Miracle-dz/UniFAR-FTUs huggingface dataset:
A Protein-Chameleon: Conformational Plasticity of α-Synuclein, a Disordered Protein Involved in Neurodegenerative Disorders

Abstract Under the physiological conditions in vitro, α-synuclein, a conservative presynaptic protein, the aggregation and fibrillation of which is assumed to be involved into the pathogenesis of Parkinson's disease and several other neurodegenerative disorders, known as synucleinopathies, is characterized by the lack of rigid well-defined structure; i.e., it belongs to the class of intrinsically unstructured proteins. Intriguingly, α-synuclein is characterized by a remarkable conformational plasticity, adopting a series of different conformations depending on the environment. For example, this protein may either stay substantially unfolded, or adopt an amyloidogenic partially folded conformation, or fold into α-helical or β-structural species, both monomeric and oligomeric. Furthermore, it might form several morphologically different types of aggregates, including oligomers (spheres or doughnuts), amorphous aggregates, and or amyloid-like fibrils. The peculiarities of this astonishing conformational behavior are analyzed to shed light on structural plasticity of this protein-chameleon.
Agent-Based Document Retrieval for the European Physicists: A Project Overview

(TYPE=abstract)Today in physics, more and more scientific documents are prepared electronically, are posted and archived. At the same time, an increasing number of heterogeneous Web-servers are dedicated to hosting such archives. While this trend makes available more relevant scientific information, it also complicates the task of finding, retrieving, processing and printing scientific documents. As a consequence physicists could benefit from an efficient user-friendly tool that integrates functionalities for document retrieval and distribution. In this paper, we present a solution to this problem. Our approach links two systems together: an agent-based search engine for document retrieval and a printing-on-demand service that handles printing, binding and shipping of retrieved documents to readers who request them. We discuss a prototype already available that enables document retrieval from a number of Web servers, including the global network of physics preprints, set up by P. Ginsparg, and the PhysDoc broker which integrates 1000 distributed European Web-servers maintained by local physics departments.
Inflammatory leukocytic recruitment and diffuse neuronal degeneration are separate pathological processes resulting from traumatic brain injury

The present study characterized whether inflammatory leukocytic infiltration is temporally and regionally correlated with neuronal degeneration and/or blood brain barrier (BBB) breakdown resulting from traumatic brain injury. Adult rats were sacrificed at 5 min, 2, 4, 12, 24, and 72 hr after lateral fluid percussion brain injury. BBB breakdown, neuronal degeneration and leukocyte infiltration were assessed using immunocytochemistry, silver impregnation and toluidine blue and eosin staining. BBB breakdown and neuronal degeneration occurred concomitantly in injured cortex, hippocampus, and along the dorsolateral quadrant of the diencephalon. However, neuronal degeneration within deep diencephalic structures transpired in the absence of IgG extravasation. Neutrophils were observed only in regions exhibiting BBB damage and were first apparent in injured cortex and hippocampus between 2–12 hr posttrauma lining the vasculature and filling subarachnoid/subdural spaces. Neutrophils then migrated from damaged vasculature into traumatized cortical and hippocampal parenchyma by 24 hr after lateral fluid percussion injury. Macrophages were also observed within cortical parenchyma at 24 hr and completely filled the cortical lesion site by 72 hr after injury. Macrophages were not as abundant throughout hippocampal parenchyma and were found only in hippocampal regions exhibiting focal hemorrhage at 72 hr. Finally, neutrophils did not migrate to deep diencephalic structures that showed no BBB damage despite extensive neuronal degeneration. Indeed, lateral fluid percussion elicits inflammatory leukocytic recruitment only in regions experiencing concomitant BBB damage and neuronal degeneration. In summary, inflammatory leukocytic recruitment and diffuse neuronal degeneration are separate pathological processes resulting from traumatic brain injury.
Effects of 915 MHz Electromagnetic-Field Radiation in TEM Cell on the Blood-Brain Barrier and Neurons in the Rat Brain

