Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphism of the 5-HT transporter and response to antidepressants: randomised controlled trial

Background Antidepressants exhibit a variety of pharmacological actions including inhibition of the serotonin and noradrenaline transporters. We wished to investigate whether genetic variation could be used to target or personalise treatment, in a comparison of selective serotonin reuptake inhibitors (SSRIs) with noradrenaline reuptake inhibitors (NARIs). Aims To test the hypothesis that patients homozygous for the long (insertion) polymorphism of the serotonin transporter (5-HTTLPR) have an increased response to SSRI antidepressants but not to NARI antidepressants. Method In an individually randomised, parallel-group controlled trial, people meeting criteria for a depressive episode who were referred by their general practitioner were randomised to receive either citalopram (an SSRI) or reboxetine (an NARI). Randomisation was by means of a remote automated system accessed by telephone. The main outcome was depressive symptoms, measured by Beck Depression Inventory (BDI) total score 6 weeks after randomisation. The trial was registered with the International Standard Randomised Controlled Trials Number registry (ISRCTN31345163). Results Altogether 298 participants were randomised to receive citalopram and 303 were randomised to reboxetine. At 6 weeks follow-up, complete data were available for 258 participants taking citalopram and 262 taking reboxetine. We found no evidence to support an influence of 5-HTTLPR on outcome following antidepressant treatment. The interaction term for BDI score at 6 weeks was 0.50 (95% CI −2.04 to 3.03, P = 0.70), which indicated that responses to the SSRI and NARI were similar irrespective of 5-HTTLPR genotype. Conclusions It is unlikely that the 5-HTTLPR polymorphism alone will be clinically useful in predicting response to antidepressants in people with depression.
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5′-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP–chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release.
Selectivity in the Reinnervation of the Lateral Gastrocnemius Muscle after Nerve Repair with Ethyl Cyanoacrylate in the Rat

There is a need for complementary surgical techniques that enable rapid and reliable primary repair of transected nerves. Previous studies after peripheral nerve transection and repair with synthetic adhesives have demonstrated regeneration to an extent comparable to that of conventional techniques. The aim of this study was to compare two different repair techniques on the selectivity of muscle reinnervation after repair and completed regeneration. We used the cholera toxin B technique of retrograde axonal tracing to evaluate the morphology, the number, and the three-dimensional location of α-motoneurons innervating the lateral gastrocnemius muscle and compared the results after repair with either ethyl cyanoacrylate (ECA) or epineural sutures of the transected parent sciatic nerve. In addition, we recorded the wet weight of the muscle. Six months after transection and repair of the sciatic nerve, the redistribution of the motoneuron pool was markedly disorganized, the motoneurons had apparently increased in number, and they were scattered throughout a larger volume of the spinal cord gray matter with a decrease in the synaptic coverage compared to controls. A reduction in muscle weight was observed as well. No difference in morphometric variables or muscle weight between the two repair methods could be detected. We conclude that the selectivity of motor reinnervation following sciatic nerve transection and subsequent repair with ECA is comparable to that following conventional micro suturing.
Nisin stimulates oxygen consumption by Staphylococcus aureus and Escherichia coli

Nisin stimulated oxygen consumption by nongrowing, glucose-metabolizing Staphylococcus aureus and Escherichia coli cells, indicating a protonophore mode of action. A similar stimulation in E. coli cells osmotically stressed to disrupt the outer cell membrane confirmed the cytoplasmic membrane as the site of nisin action and showed that nisin uptake was not prevented by the outer membrane.
Dynamic Clinical Data Mining: Search Engine-Based Decision Support

The research world is undergoing a transformation into one in which data, on massive levels, is freely shared. In the clinical world, the capture of data on a consistent basis has only recently begun. We propose an operational vision for a digitally based care system that incorporates data-based clinical decision making. The system would aggregate individual patient electronic medical data in the course of care; query a universal, de-identified clinical database using modified search engine technology in real time; identify prior cases of sufficient similarity as to be instructive to the case at hand; and populate the individual patient's electronic medical record with pertinent decision support material such as suggested interventions and prognosis, based on prior outcomes. Every individual's course, including subsequent outcomes, would then further populate the population database to create a feedback loop to benefit the care of future patients.
TERRESTRIAL LASER SCANNING VERSUS TRADITIONAL FOREST INVENTORY FIRST RESULTS FROM THE POLISH FORESTS

