Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning spatio-temporal dynamics Nonparametric Methods for Optimal Forecasting and Automated Pattern Discovery

Many important scientific and data-driven problems involve quantities that vary over space and time. Examples include functional magnetic resonance imaging (fMRI), climate data, or experimental studies in physics, chemistry, and biology. Principal goals of many methods in statistics, machine learning, and signal processing are to use this data and i) extract informative structures and remove noisy, uninformative parts; ii) understand and reconstruct underlying spatio-temporal dynamics that govern these systems; and iii) forecast the data, i.e., describe the system in the future. Being data-driven problems, it is important to have methods and algorithms that work well in practice for a wide range of spatio-temporal processes as well as various data types. In this thesis I present such generally applicable statistical methods that address all three problems in a unifying manner. I introduce two new techniques for optimal nonparametric forecasting of spatiotemporal data: hard and mixed LICORS (Light Cone Reconstruction of States). Hard LICORS is a consistent predictive state estimator and extends previous work from Shalizi (2003); Shalizi, Haslinger, Rouquier, Klinkner, and Moore (2006); Shalizi, Klinkner, and Haslinger (2004) to continuous-valued spatio-temporal fields. Mixed LICORS builds on a new, fully probabilistic model of light cones and predictive states mappings, and is an EM-like version of hard LICORS. Simulations show that it has much better finite sample properties than hard LICORS. I also propose a sparse variant of mixed LICORS, which improves out-of-sample forecasts even further.
Implementing OLAP Query Fragment Aggregation and Recombination for the OLAP Enabled Grid

In this paper we propose a new query processing method for the OLAP enabled grid, which blends sophisticated cache extraction techniques and data grid scheduling to efficiently satisfy OLAP queries in a distributed fashion. The heart of our approach is our query fragment aggregation and recombination (FAR) strategy that partitions OLAP queries into subqueries which can be effectively answered by retrieving and aggregating multiple fragments of cached data from nearby grid sources, or as a last resort, more remote backend data warehouses. We have implemented and experimentally evaluated our query processing method and found that our strategy reduces query time between 50% and 60% for practical user cache sizes and network parameters.
A generic camera model and calibration method for conventional, wide-angle, and fish-eye lenses

Fish-eye lenses are convenient in such applications where a very wide angle of view is needed, but their use for measurement purposes has been limited by the lack of an accurate, generic, and easy-to-use calibration procedure. We hence propose a generic camera model, which is suitable for fish-eye lens cameras as well as for conventional and wide-angle lens cameras, and a calibration method for estimating the parameters of the model. The achieved level of calibration accuracy is comparable to the previously reported state-of-the-art
Leadership in the West and the Islamic World: A Comparative Analysis

Leadership, studied by scholars for centuries, has always been a contested terrain. It is a multidisciplinary field concerned as well with ethics and morality. However, leadership is conceived differently in the West and the East and this difference is largely attributed to the differences in culture and their respective world views. The Western perspective of leadership dominates the world of learning to the total neglect of Eastern perspectives. This paper examines leadership from an Islamic perspective which has so far been neglected or misrepresented because it is studied based on European experiences. This necessitates reviewing the Western perspective on leadership as a backdrop for making a case for studying leadership from perspectives other than the West. The paper is less concerned with comparing leadership between the West and the rest. Its emphasis is upon examining roots of why the concept of leadership in Islam is different from those of the West. The final section of the paper presents the features of leadership portrayed by the Heads of State in 47 countries in which Muslims form a majority of the population and examines their congruence with the leadership concept of Islam.
Imaging the Moho and the Main Himalayan Thrust in Western Nepal With Receiver Functions

The crustal structure of Western Nepal is studied for the first time by performing receiver function analysis on teleseismic waveforms recorded at 16 seismic stations. The Moho geometry is imaged as it deepens from ~40‐km depth beneath the foothills and the Lesser Himalaya to ~58‐km depth beneath the Higher Himalayan range. A midcrustal low‐velocity zone is detected at ~15‐km depth along ~55‐km horizontal distance and is interpreted as the signature of fluids expelled from rocks descending in the footwall of the Main Himalayan Thrust. Our new image allows structural comparison of the Moho and of the Main Himalayan Thrust geometry along‐strike of the Himalayas and documents long‐wavelength lateral variations. The general crustal architecture observed on our images resembles that of Central Nepal; therefore, Western Nepal is also expected to be able to host large (MW > 8) megathrust earthquakes, as the 1505 CE event.
α-catenin

