Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Engineering Applications on Industrially Important Enzymes: Candida methylica FDH as a Case Study

Global warming and the resultant problems it could cause has made the scientific community and general public realize that there is a need to decrease dependency on oil for energy. It has also shown the need to increase the efficient use of energy in manufacturing and industrial processes. Green processes would be an alternative way of decreasing oil dependency and biotechnology is promoted as a way both to decrease oil dependency and as a source for renewable bio-based products. Biocatalysis (using enzymes or whole systems) can provide a valuable alternative to traditional chemical processes because it has many advantages such as; efficiency in enhancing the rate of chemical reactions and for their ability to discriminate between potential substrates. Therefore there is the possibility of using biological molecules to catalyse any reaction or modify any product of interest to industry. Biological catalysts from animal, plant and bacterial sources have evolved to perform most types of organic reactions, producing chirally pure and complex molecules with interesting biological properties. Biocatalysts have thus become important tools in medicine, the chemical industry, food processing and in agriculture. Industrial processes often require extreme conditions such as high pressure, temperature and extreme pH which require a large amount of energy to achieve and may produce unwanted toxic waste. Biological enzymes do not require such conditions and produce chirally pure products often without the disadvantages of unwanted toxic by-products. They offer a number of advantages over conventional chemical catalysts (Davies, 2003; Kirk et al., 2002; Perez, 2010; Tao, 2009; Wojtasiak, 2006): i) Most enzymes catalyze their reactions under mild conditions such as physiological temperature and pH (6-8) and so are therefore often compatible with one another. Compatible enzymes can be used together either in sequence or cooperatively to catalyze multistep reactions. ii) Enzymes are regioselective, and also stereospecific and this allows the production of exact chiral products from racemic mixtures. Enantiomerically pure compounds are specially demanded by the pharmaceutical, food and cosmetics industries. iii) They may be cheap and easy to use because many enzymes are commercially available. iv) They are regarded as environmentally friendly because catalysis is achieved without organic solvents or the heavy metal toxic waste.
JAM-2, a Novel Immunoglobulin Superfamily Molecule, Expressed by Endothelial and Lymphatic Cells*

Cell-cell contacts are essential for morphogenesis and tissue function and play a vital role in mediating endothelial cohesion within the vascular system during vessel growth and organization. We identified a novel junctional adhesion molecule, named JAM-2, by a selective RNA display method, which allowed identification of transcripts encoding immunoglobulin superfamily molecules regulated during coculture of endothelial cells with tumor cells. The JAM-2 transcript is highly expressed during embryogenesis and is detected in lymph node and Peyer's patches RNA of adult mice. Accordingly, antibodies specific for JAM-2 stain high endothelial venules and lymphatic vessels in lymphoid organs, and vascular structures in the kidney. Using real time video microscopy, we show that JAM-2 is localized within minutes to the newly formed cell-cell contact. The role of the protein in the sealing of cell-cell contact is further suggested by the reduced paracellular permeability of cell monolayer transfected with JAM-2 cDNA, and by the localization of JAM-2 to tight junctional complexes of polarized cells. Taken together, our results suggest that JAM-2 is a novel vascular molecule, which participates in interendothelial junctional complexes.
Depressive Symptoms in Medical Students and Residents: A Multischool Study

Background This multisite, anonymous study assessed depressive symptoms and suicidal ideation in medical trainees (medical students and residents). Method In 2003–2004, the authors surveyed medical trainees at six sites. Surveys included content from the Center for Epidemiologic Studies–Depression scale (CES-D) and the Primary Care Evaluation of Mental Disorders (PRIME-MD) (measures for depression), as well as demographic content. Rates of reported major and minor depression and of suicidal ideation were calculated. Responses were compared by level of training, gender, and ethnicity. Results More than 2,000 medical students and residents responded, for an overall response rate of 89%. Based on categorical levels from the CES-D, 12% had probable major depression and 9.2% had probable mild/moderate depression. There were significant differences in depression by trainee level, with a higher rate among medical students; and gender, with higher rates among women (&khgr;2 = 10.42, df = 2, and P = .005 and &khgr;2 = 22.1, df = 2, and P < .001, respectively). Nearly 6% reported suicidal ideation, with differences by trainee level, with a higher rate among medical students; and ethnicity, with the highest rate among black/African American respondents and the lowest among Caucasian respondents (&khgr;2 = 5.19, df = 1, and P = .023 and &khgr;2 = 10.42, df = 3, and P = .015, respectively). Conclusions Depression remains a significant issue for medical trainees. This study highlights the importance of ongoing mental health assessment, treatment, and education for medical trainees.
Some observations on transneuronal cell degeneration in the olfactory bulb of the rabbit.

