Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterozygosity and biomass production in Salix eriocephala

The relationships between heterozygosity at 11 variable isoenzyme loci and total above-ground leafless biomass production were examined in four full-sib families of Salix eriocephala, a willow species important in short-rotation intensive-culture feedstock plantations. Relationships were investigated by comparing the performance of heterozygotes with that of corresponding homozygotes in locus-by-locus comparisons, by investigating multiple regression models with individual loci as independent variables, and by employing the adaptive distance model. In all of these analytical approaches, evidence indicated the presence of positive associations between heterozygosity at enzyme loci and biomass production. The theoretical implications of these results are discussed in the specific context of this study.
A WorkFlow Management System for Bioinformatics Grid

In this paper we describe a Workflow Management System, named ProGenGrid (Proteomics and Genomics Grid, developed at the University of Lecce) which aims at providing a tool where e-scientists can simulate biological experiments through the composition of existing analysis and visualization tools, wrapped as Web Services. Since bioinformatics applications are computeand data-intensive, needing clusters or many workstations to reduce the execution time, we exploit a Grid infrastructure for interconnecting wide-spread tools and hardware resources. As an example, we are considering some algorithms and tools needed for alignment of sequences, providing them as services, through easy to use Web interfaces and Web services built using the open source gSOAP Toolkit. As Grid middleware, we are using the Globus Toolkit 4.1, exploiting some protocols such as GSI and GridFTP.
Genetics and Molecular Biology

Lung adenocarcinoma (LUAD) is the main subtype of non-small cell lung cancer with a poor survival prognosis. In our study, gene expression, DNA methylation, and clinicopathological data of primary LUAD were utilized to identify potential prognostic markers for LUAD, which were recruited from The Cancer Genome Atlas (TCGA) database. Univariate regression analysis showed that there were 21 methylation-associated DEGs related to overall survival (OS), including 9 downand 12 up-regulated genes. The 12 up-regulated genes with hypomethylation may be risky genes, whereas the other 9 down-regulated genes with hypermethylation might be protective genes. By using the Step-wise multivariate Cox analysis, a methylation-associated 6-gene (consisting of CCL20, F2, GNPNAT1, NT5E, B3GALT2, and VSIG2) prognostic signature was constructed and the risk score based on this gene signature classified patients into highor low-risk groups. Patients of the high-risk group had shorter OS than those of the low-risk group in both the training and validation cohort. Multivariate Cox analysis and the stratified analysis revealed that the risk score was an independent prognostic factor for LUAD patients. The methylation-associated gene signature may serve as a prognostic factor for LUAD patients and the represent hypermethylated or hypomethylated genes might be potential targets for LUAD therapy.
The exploration of objective task difficulty and domain knowledge effects on users' query formulation

In this paper, we explore the effects of objective task difficulty and domain knowledge on users' query formulation behaviors. The dataset from a user experiment was used in this research, which focused on the medical domain. The objective difficulty was measured by the precision level of search topics (as queries) in the search system, and searchers' domain knowledge was assessed by a self‐reported rating on the familiarity with MeSH terms that were related to the search topics in the study. We compared expert searchers' and novice searchers' query similarity and query features between easy and difficult tasks. The results showed that there was no significant difference between domain experts and novices in query similarity, but there existed an opposite pattern of task difficulty effects on query similarity for searchers with different domain knowledge levels. Domain expert searchers had more diverse vocabulary in difficult tasks than in easy tasks, whereas novice searchers had to rely heavily on task descriptions to formulate their queries. Task difficulty had also influenced searchers' performance, especially the precision measure. Novice searchers' recall was relatively low in both easy and difficult tasks. The findings in this study help us further understand users' query formulation process, and have implication for the design of query suggestion functions in search systems.
Endobronchial Ultrasound Elastography for Evaluation of Intrathoracic Lymph Nodes: A Pilot Study

Background: Endobronchial ultrasound (EBUS) elastography is a new imaging procedure for describing the elasticity of intrathoracic lesions and providing important additional diagnostic information. Objectives: The aim of this study was to utilize the feasibility of qualitative and quantitative methods to evaluate the ability of EBUS elastography to differentiate between benign and malignant mediastinal and hilar lymph nodes (LNs) during EBUS-guided transbronchial needle aspiration (EBUS-TBNA). Methods: Patients with enlarged intrathoracic LNs required for EBUS-TBNA examination at a clinical center for thoracic medicine from January 2014 to April 2014 were prospectively enrolled. EBUS sonographic characteristics on B-mode, vascular patterns and elastography, EBUS-TBNA procedures, pathological findings, and microbiological results were recorded. Furthermore, elastographic patterns (qualitative method) and the mean gray value inside the region of interest (quantitative method) were analyzed. Both methods were compared with a definitive diagnosis of the involved LNs. Results: Fifty-six patients including 68 LNs (33 benign and 35 malignant nodes) were prospectively enrolled into this study and retrospectively analyzed. Using qualitative and quantitative methods, we were able to differentiate between benign and malignant LNs with high sensitivity, specificity, positive and negative predictive values, and accuracy (85.71, 81.82, 83.33, 84.38, and 83.82% vs. 91.43, 72.73, 78.05, 88.89, and 82.35%, respectively). Conclusions: EBUS elastography is potentially capable of further differentiating between benign and malignant LNs. These proposed qualitative and quantitative methods might be useful tools for describing EBUS elastography during EBUS-TBNA.
The effects of exercise using PNF in patients with a supraspinatus muscle tear

