Miracle-dz/UniFAR-FTUs huggingface dataset:
MIPS: analysis and annotation of proteins from whole genomes in 2005

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server ().
Contraction of Experimental Skin Flaps

Contraction of experimental skin flaps in loose-skinned animals is a well-known but underestimated phenomenon that in fact may vary in different circumstances and complicate the calculations of survived and necrosed areas. A standard abdominal island skin flap design in the rat was used in this study to investigate the difference between the contraction rates of necrotic and survived tissues, and to determine its significance in the experimental models. The abdominal island skin flap was based on the inferior epigastric neurovascular bundles, and it extended from the pubis to the xiphoid and between the both midaxillary lines. The study was conducted in two steps. In the first step, contraction rates of completely necrosed (both pedicles severed) and completely survived (vascular pedicles were intact on both sides either with or without a nerve supply) flaps were assessed in 45 animals. After 1 week, area loss was highly significant in both necrosed and survived flaps (p < 0.001). The rate of contraction was significantly higher in necrosed tissues than in survived tissues (p < 0.001), and it was also significantly higher in the neurovascular flaps than in the denervated flaps (p < 0.05). The contraction of all flaps occurred in the vertical dimension, whereas the horizontal dimension stayed almost the same. In the second step of the study, a unilateral, pedicled abdominal flap was used, which had a constant necrotic zone on the nonpedicled half, either with or without a nerve supply in 30 animals. After 1 week the pedicled halves of all flaps were significantly larger than the nonpedicted halves (p < 0.001). Although the total area loss was higher in the neurovascular flaps than the denervated flaps, the difference was not significant statistically (p > 0.05). There was no statistically significant difference between the areas of necrosis seen in both groups when it was expressed as a proportion of the total flap area (p > 0.05). However, this insignificant difference became significant when the amount of necrosis was expressed as a proportion of only the nonpedicted flap half, favoring the denervated flaps (p < 0.005). It appears in this study that ultimate proportions of surviving and necrosed tissues may be inconsistent owing to the variable contraction rates of these tissues, and misleading conclusions may appear during the assessment of given treatment modalities.
Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia

Summary Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.
Combining Confocal Laser Scanning Microscopy with Serial Section Reconstruction in the Study of Adult Neurogenesis

Current advances in imaging techniques have extended the possibility of visualizing small structures within large volumes of both fixed and live specimens without sectioning. These techniques have contributed valuable information to study neuronal plasticity in the adult brain. However, technical limits still hamper the use of these approaches to investigate neurogenic regions located far from the ventricular surface such as parenchymal neurogenic niches, or the scattered neuroblasts induced by brain lesions. Here, we present a method to combine confocal laser scanning microscopy (CLSM) and serial section reconstruction in order to reconstruct large volumes of brain tissue at cellular resolution. In this method a series of thick sections are imaged with CLSM and the resulting stacks of images are registered and 3D reconstructed. This approach is based on existing freeware software and can be performed on ordinary laboratory personal computers. By using this technique we have investigated the morphology and spatial organization of a group of doublecortin (DCX)+ neuroblasts located in the lateral striatum of the late post-natal guinea pig. The 3D study unraveled a complex network of long and poorly ramified cell processes, often fascicled and mostly oriented along the internal capsule fiber bundles. These data support CLSM serial section reconstruction as a reliable alternative to the whole mount approaches to analyze cyto-architectural features of adult germinative niches.
Dielectric studies on cellulose fibers

