Miracle-dz/UniFAR-FTUs huggingface dataset:
Homophilic Clustering by Locally Asymmetric Geometry

Clustering is indispensable for data analysis in many scientific disciplines. Detecting clusters from heavy noise remains challenging, particularly for high-dimensional sparse data. Based on graph-theoretic framework, the present paper proposes a novel algorithm to address this issue. The locally asymmetric geometries of neighborhoods between data points result in a directed similarity graph to model the structural connectivity of data points. Performing similarity propagation on this directed graph simply by its adjacency matrix powers leads to an interesting discovery, in the sense that if the in-degrees are ordered by the corresponding sorted out-degrees, they will be self-organized to be homophilic layers according to the different distributions of cluster densities, which is dubbed the Homophilic In-degree figure (the HI figure). With the HI figure, we can easily single out all cores of clusters, identify the boundary between cluster and noise, and visualize the intrinsic structures of clusters. Based on the in-degree homophily, we also develop a simple efficient algorithm of linear space complexity to cluster noisy data. Extensive experiments on toy and real-world scientific data validate the effectiveness of our algorithms.
Bridging the gap: combined optical tweezers with free standing lipid membrane

This thesis presents a reliable technology to assemble free standing lipid membranes using microfabricated devices. A microfluidic cartridge consisting of parallel channels connected with a rectangular aperture was designed and characterized to assemble artificial membranes. This methodology resulted on a system capable of assembling lipid bilayer membranes of different lipid composition. Using decane as organic solvent, ~70% of the aperture was covered by the lipid bilayer, while the remaining are was occupied a pocket of solvent (annulus). An almost complete depletion of the annulus can be achieved by choosing a solvent (chloroform) capable of being absorbed by the flowcell material. In comparison with others methods, this approach is an important contribution to the field as it is allows real-time control over conditions (voltage, molecules in solution, pH) over both leaflets of the membrane. Furthermore, the lipid bilayer plane is perpendicular to the microscope focal plane, allowing observation of morphological changes in the lipid membrane and straightforward combination with optical techniques. This work shows the first successful operation of optical tweezers combined with planar lipid membranes accessible from both sides. Direct manipulation of the membrane is demonstrated with membranes with a reduced annulus. One of the microfluidic devices designed in this thesis can host several membranes simultaneously, which are all accessible with an optical tweezers. This device facilitates optical tweezers studies of by allowing to work with different membranes of same lipid composition in a same device with access to both sides of the membranes. Direct mechanical manipulation and adjustable buffer conditions both simultaneously are highly desired features that this technique offers, enabling the study of biological processes that depend on asymmetric conditions on each membrane sides. In addition, the easy access facilitates the study of the formation of lipid nanotube via the intrusion of objects on a flat membrane. The methodology developed in the context of this thesis can be used for combined electrophysiology and force spectroscopy of lipid membranes. To reach the full potential of this technique, a more complete descriptive model of the membrane is needed. More complex lipid membranes could also be implemented as future work.
Optical wireless sensor network design for a conducting chamber

Now a day's majority of the wireless sensor networks (WSNs) are based on Radio Frequency (RF) communication technology. But RF when used in an environment like that of metallic, conducting chamber exhibits large amount of interference due to multipath effects which degrades the performance of the sensor network. Infrared (IR) communication technology which is capable of overcoming the drawbacks exhibited by RF can be used in sensor networks. Suitable IR link can provide high efficiency and mobility. The paper presents design of one such sensor network based on IR communication technology to be deployed in a device known as Tokamak, used to conduct controlled nuclear fusion.
“A catalogue of biases”: The need for a European perspective on antidepressants’ evidence in general practice

