Miracle-dz/UniFAR-FTUs huggingface dataset:
New lattice based cryptographic constructions

We introduce the use of Fourier analysis on lattices as an integral part of a lattice based construction. The tools we develop provide an elegant description of certain Gaussian distributions around lattice points. Our results include two cryptographic constructions which are based on the worst-case hardness of the unique shortest vector problem. The main result is a new public key cryptosystem whose security guarantee is considerably stronger than previous results (O(n1.5) instead of O(n7)). This provides the first alternative to Ajtai and Dwork's original 1996 cryptosystem. Our second result is a collision resistant hash function which, apart from improving the security in terms of the unique shortest vector problem, is also the first example of an analysis which is not based on Ajtai's iterative step. Surprisingly, the two results are derived from the same tool which presents two indistinguishable distributions on the segment [0,1]. It seems that this tool can have further applications and as an example we mention how it can be used to solve an open problem related to quantum computation.
On the convergence time of a path-vector protocol

We study the running time of a particular path-vector protocol for distributively and asynchronously computing shortest paths in a network to a given target node t. We study two cases. In both, the protocol starts with each node possibly knowing some path to t, subject to conditions discussed in the paper. In the first case, the "withdrawal case," all edges incident to the target are cut. We prove that in this case, the protocol always terminates but may need exponential time to do so, if the nodes "fire" (i.e., execute) in an adversarially chosen order, even if the initial paths are shortest. If the graph is a clique, the protocol terminates in polynomial time. If, on the other hand, the nodes fire in random order, and the graph is arbitrary, then the algorithm terminates in polynomial expected time. In the second case, the "announcement case," in which new edges incident to t appear, we prove that the protocol terminates in polynomial time, regardless of the firing order.This protocol is interesting since it models the shortest-path protocol used by BGP, the interdomain routing protocol of the Internet, in the absence of policy.
A Novel Phytomyxean Parasite Associated with Galls on the Bull-Kelp Durvillaea antarctica (Chamisso) Hariot

Durvillaea antarctica (Fucales, Phaeophyceae) is a large kelp of high ecological and economic significance in the Southern Hemisphere. In natural beds along the central coast of Chile (Pacific Ocean), abnormal growth characterized by evident gall development and discolorations of the fronds/thallus was observed. Analysing these galls by light microscopy and scanning electron microscopy revealed the presence of endophytic eukaryotes showing typical characteristics for phytomyxean parasites. The parasite developed within enlarged cells of the subcortical tissue of the host. Multinucleate plasmodia developed into many, single resting spores. The affiliation of this parasite to the Phytomyxea (Rhizaria) was supported by 18S rDNA data, placing it within the Phagomyxida. Similar microorganisms were already reported once 23 years ago, indicating that these parasites are persistent and widespread in D. antarctica beds for long times. The symptoms caused by this parasite are discussed along with the ecological and economic consequences. Phytomyxean parasites may play an important role in the marine ecosystem, but they remain understudied in this environment. Our results demonstrate for the first time the presence of resting spores in Phagomyxida, an order in which resting spores were thought to be absent making this the first record of a phagomyxean parasite with a complete life cycle so far, challenging the existing taxonomic concepts within the Phytomyxea. The importance of the here described resting spores for the survival and ecology of the phagomyxid parasite will be discussed together with the impact this parasite may have on ‘the strongest seaweed of the world’, which is an important habitat forming and economic resource from the Southern Hemisphere.
Revisiting the codon adaptation index from a whole-genome perspective: gene expression, codon bias, and metabolic networks in the context of genomes comparison

