gebhart/patrepeval huggingface dataset:
Neural Organization: Structure, Function, and Dynamics (1997)

Part 1 Overview: the many themes of neural organization - structure, function, dynamics a structural overview - an embryological perspective on neural structure and motility, the modular architectonics principle, multiple models of modularity a functional overview - schema theory and functional neuroscience, schemas for rana computatrix, schemas for Saccades, schemas for reaching and grasping, representing space and time a dynamical overview - neurodynamical system theory, oscillatory behaviour in neural systems, chaotic behaviour in neural systems - some facts and models, self-organization and the development of the nervous system, learning rules. Part 2 Interacting systems of the brain: the olfactory system - anatomical system, electrical patterns in the olfactory bulb and olfactory cortex, development, learning and memory in the olfactory system hippocampus - anatomical organization, electrical activity patterns, brain states and long-term potentiation, hippocampal function and cognitive maps, hippocampal function and human memory thalamus - nuclei of the thalamus, thalamus and sensory systems, thalamocortical loops and cooperative computation cerebral cortex -structural overview, primary visual cortex - the paradigm of modular architectonics, thalamocortical oscillators, frontoparietal interactions, learning of coordinated behaviours, from action-oriented perception to cognition cerebellum - phylogeny and ontogeny of the cerebellum, structural organization of the cerebellar cortex and nuclei, the cerebellum as a learning machine, cerebellar adaptation of movement generation, the cerebellum and mental activity basal ganglia -structure of the basal ganglia, diseases of the basal ganglia, self-reorganization of the striatum, role of basal ganglia in saccade control, roles of the basal ganglia in motor coordination and learning prospects for a neuroscience of cognition - following the threads - the book in perspective, multiple levels, multiple methodologies and the need for their integration, implications and outlook for cognitive neuroscience. Part 3 Appendices: A - neural simulation language B -brain models on the Web.
Release of neutrophil proteinase 4(3) and leukocyte elastase during phagocytosis and their interaction with proteinase inhibitors (1992)

Neutrophil proteinase 4 (NP4) is a major neutral proteinase of the human polymorphonuclear (PMN) leukocyte, which is present in amounts similar to leukocyte elastase. NP4(3) is a potent, non-specific proteinase, which may degrade structural and soluble proteins in the tissues and body fluids, and it has been implicated as an important pathogenetic factor in lung emphysema. We have studied the release of elastase and NP4(3) in an in vitro model of phagocytosis. alpha 1-proteinase inhibitor (alpha 1-PI) is the major plasma inhibitor of both leukocyte elastase and NP4(3), but alpha 1-PI bound leukocyte elastase more readily than NP4(3). The basic conditions were designed so that some proteolytic activity was present in the medium. Addition of increasing amounts of Secretory leukocyte protease inhibitor (SLPI) to the incubation mixtures resulted in binding of leukocyte elastase to this inhibitor and extinction of free proteolytic activity against both natural and synthetic substrates. The progressive binding of leukocyte elastase to SLPI instead of alpha 1-PI was paralleled by an increasing binding of NP4(3) to alpha 1-PI. SLPI is a potent inhibitor of leukocyte elastase and cathepsin G, and although it lacks inhibitory effect on NP4(3), it may obviously indirectly aid in the binding and inhibition of NP4(3) to alpha 1-PI, by taking care of at least part of the leukocyte elastase. As a specific NP4(3)-inhibitor is not readily available for therapeutic use, this effect may prove useful under in vivo conditions and enhance the protective effect of administered recombinant human SLPI.
Pharmacodynamics of mitomycin C in cultured human bladder tumors. (1991)

The effects of mitomycin C (MMC) concentration and exposure time on the inhibition of tumor cell labeling index (LI) were studied using surgical bladder tumor samples from 14 patients. The bladder tumors were cultured as 1-mm3 fragments on collagen gels. LI was determined by incorporation of [3H]thymidine and autoradiography. All tumors responded to MMC. However, the sensitivity varied significantly between tumors. At a 2-h exposure, the concentrations required for 50 and 90% inhibition (IC50 and IC90) ranged from 0.237 to 14.9 and 2.76 to 74.5 micrograms/ml, respectively. There was an inverse correlation between MMC activity and tumor LI; the IC values were higher for the more rapidly proliferating tumors. Exposure time had a pronounced effect on MMC activity. Shortening the exposure time from 2 to 0.5 h increased the IC50 3-fold, while prolonging the exposure time from 2 to 24 h decreased the IC50 6-fold. To determine the minimum concentration and exposure time necessary to reduce tumor LI by 90%, the data for 6 tumors were computer fitted to the pharmacodynamic relationship Cn x T = k. The analysis showed that, on average, a 2.5-h exposure of 3 micrograms/ml was needed for 50% inhibition and a 7-h exposure of 8 micrograms/ml was needed for 90% inhibition. A comparison of the IC values of MMC determined in this study with the literature values determined using monolayer and spheroid cultures of established human bladder tumor cell lines showed that the drug activity in cultured tumor fragments ranged from 7- to 5300-fold lower than that in established cell lines. In summary, our data demonstrate a heterogeneity in the response of bladder tumors from individual patients to MMC, a decreased sensitivity to MMC with increasing tumor proliferation, and that drug concentration and exposure time are critical determinants of MMC activity.
Gas-Bubble Effects on the Formation of Colloidal Iron Oxide Nanocrystals (2011)

