Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomic structure and dynamics of pentameric ligand‐gated ion channels: new insight from bacterial homologues

Pentameric ligand‐gated ion channels (pLGICs) are widely expressed in the animal kingdom and are key players of neurotransmission by acetylcholine (ACh), γ‐amminobutyric acid (GABA), glycine and serotonin. It is now established that this family has a prokaryotic origin, since more than 20 homologues have been discovered in bacteria. In particular, the GLIC homologue displays a ligand‐gated ion channel function and is activated by protons. The prokaryotic origin of these membrane proteins facilitated the X‐ray structural resolution of the first members of this family. ELIC was solved at 3.3 Å in a closed‐pore conformation, and GLIC at up to 2.9 Å in an apparently open‐pore conformation. These data reveal many structural features, notably the architecture of the pore, including its gate and its selectivity filter, and the interactions between the protein and lipids. In addition, comparison of the structures of GLIC and ELIC hints at a mechanism of channel opening, which consists of both a quaternary twist and a tertiary deformation. This mechanism couples opening–closing motions of the channel with a global reorganization of the protein, including the subunit interface that holds the neurotransmitter binding sites in eukaryotic pLGICs.
Abnormal Scene Change Detection From a Moving Camera Using Bags of Patches and Spider-Web Map

This paper proposes a novel surveillance system for detecting exceptional scene changes as abnormal events with a mobile camera mounted on a robot. In contrast to abnormal event analysis using fixed cameras, three key problems should be tackled in this system, i.e., scene construction, robot localization, and scene comparison. For the first problem, scene construction, a clustering scheme is proposed for extracting a set of key frames from the surveillance environment. Each key frame is further divided into a set of patches, which forms a sparse representation for representing scene contents. In addition to the compression effect, the scheme can tackle the effects of misalignment and lighting changes well. For the localization problem, a novel patch matching method is proposed to reduce not only the size of the search space but also the size of the feature dimensions in similarity matching. To prune the search space, a set of projection kernels is used to construct a ring structure. Then, one order of time complexity in the similarity calculation can be reduced from the structure. After scene searching, the robot location is not always guaranteed to be successfully registered to the scene map. Thus, a novel spider-web map is proposed to tackle the effect of misalignment and then detect different exceptional scene changes from the videos. The proposed method has been rigorously tested on a variety of videos to demonstrate its superiority in object detection and abnormal scene change detection.
Automatic Determination of Left- and Right-Hand Bone Age in the First Zurich Longitudinal Study

Background/Aims: A more advanced bone age (BA) has been reported for the left hand relative to the right hand, while another study has found no such effect. The aim was to study the average difference of automated BoneXpert BA determination (left- vs. right-hand) for normal children, examine the precision of automatic BA and provide a BA reference for normal Caucasian children. Methods: Radiographs of both hands (age range: 2–20 years) were digitised and analysed automatically to determine Greulich-Pyle BA, producing analysis results for 3,374 left-hand and 2,752 right-hand images. Results: Comparison of left- and right-hand BA showed no average difference (<0.07 years, 95% confidence). The SD of the differences between left and right sides was 0.25 years for boys as well as girls, implying the precision of automated Greulich-Pyle BA determination was 0.18 years or better. Greulich-Pyle BA for boys and girls were on average 0.10 and 0.21 years below the chronological age. Conclusion: The left and right hand give the same BA on average and the SD between the sides is 0.25 years, indicating an excellent precision of the automated method.
Background Paper: Research and Development and Extension Services in Agriculture and Food Security

Investments in agricultural research and extension have consistently demonstrated high rates of return in Asia and the Pacific. However, the recent global food crisis exposed the vulnerability of food supply systems and reversed many past achievements in the fight against hunger and malnutrition. It also demonstrated the need for continued innovation. In view of the emerging economic, climatic, and political scenarios in the region, this paper explores the role of applied research for development and extension services through the two-pronged approach of boosting food production and preventing losses. Priority areas for research emphasize attention to smallholder farming systems, practical business models, the integration of gender, and multidisciplinary research that is sensitive to nutritional outcomes. In addition, pioneering mechanisms to public-private partnerships are examined towards the strategic use of renewed stakeholder commitments to achieve food security and prevent future crisis. By learning from the past and looking into the future, this paper makes a case for sustained investments in research and extension to address the numerous challenges along the pathway from agriculture production and distribution to consumption and utilization.
Phosphoinositide 3-Kinase Is Involved in the Tumor-specific Activation of Human Breast Cancer Cell Na+/H+Exchange, Motility, and Invasion Induced by Serum Deprivation*

