Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics Applications Note Systems Biology Bionet: an R-package for the Functional Analysis of Biological Networks

Motivation: Increasing quantity and quality of data in transcri-ptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules. Results: The BioNet package provides an extensive framework for integrated network analysis in R. This includes the statistics for the integration of transcriptomic and functional data with biological networks, the scoring of nodes as well as methods for network search and visualization. Availability: The BioNet package and a tutorial are available from
Modeling the Biological Nanopore Instrument for Biomolecular State Estimation

The nanopore is a powerful tool for probing biomolecular interactions at the single-molecule level, and shows great promise commercially as a next-generation deoxyribonucleic acid (DNA) sequencing technology. Coupling active voltage control with the nanopore has expanded its capabilities, for example, by allowing precise manipulation of DNA-enzyme complexes at millisecond timescales. However, any change in voltage excites capacitance in the system and results in masking the molecule's contribution to the measured current. To improve active control capabilities, a method is needed for continuous monitoring of the molecule's contribution to the current during voltage-varying experiments. The method must be able to separate the capacitive effects from the channel conductance, which is the parameter that can be used to infer the state of the molecule in the pore. The contributions of this paper are: 1) to develop a dynamic model of the nanopore instrument which includes capacitance and conductance parameters and 2) to develop model-based algorithms for estimating the conductance parameter during voltage varying experiments. First, grey- and black-box state-space models are estimated and compared using nanopore experimental data and system identification tools. Next, a validated grey-box model is used to derive two methods for estimating the channel conductance under voltage-varying conditions: one based on least-squares, and one based on the extended Kalman filter. In simulations and experiments, the Kalman filter outperforms the simpler least-squares method.
Evaluation of Herbal Methionine and Mangifera Indica Against Lead-induced Organ Toxicity in Broilers

Lead toxicity was studied in male broiler chicks (Cobb strain) of a day-old age. The chicks were randomly divided into six groups consisting of 15 in each group. Group 1 was maintained as basal diet control and group 2 was kept on lead at 300 ppm in feed throughout 5 wk as toxic control without any treatment. Groups 3 and 4 were maintained on herbal methionine at 1.4 g/kg feed + Mangifera indica at 0.1% in feed, respectively. Groups 5 and 6 were treated with lead + herbal methionine and lead + M.indica, respectively, for the 5 wk. The concentration of thiobarbituric acid reactive substances (TBARS) and protein carbonyls, and the activities of superoxide dismutase (SOD) and catalase in liver and kidney revealed a significant (P<0.05) increase, while there was a significant (P<0.05) decrease in the concentration of reduced glutathione (GSH) in liver and kidney, and hepatocytic membrane ATPases and cytochrome P 450 (CYP 450 ) in liver in the lead toxic control group. Treatment with herbal remedies in groups 5 and 6 resulted in a marked improvement in all the above parameters as compared to those of lead toxic control. Thus, it is concluded that lead induces biological damage by means of oxidative stress and the herbs in test offered better amelioration. The beneficial effects of herbal methionine and Ma. indica may be attributed to their antioxidant, anti-stress and hepatoprotective principles.
Low-Dose Valganciclovir as Preemptive Therapy for Cytomegalovirus Infection Occurring in Allogeneic Stem Cell Transplant Recipients

Few data are available to date on the dose of oral valganciclovir as cytomegalovirus (CMV) preemptive therapy in stem cell transplantation patients. This study aimed to evaluate the efficacy and safety of low-dose valganciclovir (900 mg/day) as preemptive treatment in allotransplanted recipients. Valganciclovir was used in 34 patients who underwent allogeneic stem cell transplantation for hematological malignancies at the dose of 900 mg oral administration/day (12 patients, group 1) or 1,800 mg oral administration/day (22 patients, group 2). Thirty-two out of 34 patients (94%) obtained negativization of polymerase chain reaction for CMV at a median of 12.5 days from the beginning of valganciclovir administration (10/12 patients of group 1, 22/22 patients of group 2). We conclude that oral administration of valganciclovir can induce clearance of CMV viral load in about 2 weeks; moreover, lower-dose oral valganciclovir (900 mg/day) has a comparable efficacy to the proposed standard dose (1,800 mg/day).
Precise Delivery Into Chronic Spinal Cord Injury Syringomyelic Cysts with Magnetic Nanoparticles MRI Visualization