For the first time in its history, the board of the Dutch College of General Practitioners (GPs) decided in November 2004 that the multidisciplinary guideline about the management of patients with mood disorders is not acceptable for Dutch GPs. Their criticism concerned the lack of transparency in the process of making the guideline, and its overly positive tone about the effects of antidepressants. What went wrong? In 1999, various Dutch groups of health professionals, including GP representatives of the Dutch College, started enthusiastically to participate in the guideline process. However, we could not agree on whether or not to re-evaluate the evidence about antidepressants versus placebo. The psychiatrists involved claimed that no such comparison was needed as the drugs are already registered. However, the GP participants preferred to take a fresh look at the evidence. Most antidepressants are prescribed by GPs (1), and serious concerns have been raised lately about the methodological quality of antidepressant studies. What were those concerns? A brief and far from exhaustive overview follows:
Atypical Polyproline Recognition by the CMS N-terminal Src Homology 3 Domain*

The CIN85/CMS (human homologs of mouse SH3KBP1/CD2AP) family of endocytic adaptor proteins has the ability to engage multiple effectors and couple cargo trafficking with the cytoskeleton. CIN85 and CMS (Cas ligand with multiple Src homology 3 (SH3) domains) facilitate the formation of large multiprotein complexes required for an efficient internalization of cell surface receptors. It has recently been shown that c-Cbl/Cbl-b could mediate the formation of a ternary complex between one c-Cbl/Cbl-b molecule and two SH3 domains of CIN85, important for the ability of Cbl to promote epidermal growth factor receptor down-regulation. To further investigate whether multimerization is conserved within the family of adaptor proteins, we have solved the crystal structures of the CMS N-terminal SH3 domain-forming complexes with Cbl-b- and CD2-derived peptides. Together with biochemical evidence, the structures support the notion that, despite clear differences in the interaction surface, both Cbl-b and CD2 can mediate multimerization of N-terminal CMS SH3 domains. Detailed analyses on the interacting surfaces also provide the basis for a differential Cbl-b molecular recognition of CMS and CIN85.
Cognitive mechanisms for inferring the meaning of novel signals during symbolisation

As participants repeatedly interact using graphical signals (as in a game of Pictionary), the signals gradually shift from being iconic (or motivated) to being symbolic (or arbitrary). The aim here is to test experimentally whether this change in the form of the signal implies a concomitant shift in the inferential mechanisms needed to understand it. The results show that, during early, iconic stages, there is more reliance on creative inferential processes associated with insight problem solving, and that the recruitment of these cognitive mechanisms decreases over time. The variation in inferential mechanism is not predicted by the sign’s visual complexity or iconicity, but by its familiarity, and by the complexity of the relevant mental representations. The discussion explores implications for pragmatics, language evolution, and iconicity research.
Management of Drug Interactions in Patients with HIV

Objective To provide a compilation of relevant information on drug interactions to assist healthcare practitioners in managing complex HIV-related pharmacotherapy. Data Sources Information was retrieved via a MEDLINE search (January 1966–December 1996) using MeSH headings “human immunodeficiency virus,” “drug interactions,” and names of medications commonly prescribed for the management of HIV infection and related opportunistic infections. Abstracts of international and national conferences, review articles, textbooks, and references of all articles were also searched. Study Selection and Data Extraction All literature on pharmacokinetic or pharmacodynamic interactions was considered for inclusion. Pertinent information, as assessed by the authors, was selected and summarized for discussion. Data Synthesis Drug disposition and/or pharmacologic effect may be affected either by HIV-related physiologic changes or by the presence of concomitant drug therapy. Modifications in drug selection, dosage, dosing regimen, or route of administration may be needed to avoid or manage drug–disease, drug–drug, or drug-food interactions. Management options may depend on the mechanism and the clinical significance of the interaction, the availability of therapeutic alternatives, patient convenience, and cost restrictions. In the absence of specific data, consideration of pharmacokinetic and pharmacodynamic characteristics to assist practitioners in predicting the likelihood of possible interactions was included. Results A comprehensive table of clinically significant drug interactions is provided. Drug interaction principles and practical management strategies are also discussed. Conclusions The potential for drug interactions is extremely common, given the increasing complexity of managing patients infected with HIV. To avoid compromising therapeutic efficacy or increasing drug toxicity, practitioners need to be aware of potential interactions and are encouraged to use a systematic approach when managing patient drug therapy.
Issues in Optimization of Decision Tree Learning : A Survey