Whereas the tumor acidic extracellular pH plays a crucial role in the invasive process, the mechanism(s) behind this acidification, especially in low nutrient conditions, are unclear. The regulation of the Na+/H+ exchanger (NHE) and invasion by serum deprivation were studied in a series of breast epithelial cell lines representing progression from non-tumor to highly metastatic cells. Whereas serum deprivation reduced lactate production in all three cells lines, it inhibited NHE activity in the non-tumor cells and stimulated it in the tumor cells with a larger stimulation in the metastatic cells. The stimulation of NHE in the tumor cell lines was the result of an increased affinity of the internal H+regulatory site of the NHE without changes in sodium kinetics or expression. Serum deprivation conferred increased cell motility and invasive ability that were abrogated by specific inhibition of the NHE. Inhibition of phosphoinositide 3-kinase by overexpression of a dominant-negative mutant or wortmannin incubation inhibited NHE activity and invasion in serum replete conditions while potentiating the serum deprivation-dependent activation of the NHE and invasion. These results indicate that the up-regulation of the NHE by a phosphoinositide 3-kinase-dependent mechanism plays an essential role in increased tumor cell invasion induced by serum deprivation.
Segmentation of optic nerve head images

Segmentation of the optic nerve head or optic disc in digital retinal fundus photographs is a non-invasive procedure that plays an important role in early detection of abnormalities of the eyes, particularly glaucoma diseases. Developing an automatic system, we employ image processing techniques coupled with graph cut algorithms from combinatorial optimization. Avoiding the need of manual pre-segmentation for constructing an initial graph, a supervised learning approach is effectively and efficiently applied. Crucial information is extracted from a set of labeled binary masks and integrated into weight assignments of the edges of the graph. We associate the characteristically bell-shape of a Gaussian distribution with the rounded circular-shape of the optic disc. Our approach was validated and evaluated on the RIM-ONE open database. Segmentation is successful on 91.12% of the entire 169 images, achieving 91% sensitivity and 88% accuracy.
Connexin43 Expression Levels Influence Intercellular Coupling and Cell Proliferation of Native Murine Cardiac Fibroblasts

Little is known about connexin expression and function in murine cardiac fibroblasts. The authors isolated native ventricular fibroblasts from adult mice and determined that although they expressed both connexin43 (Cx43) and connexin45 (Cx45), the relative abundance of Cx45 was greater than that of Cx43 in fibroblasts compared to myocytes, and the electrophoretic mobility of both Cx43 and Cx45 differed in fibroblasts and in myocytes. Increasing Cx43 expression by adenoviral infection increased intercellular coupling, whereas decreasing Cx43 expression by genetic ablation decreased coupling. Interestingly, increasing Cx43 expression reduced fibroblast proliferation, whereas decreasing Cx43 expression increased proliferation. These data demonstrate that native fibroblasts isolated from the mouse heart exhibit intercellular coupling via gap junctions containing both Cx43 and Cx45. Fibroblast proliferation is inversely related to the expression level of Cx43. Thus, connexin expression and remodeling is likely to alter fibroblast function, maintenance of the extracellular matrix, and ventricular remodeling in both normal and diseased hearts.
Alignment of a Vertical Migrated Periodontal Pre-injured Upper CentralIncisor

Introduction: Labial and vertical migration of maxillary incisors is a common complication of moderate to severe periodontitis and it is often the motivation for patients to seek periodontal and orthodontic treatment. Aims: This case report demonstrates a minimal invasive orthodontic therapy with modified aligners to straighten a periodontal pre-injured upper central incisor with sophisticated bone defect. Methods: A female patient, aged 36 years, presented in our department with the chief complaint of elongation and protrusion of her right upper central incisor, which had strongly changed its position within at least the last year on account of a sophisticated periodontal injury and it had already been incisal grinded by her general dentist up to the exposure of dentin. The clinical evaluation revealed a vertical divergence and protrusion of 2 mm, respectively, frontal dental crowding, and distinctive vertical bone loss with probing depth of at least 8 mm at the most affected side, mild loosening, but no signs of periodontal inflammation. A minimal invasive treatment with a modified aligner appliance, including a total of 3 aligner series and 6 set-ups, was carried out. Intrusion was realized with vertical elastic, little buttons bonded at the aligner and an incisal slot opening. Results: Total treatment time amounted 6 months. The result was stabilized with a bonded retainer. Radiologic control revealed no variation in tooth length and a stable periodontal pocket after active orthodontic treatment. Discussion and conclusion: This case report demonstrates that orthodontic aligner treatment in the aesthetical area is possible and can be safely performed even in case of distinctive bone loss.
Visual detection of motion speed in humans: spatiotemporal analysis by fMRI and MEG