Background Traumatic spinal cord injury (SCI) often results in the deficiency of glia and neurons in cystic cavities. These syringomyelic cysts can prevent axonal regeneration and sprouting. Details of the mechanism of syringomyelic cyst formation are unknown and an effective treatment for overcoming syringomyelic cysts is not available. Material/Methods Ten adult female Wistar rats underwent contusion SCI modeling resulting in syringomyelic cyst formation. A novel method for locating the cysts was developed and employed. MRI safe silver needles were inserted through the erector spinae of anesthetized rats to create a stable reference point. MRI images of the rodent spine were taken with the needles in situ. This information was used to accurately locate the cyst and determine the 3-dimensional entry point coordinates for nanoparticle delivery. Nanoparticles were injected into the cyst during a primary injection of 8 ul and a secondary injection of 8 ul, to prove the procedure can be accurately repeated. Results None of the rats died intra- or post-operatively. The syringomyelic cysts were accurately located with the 3-dimensional entry point coordinates. After nanoparticle delivery twice into each rat, the visualized syringomyelic cyst volume significantly decreased from 5.71±0.21 mm3 to 3.23±0.364 mm3 and to 1.48±0.722 mm3. Conclusions The present study describes a novel strategy for precise nanoparticle delivery into a syringomyelic cyst, using measurements obtained from MRI images. This strategy may aid in developing a new method for studying chronic spinal cord injury and a novel treatment for syringomyelic cysts.
Age and petrogenesis of volcanic and intrusive rocks in the Sulphur Spring Range, central Nevada: Comparisons with ore-associated Eocene magma systems in the Great Basin

Widespread base- and precious-metal anomalies, oxidized sulfi de veins, silicifi ed calcareous shales and carbonates, and altered porphyry intrusions occur in the northeastern Sulphur Spring Range, Nevada, 80 km south of important gold deposits in the Carlin trend. The small historic mines and prospects in the area are spatially and perhaps genetically related to a suite of variably altered dikes, small lava fl ows, silicic domes, and related pyroclastic rocks. New major- and trace-element data and U-Pb zircon ages show that the East Sulphur Spring volcanic suite is Eo-Oligocene in age (36‐31 Ma) and ranges in composition from high MgO- basaltic andesite to peraluminous rhyolite. The major- and trace-element compositions of the volcanic rocks are characteristic of continental margin subduction zone magmas and form a high-K, calc-alkaline suite with low Fe/Mg ratios. In addition, the rocks have negative Nb and Ti anomalies and elevated Ba, K, and Pb on normalized trace-element diagrams. Crustal melting is indicated by the eruption of a peraluminous garnet-bearing ignimbrite and as a component in hybridized andesite. The nature of this suite and its potential for mineralization is elucidated via comparisons to other Eocene age volcanic rocks associated with much larger gold and copper deposits in the Great Basin. The East Sulphur Spring suite is more similar to Eocene igneous rocks found along and near the Carlin trend than it is to those erupted while the Bingham porphyry copper deposit developed 300 km farther to the east. For example, the East Sulphur Spring suite and the Eocene magmatic rocks along the Carlin trend are less alkaline than the Bingham suite and lack its unusual enrichment of Cr, Ni, and Ba in intermediate composition rocks (58‐68 wt% silica). Nonetheless, the Bingham and East Sulphur Spring volcanic suites both preserve evidence of mixing that created intermediate compositions. For example, an andesite has obvious mineral disequilibrium with plagioclase, biotite, clinopyroxene, orthopyroxene, olivine, and amphibole coexisting with extensively resorbed megacrysts of quartz, K-feldspar, and garnet—indicative of mixing basaltic andesite or andesite and largely crystallized garnet-bearing rhyolite. On the other hand, we found no evidence for mixing with a mafi c alkaline magma like that in the Bingham Canyon magma-ore system. We conclude that: (1) an unusual tectonic setting prevailed during the Eocene and Oligocene of the western United States that promoted the production of oxidized mafi c magma in an arclike setting, but far inland as a result of the rollback of the Farallon slab; (2) the mafi c magmas intruded or erupted separately, or mixed with more silicic magma generated by fractional crystallization and assimilation of crustal materials; and (3) these mafi c magmas may have delivered signifi cant amounts of sulfur and chalcophile metals to upper crustal magma chambers and eventually to Paleogene ore deposits in the eastern Great Basin.
L-Selectin and chemokine response after liver ischemia and reperfusion.