Downregulation or loss of α-catenin occurs in multiple human cancer types. The traditional view of α-catenin is that it is one of the core components of the E-cadherin-catenin complex and is required for maintaining the integrity of the intercellular adherens junction, a cell junction whose cytoplasmic face is linked to the actin cytoskeleton. Therefore, loss of α-catenin can result in loss of cell-cell adhesion, a common characteristic of cancer cells. There is an emerging recognition; however, that α-catenin also regulates multiple signaling pathways independent of adherens junctions. For instance, α-catenin functions as a tumor suppressor in E-cadherin-negative basal like breast cancer cells by inhibiting NF-κB signaling. In this perspective, we discuss the role and mechanisms of α-catenin in regulating several signaling pathways in cancer.
PMG: online generation of high-quality molecular pictures and storyboarded animations

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs. jussieu.fr/PMG.html.
CHOROIDAL MELANOMA

DEAR SIRS,-Mr. Foster AMoore has very kindly shown us his letter (p. 46). The question of a congenital patch in the pigment epithelium was considered;but we had not thought such a patch could enlarge. The letter relieves my mind very much. Pritchard and I got to know and like the patient, and wehad an unpleasantly guilty feeling that perhaps we were failing in our duty in not removing his eye. After Mr. Foster Moore's letter we shall watch the case with diminished apprehension. Yours sincerely,
Characterizing hydrogeological properties and monitoring biogeochemical processes using geophysical data

the distribution of a slow release polylactate and to monitor the distribution of the amendment and changes in geochemical phase and pore fluid composition associated with a biostimulation experiment. This case study illustrates the value of using multiple types of geophysical datasets to investigate complex and dynamic systems. Finally, at the Uranium-contaminated Rifle UMTRA site in Colorado, surface-and borehole-based complex resistivity techniques were used to monitor changes in mineralogy associated with both iron and sulfate reduction processes that occurred in
Alarm correlation engine (ACE)

Networks are growing in size and complexity, resulting in increased alarm volume and number of unfamiliar alarms. Often, there is no proportional increase in monitoring personnel and response time to faults suffers. GTE deployed Telephone Operations Network Integrated Control System (TONICS) in 1993 to support its network management operations. To stay competitive in the face of continued staff reductions, increase in network size, and monitoring complications related to deregulation of the telephone industry, GTE is introducing artificial intelligence techniques into TONICS. Alarm Correlation Engine (ACE), the system described in this paper, is part of the effort. ACE aids network management by correlating alarms on the basis of common cause to provide alarm compression, filtering, and suppression. In conjunction with its ability to carry out prescribed responses, it improves response times and increases productivity. ACE was developed with the following requirements: reliability, speed, versatility (handle alarms from different switches and networks), ease of knowledge engineering (field technicians must be able to construct, test, and modify correlation patterns), handle in real time multiple network problems, and finally, interface smoothly with GTE's TONICS system. ACE's strength lies in its domain specific correlation language which facilitates knowledge engineering and in its asynchronous processing core that enables integration into a real-time monitoring system.
Maximum SINR-based beamforming for the MISO interference channel

Multi-antenna wireless mesh networks are a promising means to achieve high data rate in next generation of wireless networks. However, because co-channel interference (CCI) is a major source of performance degradation in such networks, cooperative techniques have been proposed to cope with CCI. Nevertheless, these techniques require the exchange of information between the transmit nodes (e.g. channel knowledge acquisition, synchronization, etc.) and are thus very complex to implement. Conversely, non-cooperative techniques have limited complexity and are therefore an interesting alternative. Two non-cooperative methods have been proposed in the literature: the zero-forcing and the maximal signal-to-noise ratio beamformers. However, those two schemes do not maximize the aggregate capacity of the network nor minimize the bit error rate (BER) of each communication channel. In this paper, we consider a different optimization metric based on maximizing the SINR at the transmitters. We show that the proposed scheme achieves maximal capacity and outperforms the two existing non-cooperative schemes in terms of BER.
Clostridium difficile Associated Diarrhea

To the Editor: Clostridium difficile-associated diarrhea and colitis is frequently noted in patients receiving antibiotic therapy in hospitalsi and chronic-care facilities2 The organism is usually acquired nosocomially through human contact or from the hospital environment that is frequently contaminated with C difficile spores.3 Immunoblot typing has been used to demonstrate nosocomial infection.4 As part of an investigation of an outbreak of C difficile-associated diarrhea, we studied the possible role of rectal thermometers as a source of nosocomial transmissions. Over a one-month interval, a total of 72 electronic rectal thermometers and 16 electronic oral thermometers were tested for C difficile. The portion of the handle nearest the base of the disposable plastic temperature probe sheath was sampled using a sterile moist swab that was then inoculated into chopped meat broth containing cefoxitin (40 p&ml) to suppress contaminants, and sodium taurocholate (1 mg/ml) to promote spore germination. Alter 24 hours of incubation, the broths were screened for C dificile antigen (Marion Latex Test), and those that tested positive were futher evaluated by C difficile isolation and identification. Fifteen of 72 rectal thermometers (20.8%) were positive for C difficile antigen, and of these, seven were confirmed by isolation and identification of the organism. The remaining eight specimens were overgrown with enterococcus, which interfered with the attempted isolation of C difitile. None of the oral thermometers were positive for C difficile by the antigen screen. Electronic rectal thermometers, which are used extensively in many institutions, are designed for multiple patient use. Our study shows that the handles often become contaminated with C difficile spores. Although the temperature probe is covered by a disposable plastic sheath that is changed between each patient, the newly installed sheath may be easily contaminated by hand carriage of spores from the handle of the thermometer. Insertion of a temperature probe carrying C difficile spores directly into the rectum might be a mechanism of nosocomial transmission of the organisms between patients. Thorough cleaning of the handle of the thermometer between patient use may help reduce the transmission of C diffitile by this route.
Quantitation of mitochondrial DNA in human lymphoblasts by a competitive polymerase chain reaction method: application to the study of inhibitors of mitochondrial DNA content.

