Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical target volume delineation in glioblastomas: pre-operative versus post-operative/pre-radiotherapy MRI.

OBJECTIVES Delineation of clinical target volume (CTV) is still controversial in glioblastomas. In order to assess the differences in volume and shape of the radiotherapy target, the use of pre-operative vs post-operative/pre-radiotherapy T(1) and T(2) weighted MRI was compared. METHODS 4 CTVs were delineated in 24 patients pre-operatively and post-operatively using T(1) contrast-enhanced (T1(PRE)CTV and T1(POST)CTV) and T(2) weighted images (T2(PRE)CTV and T2(POST)CTV). Pre-operative MRI examinations were performed the day before surgery, whereas post-operative examinations were acquired 1 month after surgery and before chemoradiation. A concordance index (CI) was defined as the ratio between the overlapping and composite volumes. RESULTS The volumes of T1(PRE)CTV and T1(POST)CTV were not statistically different (248 ± 88 vs 254 ± 101), although volume differences >100 cm(3) were observed in 6 out of 24 patients. A marked increase due to tumour progression was shown in three patients. Three patients showed a decrease because of a reduced mass effect. A significant reduction occurred between pre-operative and post-operative T(2) volumes (139 ± 68 vs 78 ± 59). Lack of concordance was observed between T1(PRE)CTV and T1(POST)CTV (CI = 0.67 ± 0.09), T2(PRE)CTV and T2(POST)CTV (CI = 0.39 ± 0.20) and comparing the portion of the T1(PRE)CTV and T1(POST)CTV not covered by that defined on T2(PRE)CTV images (CI = 0.45 ± 0.16 and 0.44 ± 0.17, respectively). CONCLUSION Using T(2) MRI, huge variations can be observed in peritumoural oedema, which are probably due to steroid treatment. Using T(1) MRI, brain shifts after surgery and possible progressive enhancing lesions produce substantial differences in CTVs. Our data support the use of post-operative/pre-radiotherapy T(1) weighted MRI for planning purposes.
Human Brain Physiology Investigated in the Disorder of Consciousness

Neuroimaging research has shown that subjects in vegetative state (or unresponsive wakefulness syndrome; VS/UWS) may retain high-level aspects of brain activity across sensory modalities, language and learning dynamics, emotions, or pain. Brain responses vary in complexity, from local activation of primary sensory cortices, to the involvement of associative areas, to activation of cortical–subcortical networks to either mental imagery tasks or distinction of ambiguous/non-ambiguous words or figures (1–3). These observations document the capability of the severely damaged brain to express surviving modular functions despite impaired corticocortical and cortico-subcortical connectivity and are understood as indicative of retained, covert cognition, or consciousness as opposed to interpretations that markers of neural activity not necessarily are surrogates for conscious activity (1–4). The controversy challenges our definitions of phenomenal consciousness, and blurs the extent to which the classical binary conscious/unconscious separation may serve. The implications can entangle the current diagnostic criteria as well as medical care, legal or popular perception of bioethical issues, allocation of human resources and logistics, and healthcare policies for VS/UWS. The issue nevertheless is mainly scientific and remains unsolved (2, 3). The task- or stimulus-related brain activation in fMRI studies may or may not be indicative of residual, covert consciousness in VS/UWS (2), but neuroimaging research on the disorder of consciousness is certainly seminal. In particular, it should be emphasized how the surviving brain structures and networks identified in VS/UWS compare as to anatomy and modes of activation to those observed in healthy subjects under comparable stimulus/task conditions. This similarity indicates that brain activation is not at random. It also compels the evidence that the brain can operate in sensory data processing or motor action with limited or null control from conscious processes: where and how, in the brain, sensory information processing becomes conscious perception or intentional planning becomes movement remains undocumented (5). In VS/UWS, interference on bottom-up processes from top-down controlling brain systems is peculiarly negligible due to the selective disruption of the top-down projections from high-order associative cortices (6); modulation by attentional processes, spontaneous fluctuations in the brain functional state (e.g., in vigilance), and interaction with the environment are conceivably also irrelevant. In a reversed perspective, the findings of neuroimaging research (and the experimental approach itself) would thus provide unique information about unconscious brain mechanisms or functions that in VS/UWS have been investigated in experimental conditions that happen to be ideally controlled. This rationale should be discussed and submitted to a strict logical interpretation in view of application in research.
Biocontrol strain Pseudomonas fluorescens WCS365 inhibits germination of Fusarium oxysporum spores in tomato root exudate as well as subsequent formation of new spores.