[Purpose] The aim of this study was to examine the effects of proprioceptive neuromuscular facilitation techniques and simple exercise on subjective pain reduction and blood flow velocity in supraspinatus tear patients and to evaluate muscle recovery. [Subjects and Methods] The 20 subjects of this study were diagnosed with supraspinatus tears by MRI. The subjects have performed PNF techniques and Simple exercise for 12 weeks. [Results] After 12 weeks of proprioceptive neuromuscular facilitation techniques and simple exercise, the blood flow velocity, Visual Analogue Scale, and disabilities of the arm, shoulder, and hand score showed statistically significant difference. Also, the difference between the proprioceptive neuromuscular facilitation techniques and simple exercise was statistically significant. [Conclusion] In conclusion, 12 weeks of proprioceptive neuromuscular facilitation treatment and simple exercise therapy had no effect on pain reduction in patients with supraspinatus tear, but in terms of functionality, the proprioceptive neuromuscular facilitation treatment was effective.
Loss of linker histone H1 in cellular senescence

Cellular senescence is a tumor-suppressing mechanism that is accompanied by characteristic chromatin condensation called senescence-associated heterochromatic foci (SAHFs). We found that individual SAHFs originate from individual chromosomes. SAHFs do not show alterations of posttranslational modifications of core histones that mark condensed chromatin in mitotic chromosomes, apoptotic chromatin, or transcriptionally inactive heterochromatin. Remarkably, SAHF-positive senescent cells lose linker histone H1 and exhibit increased levels of chromatin-bound high mobility group A2 (HMGA2). The expression of N-terminally enhanced green fluorescent protein (EGFP)–tagged histone H1 induces premature senescence phenotypes, including increased levels of phosphorylated p53, p21, and hypophosphorylated Rb, and a decrease in the chromatin-bound endogenous histone H1 level but not in p16 level accumulation or SAHF formation. However, the simultaneous ectopic expression of hemagglutinin-tagged HMGA2 and N-terminally EGFP-tagged histone H1 leads to significant SAHF formation (P < 0.001). It is known that histone H1 and HMG proteins compete for a common binding site, the linker DNA. These results suggest that SAHFs are a novel type of chromatin condensation involving alterations in linker DNA–binding proteins.
Subdural haematoma in a patient with meningioma.

CaSe A 64-year old male patient, smoker, had a loss of consciousness with mild headache during a spirometric exam. He was medicated with analgesics and remained with headache for 12 hours and was discharged from hospital. He persisted with chronic headache and developed a gradual confusional state and left hemiparesia. After the initial episode, five days after the spiro metric test, he returned to the hospital for a computed tomography (CT) of the head (Figs 1 and 2). The CT showed a right subdural haematoma with a fresh clot in the anterior skull base with bone thickness of the anterior fossa besides meningioma of the falx with adjacent edema. The patient had no prior history of trauma or alcoholism. He was using (AAS) 200 mg/day. Coagulation tests were normal. A right frontal osteoplastic craniotomy was performed draining the haematoma, and during the same surgical procedure the tumor was removed using microscopy. A dark, thick, red blood clot was drained. During the surgical drainage of the subdural haematoma two findings were ob served by the surgeon: 1) the homolateral side of the subdural haematoma presented with greater vascular density. 2) the clot surface on this side showed a variable aspect, suggesting ac
PATTERNS OF GENETIC ARCHITECTURE FOR LIFE‐HISTORY TRAITS AND MOLECULAR MARKERS IN A SUBDIVIDED SPECIES

Abstract Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with QST generally exceeding GST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character‐specific comparison of QST and GST support divergent selection pressures among populations for the majority of life‐history traits in both coast and mountain regions. The level of within‐population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within‐population quantitative‐genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary‐pond species, D. pulex.
Impaired fear conditioning following unilateral temporal lobectomy in humans