A method for obtaining the intrinsic dielectric constant and loss factor of dry cellulose fiber along the fiber axis was developed, and the dielectric properties of viscose rayon, Bemberg (cuprammonium rayon), and cotton sliver were measured over the frequency range from 500 cycles/sec. to 3 Mcycles/sec. and the temperature range from −60 to + 20°C. by using the mutual inductance bridge. Only one dispersion could be observed in this temperature and frequency range. Cole-Cole's circular are law could be satisfactorily applied to the data obtained, and the parameters of the are (ϵ0 – ϵ∞) and β for the three samples could be determined at each temperature. The value of (ϵ0 – ϵ∞), which is proportional to concentration of the dipoles contributing to the orientation, increased with rising temperature and reached a limiting value at about −20°C. The value of β relating to the width of the distribution of relaxation times also increased with rising temperature, showing a little rise in the degree of increase at temperatures above −20°C. On the other hand, the apparent activation energy for dipole orientation, as calculated from the temperature dependence of the dispersion frequency, reached a maximum around −20°C. All these facts suggest that some transition will take place in the neighborhood of −20°C. This temperature is not considered to be likely to be the glass transition temperature for dry cellulose, since −20°C. is too low for a primary transition in stiff molecules such as cellulose, and since the observed value of the apparent activation energy is too small to activate the segmental movement of the main chains. It might be possible to expect some secondary transition, probably of a thermodynamical nature, relating to the movement of local parts such as side chains, especially methylol groups on glucose residue, at about −20°C. , though there is no other support for this expectation. Moreover, the effect of the fine structures on the dielectric properties is that the magnitude of (ϵ0 – ϵ∞) at each temperature decreases in the order, viscose rayon > Bemberg > cotton sliver, and this order parallels that of the accessibility of the three samples. This fact suggests that the dipoles in the amorphous region and on the surface of the crystallite provide the chief contribution to this dispersion.
Differentiating Sensitivity of Post-Stimulus Undershoot under Diffusion Weighting: Implication of Vascular and Neuronal Hierarchy

The widely used blood oxygenation level dependent (BOLD) signal during brain activation, as measured in typical fMRI methods, is composed of several distinct phases, the last of which, and perhaps the least understood, is the post-stimulus undershoot. Although this undershoot has been consistently observed, its hemodynamic and metabolic sources are still under debate, as evidences for sustained blood volume increases and metabolic activities have been presented. In order to help differentiate the origins of the undershoot from vascular and neuronal perspectives, we applied progressing diffusion weighting gradients to investigate the BOLD signals during visual stimulation. Three distinct regions were established and found to have fundamentally different properties in post-stimulus signal undershoot. The first region, with a small but focal spatial extent, shows a clear undershoot with decreasing magnitude under increasing diffusion weighting, which is inferred to represent intravascular signal from larger vessels with large apparent diffusion coefficients (ADC), or high mobility. The second region, with a large continuous spatial extent in which some surrounds the first region while some spreads beyond, also shows a clear undershoot but no change in undershoot amplitude with progressing diffusion weighting. This would indicate a source based on extravascular and small vessel signal with smaller ADC, or lower mobility. The third region shows no significant undershoot, and is largely confined to higher order visual areas. Given their intermediate ADC, it would likely include both large and small vessels. Thus the consistent observation of this third region would argue against a vascular origin but support a metabolic basis for the post-stimulus undershoot, and would appear to indicate a lack of sustained metabolic rate likely due to a lower oxygen metabolism in these higher visual areas. Our results are the first, to our knowledge, to suggest that the post-stimulus undershoots have a spatial dependence on the vascular and neuronal hierarchy, and that progressing flow-sensitized diffusion weighting can help delineate these dependences.
Exploring the concept of respite.

AIM To report an analysis of the concept of respite for older people. BACKGROUND Respite is an important support strategy for family carers of older people. However, there is considerable confusion in the literature about the nature, scope, and outcomes of respite services. DATA SOURCES The data source for the concept analysis was a review of literature addressing respite for older people. There were no publication date restrictions for the review and literature was searched up to 2010. DESIGN Concept analysis that was informed by the work of Dubin and the operationalization of Dubin's work by Holton and Lowe. REVIEW METHOD A review of the literature was undertaken to better understand the nature of respite for older people. The review investigated the views of respite from the perspective of the service provider, family carer, and care-recipient. A conceptual model of respite was developed using a four-step approach: gaining an understanding of the phenomenon; identifying and retrieving relevant studies; analysing the construct; and developing the conceptual model. RESULTS The conceptual model that emerged from this process consisted of three attributes, Partnership, Service, and Respite. The attribute of Partnership concerned the relationship between the service provider, carer and care-recipient. The attribute of Service concerned what the provider offered and focused on two important areas, assistance and engagement. The attribute of Respite concerned the outcomes that the family carer and care-recipient gained from respite and focused on freedom, support, and connection. CONCLUSION The conceptual model provides a framework to assist in the development of respite services.
Effects of Short-Term Exenatide Treatment on Regional Fat Distribution, Glycated Hemoglobin Levels, and Aortic Pulse Wave Velocity of Obese Type 2 Diabetes Mellitus Patients