Abstract Masuda, H. , Ushiyama, A. , Takahashi, M. , Wang, J., Fujiwara, O. , Hikage, T. , Nojima, T. , Fujita, K. , Kudo, M. and Ohkubo, C. Effects of 915 MHz Electromagnetic-Field Radiation in TEM Cell on the Blood-Brain Barrier and Neurons in the Rat Brain. Radiat. Res. 172, 66-73 (2009). The aim of this study was to determine whether albumin leakage and dark neurons were present in rat brains 14 and 50 days after a single 2-h exposure to a 915 MHz electromagnetic field, as reported by Salford et al. (Environ. Health Perspect. 111, 881–883, 203). Sixty-four male F344 rats (12 weeks old) were exposed to a 915 MHz electromagnetic field at whole-body average specific absorption rates of 0, 0.02, 0.2 and 2.0 W/kg in TEM cells for 2 h, following the protocol reported by Salford et al. The brains were examined histologically and immunohistochemically. No albumin immunoreactivity was observed in the exposed groups. In addition, dark neurons, assessed using hematoxylin and eosin staining, were rarely present, with no statistically significant difference between exposed and sham-exposed animals. This study thus failed to confirm the results of Salford et al.
Intentionally inserted oxygen depleted (Ba/sub 0.5/Sr/sub 0.5/)TiO/sub 3/ layers as a model of DC-electrical degradation

The relative dielectric constant versus voltage (/spl epsiv//sub r/-V) characteristics and the current density versus electric field (J-E) characteristics of (Ba/sub 0.5/Sr/sub 0.5/)TiO/sub 3/ films, which have intentionally inserted oxygen depleted layers near the bottom electrodes, were investigated as a model of dc-electrical degradation phenomena. Our investigation demonstrated that the intentionally inserted oxygen depleted layer is the cause of the tunneling conduction.
Factors Affecting Depressive Symptoms among North Korean Adolescent Refugees Residing in South Korea

We examined factors affecting the depressive symptoms and the relationship between depression and quality of life among 131 North Korean adolescent refugees aged 12–24 years. We compared sociodemographic, social, and individual characteristics and perceived the quality of life between participants with and without depression. Thirty-seven refugees (28.2%) had clinically significant depressive symptoms. The refugees with depression were younger (t = 2.67; p = 0.009), more likely to be male (χ2 = 6.98; p = 0.009), and more likely to have a Chinese father (χ2 = 9.05; p = 0.003) than those without depression. The refugees with depression had lower levels of psychological social support (t = 2.96; p = 0.004) and resilience (t = 4.24; p < 0.001) and higher levels of alcohol problems (t = −2.08; p = 0.043), aggression (t = −3.15; p = 0.003), and post-traumatic stress disorder (PTSD; t = −2.89; p = 0.004). They also reported lower levels of life satisfaction (t = 3.31; p = 0.001) and had a more negative view of their future (t = 2.68; p = 0.010). Interventions to increase resilience, to decrease the impact of traumatic events, and to provide psychological support may be helpful for North Korean adolescent refugees at risk of depression.
Fluorescence two-dimensional difference gel electrophoresis for biomaterial applications

Fluorescence two-dimensional difference gel electrophoresis (DiGE) is rapidly becoming established as a powerful technique for the characterization of differences in protein expression levels between two or more conditions. In this review, we consider the application of DiGE—both minimal and saturation labelling—to biomaterials research, considering the challenges and rewards of this approach.
Similarity in Fog and Rainfall Intermittency