Classical fear conditioning was used in the present study as a model for investigating emotional learning and memory in human subjects with lesions to the medial temporal lobe. Animal studies have revealed a critical role for medial temporal lobe structures, particularly the amygdala, in simple and complex associative emotional responding. Whether these structures perform similar functions in humans is unknown. On both simple and conditional discrimination tasks, unilateral temporal lobectomy subjects showed impaired conditioned response acquisition relative to control subjects. This impairment could not be accounted for by deficits in nonassociative sensory or autonomic performance factors, or by differences in declarative memory for the experimental parameters. These results show that temporal lobe structures in humans, as in other mammals, are important components in an emotional memory network.
Non-negative blind source separation techniques for tumor tissue typing using HR-MAS signals

Given High Resolution Magic Angle Spinning (HR-MAS) signals from several glioblastoma tumor subjects, the goal is to differentiate between tumor tissue types by separating the different sources that contribute to the profile of each spectrum. Blind source separation techniques are applied for obtaining characteristic profiles for necrosis, high cellular tumor and border tumor tissue, and providing the contribution (abundance) of each tumor tissue to the profile of the spectra. The problem is formulated as a non-negative source separation problem. We illustrate the effectiveness of the proposed methods and we analyze to which extent the dimension of the input space could influence the performance by comparing the results on the full magnitude signals and on dimensionally reduced spaces.
A Variation-Tolerant Replica-Based Reference-Generation Technique for Single-Ended Sensing in Wide Voltage-Range SRAMs

The most promising SRAM cells capable of operating over a wide range of supply voltages contain single-ended read ports. These systems require an external reference voltage that suitably scales to enable error-free operation of the memory, as the supply voltage is scaled. This paper presents a replica-based reference-generation technique for wide voltage range SRAMs. The proposed approach tracks the memory over the large range of supply voltages, and is tunable to extend functionality down to subthreshold voltages. In addition, a tunable delay-based timing-generation scheme is employed to enable memory functionality, in the presence of increased variation at subthreshold voltages. Configuration bits are set using a random-sampling-based Built-in Self-Test algorithm that significantly speeds up the tuning process. A 4-kb array, using the conventional 8T cell, implemented in the UMC 130-nm process, is demonstrated to function from 1.2 V down to 310 mV (at 1.3 MHz and 6.45 pJ/access). The memory consumes 0.115 pJ/bit/access at the energy optimum point of 400 mV.
Identification of a Novel Raf-1 Pathway Activator that Inhibits Gastrointestinal Carcinoid Cell Growth

Carcinoids are neuroendocrine tumors (NET) that secrete hormones, including serotonin, resulting in the malignant carcinoid syndrome. In addition to the significant morbidity associated with the syndrome, carcinoids are frequently metastatic at diagnosis, and untreated mortality at 5 years exceeds 70%. Surgery is the only curative option, and the need for other therapies is clear. We have previously shown that activation of Raf-1 inhibits carcinoid cell proliferation. We investigated the ability of leflunomide (LFN), a Food and Drug Administration–approved medication for the treatment of rheumatoid arthritis, and its active metabolite teriflunomide (TFN) as a potential anti-NET treatment. LFN and TFN inhibit the in vitro proliferation of gastrointestinal carcinoid cells and induce G2-M phase arrest. Daily oral gavage of nude mice with subcutaneous xenografted carcinoid tumors confirms that LFN can inhibit NET growth in vivo. Treatment with TFN suppresses the cellular levels of serotonin and chromogranin A, a glycopeptide co-secreted with bioactive hormones. Additionally, TFN reduces the level of achaete-scute complex-like 1 (ASCL1), a NET marker correlated with survival. These effects are associated with the activation of the Raf-1/mitiogen-activated protein kinase kinase/extracellular signal–regulated kinase-1/2 pathway, and blockade of mitiogen-activated protein kinase kinase signaling reversed the effects of TFN on markers of the cell cycle and ASCL1 expression. In summary, LFN and TFN inhibit carcinoid cell proliferation in vitro and in vivo and alter the expression of NET markers. This compound thus represents an attractive target for further clinical investigation. Mol Cancer Ther; 9(2); 429–37
ISLET TRANSPLANTATION : ADVANCES AND IMMUNOLOGICAL CHALLENGES

