Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods.

A method for estimating protein secondary structure from infrared spectra has been developed. The infrared spectra of H2O solutions of 13 proteins of known crystal structure have been recorded and corrected for the spectral contribution of water in the amide I and II region by using the algorithm of Dousseau et al. [Dousseau, F. , Therrien, M. , & Pézolet, M. (1989) Appl. Spectrosc. 43, 538-542]. This calibration set of proteins has been analyzed by using either a classical least-squares (CLS) method or the partial least-squares (PLS) method. The pure-structure spectra calculated by the classical least-squares method are in good agreement with spectra of poly(L-lysine) in the alpha-helix, beta-sheet, and undefined conformations. The results show that the best agreement between the secondary structure determined by X-ray crystallography and that predicted by infrared spectroscopy is obtained when both the amide I and II bands are used to generate the calibration set, when the PLS method is used, and when it is assumed that the secondary structure of proteins is composed of only four types of structure: ordered and disordered alpha-helices, beta-sheet, and undefined conformation. Attempts to include turns in the secondary structure estimation have led to a loss of accuracy. The standard deviation of the difference between X-ray and infrared secondary structure estimates with this method is 4.8% for the alpha-helix, 3.7% for the beta-sheet, and 5.1% for the undefined structure, whereas the regression coefficients are 0.95, 0.96, and 0.56, respectively. The spectra of the calibration proteins were also recorded in 2H2O solution. (ABSTRACT TRUNCATED AT 250 WORDS)
Twenty Years of Universal Vaccination Against Hepatitis B in Italy: Achievements and Challenges

Viral hepatitis B is a vaccine-preventable disease. Vaccination has proved to be safe and highly effective in reducing the incidence, the carrier rate and HBV-related mortality on a global scale. In Italy, universal vaccination against hepatitis B started in 1991 in infants as well as in adolescents, providing an outstanding record of safety and effectiveness. Within a few years, over 95% coverage was consistently reported. Today, some 17 million people are immune against hepatitis B and their immunity has been shown to be long-lasting. At present, no booster is required in healthy vaccinated people to sustain protection. Surveillance data from Italy have shown a clear overall decline in hepatitis B among successfully vaccinated individuals. Furthermore, a generation of children and young people (at present cohorts ranging from 0 to 32 years) is emerging with practically no markers of HBV infection. Italy’s vaccination programme has resulted in substantial progress towards the prevention and control of hepatitis B. The vaccination programme must continue. Maintaining mandatory vaccination of infants and increasing HBV vaccination coverage in high-risk groups, including households of HBsAg carriers as well as immigrants, remain a priority for the future. Acknowledgments Data reported in this paper were presented at a national Meeting, Towards the elimination of hepatitis B: celebrating 20 years of vaccination in Italy, held in Milano (19 November 2011) under the high patronage of the President of the Italian Republic. Distinguished figures from the world of Italian Public Health as well as international experts participated and paid tribute to the work of those who had contributed to the saving of lives, prevention of suffering, and the savings made to the State.
Adrenergic and Reflex Abnormalities in Obesity-Related Hypertension

Previous studies have shown that essential hypertension and obesity are both characterized by sympathetic activation coupled with a baroreflex impairment. The present study was aimed at determining the effects of the concomitant presence of the 2 above-mentioned conditions on sympathetic activity as well as on baroreflex cardiovascular control. In 14 normotensive lean subjects (aged 33.5±2.2 years, body mass index 22.8±0.7 kg/m2 [mean±SEM]), 16 normotensive obese subjects (body mass index 37.2±1.3 kg/m2), 13 lean hypertensive subjects (body mass index 24.0±0.8 kg/m2), and 16 obese hypertensive subjects (body mass index 37.5±1.3 kg/m2), all age-matched, we measured beat-to-beat arterial blood pressure (by Finapres device), heart rate (HR, by ECG), and postganglionic muscle sympathetic nerve activity (MSNA, by microneurography) at rest and during baroreceptor stimulation and deactivation induced by stepwise intravenous infusions of phenylephrine and nitroprusside, respectively. Blood pressure values were higher in lean hypertensive and obese hypertensive subjects than in normotensive lean and obese subjects. MSNA was significantly (P <0.01) greater in obese normotensive subjects (49.1±3.0 bursts per 100 heart beats) and in lean hypertensive subjects (44.5±3.3 bursts per 100 heart beats) than in lean normotensive control subjects (32.2±2.5 bursts per 100 heart beats); a further increase was detectable in individuals with the concomitant presence of obesity and hypertension (62.1±3.4 bursts per 100 heart beats). Furthermore, whereas in lean hypertensive subjects, only baroreflex control of HR was impaired, in obese normotensive subjects, both HR and MSNA baroreflex changes were attenuated, with a further attenuation being observed in obese hypertensive patients. Thus, the association between obesity and hypertension triggers a sympathetic activation and an impairment in baroreflex cardiovascular control that are greater in magnitude than those found in either of the above-mentioned abnormal conditions alone.
Dynamics and Plasticity of Weibel-Palade Bodies in Endothelial Cells