The goal of this paper was to present the pilot stu dy ongoing in the Polish State Forests on the appli cation of gathering basic forest parameters using the terrestrial laser scanner (TLS ) technology. The 3D point cloud was created using scanner based on the “phaseshift” technology. The first part of the paper show s the comparison of two manual methods of TLS data processing, i.e. the directly measurement on the planar image so called - „pixel method” and semi-automatic „pipe method”, in the context of the results obtained with traditional forest inventory. The second part of the article refers to author’s algorithms, the p urpose of which was to make the process of obtained the stand basal area (G) from a scanned tree trunks (also partially scanned) autom atic. The first stage of work over algorithms resulted in precise definition of t he: location of tree trunks on the inventory plot a nd such elements: tree basal area (g), stand basal area (G) and BHD.
Unearthing the impact of human disturbance on a notorious weed

Large‐scale anthropogenic changes in the environment are reshaping global biodiversity and the evolutionary trajectory of many species. Evolutionary mechanisms that allow organisms to thrive in this rapidly changing environment are just beginning to be investigated (Hoffmann & Sgrò ; Colautti & Barrett ). Weedy and invasive species represent ‘success stories’ for how species can cope with human modified environments. As introduced species have spread within recent times, they provide the unique opportunity to track the genetic consequences of rapid range expansion through time and space using historic DNA samples. Using modern collections and herbarium specimens dating back to 1873, Martin et al. ( ) have provided a more complete understanding of the population history of the invasive, agricultural weed, common ragweed (Ambrosia artemisiifolia; Fig. ) in its native range with surprising results. They find that the recent population explosion of common ragweed in North America coincided with substantial shifts in population genetic structure with implications for invasion.
Adenovirus retargeting to surface expressed antigens on oral mucosa

Head and neck squamous cell carcinomas develop in preneoplastic mucosal fields that can extend over several centimeters in diameter. Most of these fields are microscopically recognized as dysplasias. These fields are often not adequately treated and might cause local relapse. Previous investigations demonstrated that mouthwash therapy with oncolytic adenoviruses appears to be a good option for the treatment of these fields, although, at present, with limited efficacy.
Does balloon catheter sinuplasty have a role in the surgical management of pediatric sinus disease?

BACKGROUND The surgical management of chronic recurrent sinusitis (CRS) recalcitrant to medical therapy in the pediatric population has traditionally consisted of adenoidectomy and functional endoscopic sinus surgery (FESS), depending on age and imaging findings. Adenoidectomy relieves nasopharyngeal airway obstruction as well as potentially eradicates a bacterial reservoir. FESS, as in adults, promotes paranasal sinus ventilation and drainage. Pediatric FESS most commonly consists of uncinectomy, maxillary antrostomy, and/or ethmoidectomy due to the relative underdevelopment of the sphenoid and especially the frontal sinuses in preadolescent children. FESS is generally considered to be safe, with major complications such as cerebrospinal fluid leak, meningitis, or orbital violation occurring in <1% of cases. Initial concerns that FESS in the pediatric population may lead to retardation of facial growth have proven to be unsubstantiated. Balloon catheter sinuplasty (BCS) was first introduced as a therapeutic modality of CRS in adults in 2006. In BCS a guidewire, passed into the target maxillary, sphenoid, or frontal sinus under endoscopic visualization with either fluoroscopic or fiberoptic light confirmation, is used to position a deflated oblong balloon across the natural sinus ostium. This balloon is subsequently inflated to a maximum diameter of 5 to 7 mm, dilating the natural ostium. In contrast to FESS, BCS does not involve tissue removal and theoretically is mucosal sparing. Purported limitations of BCS include the inability to address alternative predisposing anatomical abnormalities (the uncinate process, for example, is not removed in maxillary procedures) or to treat concurrent ethmoid sinus disease. The efficacy of BCS in adults with frontal, sphenoid and maxillary sinus disease is reported to be on par with FESS, suggesting a potential role for BCS in the treatment armamentarium of pediatric rhinosinusitis as well.
Self-Amplification of Nigral Degeneration in Parkinson's Disease: A Hypothesis

This review analyzes current evidence regarding possible mechanisms of nigral damage in idiopathic Parkinson's disease (iPD). In normal brain, a specific interplay among the blood–brain barrier (BBB), substantia nigra (SN), and locus coeruleus (LC) creates the condition for a self-accelerating damage to the SN. Three vicious circles involving SN-BBB, LC-SN-BBB, and histamine-BBB-SN interactions are described. In iPD, a self-accelerating loss of nigral cells can be triggered by brain hypoperfusion and by an increased blood histamine level. iPD-associated factors such as decreased CSF levels of substance P, somatostatin, and glutamate can aggravate the vicious-circle-induced damage to the SN.
Identification of 2,3-dihydroxybenzoic acid as a Brucella abortus siderophore