NATURE REVIEWS | IMMUNOLOGY VOLUME 4 | APRIL 2004 | 259 Diabetes mellitus comprises a series of clinically and genetically heterogeneous disorders associated by disturbances of carbohydrate, fat and protein metabolism, the most common sign of which is HYPERGLYCAEMIA. The prevalence of diabetes increases with age, from less than 1% of western populations affected before age 20 to more than 13% above age 75. Approximately 90% of adult patients with diabetes have the ‘type 2’ variant, previously referred to as non-insulin dependent, which is generally associated with hyperglycaemia and insulin resistance, eventually leading to defects in insulin secretion. The most severe form of diabetes is the ‘type 1’ variant, which results from autoimmune destruction of the insulin-secreting cells (β-cells) contained in the pancreatic islets. In type 1 diabetes, daily treatment with exogenous insulin is required to support life. The metabolic abnormalities associated with diabetes can lead to a significant percentage of patients developing a series of chronic and degenerative complications, including retinopathy, nephropathy, neuropathy, atherosclerosis and lipid disorders. Experimental models and recent clinical trials have shown that islet transplantation could be an alternative to exogenous insulin treatment, as it results in normalization of metabolic control, which has been almost impossible to obtain with administration of exogenous insulin. The results of clinical islet transplantation have greatly improved owing to the introduction of more efficient methods for the separation of islets and more effective immunosuppressive strategies. The marked improvement in clinical results has been paralleled by a renewed enthusiasm and interest in this approach, but major challenges remain to be addressed, including the need for life-long recipient immunosuppression, which severely limits the current indications for islet transplantation. This article outlines the history of and recent progress in the field (TIMELINE), as well as the present immunological challenges and strategies for tolerance induction to avoid continuous recipient immunosuppression after islet transplantation.
Suppression of ERK signalling abolishes primitive endoderm formation but does not promote pluripotency in rabbit embryo

Formation of epiblast (EPI) – the founder line of all embryonic lineages – and extra-embryonic supportive tissues is one of the key events in mammalian development. The prevailing model of early mammalian development is based almost exclusively on the mouse. Here, we provide a comprehensive, stage-by-stage analysis of EPI and extra-embryonic primitive endoderm (PrE) formation during preimplantation development of the rabbit. Although we observed that rabbit embryos have several features in common with mouse embryos, including a stage-related initiation of lineage specification, our results demonstrate the existence of some key differences in lineage specification among mammals. Contrary to the current view, our data suggest that reciprocal repression of GATA6 and NANOG is not fundamental for the initial stages of PrE versus EPI specification in mammals. Furthermore, our results provide insight into the observed discrepancies relating to the role of FGF/ERK signalling in PrE versus EPI specification between mouse and other mammals. Highlighted Article: A comprehensive analysis of rabbit preimplantation development reveals key differences between rabbit and mouse, with some aspects of lineage specification in rabbit more closely resembling that of human and primate embryos.
CCL3 Production by Microglial Cells Modulates Disease Severity in Murine Models of Retinal Degeneration

Many degenerative retinal diseases illustrate retinal inflammatory changes that include infiltration of microglia and macrophages into the subretinal space. In this study, we examined the role of chemokines in the Abca4−/−Rdh8−/− mouse model of Stargardt disease and the Mertk−/− mouse model of retinitis pigmentosa. PCR array analysis of 84 chemokines and related molecules revealed 84.6-fold elevated expression of Ccl3 (MIP-1a) 24 h after light exposure in Abca4−/−Rdh8−/− mice. Only MIP-1 chemokines, including Ccl3 and Ccl4, displayed peak expression 24 h after light exposure, and peaked earlier than the other chemokines. Secretion of Ccl3 was documented only in microglia, whereas both microglia and retinal pigment epithelium cells produced Ccl2. Exposure of Cx3Cr1gfp/ΔAbca4−/−Rdh8−/− mice to intense light resulted in the appearance of Cx3Cr1GFP+ monocytes in the subretinal space. To address the in vivo role of CCL3 in retinal degeneration, Ccl3−/−Abca4−/−Rdh8−/− mice and Ccl3−/−Mertk−/− mice were generated. Following intense light exposure, Ccl3−/−Abca4−/−Rdh8−/− mice displayed persistent retinal inflammation with appearance of Iba-1+ cells in the subretinal space, severe photoreceptor cell death, and increased Ccl4 expression compared with Abca4−/−Rdh8−/− mice. In contrast, Ccl3−/−Abca4−/−Rdh8−/− mice exhibited a milder retinal inflammation and degeneration than Abca4−/−Rdh8−/− mice did in age-related chronic retinal degeneration under room light conditions. The deficiency of Ccl3 also attenuated the severity of retinal degeneration in Mertk−/− mice. Taken together, our results indicate that Ccl3 has an essential role in regulating the severity of retinal inflammation and degeneration in these mouse models.
A probabilistic poly-time framework for protocol analysis

We develop a framework for analyzing security protocols in which protocol adversaries may be arbitrary probabilistic polynomial-time processes. In this framework, protocols are written in a restricted form of pi-calculus and security may expressed as a form or observational equivalence, a standard relation from programming language theory that involves quantifying over possible environments that might interact with the protocol. Using an asymptotic notion of probabilistic equivalence, we relate observational equivalence to polynomial-time statistical tests and discuss some example protocols to illustrate the potential strengths of our approach.