The degeneration, or atrophy, which may ensue in neurons deprived of their afferent connexions was first convincingly described in the lateral geniculate nucleus, after interruption of optic nerve fibres (Minkowski, 1913), and for many years this remained the only site in which it had been demonstrated unequivocally. It seemed to depend upon the completeness of the deafferentation. For example, Cook, Walker & Barr (1951) failed to find transneuronal degeneration in the spinal cord after section either of dorsal roots or of cortico-spinal fibres, although it had been claimed to occur by earlier workers (Barron, 1933); and Glees & Le Gros Clark (1941) noted that it did not occur in the ventral posterior nucleus of the thalamus following section of the medial fillet. These and other studies were based upon the qualitative examination of Nisslstained sections. An important contribution was made by the careful quantitative study of Cook et. al (1951) of the cytological changes produced by transneuronal atrophy in the lateral geniculate nuclei of the cat and rabbit. They showed the changes in these species to be rather slow and slight, though reasonably consistent. Following this work, closely similar transneuronal degeneration has been shown to occur both in the superior cervical ganglion of the rabbit (Hamlyn, 1945) and in the cochlear nuclei of the cat (Powell & Erulkar, unpublished observations). In each of these regions it is possible to achieve more or less complete destruction of afferents. The populations of neurons are relatively homogenous. They are therefore suitable for study by quantitative methods, which are a valuable aid to the confirmation of slight changes. Transneuronal degeneration has now, however, been found to occur in situations in which the destruction of afferents is by no means complete, and this positive finding also may be attributed to the choice of technique or of preparation. The experiments already mentioned were made upon mature animals. Torvik (1956), using very young kittens, found rapid and severe cell degeneration in the pontine and olivary nuclei following unilateral lesions in the cortex or brain-stem which he considered could not have destroyed more than half the afferent connexions. Le Gros Clark (1957) has recorded that, as seen in sections prepared by the protargol technique, the principal dendrites of mitral cells in the olfactory bulb of the rabbit degenerate following destruction of the olfactory mucosa. This phenomenon seems of particular interest, since the structure of the mammalian olfactory bulb has been worked out in considerable detail by Cajal (1911) and the principal dendrite is known to be the only part of the mitral cell which is directly related to the incoming olfactory nerve
Active microwave remote sensing for soil moisture measurement: a field evaluation using ERS‐2

Active microwave remote sensing observations of backscattering, such as C‐band vertically polarized synthetic aperture radar (SAR) observations from the second European remote sensing (ERS‐2) satellite, have the potential to measure moisture content in a near‐surface layer of soil. However, SAR backscattering observations are highly dependent on topography, soil texture, surface roughness and soil moisture, meaning that soil moisture inversion from single frequency and polarization SAR observations is difficult. In this paper, the potential for measuring near‐surface soil moisture with the ERS‐2 satellite is explored by comparing model estimates of backscattering with ERS‐2 SAR observations. This comparison was made for two ERS‐2 overpasses coincident with near‐surface soil moisture measurements in a 6 ha catchment using 15‐cm time domain reflectometry probes on a 20 m grid. In addition, 1‐cm soil moisture data were obtained from a calibrated soil moisture model. Using state‐of‐the‐art theoretical, semi‐empirical and empirical backscattering models, it was found that using measured soil moisture and roughness data there were root mean square (RMS) errors from 3·5 to 8·5 dB and r2 values from 0·00 to 0·25, depending on the backscattering model and degree of filtering. Using model soil moisture in place of measured soil moisture reduced RMS errors slightly (0·5 to 2 dB) but did not improve r2 values. Likewise, using the first day of ERS‐2 backscattering and soil moisture data to solve for RMS surface roughness reduced RMS errors in backscattering for the second day to between 0·9 and 2·8 dB, but did not improve r2 values. Moreover, RMS differences were as large as 3·7 dB and r2 values as low as 0·53 between the various backscattering models, even when using the same data as input. These results suggest that more research is required to improve the agreement between backscattering models, and that ERS‐2 SAR data may be useful for estimating fields‐scale average soil moisture but not variations at the hillslope scale. Copyright © 2004 John Wiley & Sons, Ltd.
Lithium Enhances Synaptic Plasticity: Implication for Treatment of Bipolar Disorder

