gebhart/patrepeval huggingface dataset:
Early Root Transcriptomic Changes in Wheat Seedlings Colonized by Trichoderma harzianum Under Different Inorganic Nitrogen Supplies (2019)

Wheat is one of the most important crops worldwide. The use of plant growth promoting microorganisms, such as those of the genus <i>Trichoderma</i>, constitutes an alternative to chemical fertilizers, since they are cheaper and are not detrimental to the environment. However, the interaction between <i>Trichoderma</i> and wheat plants has been scarcely studied, at least at a molecular level. In the present work, a microarray approach was used to study the early transcriptomic changes induced in wheat roots by <i>Trichoderma harzianum</i>, applied alone or in combination with different concentrations of calcium nitrate [Ca(NO<sub>3</sub>)<sub>2</sub>], which was last used as nitrogen (N) source. Our results show that <i>T. harzianum</i> causes larger transcriptomic changes than Ca(NO<sub>3</sub>)<sub>2</sub> in wheat roots, and such changes are different when plants are challenged with <i>Trichoderma</i> alone or treated with a combination of <i>T. harzianum</i> and Ca(NO<sub>3</sub>)<sub>2</sub>. Overall, <i>T. harzianum</i> activates the expression of defense-related genes at early stages of the interaction with the roots, while this fungus reduces the expression of genes related to plant growth and development. Moreover, the current study in wheat roots, subjected to the different <i>T. harzianum</i> and Ca(NO<sub>3</sub>)<sub>2</sub> combinations, reveals that the number of transcriptomic changes was higher when compared against those caused by the different Ca(NO<sub>3</sub>)<sub>2</sub> concentrations than when it was compared against those caused by <i>T. harzianum</i>. N metabolism gene expression changes were in agreement with the levels of nitrate reductase activity measured in plants from <i>Trichoderma</i> plus Ca(NO<sub>3</sub>)<sub>2</sub> conditions. Results were also concordant with plant phenotypes, which showed reduced growth at early interaction stages when inoculated with <i>T. harzianum</i> or with its combination with Ca(NO<sub>3</sub>)<sub>2</sub> at the lowest dosage. These results were in a good agreement with the recognized role of <i>Trichoderma</i> as an inducer of plant defense.
Nucleotide-binding Oligomerization Domain-1 and Epidermal Growth Factor Receptor (2006)

Host-pathogen interactions that allow Helicobacter pylori to survive and persist in the stomach of susceptible individuals remain unclear. Human beta-defensins (hBDs), epithelial-derived antimicrobial peptides are critical components of host-defense at mucosal surfaces. The role of H. pylori-mediated NF-kappaB and epidermal growth factor receptor (EGFR) activation on beta-defensin expression was investigated. Transient transfection studies utilizing beta-defensin promoter constructs were conducted in gastric cells with contribution of individual signaling events evaluated by the addition of specific inhibitors, small interference nucleotide-binding oligomerization domain 1 (NOD1) RNA or plasmids encoding Vaccinia virus proteins that interrupt interleukin-1 and Toll-like receptor signaling. The role of individual MAPK pathways was further delineated in HEK-293 cells expressing conditional MAPK mutants. We found hBD2 expression exclusively dependent on the presence of the bacterial cag pathogenicity island, with NOD1 a critical host sensor. Impairment of murinebeta-defensin 4 (an orthologue of hBD2) expression in NOD1-deficient mice 7-days post-infection further confirmed the role of this cytoplasmic pattern-recognition receptor in eliciting host innate immunity. In contrast to hBD2, hBD3 expression was NOD1-independent but EGFR and ERK pathway-dependent. Importantly, Toll-like receptor signaling was not implicated in H. pylori-mediated hBD2 and hBD3 gene expression. The divergent signaling events governing hBD2 and hBD3 expression suggest temporal functional variation, such that hBD2 may contribute to antimicrobial barrier function during the inflammatory phase with hBD3 playing a greater role during the repair, wound healing phase of infection.
Tissue-Engineered Cartilage: The Crossroads of Biomaterials, Cells and Stimulating Factors (2014)