Brucella abortus grown in low-iron medium or in the presence of iron chelators [ethylenediamine-di(o-hydroxyphenylacetic acid) and 2,2-dipyridyl] showed reduced cell yields and released a material positive in chemical and biological assays for catechols. This material was purified from culture fluids of B. abortus 2308 by chromatography on agarose-iminodiacetic acid-Fe3+ and identified as 2,3-dihydroxybenzoic acid (2,3-DHBA) by thin-layer chromatography, paper electrophoresis, and UV-visible nuclear magnetic resonance and mass spectroscopy. No other major catechols were observed at different stages of growth, and 2,3-DHBA was also produced upon iron limitation by representative strains of B. abortus biotypes 1, 5, 6, and 9. Both synthetic 2,3-DHBA and the natural catechol relieved the growth inhibition of B. abortus 2308 by ethylenediamine-di(o-hydroxyphenylacetic acid), and 2,3-DHBA promoted 55Fe uptake by B. abortus 2308 by an energy-dependent mechanism. Two other monocatechols tested, 2,3-dihydroxybenzoyl-Ser and 2,3-dihydroxybenzoyl-Gly, also promoted 55Fe uptake. More complex catechol siderophores (agrobactin and enterobactin), hydroxamate siderophores (aerobactin, ferrichrome, and deferriferrioxamine mesylate [Desferal]), and an EDTA-related siderophore (rhizobactin) failed to mediate 55Fe uptake. B. abortus cells grown in low-iron medium or in medium with iron had similar rates of iron uptake when supplied with 55Fe-2,3-DHBA, and the release of 2,3-DHBA under iron starvation was not associated with the expression of new outer membrane proteins. These results suggest an uptake system in which only the synthesis of the siderophore is regulated by the iron available for growth.
MR Imaging Detection of Cerebral Microbleeds: Effect of Susceptibility-Weighted Imaging, Section Thickness, and Field Strength

BACKGROUND AND PURPOSE: The emergence of cerebral microbleeds (CMB) as common MR imaging findings raises the question of how MR imaging parameters influence CMB detection. To evaluate the effects of modified gradient recalled-echo (GRE) MR imaging methods, we performed an analysis of sequence, section thickness, and field strength on CMB imaging properties and detection in subjects with cerebral amyloid angiopathy (CAA), a condition associated with microhemorrhage. MATERIALS AND METHODS: Multiple MR images were obtained from subjects with probable CAA, with varying sequences (GRE versus susceptibility-weighted imaging [SWI]), section thicknesses (1.2–1.5 versus 5 mm), and magnetic field strengths (1.5T versus 3T). Individual CMB were manually identified and analyzed for contrast index (lesion intensity normalized to normal-appearing white matter signal intensity) and diameter. CMB counts were compared between 1.5T thick-section GRE and thin-section SWI for 3 subjects who underwent both protocols in the same scanning session. RESULTS: With other parameters constant, use of SWI, thinner sections, and a higher field strength yielded medium-to-large gains in CMB contrast index (CI; Cohen d 0.71–1.87). SWI was also associated with small increases in CMB diameter (Cohen d <0.3). Conventional thick-section GRE identified only 33% of CMB (103 of 310) seen on thin-section SWI. Lesions prospectively identified on GRE had significantly greater CI and diameter measured on the GRE image than those not prospectively identified. CONCLUSIONS: The examined alternatives to conventional GRE MR imaging yield substantially improved CMB contrast and sensitivity for detection. Future studies based on these techniques will most likely yield even higher prevalence estimates for CMB.
A Bridge Too Far – Revisited: Reframing Bruer’s Neuroeducation Argument for Modern Science of Learning Practitioners

In Education and the Brain: A Bridge Too Far, John Bruer argues that, although current neuroscientific findings must filter through cognitive psychology in order to be applicable to the classroom, with increased knowledge the neuroscience/education bridge can someday be built. Here, we suggest that translation cannot be understood as a single process: rather, we demonstrate that at least four different ‘bridges’ can conceivably be built between these two fields. Following this, we demonstrate that, far from being a matter of information lack, a prescriptive neuroscience/education bridge (the one most relevant to Bruer’s argument) is a practical and philosophical impossibility due to incommensurability between non-adjacent compositional levels-of-organization: a limitation inherent in all sciences. After defining this concept in the context of biology, we apply this concept to the learning sciences and demonstrate why all brain research must be behaviorally translated before prescriptive educational applicability can be elucidated. We conclude by exploring examples of how explicating different forms of translation and adopting a levels-of-organization framework can be used to contextualize and beneficially guide research and practice across all learning sciences.
Sustaining superior performance in an emerging economy: an empirical test in the Indian context

We demonstrate a negative relationship between pro‐market reforms and the sustainability of superior profits in an emerging economy. The decline in sustainability of superior profits shows that pro‐market reforms bring significant threats in addition to the various opportunities such as greater availability of production factors and greater freedom to enter and operate businesses highlighted in the extant literature. Our study thus contributes to a more complete conceptual understanding of the performance consequences of pro‐market reforms in emerging economies. We also show that investment in research and development and greater investments in marketing and advertising are firm‐level resources that provide a measure of protection against the erosion in sustainability of superior profits associated with pro‐market reforms. Copyright © 2011 John Wiley & Sons, Ltd.
Pneupard: A biomimetic musculoskeletal approach for a feline-inspired quadruped robot

