Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal food web dynamics along a desert riparian–upland transition

Increased awareness of spatiotemporal variation in species interactions has motivated the study of temporally-resolved food web dynamics at the landscape level. Empiricists have focused attention on cross-habitat flows of materials, nutrients, and prey, largely ignoring the movement of predators between habitats that differ in productivity (and how predators integrate pulses in resource availability over time). We set out to study seasonal variation in food web interactions between mammalian carnivores and their rodent prey along a riparian-upland gradient in semi-arid southeastern Arizona which features both spatial and temporal heterogeneity in resource availability. Specifically, we tested whether mammalian carnivores spill over from productive, near-river habitats into adjacent, desert-scrub habitats; and if they do, to document the effects of this spillover on rodent communities. Furthermore, we examined seasonal variation in top-down effects by measuring changes in carnivore diet and distribution patterns and rodent populations over time. The results indicate that carnivores track seasonally-abundant resources across the landscape, varying both their diet and movement patterns. In turn, desert-scrub rodent population dynamics track seasonal shifts in carnivore habitat use but not resource availability, suggesting that predation plays a role in structuring rodent communities along the San Pedro River. Further evidence comes from data on rodent community composition, which differs between desert-scrub habitats near and far from the river, despite similarities in resource availability. Our data also suggest that seasonal omnivory helps predators survive lean times, increasing their effects on prey populations. Taken together, these results underscore the importance of spatiotemporal variation in species interactions, highlighting the complexity of natural systems and the need for further detailed studies of food web dynamics.
Evaluating the Utility of Circulating Biomarkers of Collagen Synthesis in Hypertrophic Cardiomyopathy

Background— In hypertrophic cardiomyopathy (HCM), accumulation of myocardial collagen may play a central role in the pathogenesis of diastolic dysfunction and arrhythmia. Previous studies have suggested that peripheral levels of byproducts of collagen synthesis are reflective of myocardial extracellular matrix metabolism, although this has not been validated in detail. Given the potential clinical utility of such biomarkers, we sought to validate the assumed relationship between peripheral markers and myocardial fibrosis in HCM. Methods and Results— Fifty patients with HCM and 25 healthy controls underwent peripheral venous sampling to determine plasma concentrations of key collagen precursors (procollagen I and III N-terminal propeptides [PINP, PIIINP]). Contrast-enhanced cardiac magnetic resonance imaging was performed to quantify regional (by late-gadolinium enhancement) and diffuse (by T1 mapping) myocardial fibrosis. Nineteen subjects also underwent simultaneous arterial and coronary sinus blood sampling (to derive transcardiac concentration gradients of PINP, PIIINP, and C-terminal telopeptide of type I collagen) and right heart catheterization. Despite cardiac magnetic resonance evidence of regional (late-gadolinium enhancement quantity, 6.4±8.0%) and diffuse (T1 time, 478±79 ms) myocardial fibrosis in patients with HCM, peripheral levels of collagen precursors were similar compared with control subjects (PINP, 45.9±22.9 versus 53.4±25.9 &mgr;g/L; P=0.21; PIIINP, 4.8±1.7 versus 4.4±1.1 &mgr;g/L; P=0.26). No significant net positive transcardiac concentration gradient was detected for either biomarker of collagen synthesis. Conclusions— The cardiac contribution to peripheral levels of byproducts of collagen synthesis in patients with HCM is insignificant. Furthermore, peripheral levels of these biomarkers do not accurately reflect myocardial collagen content in these patients.
MINT, the molecular interaction database: 2012 update

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein–protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235 000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio. uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.
An analysis on students’ errors in using relative pronouns (Who, Whom, Which, Whose): a case study in the second year of Fatahillah senior high school

i ACKNOWLEDGEMENT . iii TABLE OF CONTENTS . iv LIST OF TABLES . vi LIST OF CHARTS . vii LIST OF APPENDICES . viii CHAPTER I : INTRODUCTION A. Background of Study . 1 B. Identification of the Problem . 4 C. Limitation of the Problem . 4 D. Formulation of Problem . 5 E. Objectives of Study . 5 F. Significance of Study . 5 CHAPTER II: THEORETICAL FRAMEWORK A. Adjective Clause . 7 1. The Definition of Adjective . 7 2. The Types of Adjective Clause.8 B. Relative Pronouns . 9 1. The Understanding of Relative Pronous . 9 2. The Types of Relative Pronouns . 9 3. Error Analysis . 10 1. The Definition of Error Analysis . 10 2. The Differences Between Errors and Mistakes . 11 3. The Sources of Error . 12 4. The Types of Errors . 13 5. The Procedure of Error . 18
SNIF: Sensor Network Inspection Framework