Humans take a long time to respond to the slow visual motion of an object. It is not known what neural mechanism causes this delay. We measured magnetoencephalographic neural responses to light spot motion onset within a wide speed range (0.4–500°/sec) and compared these with human reaction times (RTs). The mean response latency was inversely related to the speed of motion up to 100°/sec, whereas the amplitude increased with the speed. The response property at the speed of 500°/sec was different from that at the other speeds. The speed‐related latency change was observed when the motion duration was 10 msec or longer in the speed range between 5 and 500°/sec, indicating that the response is directly related to the speed itself. The source of the response was estimated to be around the human MT+ and was validated by functional magnetic imaging study using the same stimuli. The results indicate that the speed of motion is encoded in the neural activity of MT+ and that it can be detected within 10 msec of motion observation. RT to the same motion onset was also inversely related to the speed of motion but the delay could not be explained by the magnetic response latency change. Instead, the reciprocal of RT was linearly related to the reciprocal of the magnetic response latency, suggesting that the visual process interacts with other neural processes for decision and motor preparation. Hum. Brain Mapping 16:104–118, 2002. © 2002 Wiley‐Liss, Inc.
Provigil (Modafinil) Plus Cognitive Behavioral Therapy for Methamphetamine Use in HIV+ Gay Men: A Pilot Study

Objectives: To evaluate the efficacy of modafinil combined with cognitive behavioral therapy (CBT) for treatment of methamphetamine (MA) dependence among HIV+ gay men. Methods: In a single blind trial, modafinil was administered for 12 weeks, followed by a 4-week placebo phase. CBT was conducted for 18 sessions over the 16-week study. Primary outcome measures were self-reported use of days per week plus urine toxicology assays. Additional measures included the Beck Depression Inventory, Cravings Scale, and O/C Crystal Use Scale. Response was defined as > 50% decline in days used per week. Thirteen patients were enrolled over an 18-month period. Results: Ten patients (77%) completed the trial, although two discontinued modafinil due to side effects. Six of the ten study completers reduced their MA use by > 50%. Conclusions: These preliminary results suggest good retention using combined medication and psychotherapy, and support further examination of modafinil and CBT in double-blind placebo controlled trials.
Ultra-Low-Power Optimizations for the IEEE 802.15.4 Networking Protocol

IEEE 802.15. 4 is a recent low-rate/low-power standard for wireless personal area and sensor networks. Its simple infrastructure, intermediate range and reasonable power performance make it a candidate for a wide range of applications that require a low throughput but a reasonable device lifetime and consequently a certain power efficiency. Anyway there are some main inefficiencies of the protocol that limit its power performance and cause unnecessary power waste in some situations. In this paper these limitations of the standard in terms of power performance are investigated. Possible optimizations that can be achieved with minimal or null changes on available 802.15. 4 compliant hardware platforms are suggested. We use our modeling technique and our simulator validated for 802.15. 4 in to provide a complete evaluation of proposed optimizations.
Dynamic assessment of visual neglect: The Mobility Assessment Course as a diagnostic tool

ABSTRACT Introduction: Visual neglect is a frequent disorder following stroke and is often diagnosed by neuropsychological assessment. However, paper-and-pencil tasks have low predictive value as they lack sensitivity to capture neglect in complex, dynamic situations, such as activities of daily living. Aims of the current study were to assess the feasibility of the Mobility Assessment Course (MAC), a visual search multitask, to assess neglect, and its relation with existing neglect tasks. Method: Stroke patients admitted for inpatient rehabilitation and healthy controls were tested with the MAC in different corridors. Participants had to move through a corridor, finding and reporting 24 targets attached to the walls. In addition, the shape cancellation, line bisection, and Catherine Bergego Scale (CBS) were used in order to compare the MAC with existing diagnostic tools for neglect. Results: Administering the MAC was feasible, as 112 of 113 patients completed the MAC with a median duration of 4.09 min. Depending on the corridor where the assessment took place, in 88.5–93.3% of assessments all targets were visible. The number of omissions (total and contralesional) and the asymmetry score (contralesional–ipsilesional omissions) on the MAC as well as collisions and corrections, were higher for patients with neglect than for those without neglect. Depending on the neglect task used, 4.0–18.6% of patients without neglect on neuropsychological tasks or the CBS showed neglect on the MAC. Vice versa, 17.2–29.3% of patients who showed neglect at neuropsychological assessment or the CBS did not do so on the MAC. Finally, a moderate to strong positive relation was seen between neglect at neuropsychological assessment, the CBS, and the MAC. Conclusions: The MAC is an ecological task in which both quantitative and qualitative data on neglect can be collected. In order to assess the presence of neglect and neglect severity in a dynamic way, the MAC could be administered in conjunction with neuropsychological assessment.
3-D Microwave Magnitude Combined Tomography for Breast Cancer Detection Using Realistic Breast Models