Fusarium oxysporum f.sp. radicis-licopersici (Forl) is a soilborne pathogenic fungus which can cause tomato foot and root rot (TFRR). Tomato root exudate is a good source of nutrients for both Forl and the TFRR-suppressing biocontrol bacterium Pseudomonas fluorescens strain WCS365. Incubation of Forl microconidia in tomato root exudate stimulates their germination. This phenomenon is observed, to a lesser extent, upon incubation in plant nutrient solution supplemented with citrate or glucose, the major organic acid and sugar components, respectively, of tomato root exudate. Here we show that induction of germination of microconidia is significantly reduced in the presence of P. fluorescens WCS365 in all tested media. Scanning electron microscopy revealed that P. fluorescens WCS365 colonizes developing hyphae. Efficient colonization correlates with low nutrient availability. Eventually, new microconidia are formed. The presence of P. fluorescens WCS365 reduces the number of newly formed microconidia. This reduction does not depend on physical contact between bacteria and hyphae. We discuss that the ability of P. fluorescens WCS365 to slow down the processes of microconidia germination and development of new microconidia of the phytopathogen, and therefore the ability to reduce fungal dissemination, is likely to contribute to the biocontrol efficacy of this strain.
PHOSPHOLIPIDS IN SYNAPTIC FUNCTION

THERE is a long and honourable connection between the brain and phospholipid chemistry. While Napolean was retreating from Moscow, another Frenchman (VAUQUELIN, 1812) published the first account of a lipid which contained phosphorus. His source was an ethanol extract of brain. Much later, in Victorian London, a German physician laid the foundations of our knowledge of brain phospholipids (THUDICHUM, 1884). His work centred on the nitrogenous phospholipids which are major components of all membranes in nerve tissue, but in this review we shall be concerned mostly with a relatively minor group of phospholipids containing inositol, and their precursors phosphatidate and CDP-diacylglycerol. Interest in the possible connections between the metabolism of these acidic phospholipids and synaptic transmission began with the observation of HOKIN & HOKIN (1954) that acetylcholine increased the incorporation of labelled phosphate into phosphatidate and phosphatidylinositol of brain slices. This ‘phospholipid effect’ is not limited to the nervous system or to acetylcholine, but is seen in a wide variety of tissues in response to activation of various plasma membrane receptors. Examples include platelet and lymphocyte activation, phagocytosis by polymorphonuclear leucocytes and enzyme secretion from the pancreas. The whole field has been comprehensively reviewed by MICHELL (1975). To return to the nervous system, HOKIN & HOKIN (1959) went on to observe a similar phospholipid effect in a crude microsomal fraction from brain and DURELL & SODD (1966) showed that synaptosomes were responsible. This explained the Hokins’ observation that freezing or deoxycholate treatment abolished the acetylcholine-induced phospholipid effect. The synaptosome was behaving like a miniature cell and only intact cells produce the characteristic response, a fact which accounts for some of the difficulties biochemists have in this field. Synaptosomal localization of the phospholipid effect suggested a relationship with chemical transmission and this view was reinforced by the work of Larrabee and his colleagues on isolated sympathetic ganglia. In this research the preganglionic nerve was stimulated electrically and postganglionic action potentials were recorded (LARRABEE et a/., 1963). Rat superior cervical ganglia were surrounded by oxygenated saline containing suitable radioactive pre-
Effect of glucagon on food-induced gastrointestinal secretions.

The action of glucagon on gastrointestinal secretion has been studied in two groups of 3 dogs each. The group-A dogs were prepared with gastric fistulas, Pavlov pouches and pancreatic fistulas, while the dogs in group B possessed only gastric fistulas and biliary fistulas. Glucagon infused intravenously in a dose of 25 μg/kg-h, during a steady state of half maximal secretory response to food caused a marked inhibition of acid secretion from Pavlov pouches and bicarbonate and protein secretion from pancreatic fistula. Biliary secretion was not affected by glucagon.
Directly Reflective MetaProgramming ∗

Existing meta-programming languages operate on encodings of programs as data. This paper presents a new meta-programming language, based on an untyped lambda calculus, in which structurally reflective programming is supported directly, without any encoding. The language features call-by-value and call-by-name lambda abstractions, as well as novel reflective features enabling the intensional manipulation of arbitrary program terms. The language is scope safe, in the sense that variables can neither be captured nor escape their scopes. The expressiveness of the language is demonstrated by showing how to implement quotation and evaluation operations, as proposed by Wand. The language's utility for meta-programming is further demonstrated through additional representative examples. A prototype implementation is described and evaluated.
Cytochrome P450 reaction-phenotyping: an industrial perspective