Recent experience with the deployment of sensor networks demonstrates that it is far from trivial to setup a working larger-scale sensor network in the field. Even though simulations and experiments with lab testbeds confirmed a working system, subtle real-world influences lead to frequent failures in the field. Identifying and fixing these problems in the field is currently a difficult and cumbersome task due to the lack of appropriate concepts and tools. In this paper we address this issue by, firstly, classifying common problems that have been encountered during deployment. We then show that many of these problems can be detected by overhearing and analyzing sensor network traffic without need for an instrumentation of sensor nodes. Based on this observation, we develop a tool to inspect a deployed sensor network, consisting of a distributed network sniffer and a data-stream-based framework for online traffic analysis. We demonstrate and evaluate how this tool can be used to debug a typical data gathering application. 1
Epithelial Ca(2+) channel (ECAC1) in autosomal dominant idiopathic hypercalciuria.

BACKGROUND The epithelial Ca(2+) channel (ECaC) exhibits the defining properties for being the gatekeeper in 1,25-dihydroxyvitamin D(3)-regulated Ca(2+) (re)absorption. Its recently cloned human orthologue (ECaC1) could, therefore, represent a crucial molecule in human disorders related to Ca(2+)-wasting such as idiopathic hypercalciuria (IH). METHODS Fifty-seven members of nine families with IH were investigated. Phenotyping was performed by measurements of urinary Ca(2+) excretion, while other underlying disorders were appropriately excluded. Initially, the recently suggested locus for kidney stone-associated hypercalciuria on chromosome 1q23.3-q24 was investigated. Next, direct mutation analysis of all 15 exons of the ECAC1 gene and 2.9 kb upstream from the start codon was performed. hECaC1, heterologously expressed in human embryonic kidney 293 cells, was characterized by patch-clamp analysis. RESULTS The mode of inheritance in the studied pedigrees is consistent with an autosomal dominant trait. Haplotype analysis did not implicate a role of the locus on chromosome 1. The coding sequence of the ECAC1 gene was not different between the affected and the non-affected family members. In the 5'-flanking region, three single nucleotide polymorphisms were encountered, but these polymorphisms were observed regardless of the affection status of the screened family members. Patch-clamp analysis of hECaC1 was performed as the putative pore region contains four non-conserved amino acid substitutions compared with the other species. This analysis revealed the distinctive properties of ECaC, including a high Ca(2+) selectivity, inward rectification, and Ca(2+)-dependent inactivation. CONCLUSION These results do not support a primary role for hECaC1 in IH in nine affected families. Because of the heterogeneity of the disease, however, the involvement of ECaC1 in other subtypes of IH cannot be excluded and needs further investigation. The electrophysiological properties of hECaC1 further substantiate its prime role in Ca(2+) (re)absorption.
A successive-approximation ADC for CMOS image sensors

The CMOS image sensors are achieving a growing presence in today's mobile applications as the industry acknowledges the advances of the CMOS-based technology and its scaling possibilities. The roadmap recently unveiled for CMOS Image Sensor is announcing ever smaller pixels, after 1. 4μm pixel pitch, demos with a pitch of 1. 1μm were presented, and it also announces the future generation of pixels with 0. 9μm pixel size. This steady decrease in pixel size has had a profound impact on sensors analog readout electronics, and, in particular, on their ADC architecture. For mobile applications, the ADCs are mostly placed in each column of image arrays, as the width of each converter need to fit in the image array pitch. The design becomes a true challenge as the available area for layout is very critical. To overcome this limitation, a compromise between column level and chip level ADCs can be used. A solution using a converter per 32 columns of the pixel array is proposed. The converter is a Successive Approximation (SA) ADC of apparent resolution 12 bits and is obtained from a 9 bits converter. This work presents a conversion architecture, particularly well adapted to image sensors where the noise level varies along with the amplitude of the useful signal. The proposed design presents the benefit of increasing the number of bits of the ADC without excessively increasing its complexity or its processing time. The converter is designed in CMOS 65nm technology, and will be implemented in a 5Megapixel sensor, at a sampling rate of 8.33MS/s. The simulations show good linearity and verify the concept of the new architecture.
Energy-aware routing in multiple domains software-defined networks

The growing energy consumption of communication networks has attracted the attention of the networking researchers in the last decade. In this context, the new architecture of Software-Defined Networks (SDN) allows a flexible programmability, suitable for the power-consumption optimization problem. In this paper we address the issue of designing a novel distributed routing algorithm that optimizes the power consumption in large scale SDN with multiple domains. The solution proposed, called DEAR (Distributed Energy-Aware Routing), tackles the problem of minimizing the number of links that can be used to satisfy a given data traffic demand under performance constraints such as control traffic delay and link utilization. To this end, we present a complete formulation of the optimization problem that considers routing requirements for control and data plane communications. Simulation results confirm that the proposed solution enables the achievement of significant energy savings.
A new mechanism to render clinical isolates of Escherichia coli non-susceptible to imipenem: substitutions in the PBP2 penicillin-binding domain.