Damage to cartilage represents one of the most challenging tasks of musculoskeletal therapeutics due to its limited propensity for healing and regenerative capabilities. Lack of current treatments to restore cartilage tissue function has prompted research in this rapidly emerging field of tissue regeneration of functional cartilage tissue substitutes. The development of cartilaginous tissue largely depends on the combination of appropriate biomaterials, cell source, and stimulating factors. Over the years, various biomaterials have been utilized for cartilage repair, but outcomes are far from achieving native cartilage architecture and function. This highlights the need for exploration of suitable biomaterials and stimulating factors for cartilage regeneration. With these perspectives, we aim to present an overview of cartilage tissue engineering with recent progress, development, and major steps taken toward the generation of functional cartilage tissue. In this review, we have discussed the advances and problems in tissue engineering of cartilage with strong emphasis on the utilization of natural polymeric biomaterials, various cell sources, and stimulating factors such as biophysical stimuli, mechanical stimuli, dynamic culture, and growth factors used so far in cartilage regeneration. Finally, we have focused on clinical trials, recent innovations, and future prospects related to cartilage engineering.
LAS CAUSAS GENÉTICAS DE ENFERMEDADES VARÍAN SEGÚN EL TIPO DE POBLACIÓN (2000)

ENFERMEDADES COMO LA DIABETES Y LA ARTERIOSCLEROSIS --DE GRAN PREVALENCIA EN MEXICO-- TIENEN UN COMPONENTE HEREDITARIO CLARO DEBIDO A QUE LAS PERSONAS QUE LAS PADECEN PUEDEN HEREDARLAS A SUS HIJOS POR MEDIO DE LOS GENES. SENALO LO ANTERIOR LA DOCTORA TERESA TUSIE LUNA, DEL INSTITUTO DE INVESTIGACIONES BIOMEDICAS (IIBM), AL DICTAR EL SEMINARIO INSTITUCIONAL IDIOSINCRASIA GENETICA DE LA POBLACION MEXICANA Y EL MAPEO DE GENES EN DIABETES TIPO II Y ARTERIOSCLEROSIS, EN EL AUDITORIO FRANCISCO ALONSO DE FLORIDA DE ESA DEPENDENCIA UNIVERSITARIA. EXPLICO QUE, SIN EMBARGO, LOS GENES QUE PREDISPONEN ESTAS ENFERMEDADES SON DISTINTOS ENTRE LOS DIVERSOS TIPOS DE POBLACIONES. POR ELLO, PLANTEO QUE INVESTIGADORES MEXICANOS ESTUDIEN ESTAS ENFERMEDADES EN LA POBLACION DEL PAIS. SOLO ASI VA A DEFINIRSE EL COMPONENTE GENETICO QUE PARTICIPA EN ESTA POBLACION, INDEPENDIENTEMENTE DE LOS HALLAZGOS QUE SE HAYAN HECHO EN OTROS LUGARES. NO SE PUEDE, COMO EN FARMACOLOGIA, DEPENDER DE LOS DESARROLLOS EXTRANJEROS, PORQUE SI SE DISENA UN METODO DIAGNOSTICO A NIVEL MOLECULAR PARA DIABETES EN SUIZA O INGLATERRA, AL PROBARLO EN LA POBLACION MEXICANA LOS RESULTADOS SALDRIAN NEGATIVOS, PORQUE ESTARA BASADO EN LOS GENES QUE CAUSAN LA ENFERMEDAD EN LAS PERSONAS QUE HABITAN ESOS LUGARES. EXPLICO QUE EN SU LABORATORIO RELATIVAMENTE CUENTA CON LO NECESARIO PARA DESARROLLAR ESTE TIPO DE INVESTIGACION; HA RECIBIDO APOYO DE CONACYT, DE LA DIRECCION GENERAL DE ASUNTOS DE PERSONAL ACADEMICO, FUNSALUD, LA FUNDACION ROCKEFELLER Y DE LA ACADEMIA DE CIENCIAS DEL TERCER MUNDO, PERO AUN ASI LOS RECURSOS SON LIMITADOS, PUES REQUIEREN DE MAS ESPACIO Y GENTE PREPARADA PARA ELLO.
Far-Field Diversion Agent Using a Combintion of a Soluble Particle Diverter with Specially Engineered Proppant (2016)

