGB1 inactivation or RAGE blockade also reversed the established bladder pain symptoms. HMGB1 and RAGE are thus considered to serve as therapeutic targets for BPS.