BACKGROUND L-selectin plays an important role in the early phase of PMNs recruitment in the hepatic microvasculature following liver ischemia and reperfusion (I/R). Leukocyte cytokine chemoattractants (chemokines) cause polymorphonuclear neutrophil (PMN) activation in I/R injury. In this study, we examined the role of L-selectin in the production of chemokines in the liver and lung inflammatory response following 90 min of warm ischemia. STUDY DESIGN Thirty-six C57BL/6 mice were subjected to partial liver ischemia for a period of 90 min. Three groups of animals were included (n = 12 per group)-sham group, ischemic control, and the ischemic group receiving monoclonal antibody against L-selectin. We evaluated at 3 h: liver injury measurements, serum chemokines (MIP-2 and MIP-1alpha), liver and lung tissue myeloperoxidase (MPO), and liver and lung histology. Statistical analysis included ANOVA, Student-Newman-Keuls', and Kruskal-Wallis multiple comparison Z-value tests. RESULTS The ischemic group treated with anti-L-selectin showed significant decreases in liver enzyme levels and a marked decrease in serum MIP-2 (P < 0.05) when compared to ischemic controls. No reduction in serum MIP-1alpha was noted; however, neutrophil infiltration was significantly ameliorated in the liver and in the lung, as reflected by decreased MPO levels (P < 0.05). Improved histopathological features were observed in the anti-L-selectin-treated group compared to ischemic controls in the liver and the lung. CONCLUSIONS Our study suggests an important role for L-selectin in the pathogenesis of liver I/R and the production of chemokines. Anti-L-selectin treatment resulted in improved liver function, decreased neutrophil infiltration, and decreased MIP-2 chemokine response.
βII-tubulin and phospho-tau aggregates in Alzheimer's disease and Pick's disease

The expression of betaI-, betaII- and betaIII-tubulin isotypes was examined by immunohistochemistry in the entorhinal and transentorhinal cortices, hippocampus and dentate gyrus in normal human brains and in cases with Alzheimer's disease (AD), Pick's disease (PiD) and in argyrophilic grain disease (AGD). The results showed that betaII-tubulin predominated in the upper layers (mainly layer II) and betaIII-tubulin in the inner layers of the entorhinal and transentorhinal cortices in control brains. betaII-tubulin immunoreactivity was higher than betaIII-tubulin immunoreactivity in granular neurons of the dentate gyrus, whereas pyramidal neurons of the hippocampus proper were stained equally with anti-betaII-tubulin andbetaIII-tubulin antibodies. No preferential layering distribution was observed for betaI-tubulin. Polymerization assays with tubulin peptides following the method of microtubule-associated protein displacement demonstrated that the betaI and betaIII isotypes have a higher binding capacity for tau than does the betaII isotype. Interestingly, about 60% of neurons with neurofibrillary tangles in layer II of the entorhinal and transentorhinal cortices in AD were selectively stained with anti-betaII-tubulin antibodies. Moderate betaII-tubulin immunoreactivity was also observed in Pick bodies in PiD. Taken together, these findings support the view that high betaII-tubulin content is a contributing factor in the formation of abnormal hyper-phosphorylated tau aggregates.
The association of mean platelet volume levels with hypertensive retinopathy