It is now widely accepted that the fraction of the dose metabolized by a given drug-metabolizing enzyme is one of the major factors governing the magnitude of a drug interaction and the impact of a polymorphism on (total) drug clearance. Therefore, most pharmaceutical companies determine the enzymes involved in the metabolism of a new chemical entity (NCE) in vitro, in conjunction with human data on absorption, distribution, metabolism and excretion. This so called reaction-phenotyping, or isozyme-mapping, usually involves the use of multiple reagents (e.g., recombinant proteins, liver subcellular fractions, enzyme-selective chemical inhibitors and antibodies). For the human CYPs, reagents are readily available and in vitro reaction-phenotyping data are now routinely included in most regulatory documents. Ideally, the various metabolites have been definitively identified, incubation conditions have afforded robust kinetic analyses, and well characterized (high quality) reagents and human tissues have been employed. It is also important that the various in vitro data are consistent (e.g., scaled turnover with recombinant CYP proteins, CYP inhibition and correlation data with human liver microsomes) and enable an integrated in vitro CYP reaction-phenotype. Results of the in vitro CYP reaction-phenotyping are integrated with clinical data (e.g., human radiolabel and drug interaction studies) and a complete package is then submitted for regulatory review. If the NCE receives market approval, information on key routes of clearance and their associated potential for drug–drug interactions are included in the product label. The present review focuses on in vitro CYP reaction-phenotyping and the integration of data. Relatively simple strategies enabling the design and prioritization of follow up clinical studies are also discussed.
Contribution of transcranial magnetic stimulation to the understanding of cortical mechanisms involved in motor control

Transcranial magnetic stimulation (TMS) was initially used to evaluate the integrity of the corticospinal tract in humans non‐invasively. Since these early studies, the development of paired‐pulse and repetitive TMS protocols allowed investigators to explore inhibitory and excitatory interactions of various motor and non‐motor cortical regions within and across cerebral hemispheres. These applications have provided insight into the intracortical physiological processes underlying the functional role of different brain regions in various cognitive processes, motor control in health and disease and neuroplastic changes during recovery of function after brain lesions. Used in combination with neuroimaging tools, TMS provides valuable information on functional connectivity between different brain regions, and on the relationship between physiological processes and the anatomical configuration of specific brain areas and connected pathways. More recently, there has been increasing interest in the extent to which these physiological processes are modulated depending on the behavioural setting. The purpose of this paper is (a) to present an up‐to‐date review of the available electrophysiological data and the impact on our understanding of human motor behaviour and (b) to discuss some of the gaps in our present knowledge as well as future directions of research in a format accessible to new students and/or investigators. Finally, areas of uncertainty and limitations in the interpretation of TMS studies are discussed in some detail.
Motion Sickness Prevention System (MSPS): Reading Between the Lines

Travel sickness, which is a special kind of motion sickness or kinetosis, is unpleasant for many people while traveling. It is often caused by a mismatch between the perceived movement of the eyes and the movement sensed by the vestibular system. In a car, this condition is often caused by reading or staring at a mobile phone for a longer period of time. Looking outside the window at the trajectory of the vehicle helps most of those affected by kinetosis. But what if you want to read a book while traveling? In this paper, we present the Motion Sickness Prevention System (MSPS) --an approach that allows reading while driving easing the symptoms of kinetosis. It simply uses the live video stream of the road ahead as a background for reading. A preliminary study (N=12) shows that the MSPS, while not able to eliminate the symptoms of kinetosis, can still significantly decrease it.
Topic evolution based on LDA and HMM and its application in stem cell research

This paper analyses topic segmentation based on the LDA (Latent Dirichlet Allocation) model, and performs the topic segmentation and topic evolution of stem cell research literatures in PubMed from 2001 to 2012 by combining the HMM (Hidden Markov Model) and co-occurrence theory. Stem cell research topics were obtained with LDA and expert judgements made on these topics to test the feasibility of the model classification. Further, the correlation between topics was analysed. HMM was used to predict the trend evolution of topics over various years, and a time series map was used to visualize the evolutional relationships among the stem cell topics.
Acoustic Analysis of PD Speech

According to the U.S. National Institutes of Health, approximately 500,000 Americans have Parkinson's disease (PD), with roughly another 50,000 receiving new diagnoses each year. 70%–90% of these people also have the hypokinetic dysarthria associated with PD. Deep brain stimulation (DBS) substantially relieves motor symptoms in advanced-stage patients for whom medication produces disabling dyskinesias. This study investigated speech changes as a result of DBS settings chosen to maximize motor performance. The speech of 10 PD patients and 12 normal controls was analyzed for syllable rate and variability, syllable length patterning, vowel fraction, voice-onset time variability, and spirantization. These were normalized by the controls' standard deviation to represent distance from normal and combined into a composite measure. Results show that DBS settings relieving motor symptoms can improve speech, making it up to three standard deviations closer to normal. However, the clinically motivated settings evaluated here show greater capacity to impair, rather than improve, speech. A feedback device developed from these findings could be useful to clinicians adjusting DBS parameters, as a means for ensuring they do not unwittingly choose DBS settings which impair patients' communication.
On Abstract Finite-State Morphology

