Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing exact genetic linkage computations

Genetic linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the likelihood of data, which is needed for learning linkage parameters, using exact inference procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of superlink, which is currently the fastest genetic linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm, and hence enlarge the class of problems that can be handled effectively by exact computations.
Water Distribution System Monitoring and Decision Support Using a Wireless Sensor Network

Water distribution systems comprise labyrinthine networks of pipes, often in poor states of repair, that are buried beneath our city streets and relatively inaccessible. Engineers who manage these systems need reliable data to understand and detect water losses due to leaks or burst events, anomalies in the control of water quality and the impacts of operational activities (such as pipe isolation, maintenance or repair) on water supply to customers. Water Wise is a platform that manages and analyses data from a network of wireless sensor nodes, continuously monitoring hydraulic, acoustic and water quality parameters. Water Wise supports many applications including rolling predictions of water demand and hydraulic state, online detection of events such as pipe bursts, and data mining for identification of longer-term trends. This paper illustrates the advantage of the Water Wise platform in resolving operational decisions.
Photoaffinity labeling of parathyroid hormone receptors: comparison of receptors across species and target tissues and after desensitization to hormone.

Cells derived from human giant cell tumors of bone and fibroblasts derived from human neonatal foreskin respond to parathyroid hormone (PTH) by increasing the intracellular and extracellular levels of adenosine cyclic 3',5'-phosphate (cAMP). Using photoaffinity labeling methods, we examined these cells for the presence of a PTH receptor or a binding subunit of a receptor complex. A previously designed biologically active and photolabile radioligand analogue of PTH was reacted with these intact cells. After photolysis, the cells were extracted, and the proteins were denatured, reduced, and separated by electrophoresis on sodium dodecyl sulfate (Na-DodSO4)-polyacrylamide gels followed by autoradiography. A single membrane component, Mr 70 000, was labeled specifically in intact cells cultured from skeletal and dermal tissue. By mixing, in pairs, photolabeled proteins from (a) intact human cells derived from giant cell tumors of bone, (b) intact human fibroblasts, and (c) canine renal cortical membranes, the receptors (or their binding subunits) for PTH were compared directly and found to be identical in terms of molecular size (as determined by the migration position on NaDod-SO4-polyacrylamide gels) across species (dog and human) and target tissue (bone, skin, and kidney). Preincubation of cells cultured from giant cell tumors of bone with PTH resulted in loss of the PTH-induced cAMP response (desensitization). Preincubation with PTH was accompanied by a marked decrease in photoaffinity labeling of the PTH binding component and suggests that the loss of hormone response in cells preincubated with PTH was related to a decrease in the number or availability of PTH receptors. (ABSTRACT TRUNCATED AT 250 WORDS)
Tweeting Links to Academic Articles 1

attribution 6 1 0 0 1 0 1 0 0 9 (3%) Target 0 0 0 0 0 0 0 0 0 0 (0%) None 19 23 25 26 29 27 28 27 18 222 (82%) Total 30 30 30 30 30 30 30 30 30 270 (100%) Table 4. Sentiment in the tweets of article links. Sentiment Wiley Science Direct Springer JSTOR PLOS ONE PNAS Science Nature DOI Total Neutral 29 28 29 27 30 29 28 30 30 260 (96%) Positive 1 2 1 3 0 1 2 0 0 10 (4%) Negative 0 0 0 0 0 0 0 0 0 0 (0%) Total 30 30 30 30 30 30 30 30 30 270 (100%) Table 5. Interest expressed in the tweets of articl e links. Interest Wiley Science Direct Springer JSTOR PLOS ONE PNAS Science Nature DOI Total No comment 30 29 30 28 29 29 27 29 26 257 (95%) Interesting 0 1 0 2 1 1 3 1 4 13 (5%) Boring 0 0 0 0 0 0 0 0 0 0 (0%) Total 30 30 30 30 30 30 30 30 30 270 (100%)
Accelerating multi-media processing by implementing memoing in multiplication and division units

This paper proposes a technique that enables performing multi-cycle (multiplication, division, square-root &hellip;) computations in a single cycle. The technique is based on the notion of memoing: saving the input and output of previous calculations and using the output if the input is encountered again. This technique is especially suitable for Multi-Media (MM) processing. In MM applications the local entropy of the data tends to be low which results in repeated operations on the same datum.The inputs and outputs of assembly level operations are stored in cache-like lookup tables and accessed in parallel to the conventional computation. A successful lookup gives the result of a multi-cycle computation in a single cycle, and a failed lookup doesn't necessitate a penalty in computation time.Results of simulations have shown that on the average, for a modestly sized memo-table, about 40% of the floating point multiplications and 50% of the floating point divisions, in Multi-Media applications, can be avoided by using the values within the memo-table, leading to an average computational speedup of more than 20%.
Adaptive polygon simplification basing on Delaunay triangulation and its application in high speed PCBs and IC packages simulation