Abstract The objective of this study is to introduce a technique of far-field diversion using a mixture of soluble solid particles and an engineered proppant to ensure the temporarily bridged fractures re-open and remain propped for hydrocarbon flow after the soluble material has fully dissolved. Far-field diversion is required inside the fracture network to increase complexity by creating additional branch fractures through overcoming stresses holding the natural fractures closed. Usually, diverter particles temporarily bridge inside the fracture to create a low-permeability zone that increases the net pressure within the fracture and enables redirection of the next fluid stage to previously unstimulated intervals. However, if the diversion does not include proppant, the created fracture may close after particle dissolution. The tests performed in this study were: bridging tests to determine the optimal particle size and loadings for a fracture width of 0.04 in.; pack permeability tests to optimize the particle size distribution, temporarily reduce fracture conductivity and increase pressure; and full characterization testing of the proppant as it will remain in the fractures after the soluble particles disappear. Conductivity of the proppant pack was also determined. Two types of particle diverters (Diverter A and B) were tested. Diverter A is typically used for low- to medium-temperature application (less than 225°F) and Diverter B for high-temperature applications (greater than 225°F). The two diverters have nearly the same particle size and distribution, the only difference being a variance in particle shape. Results obtained highlighted reducing the proppant size to a larger mesh number to better place the proppant inside the far-field area with good vertical coverage. Therefore, the diverter particles were selected to be in the medium size range (10 to 50 mesh) while the proppant particles were selected to be in the fine size range (70 to 140 mesh). The crush stress at which the proppant generated less than 10 wt-% fines was 14,000 psi, while at 15,000 psi the proppant generated exactly 10 wt-% fines. The average acid solubility of this proppant in the mixture of HCl:HF was 3.4%, well below the 7% API requirements. A loading of 0.5 ppg of Diverter A was needed to bridge and plug the 0.04-in. slot width, while it needed only 0.25 ppga of Diverter B to plug the same width. Both diverters significantly reduced the conductivity of the test slot discs. After the soluble particles dissolved, conductivity was provided through the 100 mesh ceramic proppant pack that was not previously attainable because there was no proppant.
A dietary pattern rich in animal organ, seafood and processed meat products is associated with newly diagnosed hyperuricaemia in Chinese adults: a propensity score-matched case–control study (2018)

Previous studies have indicated that some food items and nutrients are associated with uric acid metabolism in humans. However, little is known about the role of dietary patterns in hyperuricaemia. We designed this case-control study to evaluate the associations between dietary patterns and newly diagnosed hyperuricaemia in Chinese adults. A total of 1422 cases and 1422 controls were generated from 14 538 participants using the 1:1 ratio propensity score matching methods. Dietary intake was assessed using a validated self-administered FFQ. Dietary patterns were derived by factor analysis. Hyperuricaemia was defined as concentrations of serum uric acid higher than 7 mg/dl (416·5 μmol/l) for men and 6 mg/dl (357 μmol/l) for women. Three dietary patterns were derived by factor analysis: sweet pattern; vegetable pattern; animal foods pattern. The animal foods pattern characterised by higher intake of an animal organ, seafood and processed meat products was associated with higher prevalence of newly diagnosed hyperuricaemia (P for trend<0·01) after adjustment. Compared with the participants in the lowest quartile of the animal foods pattern, the OR of newly diagnosed hyperuricaemia in the highest quartile was 1·50 (95 % CI 1·20, 1·87). The other two dietary patterns were not associated with the prevalence of newly diagnosed hyperuricaemia after adjustment. In conclusion, a diet rich in animal organ, seafood and processed meat products is associated with higher prevalence of newly diagnosed hyperuricaemia in a Chinese population. Further cohort studies and randomised controlled trials are required to clarify these findings.
A new standard for deposit insurance and government guarantees after the crisis (2009)

Purpose The purpose of this paper is to explore the arrangements that have been used in the present crisis and their relative success and to look to the post‐crisis situation. Design/methodology/approach The paper examines and explains the crisis and the roles of deposit insurance and government guarantees. It deals with coverage, funding, institutional structure, speed of payout, incentives, accountability and, in particular, considers how such systems should function in a world of cross‐border institutions. Findings The paper suggests how such principles and standards should be set either through International Association of Deposit Insurers or some more efficient means to complement an international approach to financial stability being addressed by the Basel institutions. Originality/value There is no widely accepted standard over what the reformed financial system safety net should look like with respect to the protection of deposits and the wider guaranteeing of creditors and other stakeholders. This paper, therefore, makes an attempt to fill that gap.
Fast and Accurate Video PQoS Estimation over Wireless Networks (2008)