Decision tree induction is a simple but powerful learning and classification model. Decision tree learning offers tools for discovery of relationships, patterns and knowledge from data in databases. The volume of data in databases is growing to quite large sizes, both in the number of attributes and instances. Decision tree learning from a very large set of records in a database is quite complex task and is usually a very slow process, which is often beyond the capabilities of existing computers. There are various issues and problems related to decision trees. To handle these issues various approaches have been proposed in the past by different researchers. This paper is an attempt to summarize the proposed approaches, tools etc. for decision tree learning with emphasis on optimization of constructed trees and handling large datasets.
Effect of Annealing on Some Properties of Zn2SnO4 Thin Films Prepared by PLD Technique

In this paper, the investigation of structural and optical properties of Zn2SnO4 thin films were studied. The films are performed on glass substrates by pulsed laser technique (PLD) using laser Nd: YAG at wavelength of 1064 nm with 800 mj laser energy using repetition rate of 6 Hz. and average 400 laser pulses at room temperature and annealing by tubular quartz furnace at temperature (573,773) K for 2 hours with air. XRD measurements showed that the structure for all samples is polycrystalline with a cubic nanostructure. Surface morphology was studied using scanning electron microscopy SEM and atomic force microscopy AFM. After annealing, the roughness of the surface and the mean grain size were increased. Optical properties as a function to wavelength in the range (300-1100 nm) have been studied. Absorption spectra of Zn2SnO4 thin films showed that absorption decreases with increasing annealing temperature. Direct energy gap for a Zn2SnO4 thin film was increases with increasing temperature for all samples due to crystal growth. The optical properties such as extinction coefficient, refractive index, and dielectric constant were also studied.
Electronic Reprint Biological Crystallography Phasing on Anomalous Signal of Sulfurs: What Is the Limit? Biological Crystallography Phasing on Anomalous Signal of Sulfurs: What Is the Limit?

Author(s) of this paper may load this reprint on their own web site provided that this cover page is retained. Republication of this article or its storage in electronic databases or the like is not permitted without prior permission in writing from the IUCr. Recent years have witnessed signi®cant advancements in X-ray data-acquisition techniques and phasing algorithms, which have made possible the successful use of a very small anomalous diffraction signal for the solution of crystal structures of macromolecules. Two crystal structures, a 44 kDa glucose isomerase containing nine sulfurs and a 33 kDa xylanase containing ®ve sulfurs, have been solved from single-wavelength anomalous data using widely available methods and programs. These two enzymes contain less sulfur than most proteins in the bacterial or eukaryotic proteomes, providing a Bijvoet ratio of about 0.6%. For glucose isomerase the automatically interpretable electron-density maps could be obtained at high as well as low resolution. The S-SAD approach relies on the anomalous signal of sulfur naturally occurring in proteins and alleviates all need for sample derivatization. It may therefore be applicable to all protein crystals able to provide accurate diffraction data.
Flap selection as a determinant of success in pressure sore coverage.