With increasing awareness of the mitochondrial toxicity associated with certain 2',3'-dideoxynucleosides used in anti-human immunodeficiency virus therapy, procedures for quantitative analyses of drug effects on mitochondrial DNA (mtDNA) have assumed enhanced importance. For this reason we have developed a method to measure the copy numbers of mtDNA in cultured MOLT-4 cells. First a hybrid competitive DNA template was synthesized by conventional polymerase chain reaction (PCR), using two custom-synthesized 40-mer composite primers incorporating mitochondrial displacement loop sequences linked by a non-mitochondrial cDNA template (a 76-base pair sequence from the tat/rev region of human immunodeficiency virus cDNA). For the competitive assay, increasing known copy numbers of the hybrid competitive template were added as an internal control to samples containing total cellular DNA. With this approach, two competitive PCR products were generated, 1) a mitochondrial displacement loop-derived fragment (182 base pairs) and 2) a competitive DNA template-derived fragment (156 base pairs). Absolute quantitation was achieved by radiometric comparison of the relative amounts of the two products. To test the versatility of this method, varying amounts of competitive template (6.6 x 10(4) to 6.6 x 10(9) copies) were used with a fixed quantity of total cellular DNA taken from cells cultured for 9 days in the presence or absence of selected pyrimidine and purine dideoxynucleosides. The results showed that the copy number of cellular mtDNA is 823 +/- 71 copies/cell in MOLT-4 cells. Little selective depletion of mtDNA, compared with total cellular DNA, was seen with the purine dideoxynucleosides examined; however, when the cells were exposed to the pyrimidine dideoxynucleoside 2',3'-dideoxycytidine (50 nM) for 9 days, mtDNA content was specifically depleted, although total cellular DNA decreased by only 10%. Thus, in addition to the presently used methods of assessing mitochondrial impairment, i.e., Southern blot analysis and electron microscopy, the competitive PCR method provides a third and convenient assay, with particular applicability to determination of mtDNA in very small numbers of cells.
Incremental Integer Linear Programming Models for Petri Nets Reachability Problems

The operational management of complex systems is characterized, in general, by the existence of a huge number of solutions. Decision-making processes must be implemented in order to find the best results. These processes need suitable modeling tools offering true practical resolution perspectives. Among them, Petri nets (PNs) provide a simple graphical model taking into account, in the same formalism, concurrency, parallelism and synchronization. Their graphical and precise nature, their firm mathematical foundation and the aboundance of analysis methods have made them become a classical modeling tool for the study of discrete event systems, ranging from operating systems to logistic ones. However, their interest in the field of problem solving is still badly known. In this paper, we consider some PN reachability problems. Since PNs can model flows in a natural and efficient way, many operations research problems can be defined using reachability between states, e.g. scheduling (Lee and DiCesare, 1994; Van Der AAlst, 1995), planning (Silva et al., 2000), car-sequencing problems (Briand, 1999). Moreover, research on Petri nets addresses the issue of flexibility: many extensions have been proposed to facilitate the modeling of complex systems, by addition of ``color’’, ``time’’ and ``hierarchy’’ (Jensen, 1992; Wang,1998). For example, it is relatively easy to map scheduling problems onto timed PNs. Their graphical nature reinforce obviously this strength, by allowing a kind of interactivity with the system. At last, a large number of difficult PN analysis problems are equivalent to the reachability problem, or to some of its variants or sub-problems (Keller, 1976). Particularly, model-checking (Latvala, 2001) which represents a key point when dealing with systems analysis is directly linked to an exhaustive traversal of the corresponding PN reachability graph. Various methods have been suggested to handle the PNs reachability problem. In this paper, we propose to use the mathematical programming paradigm. Some PN analysis problems have already been handled using such techniques (Melzer and Esparza, 1996;Silva et al., 1998; Khomenko and Koutny, 2000), but none has considered the general PNs reachability problem. The proposed approach is based on an implicit traversal of the Petri net reachability graph, which does not need its construction. This is done by considering a unique sequence of steps growing incrementally to represent exactly the total behavior of the net. We follow here a
Insufficient islet compensation to insulin resistance vs. reduced glucose effectiveness in glucose-intolerant mice.