Facts and ideas presented in this short review concern some recent developments at the interface between sequence analysis, gene expression prediction and genome comparison carried on in our group. The guiding line to all results presented here is to derive biological information from genome sequences by means of a purely statistical analysis and an appropriate design of algorithms. 1 Some background and motivation Proteins are formed out of 20 amino-acids which are coded in triplets of nucleotides, called codons. The four nucleotides (A, T, C, G) define 64 codons used in the cell. Codons are not uniformly employed in the cell, but at the contrary, certain codons are preferred and we speak about codon bias. There are several kinds of codon biases and some of them are linked to specific biological functions. Statistical analysis of DNA sequences and in particular of codon bias were performed from the moment that long chunks of DNA sequences were publicly available in the early eighties (Grantham et al. 1980; Wada et al. 1990), and the roots for these studies can be traced back to the sixties (Sueoka 1962; Zuckerkandl and Pauling 1965). However with the increasing number of bacterial genome sequences from a broad diversity of species, this field of research has been revivified in the last few years (Koonin and Galperin 1997; Lin and Gerstein 2000; Radomski and Slonimski 2001; Knight et al. 2001; Sicheritz-Ponten and Andersson 2001; Daubin et al. 2002; Lin et al. 2002; Lobry and Chessel 2003; Sandberg et al. 2003; Jansen et al. 2003). Biased codon usage may result from a diversity of factors: GC-content, preference for codons with G or C at the third nucleotide position (Lafay et al. 1999), a leading strand richer in G+T than a lagging strand (Lafay et al. 1999), horizontal gene transfer which induces chromosome segments of unusual base composition (Moszer et al. 1999), and in particular, translational bias which has been frequently noticed in fast growing prokaryotes and eukaryotes (Sharp and Li 1987; Sharp et al. 1986; Medigue et al. 1991; Shields and Sharp 1987; Sharp et al. 1988;
The Cellular Pathway of CD1e in Immature and Maturing Dendritic Cells

Dendritic cells (DCs) present antigens to T cells via CD1, HLA class I or class II molecules. During maturation, HLA class II‐restricted presentation is optimized. The relocalization of CD1e from Golgi to endosomal compartments during DC maturation suggests also an optimization of the antigen‐presentation pathway via CD1 molecules. We here detail the biosynthesis and cellular pathway of CD1e in immature and maturing DCs. Unlike the other CD1 molecules, CD1e was found to reach late endosomes through sorting endosomes, without passing through the plasma membrane in either immature or maturing cells. After induction of DC maturation, CD1e disappeared rapidly from the Golgi and was transiently localized in HLA‐DR+ vesicles, while the number of CD1e+/CD1b+ compartments increased for at least 20 h. High‐resolution light microscopy showed that, in immature DCs, CD1e+ vesicles were often in close apposition to EEA1+ or HLA‐DR+ compartments, while CD1e displayed a nearly exclusive distribution in the lysosomes of mature DCs, a finding corroborated by immunoelectron microscopy. During maturation, CD1e synthesis progressively declined, while the endosomal cleavage of CD1e still occurred. Thus, CD1e displays peculiar properties, suggesting an unexpected role among the family of CD1 antigen‐presenting molecules.
3D localization of partially buried object in unstructured environment

This paper describes a method to localize objects which are partially buried in an unstructured environment. The objects are limited to surfaces of revolution in the present study. Candidate regions are extracted as convex surface regions from a range data that is obtained by area-based stereo matching. The surface type at each point is determined based on the signs of the maximum and minimum curvatures, which are calculated by fitting a quadric in the local window. For each candidate region, multiple hypotheses for the position and direction of the rotational axis are generated for each object model. Each hypothesis is verified and improved by an iterative method, and the most reliable hypothesis is adopted. The experimental results demonstrate the effectiveness of the proposed method for actual range data.
Learning Blocking Schemes for Record Linkage

