Miracle-dz/UniFAR-FTUs huggingface dataset:
The structure of “unstructured” regions in peptides and proteins: Role of the polyproline II helix in protein folding and recognition *

Classical descriptions of the three‐dimensional shapes of proteins usually invoke three main structures: α‐helix, β‐sheet, and β‐turn. More recently, the polyproline II (PPII) structure has been implicated in diverse biological activities including signal transduction, transcription, cell motility, and immune response. Concurrently, evidence is accumulating that PPII structure has a significant role in the unfolded states of proteins. In this article, we connect the structural properties of PPII helices to their roles in protein recognition and protein unfolded states. The properties unique to the PPII conformation are linked to the exploitation of this structure for the molecular recognition of proteins, using peptide ligands of the Src homology 3 (SH3) domain as an example. The evidence supporting a role for PPII conformation in protein‐unfolded states is also presented in the context of the forces that may stabilize the PPII conformation in unfolded polypeptides. © Wiley Periodicals Inc. Biopolymers (Pept Sci), 2005
Achieving automated intrusion response: a prototype implementation

Purpose – The increasing speed and volume of attacks against networked systems highlights the need to automate the intrusion response process. This paper proposes a means by which such automation may be achieved, and presents details of a practical implementation.Design/methodology/approach – The paper outlines the architecture of a flexible and intelligent automated response system that is able to adapt response decisions according to the context in which a detected incident has occurred. The discussion presents details of a prototype implementation that has been used to evaluate the concept in practice, and demonstrates the feasibility of assessing contextual factors associated with detected incidents.Findings – A series of worked examples are presented to show how the same incident occurring in different contexts will trigger different decisions from the response system.Originality/value – The paper contributes towards the domain of intrusion response, and proposes an approach that would enable automat.
Stability and Change in Personality Disorder Symptoms in 1-Year Follow-up of Depressed Adolescent Outpatients

Abstract We investigated stability and change in personality disorder (PD) symptoms and whether depression severity, comorbid clinical psychiatric disorders, and social support predict changes in personality pathology among adolescent outpatients. The 1-year outcome of PD symptoms among consecutive adolescent psychiatric outpatients with depressive disorders (N = 189) was investigated with symptom count of depression, comorbid psychiatric disorders, and perceived social support as predictors. An overall decrease in PD symptoms in most PD categories was observed. Decreases in depression severity and in number of comorbid diagnoses correlated positively with decreases in PD symptoms of most PD categories. Social support from close friends predicted a decrease in schizotypal and narcissistic, whereas support from family predicted a decrease in paranoid symptoms. Our results suggest that among depressed adolescent outpatients, PD symptoms are relatively unstable, changes co-occuring with changes/improvement in overall psychopathology. Social support seems a possibly effective point for intervention efforts regarding positive outcome of PD symptoms.
Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007–2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
Polarization preservation of partially coherent Hermite-Gaussian beams for multiple-degrees-of-freedom free-space communication

Multiple-degrees-of-freedom free-space communication combining polarization and high-order spatial modes promises high-capacity communication channel. While high-order spatial modes have been widely exploited for dense coding and high-dimensional quantum information processing, the properties of polarization preservation of high-order spatial beams propagating in turbulent atmosphere have not been comprehensively investigated yet. Here we focus on the properties of polarization preservation of partially coherent Hermite-Gaussian beams propagating along different atmospheric turbulence paths. The analytical expressions for the polarization of partially coherent Hermite-Gaussian beams propagating through atmospheric turbulence along different paths have been derived. It is shown that the larger the coherence length is, and the larger the beam order m, n are, the less the polarization is changed. We find that the evolution properties of the polarization in slant-down paths through turbulent atmosphere are similar to the case in free space if the condition zenith angle {\xi}<{\pi}/4 is satisfied. While at a long propagation distance, evolution properties of polarization in horizontal paths of turbulent atmosphere differs much from that in free space and in slant paths. The results may allow one to choose the optimal propagation path in terms of specific applications, which is helpful for future experimental implementation of multiple-degrees-of-freedom free-space communication.
Osteolysis and particle disease in hip replacement. A review.