As modern high speed Package Circuit Boards (PCBs) and Integrated Circuit (IC) packages become more and more complicated, the electromagnetic simulation inside the PCBs and IC packages becomes more and more difficult. The most challenge work is that complicated multiple layer shapes inside PCBs and IC packages need very huge amount of high quality meshes for electromagnetic simulation, which lead to huge memory requirement for solving the linear matrix. For most personal computers, that requirement usually lead to out of memory in matrix solution. To overcome this problem without losing the simulation precision, this article presents an algorithm to simplify complex 2-D polygons based on Delaunay triangulation. By checking the smallest angles of triangles which contain an edge of the polygons, the algorithm simplifies polygons adaptively and updates the simplified polygons' Delaunay triangulation. Different from other simplifications which try to decrease the count of vertices, this algorithm tries to delete redundant short edges, leading to greatly reduced mesh points during the process of generating the constrained and quality Delaunay triangulation. The algorithm presented here has been applied for mesh generation for finite-element analysis of complicated PCBs and IC packages. Test results show that the proposed algorithm can reduce more than 75% in total nodes in comparison with the approach without simplification, resulting in significant reduction of computer resources in numerical computation.
NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

Paraspeckles are subnuclear structures formed around NEAT1 lncRNA. Paraspeckles became enlarged after proteasome inhibition caused by NEAT1 transcriptional activation, leading to protein sequestration into paraspeckles. The NEAT1-dependent sequestration affects the transcription of several genes, arguing for a novel role for lncRNA in gene regulation.
Single-molecule optomechanics in “picocavities”

A cool route to nanospectroscopy Confining light to a cavity is often used to enhance the interaction between the light and a particle stored within the cavity. Benz et al. worked with a self-assembled monolayer of biphenyl-4-thiol molecules sandwiched between a gold film and a gold nanoparticle. They used laser irradiation to move atoms in the nanoparticle and produced a “picocavity” that was stable at cryogenic temperatures. The authors were then able to obtain time-dependent Raman spectra from individual molecules. Such subwavelength cavities that can localize light to volumes well below 1 nm3 will enable optical experiments on the atomic scale. Science, this issue p. 726 Strongly subwavelength optical cavities can be used to spectroscopically probe single molecules. Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer (“picocavities”), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 106 enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level.
Pyruvate Kinase Deficiency in Sub-Saharan Africa: Identification of a Highly Frequent Missense Mutation (G829A;Glu277Lys) and Association with Malaria

Background Pyruvate kinase (PK) deficiency, causing hemolytic anemia, has been associated to malaria protection and its prevalence in sub-Saharan Africa is not known so far. This work shows the results of a study undertaken to determine PK deficiency occurrence in some sub-Saharan African countries, as well as finding a prevalent PK variant underlying this deficiency. Materials and Methods Blood samples of individuals from four malaria endemic countries (Mozambique, Angola, Equatorial Guinea and Sao Tome and Principe) were analyzed in order to determine PK deficiency occurrence and detect any possible high frequent PK variant mutation. The association between this mutation and malaria was ascertained through association studies involving sample groups from individuals showing different malaria infection and outcome status. Results The percentage of individuals showing a reduced PK activity in Maputo was 4.1% and the missense mutation G829A (Glu277Lys) in the PKLR gene (only identified in three individuals worldwide to date) was identified in a high frequency. Heterozygous carrier frequency was between 6.7% and 2.6%. A significant association was not detected between either PK reduced activity or allele 829A frequency and malaria infection and outcome, although the variant was more frequent among individuals with uncomplicated malaria. Conclusions This was the first study on the occurrence of PK deficiency in several areas of Africa. A common PKLR mutation G829A (Glu277Lys) was identified. A global geographical co-distribution between malaria and high frequency of PK deficiency seems to occur suggesting that malaria may be a selective force raising the frequency of this 277Lys variant.
A Robust Shallow Parser for Swedish

In this paper, a robust parser for Swedish is presented. The parser identifies the internal structure of phrases, but does not build full trees. In addition to phrase identification, clause boundaries are detected. The parser is designed for robustness against noisy and ill-formed data. An evaluation on 15 000 words shows that the parser’s accuracy on phrase bracketing is 88.7 per cent and the F-score for clause boundary identification is 88.3 per cent.
Impact of Elaboration on Responding to Situational Judgment Test Items