Record linkage is the process of matching records across data sets that refer to the same entity. One issue within record linkage is determining which record pairs to consider, since a detailed comparison between all of the records is impractical. Blocking addresses this issue by generating candidate matches as a preprocessing step for record linkage. For example, in a person matching problem, blocking might return all people with the same last name as candidate matches. Two main problems in blocking are the selection of attributes for generating the candidate matches and deciding which methods to use to compare the selected attributes. These attribute and method choices constitute a blocking scheme. Previous approaches to record linkage address the blocking issue in a largely ad-hoc fashion. This paper presents a machine learning approach to automatically learn effective blocking schemes. We validate our approach with experiments that show our learned blocking schemes outperform the ad-hoc blocking schemes of non-experts and perform comparably to those manually built by a domain expert.
Pore and throat size distributions measured from synchrotron X-ray tomographic images of Fontaineble

The three-dimensional geometry and connectivity of pore space controls the hydraulic transport behavior of crustal rocks. We report on direct measurement of flow-relevant geometrical properties of the void space in a suite of four samples of Fontainebleau sandstone ranging from 7.5 to 22% porosity. The measurements are obtained from computer analysis of three-dimensional, synchrotron X-ray computed microtomographic images. We present measured distributions of coordination number, channel length, throat size, and pore volume and of correlations between throat size/pore volume and nearest-neighbor pore volume/pore volume determined for these samples. In order to deal with the ambiguity of where a nodal pore ends and a channel begins, we apportion the void space volume solely among nodal pores, with the channel throat surfaces providing the nodal pore delineations. Pore channels thus have length but no associated volume; channel length is defined by nodal pore center to nodal pore center distance. For a sample of given porosity our measurements show that the pore coordination number and throat area are exponentially distributed, whereas the channel length and nodal pore volume follow gamma and lognormal distributions, respectively. Our data indicate an overall increase in coordination number and shortening of pore channel length with increasing porosity. The average coordination number ranges from 3.4 to 3.8; the average channel length ranges from 200 to 130 μm. Average throat area increases from 1600 to 2200 μm 2 with increasing porosity, while average pore volume remains essentially unchanged at around 0.0004 mm 3 .
Track, Then Decide: Category-Agnostic Vision-Based Multi-Object Tracking

The most common paradigm for vision-based multi-object tracking is tracking-by-detection, due to the availability of reliable detectors for several important object categories such as cars and pedestrians. However, future mobile systems will need a capability to cope with rich human-made environments, in which obtaining detectors for every possible object category would be infeasible. In this paper, we address the problem of class-agnostic multi-object tracking using generic object proposals. We present an efficient segmentation mask-based tracker which associates pixel-precise masks reported by the segmentation. Our approach can utilize semantic information whenever it is available for classifying objects at the track level, while retaining the capability to track generic unknown objects in the absence of such information. We demonstrate experimentally that our approach achieves performance comparable to state-of-the-art tracking-by-detection methods for popular object categories such as cars and pedestrians. Additionally, we show that the proposed method can discover and robustly track a large variety of other objects.
Haematologic parameters in metastatic colorectal cancer patients treated with capecitabine combination therapy.

BACKGROUND The standard treatment in the metastatic colorectal cancer consists of 5-FU based infusional regimens. However, with oral fluoropyrimidines, equal tumor responses may be obtained. Capecitabine causes macrocytosis of the cells by inhibition of DNA synthesis. In this context, a relationship was found between mean corpuscular volume (MCV) and response to therapy in breast cancer patients treated with Capecitabine, but whether this relationship also pertains in colorectal cancer has not been established. MATERIALS AND METHODS A total of 102 metastatic colorectal cancer patients treated with a oxaliplatin (XELOX) ±Bevacizumab combination were retrospectively evaluated. Patients were randomized into three groups. Hematological parameters (MCV, MPV, PCT, PLT, NLR) were recorded retrospectively, before treatment and after 3 cycles of chemotherapy. RESULTS After three cycles of therapy, 20 (19.6%) patients had progressive disease (PD), 41 (40.1%) had stable disease (SD), and 41 (40.1%) demonstrated a partial response (PR). In 62 (60.7%) treatment was with capesitabin plus XELOX therapy, and in 40 (39.2%) it was XELOX-Bevacizumab combination therapy. There was no difference among three groups before the treatment in terms of MCV, MPV, PCT, PLT, and NLR. MCV showed significant increase in chemotherapy response groups (PR and SD). In addition, a significant decrease was observed for platelet count in chemotherapy response groups. While NLR decrease was seen in only a PR group, PCT decrease was observed in all three groups. PCT and PLT values were higher in patients receiving Bevacizumab. CONCLUSIONS PLT, PCT, MPV, and NLR values were decreased due to Capecitabine- based chemotherapy, however MCV was increased. PCT and PLT values were higher in patients who received Bevacizumab than those who did not. MCV, PLT, and NLR can be considered as important factors in predicting response to colorectal carcinoma treatment.
Determinants of left ventricular untwisting behaviour in patients with dilated cardiomyopathy: analysis by two-dimensional speckle tracking