Background Most type 2 diabetes mellitus patients are obese and have obesity related vascular complications. Exenatide treatment is well known for both decreasing glycated hemoglobin levels and reduction in body weight. So, this study aimed to determine the effects of exenatide on body composition, glycated hemoglobin levels, and vascular stiffness in obese type 2 diabetes mellitus patients. Methods For 1 month, 32 obese type 2 diabetes mellitus patients were administered 5 µg of exenatide twice daily. The dosage was then increased to 10 µg. Patients' height, body weight, glycated hemoglobin levels, lipid profile, pulse wave velocity (PWV), body mass index, fat mass, and muscle mass were measured by using Inbody at baseline and after 3 months of treatment. Results After 3 months of treatment, glycated hemoglobin levels decreased significantly (P=0.007). Triglyceride, total cholesterol, and low density lipoprotein levels decreased, while aspartate aminotransferase and alanine aminotransferase levels were no change. Body weight, and fat mass decreased significantly (P=0.002 and P=0.001, respectively), while interestingly, muscle mass did not decrease (P=0.289). In addition to, Waist-to-hip ratio and aortic PWV decreased significantly (P=0.006 and P=0.001, respectively). Conclusion Effects of short term exenatide use in obese type 2 diabetes mellitus with cardiometabolic high risk patients not only reduced body weight without muscle mass loss, body fat mass, and glycated hemoglobin levels but also improved aortic PWV in accordance with waist to hip ratio.
Parent-Directed Approaches to Enrich the Early Language Environments of Children Living in Poverty

Abstract Children's early language environments are critical for their cognitive development, school readiness, and ultimate educational attainment. Significant disparities exist in these environments, with profound and lasting impacts upon children's ultimate outcomes. Children from backgrounds of low socioeconomic status experience diminished language inputs and enter school at a disadvantage, with disparities persisting throughout their educational careers. Parents are positioned as powerful agents of change in their children's lives, however, and evidence indicates that parent-directed intervention is effective in improving child outcomes. This article explores the efficacy of parent-directed interventions and their potential applicability to the wider educational achievement gap seen in typically developing populations of low socioeconomic status and then describes efforts to develop such interventions with the Thirty Million Words Project and Project ASPIRE (Achieving Superior Parental Involvement for Rehabilitative Excellence) curricula.
Immature Cryopreserved Ovary Restores Puberty and Fertility in Mice without Alteration of Epigenetic Marks

Background Progress in oncology could improve survival rate in children, but would probably lead to impaired fertility and puberty. In pre-pubertal girls, the only therapeutic option is the cryopreservation of one ovary. Three births have been reported after reimplantation of cryopreserved mature ovary. Conversely, reimplantation of ovary preserved before puberty (defined as immature ovary) has never been performed in humans. Methodology/Principal Findings In order to analyze ovarian function, we performed transplantation using fresh or cryopreserved immature grafts in pre-pubertal or adult mice. Puberty as well as cyclic hormonal activity was restored. All follicle populations were present although a significant reduction in follicle density was observed with or without cryopreservation. Although fertility was restored, the graft is of limited life span. Because ex vivo ovary manipulation and cryopreservation procedure, the status of genomic imprinting was investigated. Methylation status of the H19 and Lit1 Imprinting Control Regions in kidney, muscle and tongue of offsprings from grafted mice does not show significant alteration when compared to those of unoperated mice. Conclusions/Significance These results demonstrate that immature ovarian grafting can restore spontaneous puberty and fertility. However, these data suggest that follicle depletion leads to premature ovarian failure. This study addresses the very important epigenetics issue, and provides valuable information to the study of ovarian transplantation suggesting that these procedures do not perturb normal epigenetics marks. These results are highly relevant to the reimplantation question of immature cortex in women.
Sampling Online Social Networks