Agonist-induced release of endothelial cell specific storage granules, designated Weibel-Palade bodies (WPBs), provides the endothelium with the ability to rapidly respond to changes in its micro-environment. Originally being defined as an intracellular storage pool for von Willebrand factor (VWF), it has recently been shown that an increasing number of other components, including P-selectin, interleukin (IL)-8, eotaxin-3, endothelin-1, and angiopoietin-2, is present within this subcellular organelle, implicating a role for WPB exocytosis in inflammation, hemostasis, regulation of vascular tone and angiogenesis. Recent studies emphasize that WPBs provide a dynamic storage compartment whose contents can be regulated depending on the presence of inflammatory mediators in the vascular micro-environment. Additionally, release of WPBs is tightly regulated and feedback mechanisms have been identified that prevent excessive release of bioactive components from this subcellular organelle. The ability to regulate both contents and exocytosis of WPBs endows these endothelial cell specific organelles with a remarkable plasticity. This is most likely needed to allow for controlled delivery of bioactive components into the circulation on vascular perturbation.
Inversion of P and SV waves from multicomponent offset vertical seismic profiles

Downgoing waves in multicomponent VSP experiments are used to obtain seismic P- and S-wave velocities as a function of depth and angle of incidence. If P and SV waveforms do not overlap in time at the depth of interest, local velocities of the medium are obtained by separate analysis of these events. The apparent velocity of the event (P or SV) is computed from the moveout across several neighboring depth locations. The angle of incidence of the same event is computed from the particle‐motion hodogram within an appropriately chosen time window. Then, the local medium velocity (P wave or S wave depending on the chosen event) is given by the apparent velocity multiplied by the cosine of the angle of incidence. Layer interfaces with reasonably sharp velocity contrasts are efficient P-wave to SV-wave converters, even at moderate angles of incidence. In offset VSP experiments, converted SV waves are generated with varying strengths at practically all depths. Consequently, the converted SV waveforms partially o.
Employing Satellite-Derived Sea Ice Concentration to Constrain Upper-Ocean Temperature in a Global Ocean GCM

Abstract The quality of Southern Ocean sea ice simulations in a global ocean general circulation model (GCM) depends decisively on the simulated upper-ocean temperature. This is confirmed by assimilating satellite-derived sea ice concentration to constrain the upper-layer temperature of a sea ice–ocean GCM. The resolution of the model’s sea ice component is about 22 km and thus comparable to the pixel resolution of the satellite data. The ocean component is coarse resolution to afford long-term integrations for investigations of the deep-ocean equilibrium response. Besides improving the sea ice simulation considerably, the simulations with constrained upper-ocean temperature yield much more realistic global deep-ocean properties, in particular when combined with glacial freshwater input. Both outcomes are relatively insensitive to the passive-microwave algorithm used to retrieve the ice concentration being assimilated. The sensitivity of the long-term global deep-ocean properties and circulation to the po.
Occurrence of the Pharmaceutical Drug Clofibric Acid and the Herbicide Mecoprop in Various Swiss Lakes and in the North Sea