Aspects of abstract finite-state morphology are introduced and demonstrated. The use of two-way finite automata for Arabic noun stem and verb root inflection leads to abstractions based on finite-state transition network topology as well as the form and content of network arcs. Nonconcatenative morphology is distinguished from concatenative morphology by its use of movement on the output tape rather than the input tape. The idea of specific automata for classes of inflection inheriting some or all of the nodes, arc form and arc content of the abstract automaton is also introduced. This can lead to novel linguistic generalities and application, as well as advantages in terms of procedural efficiency and representation.
Prediction of DNA-binding protein based on alpha shape modeling

Previous studies about protein-DNA interaction focused on the bound structure of DNA-binding proteins and provided good but not practical results. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and use structural alignment to develop an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of unbound DNA-binding protein. The proposed method provides good performance in predicting unbound structure of DNA-binding protein which is potentially useful in many fields. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve sensitivity ranges from 48.08% to 44.23% and specificity ranges from 73.82% to 84.29%.
New evidence in theory of mind deficits in subjects with chronic schizophrenia and first episode: correlation with symptoms, neurocognition and social function.

AIM Currently substantial evidence exists about Theory of Mind (ToM) impairment in subjects affected by chronic and first episode schizophrenia. In particular, in order to enhance the validity of our construct, we used in this study classical false beliefs tasks and advanced theory of mind tasks, together with the application of structural equation model, in order to ex-amine whether we are using ToM tasks with good psychometric properties. The main goal of the present study was to examine ToM deficits in a large sample including subjects suffering from chronic schizophrenia, first episode of schizophrenia and nor-mal controls, by observing in the same task the relationship with symptomatological gravity, neurocognition and social function.Materials and methods. A sample of 178 patients with chronic schizophrenia, a sample of 49 subjects with a first episode of psychosis and 484 healthy controls participated to this study. Measures of social cognition included task of false belief and advanced theory of mind task. RESULTS No significant differences were found on ToM tasks between subjects affected by chronic and first episode schizophrenia. Social cognition showed in both groups a strong correlation with negative symptoms and social function, but did not evidence any relationship with neurocognition. CONCLUSION; ToM deficits exist in subjects suffering from chronic and first episode schizophrenia. These impairments do not seem to be a consequence of illness condition, they are likely to be state-independent and appear to be the most important cognitive mediator of social functioning in both groups.
Responses of glomus cells to hypoxia and acidosis are uncoupled, reciprocal and linked to ASIC3 expression: selectivity of chemosensory transduction

Carotid body glomus cells are activated by hypoxia and acidosis, but their capacity to differentiate between the two has been undefined. This is the first work to quantify a differential sensory transduction of hypoxia and acidosis with reciprocal responses in individual glomus cells. Cytoplasmic [Ca2+] in clusters of glomus cells indicates 68% of glomus cells respond to both hypoxia and acidosis but are selectively more sensitive to one or the other; the rest respond to either hypoxia (19%) or acidosis (13%). This uncoupling/reciprocal response was recapitulated in a mouse model by genetically altering the expression of ASIC3, an acid‐sensing ion channel that we had identified in earlier studies as a mediator of pH sensitivity in carotid body. We speculate that selective sensory transduction of glomus cells to either hypoxia or acidosis may result in activation of afferents preferentially more sensitive to hypoxia or acidosis, perhaps evoking more specific autonomic adjustments to each stimulus.
Formalization description of genetic algorithms based on intelligent computation framework

Different computation modes of agents take on relative uniform characteristic in all kinds of intelligent algorithms, though they usually have different extrinsic forms. In this paper, formalization description of genetic algorithm is proposed; and the general framework description of genetic algorithm based on intelligent computation framework idea is discussed and validated based on the uniform framework description of intelligent computation abstracted from all kinds of intelligent computation modes.
Chase-Like Decoding of Arithmetic Codes with Image Transmission Applications

Several recent contributions have demonstrated that Joint Source/ Channel (JSC) decoding could be a powerful technique to make error correction in the case of transmission of entropy encoded streams. This paper addresses a new scheme for JSC decoding of Arithmetic Codes (AC) based on Maximum A Posteriori (MAP) sequence estimation. The proposed algorithm performs Chase-like decoding using a priori knowledge of the source symbol sequence and the compressed bit stream lengths. Simulation results show that the proposed decoding algorithm leads to significant performance gain in comparison with classical arithmetic decoding, while exhibiting very low complexity. The practical relevance of the proposed technique is validated in the case of image transmission across the AWGN channel. Lossless and lossy image compression schemes were considered, and the Chase-like arithmetic decoder shows excellent results.