Intermittent fog occurrences supply significant amounts of moisture to plants in the form of fog drip onto the soil surface thereby prompting interest in their statistical behavior at multiple timescales. A comparison of rainfall and fog measurements collected at an inland tropical cloud forest in Kenya and a coastal rangeland in Northern California is presented to explore whether fog occurrences have similar intermittency characteristics as rainfall. The results confirm that both rainfall and fog show approximate power law relations for distributions of dry period and event size consistent with predictions from self‐organized criticality. Moreover, the spectral exponents of the on‐off time series of the fog and rainfall exhibited an approximate f−0.8 over a broad range of frequencies f, which is remarkably close to scaling exponents across sites experiencing different rainfall generation mechanisms. These results suggest that fog intermittency shares some properties of critical behavior documented in numerous rainfall studies.
A system for graph-based visualization of the evolution of software

We describe GEVOL, a system that visualizes the evolution of software using a novel graph drawing technique for visualization of large graphs with a temporal component. GEVOL extracts information about a Java program stored within a CVS version control system and displays it using a temporal graph visualizer. This information can be used by programmers to understand the evolution of a legacy program: Why is the program structured the way it is? Which programmers were responsible for which parts of the program during which time periods? Which parts of the program appear unstable over long periods of time and may need to be rewritten? This type of information will complement that produced by more static tools such as source code browsers, slicers, and static analyzers.
Distribution and Effects of Nonsense Polymorphisms in Human Genes

Background A great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function. In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products. Methodology/Principal Findings To detect polymorphisms affecting gene function, we analyzed all publicly available polymorphisms in a database for single nucleotide polymorphisms (dbSNP build 125) located in the exons of 36,712 known and predicted protein-coding genes that were defined in an annotation project of all human genes and transcripts (H-InvDB ver3.8). We found a total of 252,555 single nucleotide polymorphisms (SNPs) and 8,479 insertion and deletions in the representative transcripts in these genes. The SNPs located in ORFs include 40,484 synonymous and 53,754 nonsynonymous SNPs, and 1,258 SNPs that were predicted to be nonsense SNPs or read-through SNPs. We estimated the density of nonsense SNPs to be 0.85×10−3 per site, which is lower than that of nonsynonymous SNPs (2.1×10−3 per site). On average, nonsense SNPs were located 250 codons upstream of the original termination codon, with the substitution occurring most frequently at the first codon position. Of the nonsense SNPs, 581 were predicted to cause nonsense-mediated decay (NMD) of transcripts that would prevent translation. We found that nonsense SNPs causing NMD were more common in genes involving kinase activity and transport. The remaining 602 nonsense SNPs are predicted to produce truncated polypeptides, with an average truncation of 75 amino acids. In addition, 110 read-through SNPs at termination codons were detected. Conclusion/Significance Our comprehensive exploration of nonsense polymorphisms showed that nonsense SNPs exist at a lower density than nonsynonymous SNPs, suggesting that nonsense mutations have more severe effects than amino acid changes. The correspondence of nonsense SNPs to known pathological variants suggests that phenotypic effects of nonsense SNPs have been reported for only a small fraction of nonsense SNPs, and that nonsense SNPs causing NMD are more likely to be involved in phenotypic variations. These nonsense SNPs may include pathological variants that have not yet been reported. These data are available from Transcript View of H-InvDB and VarySysDB (http://h-invitational.jp/varygene/).
Psychosocial Characteristics and Obstetric Health of Women Attending a Specialist Substance Use Antenatal Clinic in a Large Metropolitan Hospital

Objective. This paper reports the findings comparing the obstetrical health, antenatal care, and psychosocial characteristics of pregnant women with a known history of substance dependence (n = 41) and a comparison group of pregnant women attending a general antenatal clinic (n = 47). Method. Face-to-face interviews were used to assess obstetrical health, antenatal care, physical and mental functioning, substance use, and exposure to violence. Results. The substance-dependent group had more difficulty accessing antenatal care and reported more obstetrical health complications during pregnancy. Women in the substance-dependent group were more likely to report not wanting to become pregnant and were less likely to report using birth control at the time of conception. Conclusions. The profile of pregnant women (in specialised antenatal care for substance dependence) is one of severe disadvantage and poor health. The challenge is to develop and resource innovative and effective multisectoral systems to educate women and provide effective care for both women and infants.
The Rise of Expanded Hemodialysis