Clofibric acid (CA) and the herbicide mecoprop (MCPP) were detected in Swiss lakes from populated areas and in the North Sea in the low nanograms per liter range. Gas chromatography/mass spectrometry (GC/MS) and MS/MS were used to distinguish the two isomeric compounds (analyzed as the methyl esters). The concentrations of CA in the North Sea (1−2 ng/L) reach levels of those of “classical” environmental pollutants such as α- and γ-hexachlorocyclohexane. The data suggest a high mobility of CA in the aquatic environment. The changed relative concentrations of CA and MCPP in the North Sea as compared to those in the lakes and in comparison to produc tion figures indicate a much more persistent behavior for CA than for MCPP. The data also indicate that some pharmaceutical compounds need evaluation on ecotoxicological grounds in very much the same way as do agricultural chemicals.
Behavioral and Brain Functions

Background: Motor system excitability is based on a complex interaction of excitatory and inhibitory processes, which in turn are modulated by internal (e.g., volitional inhibition) and external (e.g., drugs) factors. A well proven tool to investigate motor system excitability in vivo is the transcranial magnetic stimulation (TMS). In this study, we used TMS to investigate the effects of methylphenidate (MPH) on the temporal dynamics of motor system excitability during a go/nogo task. Methods: Using a double-blind, placebo-controlled, crossover design, 14 healthy adults (8 male, 6 female; aged 20–40 yrs) performed a spatial go/nogo task (S1-S2 paradigm) either under dlmethylphenidate (MPH, 20 mg) or placebo. TMS single and double-pulses (interstimulus interval: 3 ms) were delivered either at 120, 230 or 350 ms after the S2 stimulus (control, go and nogo trials). Results: At the performance level, faster reaction times and a trend towards less impulsivity errors under MPH vs. placebo were observed. In nogo trials, i.e., when a prepared response had to be inhibited, motor evoked potentials (MEPs) had a smaller amplitude at an interval of 230 ms compared to 120 and 350 ms. The short-interval intracortical inhibition (SICI) increased over time. Under MPH, SICI in nogo trials was larger compared to placebo. With the interval between S2 and the TMS-pulse increasing, MEP amplitudes increased under MPH in nogo trials but an early inhibitory effect (at 120 ms) could also be observed. Conclusion: Our results show a distinct pattern of excitatory and inhibitory phenomena in a go/ nogo task. MPH appears to significantly alter the dynamics of motor system excitability. Our findings suggest that a single dose of 20 mg MPH provides some fine-tuning of the motor system in healthy adults. Published: 27 February 2009 Behavioral and Brain Functions 2009, 5:12 doi:10.1186/1744-9081-5-12 Received: 11 September 2008 Accepted: 27 February 2009 This article is available from: http://www.behavioralandbrainfunctions. com/content/5/1/12 © 2009 Kratz et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Omega-3 fatty acids: evidence basis for treatment and future research in psychiatry.

OBJECTIVE To determine if the available data support the use of omega-3 essential fatty acids (EFA) for clinical use in the prevention and/or treatment of psychiatric disorders. PARTICIPANTS The authors of this article were invited participants in the Omega-3 Fatty Acids Subcommittee, assembled by the Committee on Research on Psychiatric Treatments of the American Psychiatric Association (APA). EVIDENCE Published literature and data presented at scientific meetings were reviewed. Specific disorders reviewed included major depressive disorder, bipolar disorder, schizophrenia, dementia, borderline personality disorder and impulsivity, and attention-deficit/hyperactivity disorder. Meta-analyses were conducted in major depressive and bipolar disorders and schizophrenia, as sufficient data were available to conduct such analyses in these areas of interest. CONSENSUS PROCESS The subcommittee prepared the manuscript, which was reviewed and approved by the following APA committees: the Committee on Research on Psychiatric Treatments, the Council on Research, and the Joint Reference Committee. CONCLUSIONS The preponderance of epidemiologic and tissue compositional studies supports a protective effect of omega-3 EFA intake, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in mood disorders. Meta-analyses of randomized controlled trials demonstrate a statistically significant benefit in unipolar and bipolar depression (p = .02). The results were highly heterogeneous, indicating that it is important to examine the characteristics of each individual study to note the differences in design and execution. There is less evidence of benefit in schizophrenia. EPA and DHA appear to have negligible risks and some potential benefit in major depressive disorder and bipolar disorder, but results remain inconclusive in most areas of interest in psychiatry. Treatment recommendations and directions for future research are described. Health benefits of omega-3 EFA may be especially important in patients with psychiatric disorders, due to high prevalence rates of smoking and obesity and the metabolic side effects of some psychotropic medications.
Hemodialysis Patients: a High Risk Group for Hepatitis C