Although faking has been identified as a potential problem in situational judgment tests (SJTs), no studies have investigated proactive approaches for controlling faking in SJTs. Therefore, this study examined the impact of elaboration on responding to SJT items. Elaboration was operationalized as reason-giving. Two hundred and forty-seven master students were assigned to either an honest or a fake condition, and to a non-elaboration or an elaboration condition. Results showed that elaboration decreased the effect of faking for items with high familiarity. Elaboration on familiar items also decreased the percentage of fakers in the top of the distribution. Next, participants in the elaboration condition rated the SJT significantly higher in terms of allowing them to present themselves more realistically and to demonstrate their knowledge, skills, and abilities. Finally, there were no significant differences in participants' satisfaction with the SJT across the elaboration and non-elaboration condition.
Energy-efficient multi-hop broadcasting in low power and lossy networks

In this paper, we investigate schemes for energy-efficient multi-hop broadcasting in large-scale dense Wireless Sensor Networks. We begin with an initial simplified study of the schemes for relay selection. Our first finding is that MPR-based (Multipoint Relay) mechanisms work poorly in a dense network while the recently proposed Multicast Protocol for Low power and Lossy Networks (MPL) protocol based on Trickle performs better. However, Trickle requires to overhear packet retransmissions in the vicinity, while sensor nodes try to avoid overhearing by periodically waking up and going to sleep to save energy. We propose Beacon-based Forwarding Tree (BFT), a new scheme that achieves similar performance to MPL, although it fits better the case of nodes with low radio duty cycling MACs of the type of beacon-enabled IEEE 802.15. 4. Our scheme also guarantees network coverage and its optimized version results in the shortest path distance to the broadcast source at a cost of lesser load mitigation. We compare and discuss the measured performance of MPL on top of ContikiMAC and BFT over beacon-enabled 802.15. 4 on a Contiki testbed. The experimental results of the comparisons show that BFT may achieve very good performance for a range of broadcast intensity, it has a predictable power consumption, a remarkable low power consumption for leaf nodes, and low loss rates. On the other hand, MPL over ContikiMAC can obtain very low duty cycles for low broadcast traffic.
Unsupervised Knowledge-Free Morpheme Boundary Detection

A new algorithm is presented which performs fully unsupervised basic morphologic analysis in any desired language without prior knowledge of that language. The algorithm detects morpheme boundaries and can also be modified to perform other tasks, e.g. clustering of word forms of the same lemma and the classification of the found morphemes. The primary aim is to reach maximum precision, so that the output can be used in a postprocessing machine learning step to increase recall. The algorithm is based on cooccurrence measures and letter successor variety and does not use any complex or computationally intense methods such as LSA. Consequently it is fast, efficient and scales well.
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

Significance Chromatin immunoprecipitation (ChIP) is a gold standard technique for genomic protein localization. We have discovered an artifact in ChIP that leads to reproducible but biologically meaningless enrichment of proteins at highly expressed genes, caused by high levels of polymerase II and polymerase III transcription. These findings call into question reports of unexpected localization of transcription factors, repressors, and cytosolic proteins to highly expressed genes. We suggest caution when interpreting ChIP enrichment at highly expressed genes and suggest a heterologous protein control in ChIP experiments to discern biologically meaningful from artifactual enrichment. Chromatin immunoprecipitation (ChIP) is the gold-standard technique for localizing nuclear proteins in the genome. We used ChIP, in combination with deep sequencing (Seq), to study the genome-wide distribution of the Silent information regulator (Sir) complex in Saccharomyces cerevisiae. We analyzed ChIP-Seq peaks of the Sir2, Sir3, and Sir4 silencing proteins and discovered 238 unexpected euchromatic loci that exhibited enrichment of all three. Surprisingly, published ChIP-Seq datasets for the Ste12 transcription factor and the centromeric Cse4 protein indicated that these proteins were also enriched in the same euchromatic regions with the high Sir protein levels. The 238 loci, termed ”hyper-ChIPable“, were in highly expressed regions with strong polymerase II and polymerase III enrichment signals, and the correlation between transcription level and ChIP enrichment was not limited to these 238 loci but extended genome-wide. The apparent enrichment of various proteins at hyper-ChIPable loci was not a consequence of artifacts associated with deep sequencing methods, as confirmed by ChIP-quantitative PCR. The localization of unrelated proteins, including the entire silencing complex, to the most highly transcribed genes was highly suggestive of a technical issue with the immunoprecipitations. ChIP-Seq on chromatin immunoprecipitated with a nuclear-localized GFP reproduced the above enrichment in an expression-dependent manner: induction of the GAL genes resulted in an increased ChIP signal of the GFP protein at these loci, with presumably no biological relevance. Whereas ChIP is a broadly valuable technique, some published conclusions based upon ChIP procedures may merit reevaluation in light of these findings.
Analyzing the Effects of Reordering Work List Items for Selected Control Flow Patterns