Feline locomotion combines great acrobatic proficiency, unparalleled balance and higher accelerations than other animals. Capable of accelerating from 0 to 100 km h-1 in three seconds, the cheetah (Acinonyx jubatus) is still a mystery which intrigues scientists. Aiming for a better understanding of the source of such higher speeds, we develop a biomimetic platform, where musculoskeletal parameters (range of motion and moment arms) from the biological system can be evaluated with air muscles within a lightweight robotic structure. We performed experiments validating the muscular structure during a treadmill walk, successfully reproducing animal locomotion while adopting an EMG based control method.
A Fast-Convergence Decoding Method and Memory-Efficient VLSI Decoder Architecture for Irregular LDPC Codes in the IEEE 802.16e Standards

In this paper, we propose a modified iterative decoding algorithm to decode a special class of quasi-cyclic low- density parity-check (QC-LDPC) codes such as QC-LDPC codes used in the IEEE 802.16e standards. The proposed decoding is implemented by serially decoding block codes with identical parity-check matrix H1 derived from the parity-check matrix H of the QC-LDPC codes. The dimensions of H1 are much smaller than those of H. Extrinsic values can be passed among these block codes since the code bits of these block codes are overlapped. Hence, the proposed decoding can reduce the number of iterations required by up to forty percent without error performance loss as compared to the conventional message- passing decoding algorithm. A partially-parallel very large-scale integration (VLSI) architecture is proposed to implement such a decoding algorithm. The proposed VLSI decoder can fully take advantage of the proposed decoding to increase its throughput. In addition, the proposed decoder only needs to store check-to- variable messages and hence is memory efficient.
Physical Layer Security in Cellular Networks: A Stochastic Geometry Approach

This paper studies the information-theoretic secrecy performance in large-scale cellular networks based on a stochastic geometry framework. The locations of both base stations and mobile users are modeled as independent two-dimensional Poisson point processes. We consider two important features of cellular networks, namely, information exchange between base stations and cell association, to characterize their impact on the achievable secrecy rate of an arbitrary downlink transmission with a certain portion of the mobile users acting as potential eavesdroppers. In particular, tractable results are presented under diverse assumptions on the availability of eavesdroppers' location information at the serving base station, which captures the benefit from the exchange of the location information between base stations.
Towards a Reference Architecture for Enterprise Mashups

Abstract. Mashup applications combine pieces of functionality from several existing websites to provide new integrated functionality. Existing mashup tools typically address only some aspects of the problem and use a variety of sometimes overlapping and sometimes complementary approaches that make it difficult to compare them. In this ‘work in progress’ paper, we present a first draft of one reference architecture aiming to ease this task. We also discuss in more detail two crucial layers of the architecture: the Data Mashup and Widget Assembly layers. For these layers, we identify their main design aspects and we briefly identify and compare the different approaches to address them. Keywords: enterprise mashups, REST, Web 2.0, reference architecture. 1 Introduction Mashup applications combine pieces of functionality from several existing websites to provide new integrated functionality. Many research works [5][12][16][18] and industrial tools [4][9][10][13][19][20] have appeared during the last two years to ease the creation of mashups. Nevertheless, existing tools address only some aspects of the problem and use a variety of overlapping and complementary approaches that make it difficult to compare them. We aim to create a reference model for mashups that can be used to classify the different proposals and, at the same time, can serve as a guide for the development of complete mashup offerings. We are especially interested in mashups in the corporate world (the so-called ‘enterprise mashups’), but we think the model will be useful for consumer mashups also. Our objectives are: − Providing a reference model composed of a set of layers, useful to compare the different mashup creation approaches. − Comprehensively identifying all the features and design aspects in each layer, discussing the different alternatives proposed to date. − Study in detail certain crucial design aspects of the reference architecture to provide specific recommendations about them. In this ‘work in progress’ paper, we present a first draft of the reference architecture. We also discuss in more detail two crucial layers of the architecture: the Data Mashup and Widget Assembly layers. For these layers, we identify their main design aspects and we briefly identify and compare the different approaches to address them. The rest of the paper is structured as follows: section 2 overviews the reference model, including a description of each of the layers that compose it. Section 3 illustrates the architecture with a sample mashup, explaining how each layer in the model participates to create the final application. Sections 4 and 5 respectively discuss the Data Mashup and Widget Assembly layers of the architecture. Section 6 discusses related work while section 7 outlines our current and future work, and concludes the paper.