This paper reports that gas bubbles can be used to tailor the kinetics of the nucleation and growth of inorganic-nanocrystals in a colloidal synthesis. We conducted a mechanistic study of the synthesis of colloidal iron oxide nanocrystals using gas bubbles generated by boiling solvents or artificial Ar bubbling. We identified that bubbling effects take place through absorbing local latent heat released from the exothermic reactions involved in the nucleation and growth of iron oxide nanocrystals. Our results show that gas bubbles display a stronger effect on the nucleation of iron oxide nanocrystals than on their growth. These results indicate that the nucleation and growth of iron oxide nanocrystals may rely on different types of chemical reactions between the iron-oleate decomposition products: the nucleation relies on the strongly exothermic, multiple-bond formation reactions, whereas the growth of iron oxide nanocrystals may primarily depend upon single-bond formation reactions. The identification of exothermic reactions is further consistent with our results in the synthesis of iron oxide nanocrystals with boiling solvents at reaction temperatures ranging from 290 to 365 °C, by which we determined the reaction enthalpy in the nucleation of iron oxide nanocrystals to be -142 ± 12 kJ/mol. Moreover, our results suggest that a prerequisite for effectively suppressing secondary nucleation in a colloidal synthesis is that the primary nucleation must produce a critical amount of nuclei, and this finding is important for a priori design of colloidal synthesis of monodispersed nanocrystals in general.
Extreme Environment Sensing Using Femtosecond Laser-Inscribed Fiber Bragg Gratings (2017)

The femtosecond laser-induced fiber Bragg grating is an effective sensor technology that can be deployed in harsh environments. Depending on the optical fiber chosen and the inscription parameters that are used, devices suitable for high temperature, pressure, ionizing radiation and strain sensor applications are possible. Such devices are appropriate for aerospace or energy production applications where there is a need for components, instrumentation and controls that can function in harsh environments. This paper will present a review of some of the more recent developments in this field.
3D head pose estimation using the Kinect (2011)

Head pose estimation plays an essential role for bridging the information gap between humans and computers. Conventional head pose estimation methods are mostly done in images captured by cameras. However accurate and robust pose estimation is often problematic. In this paper we present an algorithm for recovering the six degrees of freedom (DOF) of motion of a head from a sequence of range images taken by the Microsoft Kinect for Xbox 360. The proposed algorithm utilizes a least-squares minimization of the difference between the measured rate of change of depth at a point and the rate predicted by the depth rate constraint equation. We segment the human head from its surroundings and background, and then we estimate the head motion. Our system has the capability to recover the six DOF of the head motion of multiple people in one image. The proposed system is evaluated in our lab and presents superior results.
Rapid prototyping from 3D scanned data through automatic surface and solid generation (2018)

Abstract: "With the introduction of solid free form fabrication techniques there has been significant interest in producing prototypes from design representations. Although free form fabrication processes require solid modeling information, the representations available in the design stage might often be of lower order dimensions. In certain cases, the design information is presented as a set of sampled points scanned from 3D objects. In this paper, we describe an implementation where scanned data is automatically converted to surface and solid representations successively using a non-manifold geometric modelling system, NOODLES. After defining valid solid models, prototypes are fabricated with streolithography [sic].The stereolithography process is planned within NOODLES by transforming solid representations into planar slice descriptions using the non-regular set operations provided by NOODLES."
An Ancient Gauge for Iron (2009)

A protein with a domain that binds to oxygen and iron acts as a sensor to control iron metabolism in human cells.
Calorie Restriction Mimetics: Examples and Mode of Action (2009)