Although lithium has remained as the drug of choice in the treatment of bipolar disorder over the past 50 years, the mechanism by which it exerts its therapeutic effects is not well understood. A large body of evidence from molecular, cellular and clinical studies proposes that lithium have positive actions in enhancing neuroplasticity and synaptic plasticity, and these actions are associated with its efficacy in the treatment of bipolar disorder and other psychiatric disorders (Manji et al. 1999; Manji and Duman 2001; Rowe and Chuang 2004; Tsaltas et al. 2009). Lithium modulates intracellular signal transduction pathways involved in the activation of transcription factors (PEBP-2β, P53, and CREB) and the gene expression of diverse neurotrophic and neuroprotective factors (Chalecka-Franaszek and Chuang 1999; Grimes and Jope 2001; Jope and Roh 2006; Manji et al. 1999; Manji and Duman 2001). Among these factors, brain derived neurotrophic factor (BDNF), B-cell CLL/lymphoma 2 (Bcl-2) and cyclic adenosine monophosphate response element-binding protein (CREB) have been the most extensively studied (Angelucci et al. 2003; Chuang et al. 2002; Fukumoto et al. 2001; Manji and Chen 2002). It is well known that BDNF, Bcl-2 and CREB play important roles in maintaining normal synaptic plasticity in diverse ways (Adams and Cory 1998; McAllister et al. 1999; ; Shaywitz and Greenberg 1999; Silva et al. 1998). Evidence from brain imaging and postmortem studies and studies with animal models suggests that in patients with bipolar disorder, diverse pathological changes in neuroplastic processes lead to impairment in synaptic communications in neuronal circuits involved in the pathophysiology of bipolar disorder. Lithium may enhance synaptic plasticity and thereby restore normal synaptic communications in the circuits by up-regulating neurotrophic and neuroprotective factor such as BDNF, Bcl-2 and activating CREB, the major transcription factor of gene expression of BDNF and Bcl-2, and this action may be associated with the efficacy of the drug. However, this theory has been developed primarily based on molecular biological and clinical studies. This theory has never been fully tested by directly examining the effects of lithium exposure on synaptic plasticity. Only few studies have specifically focused on the effects of lithium exposure on synaptic plasticity.
Suppression of skeletal muscle lipoprotein lipase activity during physical inactivity: a molecular reason to maintain daily low‐intensity activity