OBJECTIVE To establish a treatment algorithm for the long-term surgical management of pressure sores. DESIGN Retrospective case series. SETTING University-based teaching hospital. PATIENTS From March 1979 to July 1995, 280 unselected pressure sore reconstructions (113 ischial, 94 sacral, and 73 trochanteric sores) were performed in 201 patients (130 men and 71 women; age range, 16-90 years; mean, 50 years). Of the patients, 90% had severe spinal cord injuries (paraplegia or quadriplegia). Forty-one percent of the wounds were chronic (present longer than 3 months). MAIN OUTCOME MEASURES Length of stay, postoperative morbidity and mortality, and flap success (defined as a completely healed wound). RESULTS Overall, 89% of the flaps healed primarily (ischium, 83% [94/113]; sacrum, 91% [86/94]; trochanter, 93% [68/73]). Three fourths of cases were treated in a single stage (debridement and reconstruction). The inferior gluteus maximus island flap (ischium) (94% [32/ 34]), the V-Y gluteus maximus advancement flap (sacrum) (97% [36/37]), and the tensor fascia lata flap (trochanter) (95% [42/44]) had the highest success rates. Flap success was not significantly affected by the size of the pressure sore or the number of previous flaps used. Postoperative hospital stays averaged 20 days. The overall complication rate was 28%, most commonly from a slight wound edge dehiscence. CONCLUSIONS Flap selection and the appropriate short- and long-term sequence of flap use significantly improve success rates for pressure sore coverage. Reconstruction can be reliably performed in a single stage with a relatively short hospitalization.
THE STRUCTURE AND CONCENTRATION OF SOLIDS IN PHOTORECEPTOR CELLS STUDIED BY REFRACTOMETRY AND INTERFERENCE MICROSCOPY

Fragments of freshly obtained retinas of several vertebrate species were studied by refractometry, with reference to the structure of the rods and cones. The findings allowed a reassessment of previous descriptions based mainly on fixed material. The refractometric method was used also to measure the refractice indices and to calculate the concentrations of solids and water in the various cell segments. The main quantitative data were confirmed by interference microscopy. When examined by the method of refractometry the outer segments of freshly prepared retinal rods appear homogeneous. Within a few minutes a single eccentric longitudinal fiber appears, and transverse striations may develop. These changes are attributed to imbibition of water and swelling in structures normally too small for detection by light microscopy. The central "core" of outer segments and the chromophobic disc between outer and inner segments appear to be artifacts resulting from shrinkage during dehydration. The fresh outer segments of cones, and the inner segments of rods and cones also are described and illustrated. The volumes, refractive indices, concentrations of solids, and wet and dry weights of various segments of the photoreceptor cells were tabulated. Rod outer segments of the different species vary more than 100-fold in volume and mass but all have concentrations of solids of 40 to 43 per cent. Cone outer segments contain only about 30 per cent solids. The myoids, paraboloids, and ellipsoids of the inner segments likewise have characteristic refractive indices and concentrations of solids. Some of the limitations and particular virtues of refractometry as a method for quantitative analysis of living cells are discussed in comparison with more conventional biochemical techniques. Also the shapes and refractive indices of the various segments of photoreceptor cells are considered in relation to the absorption and transmission of light. The Stiles-Crawford effect can be accounted for on the basis of the structure of cone cells.
KASL Clinical Practice Guidelines: Management of Alcoholic Liver Disease

In Korea, alcoholic liver disease (ALD) is the second most common cause of chronic liver disease after viral liver disease, and the rate of alcohol-related deaths is high, at 9.6 deaths per 100,000 persons per year. Nevertheless, the Korean culture is lenient toward drinking and the inebriated state, which is due to alcohol being considered an important social lubricant for both business and private gatherings. ALD tends to be thought of as a personal problem, and as such its importance is underestimated. Furthermore, academic interest in ADL is dwindling since the advent of antiviral therapy. However, given the keen worldwide interest and research into ALD, there remains a need for clinical practice guidelines that are tailored to the Korean healthcare system for the management of this disease. This need prompted the Korean Association for the Study of the Liver (KASL) to develop the “KASL Clinical Practice Guidelines: Management of Alcoholic Liver Disease”, based on a systematic approach to reflect evidence-based medicine and expert opinion in internal medicine and psychiatry, with the aim of setting clinical practice guidelines for the management of ALD and improving public health in Korea.
Improvement in Surface Passivation of c-Si Using Gradient-Layered a-Si:H Film for High Efficiency Silicon Heterojunction Solar Cells