The search for Calorie Restriction Mimetics (CRM) -compounds that mimic the genetic, biochemical and physical actions of calorie restriction -is not a search for a 'lazy dieters pill'. It is a quest aiming to clarify the basic mechanisms of calorie restriction and develop strategies in order to prevent, treat or alleviate age-related conditions. The development of CRM will add new and important assets in our armamentarium of anti-ageing therapies, with the ultimate result of increasing healthy human lifespan. This Special Supplement on CRM is an attempt to discuss some agents which may be used instead of calorie restriction itself. Agents such as resveratrol, metformin, carnosine and Rimonabant are mainstream oral therapies already used by millions of people for other clinical indications. New CRM such as NADH, gugulipids and certain drugs that interfere with glucose metabolism can be also used as oral therapy. Less easily available CRM such as oxaloacetic acid, naloxone, leptin, adiponectin, rapamycin and sirtuins are further examples of promising agents. In order for the therapy to be effective, a combination of these must be used. This paper summarises the actions of calorie restriction and then suggests several examples of possible CRM. Some of these examples can be used in everyday clinical setting.
Examination of Correction Factor for Manganese Nodule Abundance Using the Free Fall Grab and Box Corer (2008)

Manganese nodule abundance estimated based on operation of a Free Fall Grab(FFG) needs to be corrected to make up for its incomplete recovery of nodule, because FFGs can not recover all the nodules distributed on seabed. The correction factor for nodule abundance was proposed as 1.29 and 1.13 in 1994 and 2002, respectively, mainly based on the analyses of seabed images. In this study we collected manganese nodules using both FFG and Box Corer(BC) at same stations to examine the accuracy of the previous correction factors. It was found that the nodule recovery of the BC was 1.4 times greater than that of the FFG at the same sampling station, suggesting the necessity of re-evaluation of the previously proposed correction factor for FFG. More extensive sampling and improvement of image analysis method are required to improve the precision of nodule abundance correction factor for FFG.
In vitro studies of a FLT3 inhibitor combined with chemotherapy: sequence of administration is important to achieve synergistic cytotoxic effects (2004)

Patients with acute myeloid leukemia (AML) harboring internal tandem duplication mutations of the FLT3 receptor (FLT3/ITD mutations) have a poor prognosis compared to patients lacking such mutations. Incorporation of FLT3 inhibitors into existing chemotherapeutic regimens has the potential to improve clinical outcomes in this high-risk group of patients. CEP-701, an indolocarbazole-derived selective FLT3 inhibitor, potently induces apoptosis in FLT3/ITD-expressing cell lines and primary leukemic blasts. We conducted a series of in vitro cytotoxicity experiments combining CEP-701 with chemotherapy using the FLT3/ITD-expressing cell lines MV4-11 and BaF3/ITD as well as a primary blast sample from a patient with AML harboring a FLT3/ITD mutation. CEP-701 induced cytotoxicity in a synergistic fashion with cytarabine, daunorubicin, mitoxantrone, or etoposide if used simultaneously or immediately following exposure to the chemotherapeutic agent. In contrast, the combination of pretreatment with CEP-701 followed by chemotherapy was generally antagonistic, particularly with the more cell cycle-dependent agents such as cytarabine. This effect appears to be due to CEP-701 causing cell cycle arrest. We conclude that in FLT3/ITD-expressing leukemia cells, CEP-701 is synergistic with standard AML chemotherapeutic agents, but only if used simultaneously with or immediately following the chemotherapy. These results should be considered when designing trials combining chemotherapy with each of the FLT3 inhibitors currently in clinical development.
Magnetic Nanoparticles: Surface Effects and Properties Related to Biomedicine Applications (2013)

Due to finite size effects, such as the high surface-to-volume ratio and different crystal structures, magnetic nanoparticles are found to exhibit interesting and considerably different magnetic properties than those found in their corresponding bulk materials. These nanoparticles can be synthesized in several ways (e.g., chemical and physical) with controllable sizes enabling their comparison to biological organisms from cells (10-100 μm), viruses, genes, down to proteins (3-50 nm). The optimization of the nanoparticles' size, size distribution, agglomeration, coating, and shapes along with their unique magnetic properties prompted the application of nanoparticles of this type in diverse fields. Biomedicine is one of these fields where intensive research is currently being conducted. In this review, we will discuss the magnetic properties of nanoparticles which are directly related to their applications in biomedicine. We will focus mainly on surface effects and ferrite nanoparticles, and on one diagnostic application of magnetic nanoparticles as magnetic resonance imaging contrast agents.
Transformer-based deep learning for predicting protein properties in the life sciences (2023)

Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model-the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.
Towards a Global Optimal Multi-Layer Stixel Representation of Dense 3D Data (2011)

Dense 3D data as delivered by stereo vision systems, modern laser scanners or timeof-flight cameras such as PMD is a key element for 3D scene understanding. Real-time high-level vision systems require a compact and explicit representation of that data which allows for efficient attention control, object detection, and reasoning. Because man-made environments are dominated by planar horizontal and vertical surfaces we approximate the three dimensional scenery by using sets of thin planar rectangles called Stixels. This medium level representation serves as input for further processing steps and applications. Using this novel representation those are not required to process the large amounts of raw 3D data individually. This reconstruction is addressed by means of a unified probabilistic approach. Dynamic programming allows to incorporate real-world constraints such as perspective ordering and delivers an optimal segmentation with respect to freespace and obstacle information. We present results for both stereo vision data and laser data. The real-time capable approach can also be used to fuse the information of multiple data sources.
Phosphorescence and Photostimulated Luminescence of CaSO4:Dy Embedded Polyethylene Discs at Elevated Temperature for Fast Neutron Dosimetry (1983)