Microwave imaging (MWI) is a feasible tool for medical imaging driven by its capability to discriminate between different types of tissues and abnormalities. Nowadays, a variety of reconstruction algorithms are investigated, mainly based on complex and time-consuming iterative schemes. Considering a future patient use, an algorithm requiring tens of hours seems unrealistic. In this letter, a 3-D quasi real-time algorithm, inspired in a computationally efficient modified-Born method, is assessed for early-stage breast cancer detection using 3-D anthropomorphic breast phantoms. The algorithm uses multifrequency information over a portion of the UWB range to produce robust images with a fair tradeoff between resolution and penetration.
The Sense of Mastery as a Mediator and Moderator in the Association Between Economic Hardship and Health in Late Life

Objectives: This study examines the ways in which the sense of mastery modifies the association between economic hardship experienced at different life stages and late-life depression, anxiety, and physical symptoms. Methods: Using data from a sample of 1,167 older adults, ordinary least squares regression techniques were used to estimate the main and mastery-contingent effects of economic hardship. Results: Results underscore the dual role of the sense of mastery in the stress process. First, mastery mediates the effects of both earlier- and later-life economic hardships on elders’ current physical and mental health. Second, mastery moderates the health impact of economic hardship, although those patterns depend on the period of economic hardship and health outcome. Discussion: Integrating the stress process model and a life course perspective, the authors argue that to fully understand protective capacity of psychosocial resources, stressors encountered at different life stages should be taken into account.
Experimental evidence of the physiologic mechanism of certain types of headache.

In a previous communication, 1 two of us discussed the mechanism of headache produced experimentally by the intravenous injection of histamine, emphasizing the significance of the secondary rise in arterial pressure in the production of the headache. It was found that in patients suffering from post-traumatic headaches such an injection usually "reproduced" the posttraumatic headache (i. e., was followed by a headache which was the same in character and location as the usual post-traumatic one). The conclusion was drawn that the injection of histamine activated a physiologic mechanism similar to that concerned in the production of the majority of post-traumatic headaches. In the present paper, we wish to report the results of further studies bearing on the mechanism of headaches produced by the intravenous injection of histamine and on the relation between such headaches and various other types of headache encountered clinically. From the facts observed certain conclusions can be
The architecture of diagnostic research

This is the second in a series of five articles Considerable effort has been expended at the interface between clinical medicine and scientific methods to achieve the maximum validity and usefulness of diagnostic tests. This article focuses on the specific kinds of questions that arise in diagnostic research and the study architectures (the conversions of these clinical questions into appropriate research designs) used to answer them. As an example we shall take shall take assessment of the value of the plasma concentration of B-type natriuretic peptide (BNP) in the diagnosis of left ventricular dysfunction.1 Randomised controlled trials are dealt with elsewhere. As in other forms of clinical research, there are several different ways studying the potential or real diagnostic value of a physical sign or laboratory test, and each is appropriate to one kind of question and inappropriate for others. Among the possible questions about the relation between a putative diagnostic test and a target disorder (for example, the concentration of BNP and left ventricular dysfunction), four are most relevant. #### Summary points Diagnostic studies should match methods to diagnostic questions The keys to validity in diagnostic test studies are Both specificity and sensitivity may change as the same diagnostic test is applied in primary, …
Mutation analysis of SBDS in pediatric acute myeloblastic leukemia

Shwachman–Diamond syndrome (SDS) is associated with a high risk of myelodysplasia, acute myeloid leukemia (AML), and chromosome 7 abnormalities. Ninety percent of SDS patients have mutations in SBDS on 7q11. Herein, we studied the role of genetic alterations in SBDS in AML.
Map building using fuzzy ART, and learning to navigate a mobile robot on an unknown world

This paper introduces a new approach, based on the application of the fuzzy ART neural architecture, for online map building from actual sensor data collected with a mobile robot. This method is then integrated as a complement, on the parti-game learning approach, allowing the system to make a more efficient use of collected sensor information. Also, a predictive online trajectory filtering method is introduced on the learning approach. Instead of having a mechanical device (robot) moving to search the world the idea is to have the system analysing trajectories in a predictive mode, by taking advantage of the improved world model. The real robot will only move to try trajectories that have been predicted to be successful, allowing lower exploration costs. This results on an overall new and powerful method for simultaneous and cooperative construction of a world model, and learning to navigate from an initial position to a goal region on an unknown world. It is assumed that the robot knows its own current world location. It is additionally assumed that the mobile robot is able to perform sensor-based obstacle detection (not avoidance), and straight-line motions. Results of experiments with a real Nomad 200 mobile robot will be presented, demonstrating the effectiveness of the proposed methods.