This paper proposes a curve fitting technique for fast and accurate estimation of the perceived quality of streaming media contents, delivered within a wireless network. The model accounts for the effects of various network parameters such as congestion, radio link power, and video transmission bit rate. The evaluation of the perceived quality of service (PQoS) is based on the well-known VQM objective metric, a powerful technique which is highly correlated to the more expensive and time consuming subjective metrics. Currently, PQoS is used only for offline analysis after delivery of the entire video content. Thanks to the proposed simple model, we can estimate in real time the video PQoS and we can rapidly adapt the content transmission through scalable video coding and bit rates in order to offer the best perceived quality to the end users. The designed model has been validated through many different measurements in realistic wireless environments using an ad hoc WiFi test bed.
A fast technique for identifying zerotrees in the EZW algorithm (2002)

The embedded zerotree wavelet (EZW) algorithm has become a popular benchmark for image compression algorithms. The current paper presents a fast technique for identifying zerotrees for all dominant passes in the encoder prior to encoding. The key is initializing a data structure called a zerotree map with the largest power of two smaller than a given coefficient, and then completing the zerotree map by bitwise-ORing the values of potential parents with those of their children. This simple operation can be performed in parallel with the wavelet transform operation and thus is efficient for both hardware and software implementations.
The Mesa programming environment (1985)

People everywhere are developing multi-window, integrated programming environments for their favorite computers and languages. This paper describes the Mesa programming facilities of the Xerox Development Environment (XDE). It is interesting for several reasons. It has existed in something similar to its current form for about 5 years. It has more than 500 users, many interacting with it 8 or more hours a day. Several million lines of code have been written by these users, including large, multi-author systems. Previous papers have dealt with the Mesa language [Geschke77, Mitchell79], the operating system [Redell79, Lampson80] and the processor architecture on which it runs [Johnsson82, Sweet82]. This paper describes the programming environment: the user illusion, the set of programming tools, and the facilities available for augmenting the environment. Section 2 gives a short history of the environment, including some of our original design goals. Section 3 describes the current state of the user interface and discusses a few of the schemes that were tried and discarded. Section 4 describes some of the program development tools available and discusses how features of the language have influenced their design, and indeed influenced what tools are in the set. Section 5 describes other tools that, although valuable to the programming task, are largely language independent. Section 6 talks about how easy it is to make additions to the system, and gives examples of user additions—some that modify the environment and some that simply provide new tools. Section 7 discusses what we feel are major successes and what we feel needs to be done in the future.
Mapping of Microbiological Procedures by the Members of the International Society of Orthopaedic Centers (ISOC) for Diagnosis of Periprosthetic Infections (2016)

Despite multiple efforts at drafting a general guideline or consensus document, the major international orthopedic centers and the orthopedic community in general are still searching for a definitive, comprehensive and robust approach for the diagnosis and management of prosthetic joint infections (PJIs), although in the recent past many efforts have been made to establish uniform criteria and a worldwide accepted definition (1-3).….
Domain-specific transfer learning in the automated scoring of tumor-stroma ratio from histopathological images of colorectal cancer (2023)

Tumor-stroma ratio (TSR) is a prognostic factor for many types of solid tumors. In this study, we propose a method for automated estimation of TSR from histopathological images of colorectal cancer. The method is based on convolutional neural networks which were trained to classify colorectal cancer tissue in hematoxylin-eosin stained samples into three classes: stroma, tumor and other. The models were trained using a data set that consists of 1343 whole slide images. Three different training setups were applied with a transfer learning approach using domain-specific data i.e. an external colorectal cancer histopathological data set. The three most accurate models were chosen as a classifier, TSR values were predicted and the results were compared to a visual TSR estimation made by a pathologist. The results suggest that classification accuracy does not improve when domain-specific data are used in the pre-training of the convolutional neural network models in the task at hand. Classification accuracy for stroma, tumor and other reached 96.1% on an independent test set. Among the three classes the best model gained the highest accuracy (99.3%) for class tumor. When TSR was predicted with the best model, the correlation between the predicted values and values estimated by an experienced pathologist was 0.57. Further research is needed to study associations between computationally predicted TSR values and other clinicopathological factors of colorectal cancer and the overall survival of the patients.
Methodology for in situ laser-induced fluorescence spectral analysis: application to macroalgae recognition (2002)