This study evaluated the relative contribution of insulin-dependent mechanisms vs. mechanisms independent on dynamic insulin for glucose intolerance induced by high-fat diet. C57BL/6J mice underwent a frequently sampled intravenous glucose tolerance test (1 g/kg glucose) at 1 wk and 1, 3, and 10 mo after initiation of a high-fat diet (58% fat; control diet 11% fat) to measure glucose effectiveness (S(G)) and disposition index (DI), i.e., insulin sensitivity (S(I)) times early or total insulin secretion. Glucose disappearance (K(G)) and S(I) were reduced in high-fat-fed mice at all time points. Total (50 min) insulin secretion was sufficiently increased at all time points to compensate for the reduced S(I), as judged by normal DI(50) (min). In contrast, early (10 min) insulin secretion was not sufficiently increased; DI(10) (min) was reduced after 1, 3, and 10 mo. S(G) was reduced after 1 wk; the reduction persisted throughout the study period. Thus glucose intolerance induced by high-fat diet is, in early phases, solely explained by reduced glucose effectiveness, whereas insufficient early insulin secretion is of importance after long-term feeding.
Is double inactivation of the Nf1 gene responsible for the development of congenital pseudarthrosis of the tibia associated with NF1?

The pathogenic mechanism responsible for congenital pseudarthrosis of the tibia (CPT) is not well understood although the possibility of double inactivation of the neurofibromatosis type 1 (Nf1) gene has been suggested. In the present study, loss of heterozygosity was investigated in fibrous hamartoma tissues harvested from 16 patients with CPT associated with NF1 using four genetic markers that span the Nf1 gene. Based on the assumption that a single cell with double inactivation of Nf1 would undergo clonal growth and cause fibrous hamartoma, we investigated clonality in fibrous hamartoma tissues by analyzing X‐chromosome inactivation patterns in 11 female patients. Loss of Nf1 heterozygosity in fibrous hamartoma tissues was observed at one or two genetic markers in 4 out of the 16 patients tested. In clonality assays, 3 of 11 patients showed a clonal growth pattern, 5 a non‐clonal pattern, and 3 were non‐informative. These findings support that double inactivation of the Nf1 gene and subsequent clonal growth could be a pathogenic feature of the fibrous hamartoma tissue at least in some of the CPT but might not be essential requirements of CPT development. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1535–1540, 2012
Corpus Annotation within the French FrameNet: a Domain-by-domain Methodology

This paper reports on the development of a French FrameNet, within the ASFALDA project. While the first phase of the project focused on the development of a French set of frames and corresponding lexicon (Candito et al., 2014), this paper concentrates on the subsequent corpus annotation phase, which focused on four notional domains (commercial transactions, cognitive stances, causality and verbal communication). Given full coverage is not reachable for a relatively “new” FrameNet project, we advocate that focusing on specific notional domains allowed us to obtain full lexical coverage for the frames of these domains, while partially reflecting word sense ambiguities. Furthermore, as frames and roles were annotated on two French Treebanks (the French Treebank (Abeillé and Barrier, 2004) and the Sequoia Treebank (Candito and Seddah, 2012), we were able to extract a syntactico-semantic lexicon from the annotated frames. In the resource’s current status, there are 98 frames, 662 frame evoking words, 872 senses, and about 13000 annotated frames, with their semantic roles assigned to portions of text. The French FrameNet is freely available at alpage.inria. fr/asfalda.
Sera from patients with sepsis induce nitric oxide production in vascular smooth muscle cells.

BACKGROUND: Nitric oxide (NO) is an important physiological mediator of vascular tone and is involved in pathophysiology of septic shock. Although plasma nitrite is a stable end product of NO oxidation derived from endogenous NO, the plasma nitrite level is also easily affected by the intake of various foods, bacterial products and renal functional status. AIMS: We propose an excellent alternative assay technique for measuring endogenous NO production. METHODS: We measured the nitrite level in cultured vascular smooth muscle cells (SMC) treated with serum obtained from patients with sepsis (4 patients), by means of a chemiluminescence detector. RESULTS: The nitrite concentrations in such cells were significantly higher as compared to those in the cells treated with normal serum. Moreover, the increased nitrite levels in the SMC treated with the sera obtained from patients with sepsis were completely inhibited by L-nitroarginine (1 mmol/L), a nitric oxide synthase inhibitor. CONCLUSION: These data suggest that this assay method enable us to know the ability of endogenous NO production in each patient.