The low water permeability feature of original cellulosic membranes was considered an advantage in the absence of dialysis equipment that are capable of controlling water removal. The advent of ultrafiltration control systems led to the development and use of high-flux (HF) membranes that allowed improved middle molecule removal including β-2 microglobulin. Further advances in technology allowed better control over the structure and permeability of membranes. Different polymers and improved spinning modalities led to significant advances in solute removal and hemocompatibility. Inner surface modification produced a reduction in membrane thrombogenicity and protein-membrane interaction with a less tendency to fouling and permeability decay. Further evolution in technology led to the development of a new class of membranes referred to as protein-leaking membranes or super-flux or high cutoff (HCO). These membranes are more permeable than conventional HF membranes and allow some passage of proteins, including albumin. The rationale for these membranes is the need for increased clearance of low molecular weight proteins and protein-bound solutes. However, albumin loss in protein-leaking HCO membranes represents a limitation whose effect in patients is still controversial. The last evolution in the field of membranes is the development of a new class defined as “high retention onset” (HRO) due to the peculiar high sieving value in the middle to high molecular weight range. The introduction of HRO membranes in the clinical routine has enabled the development of a new concept therapy called “expanded hemodialysis. ” Its simple set up and application offer the possibility to use it even in patients with suboptimal vascular access or even with an indwelling catheter. The system does not require particular hardware or unusual nursing skill. The quality of dialysis fluid is, however, mandatory to ensure a safe conduction of the dialysis session. This new therapy is likely to modify the outcome of end-stage kidney disease patients, thanks to the enhanced removal of molecules traditionally retained by current dialysis techniques.
A Definition of Round-trip Engineering

This paper provides a definition of Round-trip Engineering ( RE) and introduces RE-systems. Where previous definitions of RE are abstract in the sense that they treat views as black boxes this paper provides a mor e detailed definition in which views are transparent. Having transparent views en abl s us to reason about what happens to views during transformations. This wi ll enable studies on the requirements on views, view transformations and view op erations and how these relate to each other. RE-systems may include multiple domains and transformations between those domains. This will enable studies on the requirements on complete RE-systems.
Evaluation of adherence to current guidelines for treatment of hyperlipidemia in adults in an outpatient setting.

PURPOSE Adherence to the 2013 American College of Cardiology (ACC)/American Heart Association (AHA) cholesterol guideline at an outpatient clinic was evaluated. METHODS This retrospective chart review study was conducted from December 1, 2013, through November 30, 2014, at an urban outpatient clinic. Estimated 10-year atherosclerotic cardiovascular disease (ASCVD) risk was calculated based on the pooled cohort equation for all patients. Patients were categorized into one of four statin-benefit groups, in descending order of ASCVD risk. The recommended intensity of a statin and the therapeutic response were determined for each patient. If statin therapy was indicated, patients were assigned to the moderate-intensity, moderate- or high-intensity, or high-intensity group according to guideline recommendations. These guideline-recommended statin intensities were then compared to the patient's prescribed statin to determine guideline concordance. Therapeutic response, expressed as the percent decrease in low-density lipoprotein cholesterol, was determined based on recommended statin intensity. RESULTS A total of 255 patients were initiated on statin therapy; 193 were included for data analysis. Overall adherence to the guideline was 65.8%, with the highest rate in the group of patients with the lowest risk of ASCVD (97.8%). The group with the lowest rate of adherence to recommendations was patients with clinical ASCVD (46.9%). Only 31.6% of patients had a follow-up lipid panel performed, and even fewer achieved a therapeutic response. CONCLUSION A majority of patients were initiated on the appropriate intensity of statin therapy according to the ACC/AHA cholesterol guideline. Of the small number of patients who had follow-up visits, few achieved a therapeutic response based on their prescribed statin therapy.
Pyrazine Analogues Are Active Components of Wolf Urine That Induce Avoidance and Freezing Behaviours in Mice