Summary form only given. Finding an accurate and simple methodology to map the deep-sea macroalgae in the West Channel and West Brittany zones are of high interest to evaluate and survey the ecological and economical diversity of the seabed. Nowadays, only emerged or shallow-water macroalgae can be efficiently monitored by passive teledetection techniques based on the spectral analysis of their reflectance, whereas the deep-sea macroalgae are shaded by the water surface. This has led us to propose an in situ monitoring of the seabed using an active spectral methodology based on fluorescence imaging.
Toward a free inertial pedestrian navigation reference system (2014)

As free inertial pedestrian navigation systems with foot mounted inertial mobile unit mature, it becomes feasible to conceive a sufficiently accurate derived solution for assessing other indoor navigation systems and assisting research activities. The design of this reference solution and the remaining challenges are at the heart of this paper. A new filter with a quaternion based state vector exploits signals (acceleration and magnetic field) and motions of opportunity for estimating the navigation solution. Quasi Static Field (QSF) updates, Magnetic Angular Rate Updates (MARU) and Angular Gradient Update (AGU) are frequently applied for mitigating the low-cost inertial sensors errors. Experimental tests performed using a post-processed GPS differential solution as reference show an average accuracy of 1.2 m over 500 m walking path: 0.5 %. Discussions about the data acquisition protocol for meeting a 1 meter horizontal accuracy within two standard deviations of the mean (95.45%) is conducted.
Phase I and Pharmacokinetic Study of Photodynamic Therapy for High-Grade Gliomas Using a Novel Boronated Porphyrin (2001)

BOPP at a dose of 4 mg/kg was well tolerated. DLT was thrombocytopenia, and photosensitivity was the only other toxicity of note. The efficacy of PDT using BOPP requires further exploration.
Adaptive PHY-MAC Design for Broadband Wireless Systems (2022)

The next generation mobile communication networks (4G) have the challenging target of The next generation mobile communication networks (4G) have the challenging target of providing a peak data rate of 1 Gigabit per second local area and 100 Megabit per second wide area. The ability to offer such high data rates in 100MHz bandwidth requires overall a very high spectral efficiency, and hence the need for multi-antenna techniques (MIMO) with spatial multiplexing, fast dynamic link adaptation and packet scheduling, wideband access techniques, and most likely non-contention based spectrum sharing among multiple operators. Many of these required technology components and techniques are well researched and established. Adaptive PHY-MAC Design for Broadband Wireless Systems explains how one can integrate and optimise their use in providing the target cell data rates with high availability. The authors address the ability to cope with interference and enhanced physical layer processing, and simultaneously, the multifaceted system level design. Focus is also on the selection of technology components and techniques, which leads to the highest spectral efficiency and peak data rate availability with reasonable Quality of Service (QoS) support, such as improved outage scenario, reduced delay, guaranteed bit rate, etc.In short, this book will answer questions such as, how individual techniques relate to each other, how can we benefit the gains by suitable combinations of different technologies and how to choose different technological solutions in different scenarios, etc.The next generation mobile communication networks (4G) have the challenging target of The next generation mobile communication networks (4G) have the challenging target of providing a peak data rate of 1 Gigabit per second local area and 100 Megabit per second wide area.
A High Resolution Grating Microspectrofluorometer with Topographic Option for Studies in Living Cells1 (1979)

A multichannel microfluorometer allows the measurement of fluorescence spectra from living cells and the topographic study of transient coenzyme (NAD(P)H, flavoproteins) fluorescence (oxido-reduction) changes, triggered by intracellular microinjection of metabolites. The method is limited by the number, Fλ, of fluorescence photons at λ. Fλ itself is a function of the fluorescence efficiency at λ, the cell area, spectral resolution Δλ, time within which each resolution element Δλ is measured and the collected solid angle. Maximum spectral and temporal resolution is obtained via vertical illumination with high NA objectives, using combined dichroic and barrier filters, a field lens, a two-dimensional slit in the image plane, and turrets providing a topographic option with choice of magnification and a spectral option with choice of dispersion. The spectral approach allows the resolution of natural cell fluorescence and its dynamic changes (i.e. in bound, free NAD(P)H, flavoproteins) in different metabolic conditions. The fluorescence of carcinogens