OBJECTIVES So far, two types of mechanism are known to be involved in carbapenem non-susceptibility of Escherichia coli clinical isolates: reduced outer membrane permeability associated with production of ESBLs and/or overproduction of class C β-lactamases; and production of carbapenemases. Non-susceptibility to only imipenem observed in two clinical isolates suggested a new mechanism, described in the present study. METHODS The ST was determined for the two isolates of E. coli (strains LSNy and VSBj), and their chromosomal region encoding the penicillin-binding domain of PBP2 was amplified, sequenced and then used for recombination experiments in E. coli K12 C600. Antibiotic MICs were determined using the Etest method. RESULTS Strains LSNy and VSBj, which displayed ST23 and ST345, respectively, showed amino acid substitutions in their PBP2 penicillin-binding domain. Substitution Ala388Ser located in motif 2 (SXD) was common to the two strains. Two additional substitutions (Ala488Thr and Leu573Val) located outside the two other motifs were identified in strain LSNy, whereas another one (Thr331Pro) located in motif 1 was identified in strain VSBj. Recombination experiments to reproduce non-susceptibility to imipenem in E. coli K12 C600 were not successful when only the common substitution was transferred, whereas recombination with DNA fragments including either the three substitutions (strain LSNy) or the two substitutions (strain VSBj) were successful. CONCLUSIONS Substitution of amino acids in the penicillin-binding domain of PBP2 is a new mechanism by which E. coli clinical isolates specifically resist imipenem.
Tumor Necrosis Factor-&agr; Monoclonal Antibody, Infliximab, Used to Manage Severe Sciatica

Study Design. An open-label study was conducted. Objective. To evaluate the efficacy and safety of infliximab, a monoclonal chimeric antibody, against tumor necrosis factor-&agr; (TNF&agr;) for the treatment of severe sciatica. Summary of Background Data. Evidence from animal studies indicates that TNF&agr; plays a role in the pathophysiology of sciatica. Anti-TNF&agr; therapy has not been previously evaluated in sciatic patients. Methods. In this study, 10 patients with disc herniation–induced severe sciatica received infliximab (Remicade 3 mg/kg) intravenously over 2 hours. The outcome was assessed at 1 hour, 1 week, 2 weeks, 1 month, and 3 months after the infusion and compared to historical control subjects consisting of 62 patients who received saline in a trial of periradicular infiltration for sciatica. Leg pain was the primary outcome, with more than a 75% decrease from the baseline score constituting a painless state. Fisher’s exact test and repeated measures analysis of variance were used for statistical analysis. Results. At 1 hour after the infusion, leg pain had decreased by 50%. At 2 weeks, 60% of the patients in the infliximab group were painless, as compared with 16% of the control patients (P = 0.006). The difference was sustained at 3 months (90%vs 46%;P = 0.014). Infliximab was superior over the whole follow-up period in terms of leg pain (P = 0.003) and back-related disability (P = 0.004). At 1 month, every patient in the infliximab group had returned to work, whereas 38% of the control subjects still were on sick leave (P = 0.02). None of the patients treated with infliximab underwent surgery during the follow-up period. No immediate or delayed adverse drug reactions and no adverse effects related to medication were observed. Conclusions. Anti-TNF&agr; therapy is a promising treatment option for sciatica. There is an urgent need for a randomized controlled trial to evaluate whether thesepromising early results can be confirmed.
Forearm reactive hyperaemia is not mediated by nitric oxide in healthy volunteers.