Efficient resource management is an important requirement for many process-oriented applications. Typically, work items are assigned to resources through their work lists. There are many reasons for reordering work items in a resource's work list. For process scheduling, for example, swapping process instances constitutes a mean to keep due times. At the same time, reducing the throughput time of the global process is typically not the primary goal. For process optimization, in turn, the implications of reordering work items on the overall temporal performance of the process might be crucial. In this paper, we investigate how reordering work items affects performance parameters that are typically associated with a first-in-first-out processing mechanism at resources. The analysis is conducted for single process tasks and for typical control flow patterns such as sequence as well as parallel and alternative branchings. It is shown that the implications on the global throughput time are less than expected, while the effects on instance based parameters strongly depend on the control-flow pattern in which the reordering mechanism is implemented. The results are supported by means of a simulation.
La transition financière chinoise : un modèle de financement alternatif dans un contexte de libéralisation financière

Cette these etudie le processus de transformation du systeme financier chinois dans un contexte de liberalisation financiere. Son objectif est de questionner les possibilites d'etablir un modele de financement alternatif en faveur du developpement economique des pays en developpement. Cette recherche montre que l'experience de la transition financiere en Chine peut etre consideree comme un cas de figure pertinent, traduisant la portee des approches de repression financiere et les ecueils des politiques de liberalisation financiere. Elle s'attache a analyser le paradoxe de l'economie chinoise : une performance economique exceptionnelle s'accompagne de la fragilite de son systeme financier. L'objectif specifique de ce travail est de discerner les specificites de la transition financiere chinoise afin de contribuer a une meilleure comprehension de la structure financiere chinoise actuelle, de son efficacite pour le developpement economique du pays et de l'impact de l'ouverture financiere sur la stabilite de son systeme financier.
Mucormycosis in a Renal Transplant Recipient: Case Report and Comprehensive Review of Literature

Mucormycosis is a rare but devastating infection. We present a case of fatal disseminated mucormycosis infection in a renal transplant patient. Uncontrolled diabetes mellitus and immunosuppression are the major predisposing factors to infection with Mucorales. Mucorales are angioinvasive and can infect any organ system. Lungs are the predominant site of infection in solid organ transplant recipients. Prompt diagnosis is challenging and influences outcome. Treatment involves a combination of surgical and medical therapies. Amphotericin B remains the cornerstone in the medical management of mucormycosis, although other agents have been used. Newer agents are promising.
Effect of transmit correlation on the sum-rate capacity of two-user broadcast channels

This letter investigates the effect of the transmit correlation on the sum-rate capacity of a two-user broadcast channel (BC) with the use of equal-power allocation in high signal-to-noise ratio (SNR) environments. It is shown using an upper-bound analysis that the sum-rate capacity of a correlated two-user BC at high SNR highly depends on the phase difference between the transmit correlation coefficients of two users as well as the magnitude of the transmit correlation coefficients, and it is maximized (or minimized) when the principal eigenvectors of the transmit correlation matrix of two users are orthogonal (or parallel) to each other. The analytic results are verified by computer simulation.
Cooperative Strategies for Simultaneous and Broadcast Relay Channels

Consider the simultaneous relay channel (SRC) that consists of a set of relay channels where the source wishes to transmit common and private information to each of the destinations. This problem is recognized as being equivalent to that of sending common and private information to several destinations in presence of helper relays where each channel outcome becomes a branch of the broadcast relay channel (BRC). Cooperative schemes and capacity region for a set with two memoryless relay channels are investigated. The proposed coding schemes, based on decode-and-forward (DF) and compress-and-forward (CF), must be capable of transmitting information simultaneously to all destinations in such a set. Depending on the quality of source-to-relay and relay-to-destination channels, inner bounds on the capacity of the general BRC are derived. Three cases of particular interest are considered: 1) cooperation is based on DF strategy for both users, referred to as DF-DF region; 2) cooperation is based on CF strategy for both users, referred to as CF-CF region; and 3) cooperation is based on DF strategy for one destination and CF for the other, referred to as DF-CF region. These results can be seen as a generalization and hence unification of previous works. An outer bound on the capacity of the general BRC is also derived. Capacity results are obtained for the specific cases of semidegraded and degraded Gaussian SRCs. Rates are evaluated for Gaussian models where the source must guarantee a minimum amount of information to both users while additional information is sent to each of them.