Gradient-layered $i$ a-Si:H passivation is shown to enhance minority carrier lifetimes in silicon heterojunction solar cells compared to single or dual-layer passivation structures. The gradient layered passivation contains optimized interfacial and capping layers for passivating the $i$ a-Si:H/c-Si interface and a gradient layer for suppressing charge traps in bulk $i$ a-Si:H. Gradient layers were obtained by changing the hydrogen dilution ratio continuously during deposition of $i$ a-Si:H. The minority carrier lifetime of the c-Si substrate using gradient-layered passivation was as high as $2451\mu \mathbf{s}$ , compared to 1831 μs for dual-layered passivation at $2\times 10^{15}$ cm−1injection level. JV characteristics of Silicon heterojunction (SHJ) solar cell employing these gradient passivation schemes will also be discussed. When the gradient-layered passivation was implied to interdigitated back contact (IBC) SHJ solar cells, there was an improvement in efficiency, compared to other passivation schemes such as single and dual passivation.
Throughput and energy efficiency in topology-controlled multi-hop wireless sensor networks

In the context of multi-hop wireless networks, various topology control algorithms have been proposed to adapt the transmission range of nodes based on local information while maintaining a connected topology. These algorithms are particularly suited for deployment in sensor networks which typically consist of energy constrained sensors. Sensor nodes should support power adaptation in order to use the benefits of topology control for energy conservation. In this paper, we design a framework for evaluating the performance of topology control algorithms using overall network throughput, and total energy consumption per packet delivered, as the metrics. Our goal is to identify the scenarios in which topology control improves the network performance. We supplement our analysis with ns2 simulations using the cone-based topology control algorithm [10, 19]. Based on our analysis and simulations, we find that link layer retransmissions are essential with topology control to avoid throughput degradation due to increase in number of hops in lightly loaded networks. In heavily loaded networks, the throughput can be improved by a factor up to k2, where k is the average factor of reduction in transmission range using topology control. Studies of energy consumption reveal that improvements of up to $k^4$ can be obtained using topology control. However, these improvements decrease as the traffic pattern shifts from local (few hop connections) to non-local (hop lengths of the order of the diameter of the network). These results can be used to guide the deployment of topology control algorithms in sensor networks.
Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)

Rates of biodiversity loss are higher in freshwater ecosystems than in most terrestrial or marine ecosystems, making freshwater conservation a priority. However, prioritization methods are impeded by insufficient knowledge on the distribution and conservation status of freshwater taxa, particularly invertebrates. We evaluated the extinction risk of the world's 590 freshwater crayfish species using the IUCN Categories and Criteria and found 32% of all species are threatened with extinction. The level of extinction risk differed between families, with proportionally more threatened species in the Parastacidae and Astacidae than in the Cambaridae. Four described species were Extinct and 21% were assessed as Data Deficient. There was geographical variation in the dominant threats affecting the main centres of crayfish diversity. The majority of threatened US and Mexican species face threats associated with urban development, pollution, damming and water management. Conversely, the majority of Australian threatened species are affected by climate change, harvesting, agriculture and invasive species. Only a small proportion of crayfish are found within the boundaries of protected areas, suggesting that alternative means of long-term protection will be required. Our study highlights many of the significant challenges yet to come for freshwater biodiversity unless conservation planning shifts from a reactive to proactive approach.
Fast Ge p-i-n Photodetectors on Si

We report about a top-side illuminated Ge photodetector, which is appropriate for transmission of high-speed data at infrared telecommunication wavelengths and is monolithically integrated on a standard Si substrate (Jutzi et al., 2005) for 1552 nm operation. A 3-dB-bandwidth of 38.9 GHz is achieved for a 10 mum diameter detector and a reverse bias of 2 V. These results demonstrate the potential of SiGe photodiodes for Si based optical links at data rates up to 40 Gbit/s and beyond