CaSO4:Dy embedded polyethylene discs were prepared and their phosphorescence and photo-stimulated luminescence (PSL) output of CaSO4:Dy was found to increase with the temperature of stimulation and readout. At 92 oC the PSL output of 0.6 mm thick CaSO4:Dy polyethylene discs was found to be about 30 times its output at room temperature. The minimum measurable 60Co gamma ray and 14.7 MeV monoenergetic neutron doses are estimated to be 3.5 mGy and 8 mGy, respectively.
Birefringence reduction in long period gratings by the fiber-twist method (2000)

Summary form only given.Broadband gain-flattened optical amplifiers are essential for increasing the capacity of wavelength division multiplexed transmission systems. Among the several approaches to flatten the gain of an amplifier, gain flattening filters (GFFs) based on long period gratings (LPGs) are strong candidates because of the ease of fabrication, the flexibility in spectral-shaping, and very low back reflection. There are, however, two major problems that had to be overcome to use the LPGs as a GFF: temperature sensitivity and polarization dependency. UV-induced birefringence in hydrogen loaded fibers makes fiber gratings sensitive to the polarization of the incident light. In this paper, we characterize the birefringence in LPGs by the measurements of polarization dependent loss and demonstrate a fiber-twist method for reducing the birefringence LPGs.
Hardware realization of a 2 m × 1 m fully electronic real-time mm-wave imaging system (2012)

A first generation of active mm-wave imaging devices is nowadays commercially available for industrial and security applications. Mostly, these systems use mechanical scanning to reduce channel count. The availability of state-of-the-art semiconductor technology enables reliably building high-channel-count fully electronic mm-wave imaging systems at E-Band frequencies, including parallel signal processing. Without the need for mechanical scanning, true real-time operation becomes possible. This work describes a prototype of such an imaging system for personnel screening applications. For the first time, hardware that is capable of capturing full 2 m × 1 m images of living persons in the 80 GHz region in real-time is demonstrated. An overview of the imaging system is given including detailed hardware description. The measurement flow is explained and the underlying link budget is derived.
Physical, cognitive and mental health impacts of COVID-19 following hospitalisation – a multi-centre prospective cohort study (2021)

Background The impact of COVID-19 on physical and mental health, and employment following hospitalisation is poorly understood. Methods PHOSP-COVID is a multi-centre, UK, observational study of adults discharged from hospital with a clinical diagnosis of COVID-19 involving an assessment between two- and seven-months later including detailed symptom, physiological and biochemical testing. Multivariable logistic regression was performed for patient-perceived recovery with age, sex, ethnicity, body mass index (BMI), co-morbidities, and severity of acute illness as co-variates. Cluster analysis was performed using outcomes for breathlessness, fatigue, mental health, cognition and physical function. Findings We report findings of 1077 patients discharged in 2020, from the assessment undertaken a median 5 [IQR4 to 6] months later: 36% female, mean age 58 [SD 13] years, 69% white ethnicity, 27% mechanical ventilation, and 50% had at least two co-morbidities. At follow-up only 29% felt fully recovered, 20% had a new disability, and 19% experienced a health-related change in occupation. Factors associated with failure to recover were female, middle-age, white ethnicity, two or more co-morbidities, and more severe acute illness. The magnitude of the persistent health burden was substantial and weakly related to acute severity. Four clusters were identified with different severities of mental and physical health impairment: 1) Very severe (17%), 2) Severe (21%), 3) Moderate with cognitive impairment (17%), 4) Mild (46%), with 3%, 7%, 36% and 43% feeling fully recovered, respectively. Persistent systemic inflammation determined by C-reactive protein was related to cluster severity, but not acute illness severity. Interpretation We identified factors related to recovery from a hospital admission with COVID-19 and four different phenotypes relating to the severity of physical, mental, and cognitive health five months later. The implications for clinical care include the potential to stratify care and the need for a pro-active approach with wide-access to COVID-19 holistic clinical services. Funding: UKRI and NIHR
Endoplasmic Reticulum Stress Induces Different Molecular Structural Alterations in Human Dilated and Ischemic Cardiomyopathy (2014)

In the present study, we report the existence of alterations in ER stress response and shaping proteins. We show a plausible effect of the ER stress on ER structure in a suitable sample of DCM and ICM subjects. Patients with higher values of RRBP1 had worse left ventricular function.