As online social networking emerges, there has been increased interest to utilize the underlying network structure as well as the available information on social peers to improve the information needs of a user. In this paper, we focus on improving the performance of information collection from the neighborhood of a user in a dynamic social network. We introduce sampling-based algorithms to efficiently explore a user's social network respecting its structure and to quickly approximate quantities of interest. We introduce and analyze variants of the basic sampling scheme exploring correlations across our samples. Models of centralized and distributed social networks are considered. We show that our algorithms can be utilized to rank items in the neighborhood of a user, assuming that information for each user in the network is available. Using real and synthetic data sets, we validate the results of our analysis and demonstrate the efficiency of our algorithms in approximating quantities of interest. The methods we describe are general and can probably be easily adopted in a variety of strategies aiming to efficiently collect information from a social graph.
The slope of the credit yield curve for speculative-grade issuers

Many theoretical bond pricing models predict that the credit yield curve facing risky bond issuers is downward-sloping. Previous empirical research (Sarig and Warga (1989), Fons (1994)) supports these models. Our study examines sets of bonds issued by the same firm with equal priority in the liability structure, but with different maturities, thus holding credit quality constant. We find, counter to prior research, that risky bonds typically have upward-sloping credit yield curves. Moreover, when we combine our matched sets of bonds (no longer controlling credit quality), the estimated slope is negative, indicating a sample selection bias problem associated with maturity. Copyright The American Finance Association 1999.
Characterization of the vanDGlycopeptide Resistance Gene Cluster from Enterococcus faecium BM4339

ABSTRACT VanD-type resistance to glycopeptides in Enterococcus faecium BM4339 is due to constitutive synthesis ofd-alanyl-d-lactate-terminating peptidoglycan precursors (B. Périchon, P. Reynolds, and P. Courvalin, Antimicrob. Agents Chemother. 41:2016–2018, 1997). The sequence of a 5,780-bp fragment was determined and revealed six open reading frames. The 3′ distal part encoded the VanHD dehydrogenase, the VanD ligase, and the VanXDdd-dipeptidase, which were highly similar to the corresponding proteins in VanA and VanB types of resistance. The deduced VanYD protein was homologous to penicillin-binding proteins that displaydd-carboxypeptidase activity. The 5′ end coded for the putative VanRD-VanSD two-component regulatory system. Due to a frameshift mutation in the chromosomal ddlgene, BM4339 produced an impairedd-alanine:d-alanine ligase. However, since expression of the resistance genes is constitutive, growth of E. faecium BM4339 was not dependent on the presence of glycopeptides in the culture medium.
Preoperative chemotherapy in advanced resectable OCSCC: long-term results of a randomized phase III trial.

BACKGROUND Data on preoperative chemotherapy in resectable oral cavity cancer are conflicting. We present the long-term results of a randomized trial of induction chemotherapy in resectable oral cavity cancer. PATIENTS AND METHODS A randomized, parallel, multicentre trial evaluated the impact of three cycles of cisplatin 100 mg/m2 and fluorouracil 1000 mg/m2 (120-h infusion administered every 21 days) in stage T2-T4, N0-N2, previously untreated patients with advanced disease. Control group received upfront surgery. Postoperative radiation was offered to both arms when pathologic risk features were identified. The co-primary end points were the occurrence of locoregional or distant tumour relapse, and death. RESULTS Among the 198 enrolled patients, with a median follow-up of 11.5 years, there was no difference in the incidence of locoregional relapse between chemotherapy and control group (P=0.6337), nor in distant metastasis development (P=0.1527). There was also no difference between groups in overall survival (P=0.3402). Patients with a pathological complete response (pCR) had higher probability of survival than those without (10-year OS: 76.2% versus 41.3%, P=0.0004). Late toxicities in patients with a minimum follow-up of 60 months (42 in each group) were similar between arms, except from fibrosis (cumulative incidence 40% versus 22% in chemotherapy arm) and grade 2 dysphagia (14% versus 5%). CONCLUSIONS Long-term follow-up of this randomized trial confirmed the absence of survival benefit with preoperative chemotherapy in oral cavity cancer. Late toxicity was similar in the two arms except for fibrosis and dysphagia, which were less in the chemotherapy arm. The survival benefit for patients achieving a pCR was maintained.