The pathophysiological mechanism of hypertensive retinopathy (HR) is not fully established. Elevated blood pressure alone does not fully account for the extent of retinopathy so other pathogenic mechanisms may be involved, such as increased platelet activation. Mean platelet volume (MPV) is a marker of platelet activation. Therefore, this study was designed to answer the following questions: Do MPV levels change in HR? and is there any relation between degree of HR and MPV levels? This study included newly diagnosed and 57 untreated essential hypertensive patients with HR. The hypertensive patients were divided into two groups according to the Keith, Wagener classification. Group 1 comprised 29 hypertensive patients with grade 1 HR with a mean age of 56.8 ± 9.7 years. Group 2 comprised 28 hypertensive patients with grade 2 HR with a mean age of 58.1 ± 10.3 years. Twenty-seven normotensive subjects who were the healthy participants and had undergone the check-up program were used as the control group. Fundoscopic examination, metabolic parameters and MPV levels were measured in all groups. The level of MPV in group 2 was significantly higher than in group 1 (8.9 ± 0.8 fl vs.8.3 ± 0.8 fl, p = 0.02) and the normotensive control group (8.9 ± 0.8 fl vs 7.8 ± 0.7 fl, p < 0.001). It was also higher in group 1 than in normotensive control group (8.3 ± 0.8 fl vs.7.8 ± 0.7 fl, p < 0.01). In addition, MPV showed a positive correlation with the degree of HR in the hypertensive group (r = 0.41, p = 0.015). Our study suggests that platelet activation, a mechanism known to be involved in vascular lesions, may promote the development of HR.
The Dose Proportionality of the Pharmacokinetics of Ardeparin, a Low Molecular Weight Heparin, in Healthy Volunteers

Ardeparin is a low molecular weight heparin currently being evaluated as an antithrombotic agent. The objective of this investigation was to assess the effects of dose on the pharmacokinetics of ardeparin after subcutaneous administration. Eighteen healthy subjects received doses of 30 U/kg, 60 U/kg, and 100 U/kg antifactor Xa (aXa) of ardeparin by subcutaneous injection. Plasma antifactor IIa (aIIa) activity levels after the 30‐ and 60‐U/kg doses of ardeparin were too low to reliably characterize the disposition of the drug. However, the pharmacokinetics of ardeparin could be characterized by using pharmacodynamic measurements of plasma aXa activity. The rate of absorption of ardeparin after subcutaneous administration did not change with increasing dose. The volume of distribution (Vd) of ardeparin was small, reflecting minimal distribution outside the intravascular space, and was independent of dose. The total clearance of ardeparin, however, decreased with increasing dose, and half‐life (t1/2) was prolonged at the higher doses. Within the observed dose range, a doubling of the ardeparin dose resulted in an area under the plasma aXa activity‐versus‐time curve (AUC) that was approximately 25% greater than expected on the basis of linear disposition. The differences in AUC and clearance between the three doses suggest that the mechanism of elimination of ardeparin is saturable.
Technology preferences and routines for sharing health information during the treatment of a chronic illness

When a patient has a chronic illness, such as heart disease or cancer, it can be challenging for distributed family members to stay aware of the patient's health status. A variety of technologies are available to support health information sharing (e.g., phone, video chat, social media), yet we still do not have a detailed understanding of which technologies are preferred and what challenges people still face when sharing information with them. To explore this, we conducted a mixed-method study-involving a survey and in-depth interviews--with people about their health information sharing routines and preferences for different technologies. Regardless of physical distance between distributed family members, synchronous methods of communication afforded the opportunity to provide affective support while asynchronous methods of communication were deemed to be the least intrusive. With family members adopting certain roles during the treatment of chronic illnesses, our findings suggest the need to design tools that mediate sharing health information across distance and age gaps, with consideration to respecting patient privacy while sharing health information.
Functional analysis of Sox8 and Sox9 during sex determination in the mouse