We have examined the regulation of lipoprotein lipase (LPL) activity in skeletal muscle during physical inactivity in comparison to low‐intensity contractile activity of ambulatory controls. From studies acutely preventing ambulatory activity of one or both the hindlimbs in rats, it was shown that ≈90–95 % of the heparin‐releasable (HR) LPL activity normally present in rat muscle with ambulatory activity is lost, and thus dependent on local contractile activity. Similarly, ≈95 % of the differences in LPL activity between muscles of different fibre types was dependent on ambulatory activity. The robustness of the finding that physical inactivity significantly decreases muscle LPL activity was evident from confirmatory studies with different models of inactivity, in many rats and mice, both sexes, three muscle types and during both acute and chronic (11 days) treatment. Inactivity caused a local reduction of plasma [3H]triglyceride uptake into muscle and a decrease in high density lipoprotein cholesterol concentration. LPL mRNA was not differentially expressed between ambulatory controls and either the acutely or chronically inactive groups. Instead, the process involved a rapid loss of the HR‐LPL protein mass (the portion of LPL largely associated with the vascular endothelium) by an actinomycin D‐sensitive signalling mechanism (i.e. transcriptionally dependent process). Significant decreases of intracellular LPL protein content lagged behind the loss of HR‐LPL protein. Treadmill walking raised LPL activity ≈8‐fold (P < 0.01) within 4 h after inactivity. The striking sensitivity of muscle LPL to inactivity and low‐intensity contractile activity may provide one piece of the puzzle for why inactivity is a risk factor for metabolic diseases and why even non‐vigorous activity provides marked protection against disorders involving poor lipid metabolism.
The validity of linguistic specificity for N400 component in cognitive visual evoked potentials technique using a Romanian psycho-verbal stimulation interface

The experiment aims to demonstrate the validity of linguistic specificity for N400 component in cognitive visual evoked potentials technique whatever is the level and the strategy of decoding, using a Romanian patented psycho-verbal stimulation interface. The acquisition of visual evoked potentials was performed in Cz, Pz, Fz, Oz leads, using a group of 50 adult persons between 19–21 year old, students who made two recognition tasks using decoded of 500 strings of symbols and decoding 500 strings of letters (words and non-word) with an average number of 7 characters. EPs were analyzed in a 1000 ms interval, after it used Grand AVG function for 50 person's recordings at each task, on 17 of 100 ms interspersed intervals, looking through SPSS software using ANOVA method which assess the highest difference in amplitude for each interval. Averaged EPs was poor in component after 300 ms for non-linguistic strings of symbols, but for linguistic stimuli it appeared a pronounced negative wave between 350–450 ms (t=6.25, p<0.001) and others negative and positive reverberation was present after this latency (t=1.10, p>0.05), especially in Fz and Pz. P300 was present on both tasks. The N400 component is related with linguistic stimuli, regardless of semantic or non-semantic types (pseudo - words) which confirm the findings of other studies.
The study on the role of inflammatory cells and mediators in post-infectious functional dyspepsia

Abstract Objective. Functional dyspepsia is a common gastrointestinal disorder. The pathogenesis of functional dyspepsia remains unclear. Functional dyspepsia may begin after a bout of gastroenteritis (post-infectious functional dyspepsia) or de novo (nonspecific functional dyspepsia). The aim of this study was to investigate the prevalence and probable mechanisms of post-infectious functional dyspepsia. Material and methods. Functional dyspepsia patients with a history of unsanitary food intake and acute gastroenteritis 6-12 months ago were enrolled. 13C-UBT confirmed absence of H. pylori infection. Controls consisted of healthy nondyspeptic volunteers and patients with nonspecific functional dyspepsia. Gastric biopsies were used for routine histology, immunohistochemistry, electron microscopy, ELISA, HPLC assays and Western blot examination. Results. Eighty-five subjects were entered including 35 with post-infectious functional dyspepsia, 30 with nonspecific functional dyspepsia, and 20 healthy controls. The number of mast cells in post-infectious functional dyspepsia and nonspecific functional dyspepsia were significantly greater than that in healthy controls. The number of enterochromaffin cells (ECs) in post-infectious functional dyspepsia was significantly higher than those in nonspecific functional dyspepsia or in healthy controls. The number of mast cells and ECs increased with the density of chronic inflammatory cells. The release of histamine and 5-hydroxytryptamine from gastric mucosa of post-infectious functional dyspepsia patients was significantly greater than those from nonspecific functional dyspepsia or healthy controls. Tryptase protein expression was higher in post-infectious functional dyspepsia and nonspecific functional dyspepsia than in healthy controls. The histological score of chronic gastric inflammation was greater in post-infectious functional dyspepsia versus patients with nonspecific functional dyspepsia or healthy controls. Electron microscopy showed secreting granules in the cytoplasm of both mast cells and ECs. The number of activated mast cells and Ecs at a distance of < 5 μm of nerve fibers were significantly greater in post-infectious functional dyspepsia versus nonspecific functional dyspepsia or controls. Conclusions. Dyspepsia may occur after an acute onset of gastroenteritis in a part of patients. Potent chemicals derived from mast cells and ECs, including histamine, tryptase and 5-hydroxytryptamine may be involved in the pathogenesis of post-infectious functional dyspepsia.
[Tracheal intubation with Trachlight: clinical assessment in one hundred patients].