AIMS To determine the role of nitric oxide (NO) in forearm reactive hyperaemia in healthy human subjects. METHODS Ten healthy subjects aged 19-34 years underwent brachial artery cannulation. Forearm circulatory arrest was achieved by means of an upper arm cuff inflated to 200 mmHg for 5 min. The blood flow responses during reactive hyperaemia were measured using venous occlusion plethysmography following a 10 min intra-arterial infusion of 8 micromol min-1 N-monomethyl L-arginine (L-NMMA) and following matching placebo administered in random order. Results were analysed by repeated measures anova and t-tests. RESULTS L-NMMA resulted in a significant reduction of basal forearm blood flow indicating inhibition of basal NO release (P=0.005). There was no significant difference between the blood flow responses during reactive hyperaemia following L-NMMA and placebo (P=0.97). CONCLUSIONS Nitric oxide production does not make a significant contribution to the vasodilatation associated with reactive hyperaemia in the human forearm.
Modeling and Analysis for Proactive-Decision Spectrum Handoff in Cognitive Radio Networks

Spectrum handoff occurs when the primary users appear in the licensed band occupied by the secondary users. Spectrum handoff procedures aim to help the secondary users to vacate the occupied licensed spectrum and find suitable target channel to resume the unfinished transmission. In this paper, we discuss how to select the target channels to minimize the total service time with multiple spectrum handoffs. We propose a preemptive resume priority (PRP) M/G/1 queueing network model to evaluate total service time for various target channels selections. Then, we suggest a low-complexity greedy algorithm to select target channels. Numerical results show that a spectrum handoff scheme based on greedy selection strategy can reduce total service time compared to the randomly selection scheme.
A Mobile-Quiz Application in Egypt

Mobile devices such as cell phones become the widest instrument handed in the students daily activities including browsing Internet and sending e-mails. Several countries such as Japan and US have already applied it in the education and learning processes due to its outstanding characteristics including portability and accessibility. In this work, a mobile-quiz application is suggested and described to facilitate the assessment process inside the high-density classrooms and to increase the interactivity among the instructors and students. Also, a case study of the proposed application in a particular academic Egyptian institution is applied and discussed for the first time with respect of our best knowledge. Basically, three different methods have been suggested to settle this application inside the Egyptian academia according to the available e-learning resources. The preliminary outcomes of the conducted experiment demonstrated the possibility of applying mobile devices within the various academic Egyptian environments.
UvA-DARE ( Digital Academic Repository ) Epistemology and ontology in core ontologies : FOLaw and LRI-Core , two core ontologies for law

For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The first one was the result of a PhD thesis by [Valente, 1995], called FOLaw. FOLaw specifies functional dependencies between types of knowledge involved in legal reasoning. Despite the fact thatFOLaw was the starting point for a number of ontologies and legal reasoning systems in various (European) projects, it is rather an epistemological framework than a (core) ontology. We are not the only ones who easily confound epistemology with ontology. In the paper we present some examples and discuss whether this epistemological promiscuity in (core) ontology development is a serious problem. It is to some extent, as it limits the scope of re-use (if not leading to confusion). Therefore, we started about four years ago the development of a ‘real’ core-ontology for law based upon notions of common sense. The reason for a common-sense foundation is that domain independent concepts of law – the common denominator – are still tainted with a strong common-sense flavor. Moreover, domains of law refer to social activities which are generally governed by common-sense notions. This core ontology, called LRI-Core, consists of five major portions (‘worlds’): physical, mental and abstract classes; roles and occurrences.
Prospects of stem cell treatment in benign urological diseases

Stem cells (SCs) are undifferentiated cells that are capable of self-renewal and differentiation and that therefore contribute to the renewal and repair of tissues. Their capacity for division, differentiation, and tissue regeneration is highly dependent on the surrounding environment. Several preclinical and clinical studies have utilized SCs in urological disorders. In this article, we review the current status of SC use in benign urological diseases (erectile dysfunction, Peyronie disease, infertility, and urinary incontinence), and we summarize the results of the preclinical and clinical trials that have been conducted.
Constitutive Repression of E2F1 Transcriptional Activity through HDAC Proteins Is Essential for Neuronal Survival

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Why People Are (Un)willing to Share Information with Online Advertisers

Online advertisers track Internet users’ activities to deliver relevant ads. To study how dierent online advertisers’ data practices aect users’ comfort with sharing their information, we conducted a 1,882-participant between-subjects online study. We asked participants about their comfort with sharing commonly collected types of information in scenarios with varying data practices, and studied their reactions to a realistic example of a behavioral prole created by advertisers about users. We found that participants’ willingness to share information with online advertisers is not only based on the sensitivity of the information, but also on the scope of collection and use, perceived necessity of collection, and perceived benets or harms of disclosing specic data types. Qualitative data analysis revealed nuanced and contextualized reasons behind stated information-sharing preferences. Participants were particularly adverse to sharing information that they perceived as irrelevant for advertising. However, our results also reveal that, under the right circumstances, participants may be willing to share their data with advertisers to enhance the utility of shown ads.