Background The common grey wolf (Canis lupus) is found throughout the entire Northern hemisphere and preys on many kinds of mammals. The urine of the wolf contains a number of volatile constituents that can potentially be used for predator–prey chemosignalling. Although wolf urine is put to practical use to keep rabbits, rodents, deer and so on at bay, we are unaware of any prior behavioural studies or chemical analyses regarding the fear-inducing impact of wolf urine on laboratory mice. Methodology/Principal Findings Three wolf urine samples harvested at different times were used in this study. All of them induced stereotypical fear-associated behaviors (i.e., avoidance and freezing) in female mice. The levels of certain urinary volatiles varied widely among the samples. To identify the volatiles that provoked avoidance and freezing, behavioural, chemical, and immunohistochemical analyses were performed. One of the urine samples (sample C) had higher levels of 2,6-dimethylpyrazine (DMP), trimethylpyrazine (TMP), and 3-ethyl-2,5-dimethyl pyrazine (EDMP) compared with the other two urine samples (samples A and B). In addition, sample C induced avoidance and freezing behaviours more effectively than samples A and B. Moreover, only sample C led to pronounced expression of Fos-immunoreactive cells in the accessory olfactory bulb (AOB) of female mice. Freezing behaviour and Fos immunoreactivity were markedly enhanced when the mice were confronted with a mixture of purified DMP, TMP, and EDMP vs. any one pyrazine alone. Conclusions/Significance The current results suggest that wolf urinary volatiles can engender aversive and fear-related responses in mice. Pyrazine analogues were identified as the predominant active components among these volatiles to induce avoidance and freezing behaviours via stimulation of the murine AOB.
Analysis of Favorable Factors for Continued Adoption of Perennial Fodder Crops by Livestock Farmers

ABSTRACT A study to analyse the favorable factors for continued adoption of perennial fodder crops by livestock farmers was conducted. Ninety-five perennial fodder growing farmers of two districts of Karnataka, viz., Belagavi and Dharwad, identified through snowball technique were interviewed using standardized interview schedule. Out of 19 variables used for the study, 15 variables exhibited positive and significant relationship with continuance of perennial fodder crops by adopters. Four predictors have been retained at the last step of screening through regression analysis. In path analysis, 11 variables indicated positive direct effect and 8 variables shown negative direct effect on continuance of perennial fodder crops cultivation. Innovative farmers with high annual income and big land holdings should be targeted to involve in participatory approach for the production of fodder planting materials.
Radio-quiet QSO environments — I. The correlation of QSOs and bJ < 23 galaxies

ABSTRA C T In this paper we present results of an analysis of radio-quiet QSO environments. The aim is to determine the relation between QSOs, galaxies and the mass distribution as a function of redshift. We cross-correlate a sample of ,150 QSOs from optically and X-ray-selected catalogues with faint, bJ < 23, galaxies. These data allow us to probe the galaxy clustering environment of QSOs out to z , 1:0‐1:5. Far from giving a positive correlation, at z < 1:5 the QSO‐galaxy cross-correlation function is marginally negative, with q﷿v < 120 arcsec fioπ 0 :027 6 0:020. Colour information suggests that the anticorrelation is most significant between the QSOs and the red galaxy population. We construct models to predict the QSO‐galaxy cross-correlation, using the known form of the galaxy N﷿zfi at bJ < 23, and assuming a variety of clustering evolution rates. Cases in which QSOs exist in rich cluster environments are comfortably ruled out at more than 5j, and the results are more consistent with a ‘normal’ galaxy environment for radio-quiet QSOs. If the small anticorrelation is interpreted as an effect of gravitational lensing, this conclusion is not altered. In this case, the data are only ,1j below the low clustering amplitude models, while the high clustering amplitude models are still comfortably rejected. We therefore conclude that these QSOs may not be much more highly biased than optically selected galaxies.