Sex determination in mammals directs an initially bipotential gonad to differentiate into either a testis or an ovary. This decision is triggered by the expression of the sex-determining gene Sry, which leads to the activation of male-specific genes including the HMG-box containing gene Sox9. From transgenic studies in mice it is clear that Sox9 is sufficient to induce testis formation. However, there is no direct confirmation for an essential role for Sox9 in testis determination. The studies presented here are the first experimental proof for an essential role for Sox9 in mediating a switch from the ovarian pathway to the testicular pathway. Using conditional gene targeting, we show that homozygous deletion of Sox9 in XY gonads interferes with sex cord development and the activation of the male-specific markers Mis and P450scc, and leads to the expression of the female-specific markers Bmp2 and follistatin. Moreover, using a tissue specific knock-out approach, we show that Sox9 is involved in Sertoli cell differentiation, the activation of Mis and Sox8, and the inactivation of Sry. Finally, double knock-out analyses suggest that Sox8 reinforces Sox9 function in testis differentiation of mice.
Cerebral Venous Thrombosis in Adults

Cerebral venous thrombosis (CVT) is a rare form of cerebrovascular disease in which thrombus forms in the dural sinuses and cortical cerebral veins. Raised venous pressure causes venous infarction, intracranial haemorrhage and the syndrome of intracranial hypertension. The inconsistent speed of onset and overlap of clinical syndromes mean that presentation is highly variable but often includes headache, focal neurological deficits and encephalopathy. Although a variety of congenital and acquired precipitants have been implicated, gender-specific risk factors including pregnancy, the puerperium and oral contraceptive use lead to CVT being more common in younger females. Neuroimaging is required for diagnosis, with magnetic resonance venography (MRV) and computed tomography venography (CTV) both being viable options, each with advantages and disadvantages. Anticoagulation is the mainstay of treatment with emerging evidence of benefit from randomised controlled trials. Endovascular intervention also offers therapeutic options for patients with a poor prognosis and surgery for impending cerebral herniation may result in good functional outcomes. Prognosis is good with the majority of patients making a full recovery and with a low recurrence rate.
On the Practice of Action Research

Some of the major aspects of engaging in action research are presented. The triadic relationships of action research as a basic and fundamental characteristic, ranging from the very abstract to the very concrete, are discussed. In action research one experiences, on and off, all the modalities of daily reality. The dialogical, linguistic, ethical and psychodynamic features of action research are emphasized, as well as its unfolding and often unpredictable nature. The role of the researcher unfolds in the context of joint action and becomes gradually articulated through (a) experience, (b) the content of one's 'toolkit', and (c) appropriate timing.
Analysis and modeling of capacitances in halo-implanted MOSFETs

In this paper, we report the anomalous behavior of capacitances in halo channel MOSFET for the linear and saturation regions. Unlike MOSFETs these devices have different threshold voltage (VTH) for the DC and CV operations, and therefore cannot be modeled by conventional methods. We have investigated various cases of doping non-uniformity: Source side halo (SH), Drain side halo (DH), both side halos (Halo) and uniformly doped (UD) transistors using TCAD simulations under various bias conditions. A computationally efficient SPICE model is used to model these trends which shows excellent matching with the measured and TCAD data.
Kinship and friendship in modern Britain

The latest in the successful Oxford Modern Britain series, Kinship and Friendship in Modern Britain provides a succinct introduction to key aspects of kin and friend relationships in Britain today. Graham Allan reviews a cross-section of research to examine the major issues surrounding contemporary kinship and friendship, analysing the personal - and social - consequence of these ties. The author examines key aspects of interpersonal relations to discuss the nature and importance of kinship in the late twentieth century. After studying modern perspectives on informal relationships, he focuses on kinship solidarities, highlighting their increased complexity in modern Britain, and reviewing the obligations and commitments between different categories of kin. In later chapters, he examines patterns of friendship, concentrating in particular on how they are organized and their social implications. Graham Allan also studies alternative views of kinship and friendship as negotiation and as economic exchange, also analysing how relationships may change in later life. Kinship and Friendship in Modern Britain provides the student with an invaluable introduction to the fundamental aspects of the sociology of family and friendship in contemporary British life.