Much can be learned from a careful reassessment of the history of total hip replacement over the past 35 years. Such a review is revealing about certain aspects of the nature of medical science, and most importantly, about solving our current problems in total hip replacement, notably cementless surgery with the rapidly increasing incidence of major pelvic and femoral lysis, predominantly manifest after 5 years or so postoperatively.
On the characterization of models of H

We give a characterization, with respect to a large class of models of untyped λ-calculus, of those models that are fully abstract for head-normalization, i.e., whose equational theory is H*. An extensional K-model D is fully abstract if and only if it is hyperimmune, i.e., non-well founded chains of elements of D cannot be captured by any recursive function.
PTEN 2, a Golgi-associated Testis-specific Homologue of the PTEN Tumor Suppressor Lipid Phosphatase*

The tumor suppressor PTEN is a phosphatidylinositol phospholipid phosphatase, which indirectly down-regulates the activity of the protein kinase B/Akt survival kinases. Examination of sequence data bases revealed the existence of a highly conserved homologue of PTEN. This homologue, termed PTEN 2, contained an extended amino-terminal domain having four potential transmembrane motifs, a lipid phosphatase domain, and a potential lipid-binding C2 domain. Transcript analysis demonstrated that PTEN 2 is expressed only in testis and specifically in secondary spermatocytes. In contrast to PTEN, PTEN 2 was localized to the Golgi apparatus via the amino-terminal membrane-spanning regions. Molecular modeling suggested that PTEN 2 is a phospholipid phosphatase with potential specificity for the phosphate at the 3 position of inositol phosphates. Enzymatic analysis of PTEN 2 revealed substrate specificity that is similar to PTEN, with a preference for the dephosphorylation of the phosphatidylinositol 3,5-phosphate phospholipid, a known mediator of vesicular trafficking. Together, these data suggest that PTEN 2 is a Golgi-localized, testis-specific phospholipid phosphatase, which may contribute to the terminal stages of spermatocyte differentiation.
Chronic Kidney Disease Stages Are Appropriate at All Ages

Chronic kidney disease (CKD) is associated with multiple detrimental consequences to the cardiovascular and musculoskeletal systems. The effects of CKD are even more significant when they begin in childhood as they affect growth and (neuro-) development as well. The division into stages of CKD serves as a guideline for the physician to better anticipate and treat early and later manifestations of CKD. For that matter, in adults, the National Kidney Foundation’s Kidney Disease Outcomes Quality Initiative has published clinical practice guidelines, which are based on estimated glomerular filtration rate (eGFR). There are no such explicit guidelines published for the pediatric CKD population, mostly (and thankfully) due to its small number. However, given the excellent guidelines published in the adult literature and ongoing clinical work done by dedicated pediatric nephrologists, similar guidelines for children could be extrapolated and determined. As a matter of fact, the pediatric nephrology community is anxiously anticipating the results of the ongoing Chronic Kidney Disease in Children study, which is the first multicenter, prospective, observational pediatric study of such kind. This article summarizes the adequacy of CKD stages at all ages based not only on opinions of experienced clinicians, but also on evidence provided by cross-sectional data analyses of the Chronic Kidney Disease in Children study.
Visual Standards in a Sample of Dentists Working within Scotland

Introduction This study aims to measure the visual acuity of practising dentists and to establish the average time elapsed since their last routine eye examination. Materials and methods Distance visual acuity, near visual acuity, convergence, accommodation, contrast sensitivity, heterophorias and stereoscopic vision were measured in a diverse group of 46 dentists practising in Scotland. Results The results indicated that distance visual acuity was at least 6/6 for all but one of the subjects. All had acceptable near visual acuity. Accommodation followed the expected age-related trend of decreasing with age. No subjects had a definitely abnormal contrast sensitivity score although four were in the borderline zone. No subjects had a horizontal squint but two had a significant vertical phoria. Three subjects had no stereoscopic vision and one subject had a very high threshold level. All other subjects were able to see stereoscopically. Of the subjects 57% had been for an eye examination within the previous two years, with the range being from less than one month to 17 years. Conclusion The eyesight of this group of clinicians exceeds generally accepted normal population values. Although the majority of the clinicians had attended for an eye examination within two years, the large range of time since last attendance is of concern and regular eye examinations are to be encouraged.
Mechanisms of filtration failure during postischemic injury of the human kidney. A study of the reperfused renal allograft.