To The Editor: We commend Alashek et al for their excellent article [1]. However, the authors did not clarify why a very important high risk group was left out of their study, that of hemodialysis (HD) patients. Hepatitis C Virus (HCV) infection has been shown to be more prevalent among HD patients in developing countries. Hepatitis C prominently increases the burden of disease in the HD population. Furthermore, the longer patients are on HD, the more susceptible they are to HCV acquisition [2]. More importantly in Libya, HD patients seem to have a higher prevalence of the disease compared to other more developed regions. Research from Libya on this issue although scant, is available, as evident by a relatively recent publication on the matter, a study by Daw et al, conducted in Tripoli from 1999 to 2001 [3]. The study showed a 20.5% prevalence of HCV among HD patients, which is of similar prevalence to neighbouring Tunisia, and seems to be better than some of the gulf countries, where a higher sero-prevalence rate seems to exist within this patient group [2]. This percentage is still unacceptable, as emphasized when compared to the CDC's data which states that the prevalence of hepatitis C in this population averages 10%, any thing above clearly outlines flaws in the HD service [4]. Health care systems that employ strict adherence to universal preventive measures during HD have a low prevalence of HCV among their patients; an example of this is that the UK has a 4% prevalence of HCV among HD patients [2]. Hemodialysis should not be a one-way street to acquiring a blood borne viral infection and unless clinical practice is changed to avoid infection risk, the overall disease burden for this group will only increase to their detriment. The current sero-prevalence status of HD patients in Libya needs to be studied and updated. We hope Alashek et al continue in their excellent work, and we recommend that the HD patient group in Libya is studied further, and any particular flaws in the provision of their care is identified and rectified.
Detection and discrimination of flicker contrast in migraine

Aims: Flickering light is strongly aversive to many individuals with migraine. This study was designed to evaluate other abnormalities in the processing of temporally modulating visual stimulation. Methods: We measured psychophysical thresholds for detection of a flickering target and for the discrimination of suprathreshold flicker contrasts (increment thresholds) in 14 migraineurs and 14 healthy controls with and without prior adaptation to high-contrast flicker. Visual discomfort (aversion) thresholds were also assessed. Results: In the baseline (no adaptation) conditions, detection and discrimination thresholds did not differ significantly between groups. Following adaptation, flicker detection thresholds were elevated equivalently in both groups; however, discrimination thresholds were more strongly affected in migraineurs than in controls, showing greater elevation at moderate contrasts and greater threshold reduction (sensitisation) at high contrast (70%). Migraineurs also had significantly elevated discomfort scores, and these were significantly correlated with number of years with migraine. Discussion: We conclude that visual flicker not only causes discomfort but also exerts measurable effects on contrast processing in the visual pathways in migraine. The findings are discussed in the context of the existing literature on habituation, adaptation and contrast-gain control.
Autoregulation and monoamine interactions in the ventral tegmental area in the absence and presence of cocaine: a microdialysis study in freely moving rats.