BACKGROUND The lightwand device (Trachligh) is effective and safe for difficult tracheal intubation. We recorded the process of acquiring the intubation technique with Trachlight and evaluated the usefulness of Trachlight for tracheal intubation. METHODS Tracheal intubation with Trachlight was performed by inexperienced anesthesiologists in one hundred patients undergoing general anesthesia. The time to tracheal intubation was recorded. RESULTS Tracheal intubation with Trachlight was successful in 92 (92%) of 100 patients. As the experience of anesthesiologists increased, both the time to tracheal intubation and the success rate improved. There were no significant correlations between the time to tracheal intubation and any of the airway parameters for Trachlight intubation. CONCLUSIONS This study suggests that the experience of at least 30 cases is necessary to learn the intubation technique with Trachlight.
Serial Order in Planning the Production of Successive Morphemes of a Word

Abstract Five implicit priming experiments examined whether the speech production system can plan noninitial morphemes of a word in advance of initial ones. On each trial, subjects had to produce one word out of a set of three words as quickly as possible. In a homogeneous condition, the responses shared part of their form, whereas in a heterogeneous condition they did not. The first experiment shows that the task is sensitive to morphological planning. In producing disyllabic simple and compound nouns, a larger facilitatory effect was obtained when a shared initial syllable constituted a morpheme than when it did not. The next three experiments suggest that successive morphemes are planned in serial order. In producing nominal compounds, no facilitation was obtained for noninitial morphemes. In producing prefixed verbs, facilitation was obtained for the prefix but not for the noninitial base. Sharing morphemes often implies semantic overlap. The fifth experiment shows that semantic similarity per se yields inhibition rather than facilitation. Computer simulations show that the WEAVER model of word-form encoding (Roelofs, 1992b, 1994, submitted-a) accounts for the findings.
Rapid contrast adaptation in glaucoma and in aging.

PURPOSE The visual system rapidly adapts to contrast changes, often with each fixation. One key anatomical site underpinning contrast adaptation is the retinal ganglion cell dendrites, where degenerative changes occur in glaucoma. This study investigated the effects of early glaucoma and aging on rapid contrast adaptation. METHODS Contrast detection and discrimination thresholds were measured in central vision for briefly presented (94 ms) Gabor patches with and without adaptation to 50% contrast Gabor patches (1000 ms). Fourteen people with glaucoma (aged 58-77 years), 17 age-similar controls (aged 50-72 years), and 19 younger adults (aged 20-31 years) participated. Detection thresholds were measured at various time points (47, 106, 200, 400, 600, and 1000 ms) post adaptation. Discrimination thresholds were measured post adaptation relative to a reference contrast below (30%), equivalent to (50%), or above (70%) the adaptor. RESULTS The glaucoma group demonstrated elevated unadapted detection (P < 0.0001) and discrimination (P = 0.01) thresholds relative to age-similar controls. In normal observers, aging elevated unadapted thresholds (detection: P < 0.0001; discrimination: P < 0.0001). At 47 ms post adaptation, the glaucoma group demonstrated reduced effects of adaptation relative to controls (P = 0.009). Adaptation was also reduced when the reference contrast (50%) was equivalent to the adaptor (P = 0.02). Aging did not alter adaptation of normal observers. CONCLUSIONS Glaucoma alters rapid contrast adaptation while aging does not. Contrast adaptation is key to visual processing in natural visual environments. Our results imply that glaucoma produces abnormalities in natural visual experiences in central vision.
Title : Auroral electrojets during deep solar minimum at the end of solar cycle 23 Year :

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