Postischemic filtration failure in experimental animals results primarily from depression of the transcapillary hydraulic pressure difference (delta P), a quantity that cannot be determined in humans. To circumvent this limitation we determined the GFR and each of its remaining determinants in transplanted kidneys. Findings in 12 allografts that exhibited subsequent normofiltration (group 1) were compared with those in 11 allografts that exhibited persistent hypofiltration (group 2). Determinations were made intraoperatively in the exposed graft after 1-3 h of reperfusion. GFR (6 +/- 2 vs 29 +/- 5 ml/min) and renal plasma flow by Doppler flow meter (140 +/- 30 vs 315 +/- 49 ml/min) were significantly lower in group 2 than group 1. Morphometric analysis of glomeruli obtained by biopsy and a structural hydrodynamic model of viscous flow revealed the glomerular ultrafiltration coefficient to be similar, averaging 3.5 +/- 0.6 and 3.1 +/- 0.2 ml/(min.mmHg) in group 2 vs 1, respectively. Corresponding values for plasma oncotic pressure were also similar, averaging 19 +/- 1 vs 21 +/- 1 mmHg. We next used a mathematical model of glomerular ultrafiltration and a sensitivity analysis to calculate the prevailing range for delta P from the foregoing measured quantities. This revealed delta P to vary from only 20-21 mmHg in group 2 vs 34-45 mmHg in group 1 (P < 0.001). Further morphometric analysis revealed the diameters of Bowman's space and tubular lumens, as well as the percentage of tubular cells that were necrotic or devoid of brush border, to be similar in the two groups. We thus conclude (a) that delta P depression is the predominant cause of hypofiltration in this form of postischemic injury; and (b) that afferent vasoconstriction rather than tubular obstruction is the proximate cause of the delta P depression.
Comparative Analysis of Diversity and Similarity Indices with Special Relevance to Vegetations around Sewage Drains

Indices summarizing community structure are used to evaluate fundamental community ecology, species interaction, biogeographical factors, and environmental stress. Some of these indices are insensitive to gross community changes induced by contaminants of pollution. Diversity indices and similarity indices are reviewed considering their ecological application, both theoretical and practical. For some useful indices, empirical equations are given to calculate the expected maximum value of the indices to which the observed values can be related at any combination of sample sizes at the experimental sites. This paper examines the effects of sample size and diversity on the expected values of diversity indices and similarity indices, using various formulae. It has been shown that all indices are strongly affected by sample size and diversity. In some indices, this influence is greater than the others and an attempt has been made to deal with these influences. Keywords—Biogeographical factors, Diversity Indices, Ecology and Similarity Indices
GLUT2 and TAS1R2 Polymorphisms and Susceptibility to Dental Caries

Objective: Dental caries is one of the most frequent multifactorial diseases. Among the numerous factors influencing the risk of caries, genetics plays a substantial role, with heritability ranging from 40 to 60%. Gene variants affecting taste preference and glucose transport were recently associated with caries risk. The aim of this study was to analyze two common polymorphisms in the sweet taste receptor (TAS1R2) and glucose transporter (GLUT2) genes in children with dental caries and healthy controls in the Czech population. Methods: A total of 637 unrelated Caucasian children, aged 11-13 years, were included in this case-control study. One hundred and fifty-five subjects were caries-free (with decayed/missing/filled teeth, DMFT = 0) and 482 children were caries-affected (DMFT ≥ 1). The TAS1R2 (Ile191Val, rs35874116) and GLUT2 (Thr110Ile, rs5400) genotypes were determined using the 5′ nuclease TaqMan® assay for allelic discrimination. Results: Compared with subjects with the common Thr allele, carriers of the Ile allele of GLUT2 had significantly more frequently dental caries (p < 0.05, OR = 1.639, 95% CI: 1.089-2.466). Similarly, children with the Val allele for the TAS1R2 Ile191Val polymorphism were more frequently affected by caries than children who carried the Ile allele (p < 0.05, OR = 1.413, 95% CI: 1.014-1.969). In contrast, no significant associations between GLUT2 and/or TAS1R2 polymorphisms and fillings were found, but allele frequencies of the TAS1R2 variant were marginally significantly different between children with DMFT = 0 and DMFT ≥1 (p = 0.053, OR = 1.339, 95% CI: 0.996-1.799). However, no significant interaction between both genes and risk of dental caries was found. Conclusions: In conclusion, GLUT2 and TASR1 polymorphisms may influence the risk of caries in the Czech population.
Prevalence of vitamin D deficiency in apparently healthy children in north India