Background/objective: Left ventricular (LV) untwisting velocity has emerged as a novel index of LV diastolic function since it is thought to be related to LV diastolic suction. However, the pathophysiology of LV untwisting behavior has not been fully investigated. The aim of this study was to investigate the determinants of LV peak untwisting velocity in patients with dilated cardiomyopathy (DCM). Methods: 101 patients with DCM (mean age 60 (SD 13) years) and 50 control subjects were evaluated. After a standard echocardiographic examination, peak torsion and peak untwisting velocity were measured using two-dimensional speckle-tracking imaging. Radial dyssynchrony was assessed by speckle-tracking radial strain analysis. Tissue Doppler derived systolic (Ts-SD) and diastolic (Te-SD) dyssynchrony indices were also assessed. Results: The patients with DCM had significantly smaller peak torsion (p<0.001) and peak untwisting velocity (p<0.001) and greater radial dyssynchrony (p<0.001) and Ts-SD (p<0.001) and Te-SD (p = 0.001) compared with the control subjects. The peak untwisting velocity was correlated with end-systolic volume index (r = 0.524, p<0.001), E/e′ (r = 0.365, p<0.001), radial dyssynchrony (r = 0.578, p<0.001), Ts-SD (p<0.001), Te-SD (p<0.001) and peak torsion (r = −0.635, p<0.001) in patients with DCM. Multivariate analysis revealed that peak torsion, radial dyssynchrony and E/e′ were independent predictors of peak untwisting velocity in patients with DCM (standard coefficient −0.483, p<0.001, 0.330, p<0.001 and 0.241, p = 0.001, respectively). Conclusion: These results suggest that strain-based LV radial dyssynchrony and E/e′ as well as LV torsion are related to diastolic untwisting behaviour in patients with DCM.
Comparative Analysis of Muscle Hypertrophy Models Reveals Divergent Gene Transcription Profiles and Points to Translational Regulation of Muscle Growth through Increased mTOR Signaling

Skeletal muscle mass is a result of the balance between protein breakdown and protein synthesis. It has been shown that multiple conditions of muscle atrophy are characterized by the common regulation of a specific set of genes, termed atrogenes. It is not known whether various models of muscle hypertrophy are similarly regulated by a common transcriptional program. Here, we characterized gene expression changes in three different conditions of muscle growth, examining each condition during acute and chronic phases. Specifically, we compared the transcriptome of Extensor Digitorum Longus (EDL) muscles collected (1) during the rapid phase of postnatal growth at 2 and 4 weeks of age, (2) 24 h or 3 weeks after constitutive activation of AKT, and (3) 24 h or 3 weeks after overload hypertrophy caused by tenotomy of the Tibialis Anterior muscle. We observed an important overlap between significantly regulated genes when comparing each single condition at the two different timepoints. Furthermore, examining the transcriptional changes occurring 24 h after a hypertrophic stimulus, we identify an important role for genes linked to a stress response, despite the absence of muscle damage in the AKT model. However, when we compared all different growth conditions, we did not find a common transcriptional fingerprint. On the other hand, all conditions showed a marked increase in mTORC1 signaling and increased ribosome biogenesis, suggesting that muscle growth is characterized more by translational, than transcriptional regulation.
A Mechanical Musculo-Skeletal System for a Human-Shaped Robot Arm