Extracellular levels of norepinephrine (NE), dopamine (DA) and serotonin (5-HT) were measured simultaneously by microdialysis in the ventral tegmental area (VTA) of conscious rats, and locomotor activity was monitored. Extracellular NE, DA and 5-HT was increased by both local infusion (30 microM) and i.p. injection (20 and 40 mg/kg) of cocaine with 5-HT responding most rapidly. DA was the only amine that showed a significantly higher increase to the systemic cocaine dose of 40 mg/kg than 20 mg/kg, and a higher response to local cocaine (30 microM) than systemic cocaine (20 mg/kg). In the following experiments, the monoamine autoreceptor antagonists idazoxan (alpha-2, 100 microM), sulpiride (D2 DA/D3 DA, 10 microM) and methiothepin (5-HT1/5-HT2, 20 microM) were focally applied into the VTA before cocaine application. Idazoxan or methiothepin increased only local cocaine-induced NE or 5-HT output, whereas sulpiride increased both local and systemic cocaine-induced DA output, consonant with the importance of somatodendritic monoamine autoreceptors in addition to accumbens-VTA feedback pathways. Both idazoxan and methiothepin increased the basal output of all three amines without modifying cocaine (30 microM or 20 mg/kg)-induced output of DA/5-HT or NE/DA, whereas sulpiride promoted cocaine-induced NE output without modifying basal NE/5-HT output and cocaine-induced 5-HT output, implying complex interactions between monoamines. Idazoxan or methiothepin depressed, whereas sulpiride stimulated cocaine (20 mg/kg)-induced motor activity. The analysis of behavioral/neurochemical relationships revealed a negative correlation between dialysate NE output and motor activity in the cocaine alone and idazoxan/cocaine groups, and a positive correlation between dialysate DA output and motor activity in the sulpiride/cocaine and methiothepin/cocaine groups.
A Sound Foundation Through Early Amplification 214 What We Know In the

Address correspondence to: Anne Marie Tharpe, Ph.D., Professor, Vanderbilt Bill Wilkerson Center, 1215 21st Ave. So. , #8310, Medical Center East, So. Tower, Nashville, TN. 37232-8242, anne.m. tharpe@vanderbilt.edu. Since that time, others have adopted these definitions in an effort to enable meaningful comparisons of data across studies (Centers for Disease Control and Prevention 2005). Our attempts to evaluate current data obtained across studies are compromised when we are not using uniform definitions. For example, prevalence rates of minimal or mild bilateral hearing loss and unilateral hearing loss are uncertain because of the differences in defining the audiometric thresholds of these groups. Furthermore, because we do not currently target minimal and mild degrees of hearing loss with our newborn hearing screening programs, we can only estimate prevalence of such losses in the newborn period. Johnson and colleagues (2005) offered a conservative estimate of 0.55/1000 newborns with mild permanent bilateral (25–40 dB at 1.0, 2.0, or 4.0 kHz) and unilateral hearing loss. The number of babies with unilateral hearing loss in the neonatal period has been estimated at 0.7–1/1000 (Prieve et al. 2000; Davis, DeVoe and Robertson 2005) as compared to 3/100 by school age (Bess et al. 1998). Bess and colleagues also estimated 2.4/100 school-age children had minimal bilateral hearing loss. The difference between estimated prevalence rates in the newborn period and at school age can be the result of several different factors including: • misses by the early hearing detection and intervention systems (EHDI); • low follow-up rates by newborn screening programs resulting in low estimates in the newborn period; • progressive or late-onset hearing loss; and/or • differing definitions of “hearing loss”. This chapter will review what we know about the impact of minimal degrees of hearing loss on children. Perhaps more importantly, what we do not know about the effects of these degrees of hearing loss will also be discussed.
Non-Parametric ICA reveals Learning Styles in Education Activities through the Web

This paper presents a new application of independent component analysis to e-learning. An ICA model is proposed defining the sources as dimensions of the learning styles of the students. A novel non-parametric ICA and standard ICA algorithms are applied to huge historical web log data from a virtual campus in order to detect relationship between web activities and learning styles. The data are divided by the course types in: graduate and regular academic career courses and each of those divisions is separated in two subsets: cases with grades and cases with no grades. Web activities include events as course access, email exchange, forum participation, news reading, chats and achievements. Suitable learning styles of the students were positively detected for graduate courses with grades using the non-parametric ICA algorithm.
Linear projection algorithms and morphological dynamic link architecture for frontal face verification

The combined use of linear projection algorithms with a variant of dynamic link architecture based on the multi-scale morphological dilation-erosion is proposed for face verification. The performance of the combined scheme is evaluated in terms of the receiver operating characteristic (ROC) for several threshold selections on the matching error in the M2VTS database. The experimental results indicate that the incorporation of linear projections in the morphological dynamic link architecture improves significantly the verification capability of the method.