Abstract Background: The data on the prevalence of vitamin D deficiency (VDD) in apparently healthy children from India is limited. Objective: To assess the prevalence of VDD in apparently healthy children. Design: Prospective study. Setting and subjects: Apparently healthy children from the age groups of 3 months–12 years, from the upper socioeconomical status (USES), attending the outpatient department (OPD) of a private pediatric hospital in Chandigarh, India, for minor ailments were enrolled over a period of 6 months (March–August 2013). Methods: Plasma levels of 25-hydroxyvitamin D [25(OH)D] were measured by competitive electrochemiluminescence immunoassay. Results: In total, 338 children (188 boys, 150 girls) with mean age of 3.31 years were enrolled. The percentages of children with deficient, insufficient, and sufficient levels of 25(OH)D were 40.24%, 25.44%, and 34.32%, respectively. Clinical signs of VDD were seen in only 8.53% of the children. The mean (±SD) levels of 25(OH)D were 27.48 (15.99) ng/mL. On univariate analysis, deficient levels of 25(OH)D were associated with relatively younger age group, female sex, failure to thrive, exclusive breastfeeding, inadequate sun exposure, and no vitamin D supplements. Conclusion: A high prevalence of clinical and biochemical VDD was noted in apparently healthy children belonging to the USES.
Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae

The product of the Saccharomyces cerevisiae SIR4 gene, in conjunction with at least three other gene products, prevents expression of mating-type genes resident at loci at either end of chromosome III, but not of the same genes resident at the MAT locus in the middle of the chromosome. To address the mechanism of this novel position effect regulation, we have conducted a structural and genetic analysis of the SIR4 gene. We have determined the nucleotide sequence of the gene and found that it encodes a lysine-rich, serine-rich protein of 152 kilodaltons. Expression of the carboxy half of the protein complements a chromosomal nonsense mutation of sir4 but not a complete deletion of the gene. These results suggest that SIR4 protein activity resides in two portions of the molecule, but that these domains need not be covalently linked to execute their biological function. We also found that high-level expression of the carboxy domain of the protein yields dominant derepression of the silent loci. This anti-Sir activity can be reversed by increased expression of the SIR3 gene, whose product is normally also required for maintaining repression of the silent loci. These results are consistent with the hypothesis that SIR3 and SIR4 proteins physically associate to form a multicomponent complex required for repression of the silent mating-type loci.
Verbal Morphology : Return of the Affix Hopping Approach

These data demonstrate the following properties: (a) it appears that main verbs (e.g., leave) must stay in situ whereas have/be must raise to a higher position (which I assume to be a T head); and (b) a dummy auxiliary do is needed when the verb and T head are intervened by negation. There have been three major analyses of this paradigm. The affix hopping approach (Chomsky 1957) essentially proposed that the verbs are stored in bare form in the lexicon but obtain an affix via the affix hopping transformation in syntax. Chomsky (1993), however, rejected his earlier position and argued for the lexicalist approach: the verbs in the lexicon are already stored in the inflected forms, and whether they raise overtly in syntax is determined by their feature settings: main verbs have weak features and do not raise overtly, while auxiliary verbs overtly raise due to their strong features. Finally, building on the asymmetry between main verbs and auxiliary verbs in the VP ellipsis paradigm (2) reported by Warner (1986), Lasnik (1995b) argued for the hybrid approach, i.e., main verbs are bare in the lexicon (as in the affix hopping approach) but auxiliary verbs like have/be are inflected in the lexicon (as in the lexicalist approach; Section 2 presents details of Lasnik’s account).
Prevention of acquired defects in platelet function during blood processing

Two kinds of platelet concentrates were prepared in this study: one as pelleted platelets from platelet‐rich plasma (PCs), and the other as a platelet suspension from the buffy coat fraction (nonpelleted PCs). The characteristics of both platelet concentrates were studied. White cell contamination in the nonpelleted PCs was below the threshold of detection by a microcell counter (less than 300 cells/μl of concentrate); in the pelleted PCs, it was 3 ± 1 × 107 cells per concentrate. The difference between the white cell contamination in pelleted PCs and nonpelleted PCs was significant (p < 0.001). The degree of aggregation induced in pelleted PCs by ADP (9 μM) and collagen decreased to 33 and 55 percent, respectively, of that in platelet‐rich plasma. The secondary wave of platelet aggregation induced by ADP and epinephrine was absent in pelleted PCs, and ATP secretion from these platelets by ADP stimulation also decreased remarkably. However, the°of aggregation and ATP secretion in nonpelleted PCs were similar to those in platelet‐rich plasma. Furthermore, it was found that the amount of platelet factor 4 release seen in pelleted PCs was large in comparison to that in nonpelleted PCs and platelet‐rich plasma. These results suggested that the deterioration of platelet function might have resulted from the platelet activation induced by pellet formation during the preparation of PCs from platelet‐rich plasma.