This paper presents a mechanical system with a similar configuration to a human musculo-skeletal system for use in anthropomorphic robots or as artificial limbs for disabled persons. First, a mechanical module called ANLES (Actuator with Non-Linear Elasticity System) is introduced. There are two types of ANLES: the linear-type ANLES and rotary-type ANLES. They can be used as a voluntary muscle in a wide-range of musculo-skeletal structures in which at least double actuators work in an antagonistic setup via some elastic elements. Next, an application of the two types of ANLES to a two-degree-of-freedom (DOF) manipulator that has a similar configuration to the human elbow joint is shown. The experimental results of the joint stiffness and joint angle control elucidate that the developed mechanism effectively regulates joint stiffness in the same way as a musculo-skeletal system.
Edible coating application of Kecombrang leaves to reduce gourami sausage damage

Gourami sausage is a processed fish product which have short shelf life. To extend shelf life, sodium nitrate as artificial preservative (synthetic) was used. However, if it consumed continuously, the synthetic preservative induced negative effects to human health. Another alternative to avoid the use of synthetic preservative is using antimicrobial edible coatings. In this regard, Kecombrang (Nicolaiaspeciosa) leaves contain bioactive compounds that able to act as natural anti-microbial for edible coating production. This research aimed to know the effect of different level of Kecombrang leave concentrate in edible coating to the microbial growth inhibition in fish sausage gourami during storage at low-temperature storage (±4°C). The result shows that edible coating contained natural anti microbial have inhibitory effect to total mold and yeast, bacteria, and microbial. The addition of 4% concentrate of Kecombrang leaves shows better in suppressing the growth of mold and yeast, bacteria, and microbe.
Robust Document Image Binarization Technique for Degraded Document Images

Segmentation of text from badly degraded document images is a very challenging task due to the high inter/intra-variation between the document background and the foreground text of different document images. In this paper, we propose a novel document image binarization technique that addresses these issues by using adaptive image contrast. The adaptive image contrast is a combination of the local image contrast and the local image gradient that is tolerant to text and background variation caused by different types of document degradations. In the proposed technique, an adaptive contrast map is first constructed for an input degraded document image. The contrast map is then binarized and combined with Canny's edge map to identify the text stroke edge pixels. The document text is further segmented by a local threshold that is estimated based on the intensities of detected text stroke edge pixels within a local window. The proposed method is simple, robust, and involves minimum parameter tuning. It has been tested on three public datasets that are used in the recent document image binarization contest (DIBCO) 2009 & 2011 and handwritten-DIBCO 2010 and achieves accuracies of 93.5%, 87.8%, and 92.03%, respectively, that are significantly higher than or close to that of the best-performing methods reported in the three contests. Experiments on the Bickley diary dataset that consists of several challenging bad quality document images also show the superior performance of our proposed method, compared with other techniques.
The effect of topic set size on retrieval experiment error

Retrieval mechanisms are frequently compared by computing the respective average scores for some effectiveness metric across a common set of information needs or topics, with researchers concluding one method is superior based on those averages. Since comparative retrieval system behavior is known to be highly variable across topics, good experimental design requires that a "sufficient" number of topics be used in the test. This paper uses TREC results to empirically derive error rates based on the number of topics used in a test and the observed difference in the average scores. The error rates quantify the likelihood that a different set of topics of the same size would lead to a different conclusion. We directly compute error rates for topic sets up to size 25, and extrapolate those rates for larger topic set sizes. The error rates found are larger than anticipated, indicating researchers need to take care when concluding one method is better than another, especially if few topics are used.